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 for (p = 0, i = 0; p < embedDim; ++p) { 1806 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1807 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1808 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1809 ++i; 1810 } 1811 } 1812 } 1813 /* Construct graph */ 1814 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1815 for (i = 0; i < numVerts; ++i) { 1816 for (j = 0, k = 0; j < numVerts; ++j) { 1817 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1818 } 1819 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1820 } 1821 /* Build Topology */ 1822 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 1823 for (c = 0; c < numCells; c++) { 1824 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 1825 } 1826 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1827 /* Cells */ 1828 for (i = 0, c = 0; i < numVerts; ++i) { 1829 for (j = 0; j < i; ++j) { 1830 for (k = 0; k < j; ++k) { 1831 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1832 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1833 /* Check orientation */ 1834 { 1835 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}}}; 1836 PetscReal normal[3]; 1837 PetscInt e, f; 1838 1839 for (d = 0; d < embedDim; ++d) { 1840 normal[d] = 0.0; 1841 for (e = 0; e < embedDim; ++e) { 1842 for (f = 0; f < embedDim; ++f) { 1843 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1844 } 1845 } 1846 } 1847 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1848 } 1849 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 1850 } 1851 } 1852 } 1853 } 1854 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1855 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1856 ierr = PetscFree(graph);CHKERRQ(ierr); 1857 /* Interpolate mesh */ 1858 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1859 ierr = DMDestroy(dm);CHKERRQ(ierr); 1860 *dm = idm; 1861 } else { 1862 /* 1863 12-21--13 1864 | | 1865 25 4 24 1866 | | 1867 12-25--9-16--8-24--13 1868 | | | | 1869 23 5 17 0 15 3 22 1870 | | | | 1871 10-20--6-14--7-19--11 1872 | | 1873 20 1 19 1874 | | 1875 10-18--11 1876 | | 1877 23 2 22 1878 | | 1879 12-21--13 1880 */ 1881 const PetscReal dist = 1.0/PetscSqrtReal(3.0); 1882 PetscInt cone[4], ornt[4]; 1883 1884 numCells = !rank ? 6 : 0; 1885 numEdges = !rank ? 12 : 0; 1886 numVerts = !rank ? 8 : 0; 1887 firstVertex = numCells; 1888 firstEdge = numCells + numVerts; 1889 /* Build Topology */ 1890 ierr = DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1891 for (c = 0; c < numCells; c++) { 1892 ierr = DMPlexSetConeSize(*dm, c, 4);CHKERRQ(ierr); 1893 } 1894 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1895 ierr = DMPlexSetConeSize(*dm, e, 2);CHKERRQ(ierr); 1896 } 1897 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1898 /* Cell 0 */ 1899 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1900 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1901 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1902 ierr = DMPlexSetConeOrientation(*dm, 0, ornt);CHKERRQ(ierr); 1903 /* Cell 1 */ 1904 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1905 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1906 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1907 ierr = DMPlexSetConeOrientation(*dm, 1, ornt);CHKERRQ(ierr); 1908 /* Cell 2 */ 1909 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1910 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1911 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1912 ierr = DMPlexSetConeOrientation(*dm, 2, ornt);CHKERRQ(ierr); 1913 /* Cell 3 */ 1914 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1915 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1916 ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; 1917 ierr = DMPlexSetConeOrientation(*dm, 3, ornt);CHKERRQ(ierr); 1918 /* Cell 4 */ 1919 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1920 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1921 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; 1922 ierr = DMPlexSetConeOrientation(*dm, 4, ornt);CHKERRQ(ierr); 1923 /* Cell 5 */ 1924 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1925 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1926 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; 1927 ierr = DMPlexSetConeOrientation(*dm, 5, ornt);CHKERRQ(ierr); 1928 /* Edges */ 1929 cone[0] = 6; cone[1] = 7; 1930 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1931 cone[0] = 7; cone[1] = 8; 1932 ierr = DMPlexSetCone(*dm, 15, cone);CHKERRQ(ierr); 1933 cone[0] = 8; cone[1] = 9; 1934 ierr = DMPlexSetCone(*dm, 16, cone);CHKERRQ(ierr); 1935 cone[0] = 9; cone[1] = 6; 1936 ierr = DMPlexSetCone(*dm, 17, cone);CHKERRQ(ierr); 1937 cone[0] = 10; cone[1] = 11; 1938 ierr = DMPlexSetCone(*dm, 18, cone);CHKERRQ(ierr); 1939 cone[0] = 11; cone[1] = 7; 1940 ierr = DMPlexSetCone(*dm, 19, cone);CHKERRQ(ierr); 1941 cone[0] = 6; cone[1] = 10; 1942 ierr = DMPlexSetCone(*dm, 20, cone);CHKERRQ(ierr); 1943 cone[0] = 12; cone[1] = 13; 1944 ierr = DMPlexSetCone(*dm, 21, cone);CHKERRQ(ierr); 1945 cone[0] = 13; cone[1] = 11; 1946 ierr = DMPlexSetCone(*dm, 22, cone);CHKERRQ(ierr); 1947 cone[0] = 10; cone[1] = 12; 1948 ierr = DMPlexSetCone(*dm, 23, cone);CHKERRQ(ierr); 1949 cone[0] = 13; cone[1] = 8; 1950 ierr = DMPlexSetCone(*dm, 24, cone);CHKERRQ(ierr); 1951 cone[0] = 12; cone[1] = 9; 1952 ierr = DMPlexSetCone(*dm, 25, cone);CHKERRQ(ierr); 1953 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1954 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1955 /* Build coordinates */ 1956 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1957 coordsIn[0*embedDim+0] = -dist; coordsIn[0*embedDim+1] = dist; coordsIn[0*embedDim+2] = -dist; 1958 coordsIn[1*embedDim+0] = dist; coordsIn[1*embedDim+1] = dist; coordsIn[1*embedDim+2] = -dist; 1959 coordsIn[2*embedDim+0] = dist; coordsIn[2*embedDim+1] = -dist; coordsIn[2*embedDim+2] = -dist; 1960 coordsIn[3*embedDim+0] = -dist; coordsIn[3*embedDim+1] = -dist; coordsIn[3*embedDim+2] = -dist; 1961 coordsIn[4*embedDim+0] = -dist; coordsIn[4*embedDim+1] = dist; coordsIn[4*embedDim+2] = dist; 1962 coordsIn[5*embedDim+0] = dist; coordsIn[5*embedDim+1] = dist; coordsIn[5*embedDim+2] = dist; 1963 coordsIn[6*embedDim+0] = -dist; coordsIn[6*embedDim+1] = -dist; coordsIn[6*embedDim+2] = dist; 1964 coordsIn[7*embedDim+0] = dist; coordsIn[7*embedDim+1] = -dist; coordsIn[7*embedDim+2] = dist; 1965 } 1966 break; 1967 case 3: 1968 if (simplex) { 1969 DM idm; 1970 const PetscReal edgeLen = 1.0/PETSC_PHI; 1971 const PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 1972 const PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 1973 const PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 1974 const PetscInt degree = 12; 1975 PetscInt s[4] = {1, 1, 1}; 1976 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}, 1977 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 1978 PetscInt cone[4]; 1979 PetscInt *graph, p, i, j, k, l; 1980 1981 numCells = !rank ? 600 : 0; 1982 numVerts = !rank ? 120 : 0; 1983 firstVertex = numCells; 1984 /* Use the 600-cell, which for a unit sphere has coordinates which are 1985 1986 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 1987 (\pm 1, 0, 0, 0) all cyclic permutations 8 1988 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 1989 1990 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1991 length is then given by 1/\phi = 0.61803. 1992 1993 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 1994 http://mathworld.wolfram.com/600-Cell.html 1995 */ 1996 /* Construct vertices */ 1997 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1998 i = 0; 1999 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2000 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2001 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2002 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2003 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2004 ++i; 2005 } 2006 } 2007 } 2008 } 2009 for (p = 0; p < embedDim; ++p) { 2010 s[1] = s[2] = s[3] = 1; 2011 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2012 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2013 ++i; 2014 } 2015 } 2016 for (p = 0; p < 12; ++p) { 2017 s[3] = 1; 2018 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2019 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2020 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2021 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2022 ++i; 2023 } 2024 } 2025 } 2026 } 2027 if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2028 /* Construct graph */ 2029 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2030 for (i = 0; i < numVerts; ++i) { 2031 for (j = 0, k = 0; j < numVerts; ++j) { 2032 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2033 } 2034 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2035 } 2036 /* Build Topology */ 2037 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 2038 for (c = 0; c < numCells; c++) { 2039 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 2040 } 2041 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 2042 /* Cells */ 2043 for (i = 0, c = 0; i < numVerts; ++i) { 2044 for (j = 0; j < i; ++j) { 2045 for (k = 0; k < j; ++k) { 2046 for (l = 0; l < k; ++l) { 2047 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2048 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2049 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2050 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2051 { 2052 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2053 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2054 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2055 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2056 2057 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2058 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2059 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2060 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2061 2062 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2063 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2064 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2065 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2066 2067 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2068 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2069 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2070 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2071 PetscReal normal[4]; 2072 PetscInt e, f, g; 2073 2074 for (d = 0; d < embedDim; ++d) { 2075 normal[d] = 0.0; 2076 for (e = 0; e < embedDim; ++e) { 2077 for (f = 0; f < embedDim; ++f) { 2078 for (g = 0; g < embedDim; ++g) { 2079 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]); 2080 } 2081 } 2082 } 2083 } 2084 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2085 } 2086 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 2087 } 2088 } 2089 } 2090 } 2091 } 2092 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2093 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2094 ierr = PetscFree(graph);CHKERRQ(ierr); 2095 /* Interpolate mesh */ 2096 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2097 ierr = DMDestroy(dm);CHKERRQ(ierr); 2098 *dm = idm; 2099 break; 2100 } 2101 default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2102 } 2103 /* Create coordinates */ 2104 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 2105 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2106 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2107 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2108 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2109 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2110 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2111 } 2112 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2113 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2114 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2115 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2116 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2117 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2118 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2119 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2120 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2121 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2122 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 2123 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2124 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2125 PetscFunctionReturn(0); 2126 } 2127 2128 /* External function declarations here */ 2129 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 2130 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2131 extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2132 extern PetscErrorCode DMCreateLocalSection_Plex(DM dm); 2133 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 2134 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 2135 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 2136 extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field); 2137 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 2138 extern PetscErrorCode DMSetUp_Plex(DM dm); 2139 extern PetscErrorCode DMDestroy_Plex(DM dm); 2140 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 2141 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 2142 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm); 2143 extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm); 2144 static PetscErrorCode DMInitialize_Plex(DM dm); 2145 2146 /* Replace dm with the contents of dmNew 2147 - Share the DM_Plex structure 2148 - Share the coordinates 2149 - Share the SF 2150 */ 2151 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 2152 { 2153 PetscSF sf; 2154 DM coordDM, coarseDM; 2155 Vec coords; 2156 PetscBool isper; 2157 const PetscReal *maxCell, *L; 2158 const DMBoundaryType *bd; 2159 PetscErrorCode ierr; 2160 2161 PetscFunctionBegin; 2162 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 2163 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 2164 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 2165 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 2166 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 2167 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 2168 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 2169 ierr = DMSetPeriodicity(dmNew, isper, maxCell, L, bd);CHKERRQ(ierr); 2170 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 2171 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2172 dm->data = dmNew->data; 2173 ((DM_Plex *) dmNew->data)->refct++; 2174 dmNew->labels->refct++; 2175 if (!--(dm->labels->refct)) { 2176 DMLabelLink next = dm->labels->next; 2177 2178 /* destroy the labels */ 2179 while (next) { 2180 DMLabelLink tmp = next->next; 2181 2182 ierr = DMLabelDestroy(&next->label);CHKERRQ(ierr); 2183 ierr = PetscFree(next);CHKERRQ(ierr); 2184 next = tmp; 2185 } 2186 ierr = PetscFree(dm->labels);CHKERRQ(ierr); 2187 } 2188 dm->labels = dmNew->labels; 2189 dm->depthLabel = dmNew->depthLabel; 2190 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 2191 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 2192 PetscFunctionReturn(0); 2193 } 2194 2195 /* Swap dm with the contents of dmNew 2196 - Swap the DM_Plex structure 2197 - Swap the coordinates 2198 - Swap the point PetscSF 2199 */ 2200 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 2201 { 2202 DM coordDMA, coordDMB; 2203 Vec coordsA, coordsB; 2204 PetscSF sfA, sfB; 2205 void *tmp; 2206 DMLabelLinkList listTmp; 2207 DMLabel depthTmp; 2208 PetscInt tmpI; 2209 PetscErrorCode ierr; 2210 2211 PetscFunctionBegin; 2212 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 2213 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 2214 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 2215 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 2216 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 2217 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 2218 2219 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 2220 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 2221 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 2222 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 2223 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 2224 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 2225 2226 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 2227 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 2228 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 2229 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 2230 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 2231 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 2232 2233 tmp = dmA->data; 2234 dmA->data = dmB->data; 2235 dmB->data = tmp; 2236 listTmp = dmA->labels; 2237 dmA->labels = dmB->labels; 2238 dmB->labels = listTmp; 2239 depthTmp = dmA->depthLabel; 2240 dmA->depthLabel = dmB->depthLabel; 2241 dmB->depthLabel = depthTmp; 2242 tmpI = dmA->levelup; 2243 dmA->levelup = dmB->levelup; 2244 dmB->levelup = tmpI; 2245 PetscFunctionReturn(0); 2246 } 2247 2248 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2249 { 2250 DM_Plex *mesh = (DM_Plex*) dm->data; 2251 PetscErrorCode ierr; 2252 2253 PetscFunctionBegin; 2254 /* Handle viewing */ 2255 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 2256 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 2257 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 2258 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 2259 /* Point Location */ 2260 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 2261 /* Partitioning and distribution */ 2262 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 2263 /* Generation and remeshing */ 2264 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 2265 /* Projection behavior */ 2266 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 2267 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 2268 /* Checking structure */ 2269 { 2270 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE; 2271 2272 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2273 if (flg && flg2) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 2274 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); 2275 if (flg && flg2) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 2276 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); 2277 if (flg && flg2) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 2278 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2279 if (flg && flg2) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 2280 } 2281 2282 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2283 PetscFunctionReturn(0); 2284 } 2285 2286 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2287 { 2288 PetscInt refine = 0, coarsen = 0, r; 2289 PetscBool isHierarchy; 2290 PetscErrorCode ierr; 2291 2292 PetscFunctionBegin; 2293 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2294 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2295 /* Handle DMPlex refinement */ 2296 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 2297 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 2298 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2299 if (refine && isHierarchy) { 2300 DM *dms, coarseDM; 2301 2302 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2303 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2304 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2305 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2306 /* Total hack since we do not pass in a pointer */ 2307 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2308 if (refine == 1) { 2309 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2310 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2311 } else { 2312 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2313 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2314 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2315 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2316 } 2317 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2318 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2319 /* Free DMs */ 2320 for (r = 0; r < refine; ++r) { 2321 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2322 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2323 } 2324 ierr = PetscFree(dms);CHKERRQ(ierr); 2325 } else { 2326 for (r = 0; r < refine; ++r) { 2327 DM refinedMesh; 2328 2329 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2330 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 2331 /* Total hack since we do not pass in a pointer */ 2332 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 2333 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2334 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 2335 } 2336 } 2337 /* Handle DMPlex coarsening */ 2338 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 2339 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 2340 if (coarsen && isHierarchy) { 2341 DM *dms; 2342 2343 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2344 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2345 /* Free DMs */ 2346 for (r = 0; r < coarsen; ++r) { 2347 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2348 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2349 } 2350 ierr = PetscFree(dms);CHKERRQ(ierr); 2351 } else { 2352 for (r = 0; r < coarsen; ++r) { 2353 DM coarseMesh; 2354 2355 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2356 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 2357 /* Total hack since we do not pass in a pointer */ 2358 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 2359 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2360 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 2361 } 2362 } 2363 /* Handle */ 2364 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2365 ierr = PetscOptionsTail();CHKERRQ(ierr); 2366 PetscFunctionReturn(0); 2367 } 2368 2369 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2370 { 2371 PetscErrorCode ierr; 2372 2373 PetscFunctionBegin; 2374 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2375 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2376 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2377 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2378 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2379 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2380 PetscFunctionReturn(0); 2381 } 2382 2383 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2384 { 2385 PetscErrorCode ierr; 2386 2387 PetscFunctionBegin; 2388 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2389 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2390 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2391 PetscFunctionReturn(0); 2392 } 2393 2394 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2395 { 2396 PetscInt depth, d; 2397 PetscErrorCode ierr; 2398 2399 PetscFunctionBegin; 2400 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2401 if (depth == 1) { 2402 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2403 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2404 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2405 else {*pStart = 0; *pEnd = 0;} 2406 } else { 2407 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2408 } 2409 PetscFunctionReturn(0); 2410 } 2411 2412 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2413 { 2414 PetscSF sf; 2415 PetscErrorCode ierr; 2416 2417 PetscFunctionBegin; 2418 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2419 ierr = PetscSFGetRootRanks(sf, nranks, ranks, NULL, NULL, NULL);CHKERRQ(ierr); 2420 PetscFunctionReturn(0); 2421 } 2422 2423 static PetscErrorCode DMInitialize_Plex(DM dm) 2424 { 2425 PetscErrorCode ierr; 2426 2427 PetscFunctionBegin; 2428 dm->ops->view = DMView_Plex; 2429 dm->ops->load = DMLoad_Plex; 2430 dm->ops->setfromoptions = DMSetFromOptions_Plex; 2431 dm->ops->clone = DMClone_Plex; 2432 dm->ops->setup = DMSetUp_Plex; 2433 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 2434 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 2435 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 2436 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 2437 dm->ops->getlocaltoglobalmapping = NULL; 2438 dm->ops->createfieldis = NULL; 2439 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 2440 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 2441 dm->ops->getcoloring = NULL; 2442 dm->ops->creatematrix = DMCreateMatrix_Plex; 2443 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 2444 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 2445 dm->ops->createinjection = DMCreateInjection_Plex; 2446 dm->ops->refine = DMRefine_Plex; 2447 dm->ops->coarsen = DMCoarsen_Plex; 2448 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 2449 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 2450 dm->ops->adaptlabel = DMAdaptLabel_Plex; 2451 dm->ops->adaptmetric = DMAdaptMetric_Plex; 2452 dm->ops->globaltolocalbegin = NULL; 2453 dm->ops->globaltolocalend = NULL; 2454 dm->ops->localtoglobalbegin = NULL; 2455 dm->ops->localtoglobalend = NULL; 2456 dm->ops->destroy = DMDestroy_Plex; 2457 dm->ops->createsubdm = DMCreateSubDM_Plex; 2458 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 2459 dm->ops->getdimpoints = DMGetDimPoints_Plex; 2460 dm->ops->locatepoints = DMLocatePoints_Plex; 2461 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 2462 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 2463 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 2464 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 2465 dm->ops->computel2diff = DMComputeL2Diff_Plex; 2466 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 2467 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 2468 dm->ops->getneighbors = DMGetNeighbors_Plex; 2469 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 2470 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 2471 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 2472 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 2473 PetscFunctionReturn(0); 2474 } 2475 2476 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 2477 { 2478 DM_Plex *mesh = (DM_Plex *) dm->data; 2479 PetscErrorCode ierr; 2480 2481 PetscFunctionBegin; 2482 mesh->refct++; 2483 (*newdm)->data = mesh; 2484 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 2485 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 2486 PetscFunctionReturn(0); 2487 } 2488 2489 /*MC 2490 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 2491 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 2492 specified by a PetscSection object. Ownership in the global representation is determined by 2493 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 2494 2495 Options Database Keys: 2496 + -dm_plex_hash_location - Use grid hashing for point location 2497 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 2498 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 2499 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 2500 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 2501 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 2502 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 2503 . -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 2504 . -dm_plex_check_geometry - Check that cells have positive volume 2505 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 2506 . -dm_plex_view_scale <num> - Scale the TikZ 2507 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 2508 2509 2510 Level: intermediate 2511 2512 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 2513 M*/ 2514 2515 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 2516 { 2517 DM_Plex *mesh; 2518 PetscInt unit, d; 2519 PetscErrorCode ierr; 2520 2521 PetscFunctionBegin; 2522 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2523 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 2524 dm->dim = 0; 2525 dm->data = mesh; 2526 2527 mesh->refct = 1; 2528 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 2529 mesh->maxConeSize = 0; 2530 mesh->cones = NULL; 2531 mesh->coneOrientations = NULL; 2532 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 2533 mesh->maxSupportSize = 0; 2534 mesh->supports = NULL; 2535 mesh->refinementUniform = PETSC_TRUE; 2536 mesh->refinementLimit = -1.0; 2537 2538 mesh->facesTmp = NULL; 2539 2540 mesh->tetgenOpts = NULL; 2541 mesh->triangleOpts = NULL; 2542 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 2543 mesh->remeshBd = PETSC_FALSE; 2544 2545 mesh->subpointMap = NULL; 2546 2547 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 2548 2549 mesh->regularRefinement = PETSC_FALSE; 2550 mesh->depthState = -1; 2551 mesh->globalVertexNumbers = NULL; 2552 mesh->globalCellNumbers = NULL; 2553 mesh->anchorSection = NULL; 2554 mesh->anchorIS = NULL; 2555 mesh->createanchors = NULL; 2556 mesh->computeanchormatrix = NULL; 2557 mesh->parentSection = NULL; 2558 mesh->parents = NULL; 2559 mesh->childIDs = NULL; 2560 mesh->childSection = NULL; 2561 mesh->children = NULL; 2562 mesh->referenceTree = NULL; 2563 mesh->getchildsymmetry = NULL; 2564 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 2565 mesh->vtkCellHeight = 0; 2566 mesh->useAnchors = PETSC_FALSE; 2567 2568 mesh->maxProjectionHeight = 0; 2569 2570 mesh->printSetValues = PETSC_FALSE; 2571 mesh->printFEM = 0; 2572 mesh->printTol = 1.0e-10; 2573 2574 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2575 PetscFunctionReturn(0); 2576 } 2577 2578 /*@ 2579 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 2580 2581 Collective 2582 2583 Input Parameter: 2584 . comm - The communicator for the DMPlex object 2585 2586 Output Parameter: 2587 . mesh - The DMPlex object 2588 2589 Level: beginner 2590 2591 @*/ 2592 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 2593 { 2594 PetscErrorCode ierr; 2595 2596 PetscFunctionBegin; 2597 PetscValidPointer(mesh,2); 2598 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 2599 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 2600 PetscFunctionReturn(0); 2601 } 2602 2603 /* 2604 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 2605 */ 2606 /* TODO: invertCells and spaceDim arguments could be added also to to DMPlexCreateFromCellListParallel(), DMPlexBuildFromCellList_Internal() and DMPlexCreateFromCellList() */ 2607 PetscErrorCode DMPlexBuildFromCellList_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells, PetscSF *sfVert) 2608 { 2609 PetscSF sfPoint; 2610 PetscLayout vLayout; 2611 PetscHSetI vhash; 2612 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 2613 const PetscInt *vrange; 2614 PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; 2615 PetscMPIInt rank, size; 2616 PetscErrorCode ierr; 2617 2618 PetscFunctionBegin; 2619 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2620 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2621 /* Partition vertices */ 2622 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 2623 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 2624 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 2625 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 2626 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 2627 /* Count vertices and map them to procs */ 2628 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 2629 for (c = 0; c < numCells; ++c) { 2630 for (p = 0; p < numCorners; ++p) { 2631 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 2632 } 2633 } 2634 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 2635 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 2636 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 2637 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 2638 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 2639 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 2640 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 2641 for (v = 0; v < numVerticesAdj; ++v) { 2642 const PetscInt gv = verticesAdj[v]; 2643 PetscInt vrank; 2644 2645 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 2646 vrank = vrank < 0 ? -(vrank+2) : vrank; 2647 remoteVerticesAdj[v].index = gv - vrange[vrank]; 2648 remoteVerticesAdj[v].rank = vrank; 2649 } 2650 /* Create cones */ 2651 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 2652 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 2653 ierr = DMSetUp(dm);CHKERRQ(ierr); 2654 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2655 for (c = 0; c < numCells; ++c) { 2656 for (p = 0; p < numCorners; ++p) { 2657 const PetscInt gv = cells[c*numCorners+p]; 2658 PetscInt lv; 2659 2660 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 2661 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 2662 cone[p] = lv+numCells; 2663 } 2664 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2665 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2666 } 2667 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2668 /* Create SF for vertices */ 2669 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); 2670 ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 2671 ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); 2672 ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 2673 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 2674 /* Build pointSF */ 2675 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 2676 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 2677 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 2678 ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2679 ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2680 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); 2681 ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2682 ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2683 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 2684 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 2685 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 2686 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 2687 if (vertexLocal[v].rank != rank) { 2688 localVertex[g] = v+numCells; 2689 remoteVertex[g].index = vertexLocal[v].index; 2690 remoteVertex[g].rank = vertexLocal[v].rank; 2691 ++g; 2692 } 2693 } 2694 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 2695 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 2696 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2697 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 2698 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 2699 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 2700 /* Fill in the rest of the topology structure */ 2701 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2702 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2703 PetscFunctionReturn(0); 2704 } 2705 2706 /* 2707 This takes as input the coordinates for each owned vertex 2708 */ 2709 PetscErrorCode DMPlexBuildCoordinates_Parallel_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) 2710 { 2711 PetscSection coordSection; 2712 Vec coordinates; 2713 PetscScalar *coords; 2714 PetscInt numVertices, numVerticesAdj, coordSize, v; 2715 PetscErrorCode ierr; 2716 2717 PetscFunctionBegin; 2718 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2719 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 2720 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2721 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2722 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2723 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); 2724 for (v = numCells; v < numCells+numVerticesAdj; ++v) { 2725 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2726 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2727 } 2728 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2729 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2730 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 2731 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2732 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2733 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2734 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2735 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2736 { 2737 MPI_Datatype coordtype; 2738 2739 /* Need a temp buffer for coords if we have complex/single */ 2740 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 2741 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 2742 #if defined(PETSC_USE_COMPLEX) 2743 { 2744 PetscScalar *svertexCoords; 2745 PetscInt i; 2746 ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); 2747 for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 2748 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2749 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2750 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 2751 } 2752 #else 2753 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2754 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2755 #endif 2756 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 2757 } 2758 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2759 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2760 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2761 PetscFunctionReturn(0); 2762 } 2763 2764 /*@ 2765 DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2766 2767 Input Parameters: 2768 + comm - The communicator 2769 . dim - The topological dimension of the mesh 2770 . numCells - The number of cells owned by this process 2771 . numVertices - The number of vertices owned by this process 2772 . numCorners - The number of vertices for each cell 2773 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2774 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2775 . spaceDim - The spatial dimension used for coordinates 2776 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2777 2778 Output Parameter: 2779 + dm - The DM 2780 - vertexSF - Optional, SF describing complete vertex ownership 2781 2782 Note: Two triangles sharing a face 2783 $ 2784 $ 2 2785 $ / | \ 2786 $ / | \ 2787 $ / | \ 2788 $ 0 0 | 1 3 2789 $ \ | / 2790 $ \ | / 2791 $ \ | / 2792 $ 1 2793 would have input 2794 $ numCells = 2, numVertices = 4 2795 $ cells = [0 1 2 1 3 2] 2796 $ 2797 which would result in the DMPlex 2798 $ 2799 $ 4 2800 $ / | \ 2801 $ / | \ 2802 $ / | \ 2803 $ 2 0 | 1 5 2804 $ \ | / 2805 $ \ | / 2806 $ \ | / 2807 $ 3 2808 2809 Level: beginner 2810 2811 .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 2812 @*/ 2813 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) 2814 { 2815 PetscSF sfVert; 2816 PetscErrorCode ierr; 2817 2818 PetscFunctionBegin; 2819 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2820 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2821 PetscValidLogicalCollectiveInt(*dm, dim, 2); 2822 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 2823 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2824 ierr = DMPlexBuildFromCellList_Parallel_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE, &sfVert);CHKERRQ(ierr); 2825 if (interpolate) { 2826 DM idm; 2827 2828 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2829 ierr = DMDestroy(dm);CHKERRQ(ierr); 2830 *dm = idm; 2831 } 2832 ierr = DMPlexBuildCoordinates_Parallel_Internal(*dm, spaceDim, numCells, numVertices, sfVert, vertexCoords);CHKERRQ(ierr); 2833 if (vertexSF) *vertexSF = sfVert; 2834 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 2835 PetscFunctionReturn(0); 2836 } 2837 2838 /* 2839 This takes as input the common mesh generator output, a list of the vertices for each cell 2840 */ 2841 PetscErrorCode DMPlexBuildFromCellList_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscBool invertCells) 2842 { 2843 PetscInt *cone, c, p; 2844 PetscErrorCode ierr; 2845 2846 PetscFunctionBegin; 2847 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 2848 for (c = 0; c < numCells; ++c) { 2849 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 2850 } 2851 ierr = DMSetUp(dm);CHKERRQ(ierr); 2852 ierr = DMGetWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2853 for (c = 0; c < numCells; ++c) { 2854 for (p = 0; p < numCorners; ++p) { 2855 cone[p] = cells[c*numCorners+p]+numCells; 2856 } 2857 if (invertCells) { ierr = DMPlexInvertCell_Internal(spaceDim, numCorners, cone);CHKERRQ(ierr); } 2858 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 2859 } 2860 ierr = DMRestoreWorkArray(dm, numCorners, MPIU_INT, &cone);CHKERRQ(ierr); 2861 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2862 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2863 PetscFunctionReturn(0); 2864 } 2865 2866 /* 2867 This takes as input the coordinates for each vertex 2868 */ 2869 PetscErrorCode DMPlexBuildCoordinates_Internal(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 2870 { 2871 PetscSection coordSection; 2872 Vec coordinates; 2873 DM cdm; 2874 PetscScalar *coords; 2875 PetscInt v, d; 2876 PetscErrorCode ierr; 2877 2878 PetscFunctionBegin; 2879 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2880 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2881 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2882 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2883 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 2884 for (v = numCells; v < numCells+numVertices; ++v) { 2885 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2886 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2887 } 2888 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2889 2890 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2891 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 2892 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2893 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2894 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2895 for (v = 0; v < numVertices; ++v) { 2896 for (d = 0; d < spaceDim; ++d) { 2897 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 2898 } 2899 } 2900 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2901 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2902 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2903 PetscFunctionReturn(0); 2904 } 2905 2906 /*@ 2907 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2908 2909 Input Parameters: 2910 + comm - The communicator 2911 . dim - The topological dimension of the mesh 2912 . numCells - The number of cells 2913 . numVertices - The number of vertices 2914 . numCorners - The number of vertices for each cell 2915 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2916 . cells - An array of numCells*numCorners numbers, the vertices for each cell 2917 . spaceDim - The spatial dimension used for coordinates 2918 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2919 2920 Output Parameter: 2921 . dm - The DM 2922 2923 Note: Two triangles sharing a face 2924 $ 2925 $ 2 2926 $ / | \ 2927 $ / | \ 2928 $ / | \ 2929 $ 0 0 | 1 3 2930 $ \ | / 2931 $ \ | / 2932 $ \ | / 2933 $ 1 2934 would have input 2935 $ numCells = 2, numVertices = 4 2936 $ cells = [0 1 2 1 3 2] 2937 $ 2938 which would result in the DMPlex 2939 $ 2940 $ 4 2941 $ / | \ 2942 $ / | \ 2943 $ / | \ 2944 $ 2 0 | 1 5 2945 $ \ | / 2946 $ \ | / 2947 $ \ | / 2948 $ 3 2949 2950 Level: beginner 2951 2952 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 2953 @*/ 2954 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) 2955 { 2956 PetscErrorCode ierr; 2957 2958 PetscFunctionBegin; 2959 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2960 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2961 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2962 ierr = DMPlexBuildFromCellList_Internal(*dm, spaceDim, numCells, numVertices, numCorners, cells, PETSC_FALSE);CHKERRQ(ierr); 2963 if (interpolate) { 2964 DM idm; 2965 2966 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2967 ierr = DMDestroy(dm);CHKERRQ(ierr); 2968 *dm = idm; 2969 } 2970 ierr = DMPlexBuildCoordinates_Internal(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 2971 PetscFunctionReturn(0); 2972 } 2973 2974 /*@ 2975 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 2976 2977 Input Parameters: 2978 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 2979 . depth - The depth of the DAG 2980 . numPoints - Array of size depth + 1 containing the number of points at each depth 2981 . coneSize - The cone size of each point 2982 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 2983 . coneOrientations - The orientation of each cone point 2984 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 2985 2986 Output Parameter: 2987 . dm - The DM 2988 2989 Note: Two triangles sharing a face would have input 2990 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 2991 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 2992 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 2993 $ 2994 which would result in the DMPlex 2995 $ 2996 $ 4 2997 $ / | \ 2998 $ / | \ 2999 $ / | \ 3000 $ 2 0 | 1 5 3001 $ \ | / 3002 $ \ | / 3003 $ \ | / 3004 $ 3 3005 $ 3006 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 3007 3008 Level: advanced 3009 3010 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 3011 @*/ 3012 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3013 { 3014 Vec coordinates; 3015 PetscSection coordSection; 3016 PetscScalar *coords; 3017 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3018 PetscErrorCode ierr; 3019 3020 PetscFunctionBegin; 3021 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3022 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3023 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 3024 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3025 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3026 for (p = pStart; p < pEnd; ++p) { 3027 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3028 if (firstVertex < 0 && !coneSize[p - pStart]) { 3029 firstVertex = p - pStart; 3030 } 3031 } 3032 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 3033 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3034 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3035 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3036 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3037 } 3038 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3039 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3040 /* Build coordinates */ 3041 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3042 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3043 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3044 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3045 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3046 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3047 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3048 } 3049 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3050 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3051 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3052 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3053 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3054 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3055 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3056 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3057 for (v = 0; v < numPoints[0]; ++v) { 3058 PetscInt off; 3059 3060 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3061 for (d = 0; d < dimEmbed; ++d) { 3062 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3063 } 3064 } 3065 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3066 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3067 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3068 PetscFunctionReturn(0); 3069 } 3070 3071 /*@C 3072 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3073 3074 + comm - The MPI communicator 3075 . filename - Name of the .dat file 3076 - interpolate - Create faces and edges in the mesh 3077 3078 Output Parameter: 3079 . dm - The DM object representing the mesh 3080 3081 Note: The format is the simplest possible: 3082 $ Ne 3083 $ v0 v1 ... vk 3084 $ Nv 3085 $ x y z marker 3086 3087 Level: beginner 3088 3089 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3090 @*/ 3091 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3092 { 3093 DMLabel marker; 3094 PetscViewer viewer; 3095 Vec coordinates; 3096 PetscSection coordSection; 3097 PetscScalar *coords; 3098 char line[PETSC_MAX_PATH_LEN]; 3099 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 3100 PetscMPIInt rank; 3101 int snum, Nv, Nc; 3102 PetscErrorCode ierr; 3103 3104 PetscFunctionBegin; 3105 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3106 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3107 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 3108 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3109 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3110 if (!rank) { 3111 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 3112 snum = sscanf(line, "%d %d", &Nc, &Nv); 3113 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3114 } else { 3115 Nc = Nv = 0; 3116 } 3117 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3118 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3119 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 3120 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3121 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 3122 /* Read topology */ 3123 if (!rank) { 3124 PetscInt cone[8], corners = 8; 3125 int vbuf[8], v; 3126 3127 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 3128 ierr = DMSetUp(*dm);CHKERRQ(ierr); 3129 for (c = 0; c < Nc; ++c) { 3130 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 3131 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]); 3132 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3133 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 3134 /* Hexahedra are inverted */ 3135 { 3136 PetscInt tmp = cone[1]; 3137 cone[1] = cone[3]; 3138 cone[3] = tmp; 3139 } 3140 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 3141 } 3142 } 3143 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 3144 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 3145 /* Read coordinates */ 3146 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 3147 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3148 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 3149 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 3150 for (v = Nc; v < Nc+Nv; ++v) { 3151 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 3152 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 3153 } 3154 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3155 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3156 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3157 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3158 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3159 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 3160 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 3161 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3162 if (!rank) { 3163 double x[3]; 3164 int val; 3165 3166 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 3167 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 3168 for (v = 0; v < Nv; ++v) { 3169 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 3170 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 3171 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3172 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 3173 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 3174 } 3175 } 3176 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3177 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 3178 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3179 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3180 if (interpolate) { 3181 DM idm; 3182 DMLabel bdlabel; 3183 3184 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3185 ierr = DMDestroy(dm);CHKERRQ(ierr); 3186 *dm = idm; 3187 3188 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 3189 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 3190 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 3191 } 3192 PetscFunctionReturn(0); 3193 } 3194 3195 /*@C 3196 DMPlexCreateFromFile - This takes a filename and produces a DM 3197 3198 Input Parameters: 3199 + comm - The communicator 3200 . filename - A file name 3201 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 3202 3203 Output Parameter: 3204 . dm - The DM 3205 3206 Options Database Keys: 3207 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 3208 3209 Level: beginner 3210 3211 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate() 3212 @*/ 3213 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3214 { 3215 const char *extGmsh = ".msh"; 3216 const char *extGmsh2 = ".msh2"; 3217 const char *extGmsh4 = ".msh4"; 3218 const char *extCGNS = ".cgns"; 3219 const char *extExodus = ".exo"; 3220 const char *extGenesis = ".gen"; 3221 const char *extFluent = ".cas"; 3222 const char *extHDF5 = ".h5"; 3223 const char *extMed = ".med"; 3224 const char *extPLY = ".ply"; 3225 const char *extCV = ".dat"; 3226 size_t len; 3227 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV; 3228 PetscMPIInt rank; 3229 PetscErrorCode ierr; 3230 3231 PetscFunctionBegin; 3232 PetscValidPointer(filename, 2); 3233 PetscValidPointer(dm, 4); 3234 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3235 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 3236 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 3237 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 3238 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 3239 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 3240 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 3241 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 3242 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 3243 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 3244 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 3245 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 3246 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 3247 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 3248 if (isGmsh || isGmsh2 || isGmsh4) { 3249 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3250 } else if (isCGNS) { 3251 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3252 } else if (isExodus || isGenesis) { 3253 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3254 } else if (isFluent) { 3255 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3256 } else if (isHDF5) { 3257 PetscBool load_hdf5_xdmf = PETSC_FALSE; 3258 PetscViewer viewer; 3259 3260 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 3261 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 3262 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 3263 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3264 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 3265 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3266 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3267 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3268 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3269 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 3270 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 3271 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 3272 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3273 3274 if (interpolate) { 3275 DM idm; 3276 3277 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3278 ierr = DMDestroy(dm);CHKERRQ(ierr); 3279 *dm = idm; 3280 } 3281 } else if (isMed) { 3282 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3283 } else if (isPLY) { 3284 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3285 } else if (isCV) { 3286 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3287 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 3288 PetscFunctionReturn(0); 3289 } 3290 3291 /*@ 3292 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3293 3294 Collective 3295 3296 Input Parameters: 3297 + comm - The communicator 3298 . dim - The spatial dimension 3299 - simplex - Flag for simplex, otherwise use a tensor-product cell 3300 3301 Output Parameter: 3302 . refdm - The reference cell 3303 3304 Level: intermediate 3305 3306 .seealso: 3307 @*/ 3308 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 3309 { 3310 DM rdm; 3311 Vec coords; 3312 PetscErrorCode ierr; 3313 3314 PetscFunctionBeginUser; 3315 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 3316 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 3317 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 3318 switch (dim) { 3319 case 0: 3320 { 3321 PetscInt numPoints[1] = {1}; 3322 PetscInt coneSize[1] = {0}; 3323 PetscInt cones[1] = {0}; 3324 PetscInt coneOrientations[1] = {0}; 3325 PetscScalar vertexCoords[1] = {0.0}; 3326 3327 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3328 } 3329 break; 3330 case 1: 3331 { 3332 PetscInt numPoints[2] = {2, 1}; 3333 PetscInt coneSize[3] = {2, 0, 0}; 3334 PetscInt cones[2] = {1, 2}; 3335 PetscInt coneOrientations[2] = {0, 0}; 3336 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3337 3338 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3339 } 3340 break; 3341 case 2: 3342 if (simplex) { 3343 PetscInt numPoints[2] = {3, 1}; 3344 PetscInt coneSize[4] = {3, 0, 0, 0}; 3345 PetscInt cones[3] = {1, 2, 3}; 3346 PetscInt coneOrientations[3] = {0, 0, 0}; 3347 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3348 3349 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3350 } else { 3351 PetscInt numPoints[2] = {4, 1}; 3352 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3353 PetscInt cones[4] = {1, 2, 3, 4}; 3354 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3355 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3356 3357 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3358 } 3359 break; 3360 case 3: 3361 if (simplex) { 3362 PetscInt numPoints[2] = {4, 1}; 3363 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3364 PetscInt cones[4] = {1, 3, 2, 4}; 3365 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3366 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}; 3367 3368 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3369 } else { 3370 PetscInt numPoints[2] = {8, 1}; 3371 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3372 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 3373 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3374 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, 3375 -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 } 3379 break; 3380 default: 3381 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 3382 } 3383 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 3384 if (rdm->coordinateDM) { 3385 DM ncdm; 3386 PetscSection cs; 3387 PetscInt pEnd = -1; 3388 3389 ierr = DMGetLocalSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 3390 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 3391 if (pEnd >= 0) { 3392 ierr = DMClone(*refdm, &ncdm);CHKERRQ(ierr); 3393 ierr = DMCopyDisc(rdm->coordinateDM, ncdm);CHKERRQ(ierr); 3394 ierr = DMSetLocalSection(ncdm, cs);CHKERRQ(ierr); 3395 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 3396 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 3397 } 3398 } 3399 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 3400 if (coords) { 3401 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 3402 } else { 3403 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 3404 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 3405 } 3406 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 3407 PetscFunctionReturn(0); 3408 } 3409