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 PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList; 7 8 /*@ 9 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 10 11 Collective 12 13 Input Parameters: 14 + comm - The communicator for the DM object 15 . dim - The spatial dimension 16 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 17 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 18 . refinementUniform - Flag for uniform parallel refinement 19 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 20 21 Output Parameter: 22 . dm - The DM object 23 24 Level: beginner 25 26 .seealso: DMSetType(), DMCreate() 27 @*/ 28 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 29 { 30 DM dm; 31 PetscInt p; 32 PetscMPIInt rank; 33 PetscErrorCode ierr; 34 35 PetscFunctionBegin; 36 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 37 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 38 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 39 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 40 switch (dim) { 41 case 2: 42 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 43 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 44 break; 45 case 3: 46 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 47 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 48 break; 49 default: 50 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 51 } 52 if (rank) { 53 PetscInt numPoints[2] = {0, 0}; 54 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 55 } else { 56 switch (dim) { 57 case 2: 58 if (simplex) { 59 PetscInt numPoints[2] = {4, 2}; 60 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 61 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 62 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 63 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 64 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 65 66 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 67 for (p = 0; p < 4; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 68 } else { 69 PetscInt numPoints[2] = {6, 2}; 70 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 71 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 72 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 73 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}; 74 75 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 76 } 77 break; 78 case 3: 79 if (simplex) { 80 PetscInt numPoints[2] = {5, 2}; 81 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 82 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 83 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 84 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}; 85 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 86 87 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 88 for (p = 0; p < 5; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 89 } else { 90 PetscInt numPoints[2] = {12, 2}; 91 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 92 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 93 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 94 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, 95 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 96 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 97 98 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 99 } 100 break; 101 default: 102 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 103 } 104 } 105 *newdm = dm; 106 if (refinementLimit > 0.0) { 107 DM rdm; 108 const char *name; 109 110 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 111 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 112 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 113 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 114 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 115 ierr = DMDestroy(newdm);CHKERRQ(ierr); 116 *newdm = rdm; 117 } 118 if (interpolate) { 119 DM idm; 120 121 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 122 ierr = DMDestroy(newdm);CHKERRQ(ierr); 123 *newdm = idm; 124 } 125 { 126 DM refinedMesh = NULL; 127 DM distributedMesh = NULL; 128 129 /* Distribute mesh over processes */ 130 ierr = DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);CHKERRQ(ierr); 131 if (distributedMesh) { 132 ierr = DMDestroy(newdm);CHKERRQ(ierr); 133 *newdm = distributedMesh; 134 } 135 if (refinementUniform) { 136 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 137 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 138 if (refinedMesh) { 139 ierr = DMDestroy(newdm);CHKERRQ(ierr); 140 *newdm = refinedMesh; 141 } 142 } 143 } 144 PetscFunctionReturn(0); 145 } 146 147 /*@ 148 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 149 150 Collective 151 152 Input Parameters: 153 + comm - The communicator for the DM object 154 . lower - The lower left corner coordinates 155 . upper - The upper right corner coordinates 156 - edges - The number of cells in each direction 157 158 Output Parameter: 159 . dm - The DM object 160 161 Note: Here is the numbering returned for 2 cells in each direction: 162 $ 18--5-17--4--16 163 $ | | | 164 $ 6 10 3 165 $ | | | 166 $ 19-11-20--9--15 167 $ | | | 168 $ 7 8 2 169 $ | | | 170 $ 12--0-13--1--14 171 172 Level: beginner 173 174 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 175 @*/ 176 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 177 { 178 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 179 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 180 PetscInt markerTop = 1; 181 PetscInt markerBottom = 1; 182 PetscInt markerRight = 1; 183 PetscInt markerLeft = 1; 184 PetscBool markerSeparate = PETSC_FALSE; 185 Vec coordinates; 186 PetscSection coordSection; 187 PetscScalar *coords; 188 PetscInt coordSize; 189 PetscMPIInt rank; 190 PetscInt v, vx, vy; 191 PetscErrorCode ierr; 192 193 PetscFunctionBegin; 194 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 195 if (markerSeparate) { 196 markerTop = 3; 197 markerBottom = 1; 198 markerRight = 2; 199 markerLeft = 4; 200 } 201 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 202 if (!rank) { 203 PetscInt e, ex, ey; 204 205 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 206 for (e = 0; e < numEdges; ++e) { 207 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 208 } 209 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 210 for (vx = 0; vx <= edges[0]; vx++) { 211 for (ey = 0; ey < edges[1]; ey++) { 212 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 213 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 214 PetscInt cone[2]; 215 216 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 217 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 218 if (vx == edges[0]) { 219 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 220 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 221 if (ey == edges[1]-1) { 222 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 223 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);CHKERRQ(ierr); 224 } 225 } else if (vx == 0) { 226 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 227 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 228 if (ey == edges[1]-1) { 229 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 230 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);CHKERRQ(ierr); 231 } 232 } 233 } 234 } 235 for (vy = 0; vy <= edges[1]; vy++) { 236 for (ex = 0; ex < edges[0]; ex++) { 237 PetscInt edge = vy*edges[0] + ex; 238 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 239 PetscInt cone[2]; 240 241 cone[0] = vertex; cone[1] = vertex+1; 242 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 243 if (vy == edges[1]) { 244 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 245 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 246 if (ex == edges[0]-1) { 247 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 248 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);CHKERRQ(ierr); 249 } 250 } else if (vy == 0) { 251 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 252 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 253 if (ex == edges[0]-1) { 254 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 255 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);CHKERRQ(ierr); 256 } 257 } 258 } 259 } 260 } 261 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 262 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 263 /* Build coordinates */ 264 ierr = DMSetCoordinateDim(dm, 2);CHKERRQ(ierr); 265 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 266 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 267 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 268 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 269 for (v = numEdges; v < numEdges+numVertices; ++v) { 270 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 271 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 272 } 273 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 274 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 275 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 276 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 277 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 278 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 279 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 280 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 281 for (vy = 0; vy <= edges[1]; ++vy) { 282 for (vx = 0; vx <= edges[0]; ++vx) { 283 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 284 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 285 } 286 } 287 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 288 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 289 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 290 PetscFunctionReturn(0); 291 } 292 293 /*@ 294 DMPlexCreateCubeBoundary - Creates a 2D mesh that is the boundary of a cubic lattice. 295 296 Collective 297 298 Input Parameters: 299 + comm - The communicator for the DM object 300 . lower - The lower left front corner coordinates 301 . upper - The upper right back corner coordinates 302 - faces - The number of faces in each direction (the same as the number of cells) 303 304 Output Parameter: 305 . dm - The DM object 306 307 Level: beginner 308 309 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 310 @*/ 311 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 312 { 313 PetscInt vertices[3], numVertices; 314 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 315 Vec coordinates; 316 PetscSection coordSection; 317 PetscScalar *coords; 318 PetscInt coordSize; 319 PetscMPIInt rank; 320 PetscInt v, vx, vy, vz; 321 PetscInt voffset, iface=0, cone[4]; 322 PetscErrorCode ierr; 323 324 PetscFunctionBegin; 325 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"); 326 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 327 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 328 numVertices = vertices[0]*vertices[1]*vertices[2]; 329 if (!rank) { 330 PetscInt f; 331 332 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 333 for (f = 0; f < numFaces; ++f) { 334 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 335 } 336 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 337 338 /* Side 0 (Top) */ 339 for (vy = 0; vy < faces[1]; vy++) { 340 for (vx = 0; vx < faces[0]; vx++) { 341 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 342 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 343 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 344 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 345 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 346 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 347 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 348 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 349 iface++; 350 } 351 } 352 353 /* Side 1 (Bottom) */ 354 for (vy = 0; vy < faces[1]; vy++) { 355 for (vx = 0; vx < faces[0]; vx++) { 356 voffset = numFaces + vy*(faces[0]+1) + vx; 357 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 358 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 359 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 360 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 361 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 362 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 363 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 364 iface++; 365 } 366 } 367 368 /* Side 2 (Front) */ 369 for (vz = 0; vz < faces[2]; vz++) { 370 for (vx = 0; vx < faces[0]; vx++) { 371 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 372 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 373 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 374 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 375 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 376 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 377 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 378 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 379 iface++; 380 } 381 } 382 383 /* Side 3 (Back) */ 384 for (vz = 0; vz < faces[2]; vz++) { 385 for (vx = 0; vx < faces[0]; vx++) { 386 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 387 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 388 cone[2] = voffset+1; cone[3] = voffset; 389 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 390 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 391 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 392 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 393 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 394 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 395 iface++; 396 } 397 } 398 399 /* Side 4 (Left) */ 400 for (vz = 0; vz < faces[2]; vz++) { 401 for (vy = 0; vy < faces[1]; vy++) { 402 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 403 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 404 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 405 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 406 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 407 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 408 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 409 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);CHKERRQ(ierr); 410 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 411 iface++; 412 } 413 } 414 415 /* Side 5 (Right) */ 416 for (vz = 0; vz < faces[2]; vz++) { 417 for (vy = 0; vy < faces[1]; vy++) { 418 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 419 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 420 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 421 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 422 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 423 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 424 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 425 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 426 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 427 iface++; 428 } 429 } 430 } 431 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 432 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 433 /* Build coordinates */ 434 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 435 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 436 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 437 for (v = numFaces; v < numFaces+numVertices; ++v) { 438 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 439 } 440 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 441 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 442 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 443 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 444 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 445 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 446 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 447 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 448 for (vz = 0; vz <= faces[2]; ++vz) { 449 for (vy = 0; vy <= faces[1]; ++vy) { 450 for (vx = 0; vx <= faces[0]; ++vx) { 451 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 452 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 453 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 454 } 455 } 456 } 457 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 458 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 459 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 460 PetscFunctionReturn(0); 461 } 462 463 static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm) 464 { 465 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 466 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 467 PetscScalar *vertexCoords; 468 PetscReal L,maxCell; 469 PetscBool markerSeparate = PETSC_FALSE; 470 PetscInt markerLeft = 1, faceMarkerLeft = 1; 471 PetscInt markerRight = 1, faceMarkerRight = 2; 472 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 473 PetscMPIInt rank; 474 PetscErrorCode ierr; 475 476 PetscFunctionBegin; 477 PetscValidPointer(dm,4); 478 479 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 480 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 481 ierr = DMSetDimension(*dm,1);CHKERRQ(ierr); 482 ierr = DMCreateLabel(*dm,"marker");CHKERRQ(ierr); 483 ierr = DMCreateLabel(*dm,"Face Sets");CHKERRQ(ierr); 484 485 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 486 if (!rank) numCells = segments; 487 if (!rank) numVerts = segments + (wrap ? 0 : 1); 488 489 numPoints[0] = numVerts ; numPoints[1] = numCells; 490 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 491 ierr = PetscArrayzero(coneOrientations,numCells+numVerts);CHKERRQ(ierr); 492 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 493 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 494 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 495 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 496 ierr = DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 497 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 498 499 ierr = PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 500 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 501 if (!wrap && !rank) { 502 ierr = DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);CHKERRQ(ierr); 503 ierr = DMSetLabelValue(*dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 504 ierr = DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 505 ierr = DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 506 ierr = DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 507 } 508 if (wrap) { 509 L = upper - lower; 510 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 511 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 512 } 513 PetscFunctionReturn(0); 514 } 515 516 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) 517 { 518 DM boundary; 519 PetscInt i; 520 PetscErrorCode ierr; 521 522 PetscFunctionBegin; 523 PetscValidPointer(dm, 4); 524 for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 525 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 526 PetscValidLogicalCollectiveInt(boundary,dim,2); 527 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 528 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 529 ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); 530 switch (dim) { 531 case 2: ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 532 case 3: ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 533 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 534 } 535 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 536 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 537 PetscFunctionReturn(0); 538 } 539 540 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 541 { 542 DMLabel cutLabel = NULL; 543 PetscInt markerTop = 1, faceMarkerTop = 1; 544 PetscInt markerBottom = 1, faceMarkerBottom = 1; 545 PetscInt markerFront = 1, faceMarkerFront = 1; 546 PetscInt markerBack = 1, faceMarkerBack = 1; 547 PetscInt markerRight = 1, faceMarkerRight = 1; 548 PetscInt markerLeft = 1, faceMarkerLeft = 1; 549 PetscInt dim; 550 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 551 PetscMPIInt rank; 552 PetscErrorCode ierr; 553 554 PetscFunctionBegin; 555 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 556 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 557 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 558 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 559 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 560 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 561 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 562 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 563 564 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 565 } 566 switch (dim) { 567 case 2: 568 faceMarkerTop = 3; 569 faceMarkerBottom = 1; 570 faceMarkerRight = 2; 571 faceMarkerLeft = 4; 572 break; 573 case 3: 574 faceMarkerBottom = 1; 575 faceMarkerTop = 2; 576 faceMarkerFront = 3; 577 faceMarkerBack = 4; 578 faceMarkerRight = 5; 579 faceMarkerLeft = 6; 580 break; 581 default: 582 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); 583 break; 584 } 585 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 586 if (markerSeparate) { 587 markerBottom = faceMarkerBottom; 588 markerTop = faceMarkerTop; 589 markerFront = faceMarkerFront; 590 markerBack = faceMarkerBack; 591 markerRight = faceMarkerRight; 592 markerLeft = faceMarkerLeft; 593 } 594 { 595 const PetscInt numXEdges = !rank ? edges[0] : 0; 596 const PetscInt numYEdges = !rank ? edges[1] : 0; 597 const PetscInt numZEdges = !rank ? edges[2] : 0; 598 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 599 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 600 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 601 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 602 const PetscInt numXFaces = numYEdges*numZEdges; 603 const PetscInt numYFaces = numXEdges*numZEdges; 604 const PetscInt numZFaces = numXEdges*numYEdges; 605 const PetscInt numTotXFaces = numXVertices*numXFaces; 606 const PetscInt numTotYFaces = numYVertices*numYFaces; 607 const PetscInt numTotZFaces = numZVertices*numZFaces; 608 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 609 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 610 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 611 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 612 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 613 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 614 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 615 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 616 const PetscInt firstYFace = firstXFace + numTotXFaces; 617 const PetscInt firstZFace = firstYFace + numTotYFaces; 618 const PetscInt firstXEdge = numCells + numFaces + numVertices; 619 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 620 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 621 Vec coordinates; 622 PetscSection coordSection; 623 PetscScalar *coords; 624 PetscInt coordSize; 625 PetscInt v, vx, vy, vz; 626 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 627 628 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 629 for (c = 0; c < numCells; c++) { 630 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 631 } 632 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 633 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 634 } 635 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 636 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 637 } 638 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 639 /* Build cells */ 640 for (fz = 0; fz < numZEdges; ++fz) { 641 for (fy = 0; fy < numYEdges; ++fy) { 642 for (fx = 0; fx < numXEdges; ++fx) { 643 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 644 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 645 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 646 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 647 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 648 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 649 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 650 /* B, T, F, K, R, L */ 651 PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 652 PetscInt cone[6]; 653 654 /* no boundary twisting in 3D */ 655 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 656 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 657 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 658 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 659 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 660 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 661 } 662 } 663 } 664 /* Build x faces */ 665 for (fz = 0; fz < numZEdges; ++fz) { 666 for (fy = 0; fy < numYEdges; ++fy) { 667 for (fx = 0; fx < numXVertices; ++fx) { 668 PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 669 PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; 670 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 671 PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; 672 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 673 PetscInt ornt[4] = {0, 0, -2, -2}; 674 PetscInt cone[4]; 675 676 if (dim == 3) { 677 /* markers */ 678 if (bdX != DM_BOUNDARY_PERIODIC) { 679 if (fx == numXVertices-1) { 680 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 681 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 682 } 683 else if (fx == 0) { 684 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 685 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 686 } 687 } 688 } 689 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 690 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 691 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 692 } 693 } 694 } 695 /* Build y faces */ 696 for (fz = 0; fz < numZEdges; ++fz) { 697 for (fx = 0; fx < numXEdges; ++fx) { 698 for (fy = 0; fy < numYVertices; ++fy) { 699 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 700 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; 701 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 702 PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; 703 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 704 PetscInt ornt[4] = {0, 0, -2, -2}; 705 PetscInt cone[4]; 706 707 if (dim == 3) { 708 /* markers */ 709 if (bdY != DM_BOUNDARY_PERIODIC) { 710 if (fy == numYVertices-1) { 711 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 712 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 713 } 714 else if (fy == 0) { 715 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 716 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 717 } 718 } 719 } 720 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 721 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 722 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 723 } 724 } 725 } 726 /* Build z faces */ 727 for (fy = 0; fy < numYEdges; ++fy) { 728 for (fx = 0; fx < numXEdges; ++fx) { 729 for (fz = 0; fz < numZVertices; fz++) { 730 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 731 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; 732 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 733 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; 734 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 735 PetscInt ornt[4] = {0, 0, -2, -2}; 736 PetscInt cone[4]; 737 738 if (dim == 2) { 739 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 740 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 741 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 742 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 743 } else { 744 /* markers */ 745 if (bdZ != DM_BOUNDARY_PERIODIC) { 746 if (fz == numZVertices-1) { 747 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 748 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 749 } 750 else if (fz == 0) { 751 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 752 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 753 } 754 } 755 } 756 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 757 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 758 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 759 } 760 } 761 } 762 /* Build Z edges*/ 763 for (vy = 0; vy < numYVertices; vy++) { 764 for (vx = 0; vx < numXVertices; vx++) { 765 for (ez = 0; ez < numZEdges; ez++) { 766 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 767 const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; 768 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 769 PetscInt cone[2]; 770 771 if (dim == 3) { 772 if (bdX != DM_BOUNDARY_PERIODIC) { 773 if (vx == numXVertices-1) { 774 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 775 } 776 else if (vx == 0) { 777 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 778 } 779 } 780 if (bdY != DM_BOUNDARY_PERIODIC) { 781 if (vy == numYVertices-1) { 782 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 783 } 784 else if (vy == 0) { 785 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 786 } 787 } 788 } 789 cone[0] = vertexB; cone[1] = vertexT; 790 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 791 } 792 } 793 } 794 /* Build Y edges*/ 795 for (vz = 0; vz < numZVertices; vz++) { 796 for (vx = 0; vx < numXVertices; vx++) { 797 for (ey = 0; ey < numYEdges; ey++) { 798 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 799 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 800 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 801 const PetscInt vertexK = firstVertex + nextv; 802 PetscInt cone[2]; 803 804 cone[0] = vertexF; cone[1] = vertexK; 805 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 806 if (dim == 2) { 807 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 808 if (vx == numXVertices-1) { 809 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 810 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 811 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 812 if (ey == numYEdges-1) { 813 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 814 } 815 } else if (vx == 0) { 816 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 817 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 818 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 819 if (ey == numYEdges-1) { 820 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 821 } 822 } 823 } else { 824 if (vx == 0 && cutLabel) { 825 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 826 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 827 if (ey == numYEdges-1) { 828 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 829 } 830 } 831 } 832 } else { 833 if (bdX != DM_BOUNDARY_PERIODIC) { 834 if (vx == numXVertices-1) { 835 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 836 } else if (vx == 0) { 837 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 838 } 839 } 840 if (bdZ != DM_BOUNDARY_PERIODIC) { 841 if (vz == numZVertices-1) { 842 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 843 } else if (vz == 0) { 844 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 845 } 846 } 847 } 848 } 849 } 850 } 851 /* Build X edges*/ 852 for (vz = 0; vz < numZVertices; vz++) { 853 for (vy = 0; vy < numYVertices; vy++) { 854 for (ex = 0; ex < numXEdges; ex++) { 855 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 856 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 857 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 858 const PetscInt vertexR = firstVertex + nextv; 859 PetscInt cone[2]; 860 861 cone[0] = vertexL; cone[1] = vertexR; 862 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 863 if (dim == 2) { 864 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 865 if (vy == numYVertices-1) { 866 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 867 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 868 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 869 if (ex == numXEdges-1) { 870 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 871 } 872 } else if (vy == 0) { 873 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 874 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 875 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 876 if (ex == numXEdges-1) { 877 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 878 } 879 } 880 } else { 881 if (vy == 0 && cutLabel) { 882 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 883 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 884 if (ex == numXEdges-1) { 885 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 886 } 887 } 888 } 889 } else { 890 if (bdY != DM_BOUNDARY_PERIODIC) { 891 if (vy == numYVertices-1) { 892 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 893 } 894 else if (vy == 0) { 895 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 896 } 897 } 898 if (bdZ != DM_BOUNDARY_PERIODIC) { 899 if (vz == numZVertices-1) { 900 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 901 } 902 else if (vz == 0) { 903 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 904 } 905 } 906 } 907 } 908 } 909 } 910 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 911 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 912 /* Build coordinates */ 913 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 914 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 915 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 916 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 917 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 918 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 919 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 920 } 921 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 922 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 923 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 924 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 925 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 926 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 927 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 928 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 929 for (vz = 0; vz < numZVertices; ++vz) { 930 for (vy = 0; vy < numYVertices; ++vy) { 931 for (vx = 0; vx < numXVertices; ++vx) { 932 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 933 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 934 if (dim == 3) { 935 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 936 } 937 } 938 } 939 } 940 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 941 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 942 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 943 } 944 PetscFunctionReturn(0); 945 } 946 947 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) 948 { 949 PetscInt i; 950 PetscErrorCode ierr; 951 952 PetscFunctionBegin; 953 PetscValidPointer(dm, 7); 954 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 955 PetscValidLogicalCollectiveInt(*dm,dim,2); 956 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 957 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 958 switch (dim) { 959 case 2: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);CHKERRQ(ierr);break;} 960 case 3: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);CHKERRQ(ierr);break;} 961 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 962 } 963 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 964 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 965 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 966 PetscReal L[3]; 967 PetscReal maxCell[3]; 968 969 for (i = 0; i < dim; i++) { 970 L[i] = upper[i] - lower[i]; 971 maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i])); 972 } 973 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);CHKERRQ(ierr); 974 } 975 if (!interpolate) { 976 DM udm; 977 978 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 979 ierr = DMPlexCopyCoordinates(*dm, udm);CHKERRQ(ierr); 980 ierr = DMDestroy(dm);CHKERRQ(ierr); 981 *dm = udm; 982 } 983 PetscFunctionReturn(0); 984 } 985 986 /*@C 987 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 988 989 Collective 990 991 Input Parameters: 992 + comm - The communicator for the DM object 993 . dim - The spatial dimension 994 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 995 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 996 . lower - The lower left corner, or NULL for (0, 0, 0) 997 . upper - The upper right corner, or NULL for (1, 1, 1) 998 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 999 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1000 1001 Output Parameter: 1002 . dm - The DM object 1003 1004 Options Database Keys: 1005 + -dm_plex_box_lower <x,y,z> - Specify lower-left-bottom coordinates for the box 1006 . -dm_plex_box_upper <x,y,z> - Specify upper-right-top coordinates for the box 1007 - -dm_plex_box_faces <m,n,p> - Number of faces in each linear direction 1008 1009 Notes: 1010 The options database keys above take lists of length d in d dimensions. 1011 1012 Here is the numbering returned for 2 faces in each direction for tensor cells: 1013 $ 10---17---11---18----12 1014 $ | | | 1015 $ | | | 1016 $ 20 2 22 3 24 1017 $ | | | 1018 $ | | | 1019 $ 7---15----8---16----9 1020 $ | | | 1021 $ | | | 1022 $ 19 0 21 1 23 1023 $ | | | 1024 $ | | | 1025 $ 4---13----5---14----6 1026 1027 and for simplicial cells 1028 1029 $ 14----8---15----9----16 1030 $ |\ 5 |\ 7 | 1031 $ | \ | \ | 1032 $ 13 2 14 3 15 1033 $ | 4 \ | 6 \ | 1034 $ | \ | \ | 1035 $ 11----6---12----7----13 1036 $ |\ |\ | 1037 $ | \ 1 | \ 3 | 1038 $ 10 0 11 1 12 1039 $ | 0 \ | 2 \ | 1040 $ | \ | \ | 1041 $ 8----4----9----5----10 1042 1043 Level: beginner 1044 1045 .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1046 @*/ 1047 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) 1048 { 1049 PetscInt fac[3] = {0, 0, 0}; 1050 PetscReal low[3] = {0, 0, 0}; 1051 PetscReal upp[3] = {1, 1, 1}; 1052 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1053 PetscInt i, n; 1054 PetscBool flg; 1055 PetscErrorCode ierr; 1056 1057 PetscFunctionBegin; 1058 n = 3; 1059 ierr = PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);CHKERRQ(ierr); 1060 for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim)); 1061 if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i]; 1062 if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i]; 1063 if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i]; 1064 /* Allow bounds to be specified from the command line */ 1065 n = 3; 1066 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);CHKERRQ(ierr); 1067 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 1068 n = 3; 1069 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);CHKERRQ(ierr); 1070 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 1071 1072 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);CHKERRQ(ierr);} 1073 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1074 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1075 PetscFunctionReturn(0); 1076 } 1077 1078 /*@ 1079 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1080 1081 Collective 1082 1083 Input Parameters: 1084 + comm - The communicator for the DM object 1085 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1086 . lower - The lower left corner, or NULL for (0, 0, 0) 1087 . upper - The upper right corner, or NULL for (1, 1, 1) 1088 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1089 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1090 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1091 1092 Output Parameter: 1093 . dm - The DM object 1094 1095 Level: beginner 1096 1097 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1098 @*/ 1099 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1100 { 1101 DM bdm, botdm; 1102 PetscInt i; 1103 PetscInt fac[3] = {0, 0, 0}; 1104 PetscReal low[3] = {0, 0, 0}; 1105 PetscReal upp[3] = {1, 1, 1}; 1106 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1107 PetscErrorCode ierr; 1108 1109 PetscFunctionBegin; 1110 for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1; 1111 if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i]; 1112 if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i]; 1113 if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i]; 1114 for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported"); 1115 1116 ierr = DMCreate(comm, &bdm);CHKERRQ(ierr); 1117 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1118 ierr = DMSetDimension(bdm, 1);CHKERRQ(ierr); 1119 ierr = DMSetCoordinateDim(bdm, 2);CHKERRQ(ierr); 1120 ierr = DMPlexCreateSquareBoundary(bdm, low, upp, fac);CHKERRQ(ierr); 1121 ierr = DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);CHKERRQ(ierr); 1122 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1123 ierr = DMPlexExtrude(botdm, fac[2], upp[2] - low[2], orderHeight, NULL, interpolate, dm);CHKERRQ(ierr); 1124 if (low[2] != 0.0) { 1125 Vec v; 1126 PetscScalar *x; 1127 PetscInt cDim, n; 1128 1129 ierr = DMGetCoordinatesLocal(*dm, &v);CHKERRQ(ierr); 1130 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1131 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1132 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1133 x += cDim; 1134 for (i=0; i<n; i+=cDim) x[i] += low[2]; 1135 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1136 ierr = DMSetCoordinatesLocal(*dm, v);CHKERRQ(ierr); 1137 } 1138 ierr = DMDestroy(&botdm);CHKERRQ(ierr); 1139 PetscFunctionReturn(0); 1140 } 1141 1142 /*@C 1143 DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells. 1144 1145 Collective on idm 1146 1147 Input Parameters: 1148 + idm - The mesh to be extruded 1149 . layers - The number of layers, or PETSC_DETERMINE to use the default 1150 . height - The height of the extruded layer, or PETSC_DETERMINE to use the default 1151 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1152 . extNormal - The normal direction in which the mesh should be extruded, or NULL to extrude using the surface normal 1153 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1154 1155 Output Parameter: 1156 . dm - The DM object 1157 1158 Notes: 1159 The mesh created has prismatic cells, and the vertex ordering in the cone of the cell is that of the tensor prismatic cells. Not currently supported in Fortran. 1160 1161 Options Database Keys: 1162 -dm_plex_extrude_layers <k> - Sets the nubmer of layers k 1163 -dm_plex_extrude_height <h> - Sets the height h of each layer 1164 -dm_plex_extrude_order_height - If true, order cells by height first 1165 -dm_plex_extrude_normal <n0,...,nd> - Sets the normal vector along which to extrude 1166 1167 Level: advanced 1168 1169 .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMSetType(), DMCreate() 1170 @*/ 1171 PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool orderHeight, const PetscReal extNormal[], PetscBool interpolate, DM* dm) 1172 { 1173 PetscScalar *coordsB; 1174 const PetscScalar *coordsA; 1175 PetscReal *normals = NULL; 1176 PetscReal clNormal[3]; 1177 Vec coordinatesA, coordinatesB; 1178 PetscSection coordSectionA, coordSectionB; 1179 PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone; 1180 PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices; 1181 const char *prefix; 1182 PetscBool haveCLNormal; 1183 PetscErrorCode ierr; 1184 1185 PetscFunctionBegin; 1186 PetscValidHeaderSpecific(idm, DM_CLASSID, 1); 1187 PetscValidLogicalCollectiveInt(idm, layers, 2); 1188 PetscValidLogicalCollectiveReal(idm, height, 3); 1189 PetscValidLogicalCollectiveBool(idm, interpolate, 4); 1190 ierr = DMGetDimension(idm, &dim);CHKERRQ(ierr); 1191 ierr = DMGetCoordinateDim(idm, &cDim);CHKERRQ(ierr); 1192 cDimB = cDim == dim ? cDim+1 : cDim; 1193 if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim); 1194 1195 ierr = PetscObjectGetOptionsPrefix((PetscObject) idm, &prefix);CHKERRQ(ierr); 1196 if (layers < 0) layers = 1; 1197 ierr = PetscOptionsGetInt(NULL, prefix, "-dm_plex_extrude_layers", &layers, NULL);CHKERRQ(ierr); 1198 if (layers <= 0) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Number of layers %D must be positive", layers); 1199 if (height < 0.) height = 1.; 1200 ierr = PetscOptionsGetReal(NULL, prefix, "-dm_plex_extrude_height", &height, NULL);CHKERRQ(ierr); 1201 if (height <= 0.) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Height of layers %g must be positive", (double) height); 1202 ierr = PetscOptionsGetBool(NULL, prefix, "-dm_plex_extrude_order_height", &orderHeight, NULL);CHKERRQ(ierr); 1203 c = 3; 1204 ierr = PetscOptionsGetRealArray(NULL, prefix, "-dm_plex_extrude_normal", clNormal, &c, &haveCLNormal);CHKERRQ(ierr); 1205 if (haveCLNormal && c != cDimB) SETERRQ2(PetscObjectComm((PetscObject)idm), PETSC_ERR_ARG_SIZ, "Input normal has size %D != %D extruded coordinate dimension", c, cDimB); 1206 1207 ierr = DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1208 ierr = DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1209 numCells = (cEnd - cStart)*layers; 1210 numVertices = (vEnd - vStart)*(layers+1); 1211 ierr = DMCreate(PetscObjectComm((PetscObject)idm), dm);CHKERRQ(ierr); 1212 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1213 ierr = DMSetDimension(*dm, dim+1);CHKERRQ(ierr); 1214 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1215 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1216 ierr = DMCreateLabel(*dm, "celltype");CHKERRQ(ierr); 1217 for (c = cStart, cellV = 0; c < cEnd; ++c) { 1218 DMPolytopeType ct, nct; 1219 PetscInt *closure = NULL; 1220 PetscInt closureSize, numCorners = 0; 1221 1222 ierr = DMPlexGetCellType(idm, c, &ct);CHKERRQ(ierr); 1223 switch (ct) { 1224 case DM_POLYTOPE_SEGMENT: nct = DM_POLYTOPE_SEG_PRISM_TENSOR;break; 1225 case DM_POLYTOPE_TRIANGLE: nct = DM_POLYTOPE_TRI_PRISM_TENSOR;break; 1226 case DM_POLYTOPE_QUADRILATERAL: nct = DM_POLYTOPE_QUAD_PRISM_TENSOR;break; 1227 default: nct = DM_POLYTOPE_UNKNOWN; 1228 } 1229 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1230 for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++; 1231 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1232 for (l = 0; l < layers; ++l) { 1233 const PetscInt cell = orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart; 1234 1235 ierr = DMPlexSetConeSize(*dm, cell, 2*numCorners);CHKERRQ(ierr); 1236 ierr = DMPlexSetCellType(*dm, cell, nct);CHKERRQ(ierr); 1237 } 1238 cellV = PetscMax(numCorners,cellV); 1239 } 1240 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1241 1242 if (dim != cDim && !(extNormal || haveCLNormal)) {ierr = PetscCalloc1(cDim*(vEnd - vStart), &normals);CHKERRQ(ierr);} 1243 ierr = PetscMalloc1(3*cellV,&newCone);CHKERRQ(ierr); 1244 for (c = cStart; c < cEnd; ++c) { 1245 PetscInt *closure = NULL; 1246 PetscInt closureSize, numCorners = 0, l; 1247 PetscReal normal[3] = {0, 0, 0}; 1248 1249 if (normals) {ierr = DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);CHKERRQ(ierr);} 1250 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1251 for (v = 0; v < closureSize*2; v += 2) { 1252 if ((closure[v] >= vStart) && (closure[v] < vEnd)) { 1253 PetscInt d; 1254 1255 newCone[numCorners++] = closure[v] - vStart; 1256 if (normals) {for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d];} 1257 } 1258 } 1259 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1260 for (l = 0; l < layers; ++l) { 1261 PetscInt i; 1262 1263 for (i = 0; i < numCorners; ++i) { 1264 newCone[ numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells; 1265 newCone[2*numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells; 1266 } 1267 ierr = DMPlexSetCone(*dm, orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);CHKERRQ(ierr); 1268 } 1269 } 1270 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1271 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1272 ierr = PetscFree(newCone);CHKERRQ(ierr); 1273 1274 ierr = DMGetCoordinateSection(*dm, &coordSectionB);CHKERRQ(ierr); 1275 ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr); 1276 ierr = PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);CHKERRQ(ierr); 1277 ierr = PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);CHKERRQ(ierr); 1278 for (v = numCells; v < numCells+numVertices; ++v) { 1279 ierr = PetscSectionSetDof(coordSectionB, v, cDimB);CHKERRQ(ierr); 1280 ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);CHKERRQ(ierr); 1281 ierr = DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1282 } 1283 ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr); 1284 ierr = PetscSectionGetStorageSize(coordSectionB, &coordSize);CHKERRQ(ierr); 1285 ierr = VecCreate(PETSC_COMM_SELF, &coordinatesB);CHKERRQ(ierr); 1286 ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr); 1287 ierr = VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1288 ierr = VecSetBlockSize(coordinatesB, cDimB);CHKERRQ(ierr); 1289 ierr = VecSetType(coordinatesB,VECSTANDARD);CHKERRQ(ierr); 1290 1291 ierr = DMGetCoordinateSection(idm, &coordSectionA);CHKERRQ(ierr); 1292 ierr = DMGetCoordinatesLocal(idm, &coordinatesA);CHKERRQ(ierr); 1293 ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1294 ierr = VecGetArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1295 for (v = vStart; v < vEnd; ++v) { 1296 const PetscScalar *cptr; 1297 PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.}; 1298 PetscReal normal[3]; 1299 PetscReal norm, h = height/layers; 1300 PetscInt offA, d, cDimA = cDim; 1301 1302 if (normals) {for (d = 0; d < cDimB; ++d) normal[d] = normals[cDimB*(v - vStart)+d];} 1303 else if (haveCLNormal) {for (d = 0; d < cDimB; ++d) normal[d] = clNormal[d];} 1304 else if (extNormal) {for (d = 0; d < cDimB; ++d) normal[d] = extNormal[d];} 1305 else if (cDimB == 2) {for (d = 0; d < cDimB; ++d) normal[d] = ones2[d];} 1306 else if (cDimB == 3) {for (d = 0; d < cDimB; ++d) normal[d] = ones3[d];} 1307 else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unable to determine normal for extrusion"); 1308 for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d]; 1309 for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm); 1310 1311 ierr = PetscSectionGetOffset(coordSectionA, v, &offA);CHKERRQ(ierr); 1312 cptr = coordsA + offA; 1313 for (l = 0; l < layers+1; ++l) { 1314 PetscInt offB, d, newV; 1315 1316 newV = orderHeight ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells; 1317 ierr = PetscSectionGetOffset(coordSectionB, newV, &offB);CHKERRQ(ierr); 1318 for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; } 1319 for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; } 1320 cptr = coordsB + offB; 1321 cDimA = cDimB; 1322 } 1323 } 1324 ierr = VecRestoreArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1325 ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1326 ierr = DMSetCoordinatesLocal(*dm, coordinatesB);CHKERRQ(ierr); 1327 ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr); 1328 ierr = PetscFree(normals);CHKERRQ(ierr); 1329 if (interpolate) { 1330 DM idm; 1331 1332 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1333 ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr); 1334 ierr = DMDestroy(dm);CHKERRQ(ierr); 1335 *dm = idm; 1336 } 1337 PetscFunctionReturn(0); 1338 } 1339 1340 /*@C 1341 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1342 1343 Logically Collective on dm 1344 1345 Input Parameters: 1346 + dm - the DM context 1347 - prefix - the prefix to prepend to all option names 1348 1349 Notes: 1350 A hyphen (-) must NOT be given at the beginning of the prefix name. 1351 The first character of all runtime options is AUTOMATICALLY the hyphen. 1352 1353 Level: advanced 1354 1355 .seealso: SNESSetFromOptions() 1356 @*/ 1357 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1358 { 1359 DM_Plex *mesh = (DM_Plex *) dm->data; 1360 PetscErrorCode ierr; 1361 1362 PetscFunctionBegin; 1363 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1364 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1365 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1366 PetscFunctionReturn(0); 1367 } 1368 1369 /*@ 1370 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1371 1372 Collective 1373 1374 Input Parameters: 1375 + comm - The communicator for the DM object 1376 . numRefine - The number of regular refinements to the basic 5 cell structure 1377 - periodicZ - The boundary type for the Z direction 1378 1379 Output Parameter: 1380 . dm - The DM object 1381 1382 Note: Here is the output numbering looking from the bottom of the cylinder: 1383 $ 17-----14 1384 $ | | 1385 $ | 2 | 1386 $ | | 1387 $ 17-----8-----7-----14 1388 $ | | | | 1389 $ | 3 | 0 | 1 | 1390 $ | | | | 1391 $ 19-----5-----6-----13 1392 $ | | 1393 $ | 4 | 1394 $ | | 1395 $ 19-----13 1396 $ 1397 $ and up through the top 1398 $ 1399 $ 18-----16 1400 $ | | 1401 $ | 2 | 1402 $ | | 1403 $ 18----10----11-----16 1404 $ | | | | 1405 $ | 3 | 0 | 1 | 1406 $ | | | | 1407 $ 20-----9----12-----15 1408 $ | | 1409 $ | 4 | 1410 $ | | 1411 $ 20-----15 1412 1413 Level: beginner 1414 1415 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1416 @*/ 1417 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) 1418 { 1419 const PetscInt dim = 3; 1420 PetscInt numCells, numVertices, r; 1421 PetscMPIInt rank; 1422 PetscErrorCode ierr; 1423 1424 PetscFunctionBegin; 1425 PetscValidPointer(dm, 4); 1426 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1427 if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); 1428 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1429 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1430 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1431 /* Create topology */ 1432 { 1433 PetscInt cone[8], c; 1434 1435 numCells = !rank ? 5 : 0; 1436 numVertices = !rank ? 16 : 0; 1437 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1438 numCells *= 3; 1439 numVertices = !rank ? 24 : 0; 1440 } 1441 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1442 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} 1443 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1444 if (!rank) { 1445 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1446 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1447 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1448 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1449 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1450 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1451 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1452 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1453 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1454 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1455 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1456 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1457 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1458 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1459 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1460 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1461 1462 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1463 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1464 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1465 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1466 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1467 ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); 1468 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1469 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1470 ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); 1471 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1472 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1473 ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); 1474 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1475 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1476 ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); 1477 1478 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1479 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1480 ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); 1481 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1482 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1483 ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); 1484 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1485 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1486 ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); 1487 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1488 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1489 ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); 1490 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1491 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1492 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1493 } else { 1494 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1495 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1496 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1497 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1498 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1499 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1500 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1501 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1502 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1503 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1504 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1505 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1506 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1507 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1508 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1509 } 1510 } 1511 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1512 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1513 } 1514 /* Interpolate */ 1515 { 1516 DM idm; 1517 1518 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1519 ierr = DMDestroy(dm);CHKERRQ(ierr); 1520 *dm = idm; 1521 } 1522 /* Create cube geometry */ 1523 { 1524 Vec coordinates; 1525 PetscSection coordSection; 1526 PetscScalar *coords; 1527 PetscInt coordSize, v; 1528 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1529 const PetscReal ds2 = dis/2.0; 1530 1531 /* Build coordinates */ 1532 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1533 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1534 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1535 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1536 for (v = numCells; v < numCells+numVertices; ++v) { 1537 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1538 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1539 } 1540 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1541 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1542 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1543 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1544 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1545 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1546 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1547 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1548 if (!rank) { 1549 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1550 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1551 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1552 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1553 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1554 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1555 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1556 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1557 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1558 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1559 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1560 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1561 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1562 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1563 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1564 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1565 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1566 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1567 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1568 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1569 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1570 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1571 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1572 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1573 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1574 } 1575 } 1576 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1577 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1578 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1579 } 1580 /* Create periodicity */ 1581 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1582 PetscReal L[3]; 1583 PetscReal maxCell[3]; 1584 DMBoundaryType bdType[3]; 1585 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1586 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1587 PetscInt i, numZCells = 3; 1588 1589 bdType[0] = DM_BOUNDARY_NONE; 1590 bdType[1] = DM_BOUNDARY_NONE; 1591 bdType[2] = periodicZ; 1592 for (i = 0; i < dim; i++) { 1593 L[i] = upper[i] - lower[i]; 1594 maxCell[i] = 1.1 * (L[i] / numZCells); 1595 } 1596 ierr = DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1597 } 1598 /* Refine topology */ 1599 for (r = 0; r < numRefine; ++r) { 1600 DM rdm = NULL; 1601 1602 ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); 1603 ierr = DMDestroy(dm);CHKERRQ(ierr); 1604 *dm = rdm; 1605 } 1606 /* Remap geometry to cylinder 1607 Interior square: Linear interpolation is correct 1608 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1609 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1610 1611 phi = arctan(y/x) 1612 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1613 d_far = sqrt(1/2 + sin^2(phi)) 1614 1615 so we remap them using 1616 1617 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1618 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1619 1620 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1621 */ 1622 { 1623 Vec coordinates; 1624 PetscSection coordSection; 1625 PetscScalar *coords; 1626 PetscInt vStart, vEnd, v; 1627 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1628 const PetscReal ds2 = 0.5*dis; 1629 1630 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1631 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1632 ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); 1633 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1634 for (v = vStart; v < vEnd; ++v) { 1635 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1636 PetscInt off; 1637 1638 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 1639 if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; 1640 x = PetscRealPart(coords[off]); 1641 y = PetscRealPart(coords[off+1]); 1642 phi = PetscAtan2Real(y, x); 1643 sinp = PetscSinReal(phi); 1644 cosp = PetscCosReal(phi); 1645 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1646 dc = PetscAbsReal(ds2/sinp); 1647 df = PetscAbsReal(dis/sinp); 1648 xc = ds2*x/PetscAbsReal(y); 1649 yc = ds2*PetscSignReal(y); 1650 } else { 1651 dc = PetscAbsReal(ds2/cosp); 1652 df = PetscAbsReal(dis/cosp); 1653 xc = ds2*PetscSignReal(x); 1654 yc = ds2*y/PetscAbsReal(x); 1655 } 1656 coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); 1657 coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); 1658 } 1659 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1660 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1661 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); 1662 } 1663 } 1664 PetscFunctionReturn(0); 1665 } 1666 1667 /*@ 1668 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1669 1670 Collective 1671 1672 Input Parameters: 1673 + comm - The communicator for the DM object 1674 . n - The number of wedges around the origin 1675 - interpolate - Create edges and faces 1676 1677 Output Parameter: 1678 . dm - The DM object 1679 1680 Level: beginner 1681 1682 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1683 @*/ 1684 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1685 { 1686 const PetscInt dim = 3; 1687 PetscInt numCells, numVertices, v; 1688 PetscMPIInt rank; 1689 PetscErrorCode ierr; 1690 1691 PetscFunctionBegin; 1692 PetscValidPointer(dm, 3); 1693 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1694 if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1695 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1696 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1697 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1698 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1699 ierr = DMCreateLabel(*dm, "celltype");CHKERRQ(ierr); 1700 /* Create topology */ 1701 { 1702 PetscInt cone[6], c; 1703 1704 numCells = !rank ? n : 0; 1705 numVertices = !rank ? 2*(n+1) : 0; 1706 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1707 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 6);CHKERRQ(ierr);} 1708 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1709 for (c = 0; c < numCells; c++) { 1710 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1711 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1712 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 1713 ierr = DMPlexSetCellType(*dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);CHKERRQ(ierr); 1714 } 1715 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1716 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1717 } 1718 for (v = numCells; v < numCells+numVertices; ++v) { 1719 ierr = DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1720 } 1721 /* Interpolate */ 1722 if (interpolate) { 1723 DM idm; 1724 1725 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1726 ierr = DMDestroy(dm);CHKERRQ(ierr); 1727 *dm = idm; 1728 } 1729 /* Create cylinder geometry */ 1730 { 1731 Vec coordinates; 1732 PetscSection coordSection; 1733 PetscScalar *coords; 1734 PetscInt coordSize, c; 1735 1736 /* Build coordinates */ 1737 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1738 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1739 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1740 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1741 for (v = numCells; v < numCells+numVertices; ++v) { 1742 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1743 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1744 } 1745 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1746 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1747 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1748 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1749 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1750 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1751 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1752 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1753 for (c = 0; c < numCells; c++) { 1754 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; 1755 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; 1756 } 1757 if (!rank) { 1758 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1759 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1760 } 1761 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1762 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1763 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1764 } 1765 PetscFunctionReturn(0); 1766 } 1767 1768 PETSC_STATIC_INLINE PetscReal DiffNormReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1769 { 1770 PetscReal prod = 0.0; 1771 PetscInt i; 1772 for (i = 0; i < dim; ++i) prod += PetscSqr(x[i] - y[i]); 1773 return PetscSqrtReal(prod); 1774 } 1775 PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1776 { 1777 PetscReal prod = 0.0; 1778 PetscInt i; 1779 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1780 return prod; 1781 } 1782 1783 /* The first constant is the sphere radius */ 1784 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1785 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1786 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1787 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1788 { 1789 PetscReal r = PetscRealPart(constants[0]); 1790 PetscReal norm2 = 0.0, fac; 1791 PetscInt n = uOff[1] - uOff[0], d; 1792 1793 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 1794 fac = r/PetscSqrtReal(norm2); 1795 for (d = 0; d < n; ++d) f0[d] = u[d]*fac; 1796 } 1797 1798 /*@ 1799 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 1800 1801 Collective 1802 1803 Input Parameters: 1804 + comm - The communicator for the DM object 1805 . dim - The dimension 1806 . simplex - Use simplices, or tensor product cells 1807 - R - The radius 1808 1809 Output Parameter: 1810 . dm - The DM object 1811 1812 Level: beginner 1813 1814 .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1815 @*/ 1816 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 1817 { 1818 const PetscInt embedDim = dim+1; 1819 PetscSection coordSection; 1820 Vec coordinates; 1821 PetscScalar *coords; 1822 PetscReal *coordsIn; 1823 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1824 PetscMPIInt rank; 1825 PetscErrorCode ierr; 1826 1827 PetscFunctionBegin; 1828 PetscValidPointer(dm, 4); 1829 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1830 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1831 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1832 ierr = DMSetCoordinateDim(*dm, dim+1);CHKERRQ(ierr); 1833 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);CHKERRQ(ierr); 1834 switch (dim) { 1835 case 2: 1836 if (simplex) { 1837 DM idm; 1838 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI); 1839 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius); 1840 const PetscInt degree = 5; 1841 PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1842 PetscInt s[3] = {1, 1, 1}; 1843 PetscInt cone[3]; 1844 PetscInt *graph, p, i, j, k; 1845 1846 vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius; 1847 numCells = !rank ? 20 : 0; 1848 numVerts = !rank ? 12 : 0; 1849 firstVertex = numCells; 1850 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 1851 1852 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1853 1854 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1855 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 1856 */ 1857 /* Construct vertices */ 1858 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1859 if (!rank) { 1860 for (p = 0, i = 0; p < embedDim; ++p) { 1861 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1862 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1863 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1864 ++i; 1865 } 1866 } 1867 } 1868 } 1869 /* Construct graph */ 1870 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1871 for (i = 0; i < numVerts; ++i) { 1872 for (j = 0, k = 0; j < numVerts; ++j) { 1873 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1874 } 1875 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1876 } 1877 /* Build Topology */ 1878 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 1879 for (c = 0; c < numCells; c++) { 1880 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 1881 } 1882 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1883 /* Cells */ 1884 for (i = 0, c = 0; i < numVerts; ++i) { 1885 for (j = 0; j < i; ++j) { 1886 for (k = 0; k < j; ++k) { 1887 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1888 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1889 /* Check orientation */ 1890 { 1891 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}}}; 1892 PetscReal normal[3]; 1893 PetscInt e, f; 1894 1895 for (d = 0; d < embedDim; ++d) { 1896 normal[d] = 0.0; 1897 for (e = 0; e < embedDim; ++e) { 1898 for (f = 0; f < embedDim; ++f) { 1899 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1900 } 1901 } 1902 } 1903 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1904 } 1905 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 1906 } 1907 } 1908 } 1909 } 1910 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1911 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1912 ierr = PetscFree(graph);CHKERRQ(ierr); 1913 /* Interpolate mesh */ 1914 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1915 ierr = DMDestroy(dm);CHKERRQ(ierr); 1916 *dm = idm; 1917 } else { 1918 /* 1919 12-21--13 1920 | | 1921 25 4 24 1922 | | 1923 12-25--9-16--8-24--13 1924 | | | | 1925 23 5 17 0 15 3 22 1926 | | | | 1927 10-20--6-14--7-19--11 1928 | | 1929 20 1 19 1930 | | 1931 10-18--11 1932 | | 1933 23 2 22 1934 | | 1935 12-21--13 1936 */ 1937 PetscInt cone[4], ornt[4]; 1938 1939 numCells = !rank ? 6 : 0; 1940 numEdges = !rank ? 12 : 0; 1941 numVerts = !rank ? 8 : 0; 1942 firstVertex = numCells; 1943 firstEdge = numCells + numVerts; 1944 /* Build Topology */ 1945 ierr = DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1946 for (c = 0; c < numCells; c++) { 1947 ierr = DMPlexSetConeSize(*dm, c, 4);CHKERRQ(ierr); 1948 } 1949 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1950 ierr = DMPlexSetConeSize(*dm, e, 2);CHKERRQ(ierr); 1951 } 1952 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1953 if (!rank) { 1954 /* Cell 0 */ 1955 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1956 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1957 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1958 ierr = DMPlexSetConeOrientation(*dm, 0, ornt);CHKERRQ(ierr); 1959 /* Cell 1 */ 1960 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1961 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1962 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1963 ierr = DMPlexSetConeOrientation(*dm, 1, ornt);CHKERRQ(ierr); 1964 /* Cell 2 */ 1965 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1966 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1967 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1968 ierr = DMPlexSetConeOrientation(*dm, 2, ornt);CHKERRQ(ierr); 1969 /* Cell 3 */ 1970 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1971 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1972 ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; 1973 ierr = DMPlexSetConeOrientation(*dm, 3, ornt);CHKERRQ(ierr); 1974 /* Cell 4 */ 1975 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1976 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1977 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; 1978 ierr = DMPlexSetConeOrientation(*dm, 4, ornt);CHKERRQ(ierr); 1979 /* Cell 5 */ 1980 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1981 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1982 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; 1983 ierr = DMPlexSetConeOrientation(*dm, 5, ornt);CHKERRQ(ierr); 1984 /* Edges */ 1985 cone[0] = 6; cone[1] = 7; 1986 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1987 cone[0] = 7; cone[1] = 8; 1988 ierr = DMPlexSetCone(*dm, 15, cone);CHKERRQ(ierr); 1989 cone[0] = 8; cone[1] = 9; 1990 ierr = DMPlexSetCone(*dm, 16, cone);CHKERRQ(ierr); 1991 cone[0] = 9; cone[1] = 6; 1992 ierr = DMPlexSetCone(*dm, 17, cone);CHKERRQ(ierr); 1993 cone[0] = 10; cone[1] = 11; 1994 ierr = DMPlexSetCone(*dm, 18, cone);CHKERRQ(ierr); 1995 cone[0] = 11; cone[1] = 7; 1996 ierr = DMPlexSetCone(*dm, 19, cone);CHKERRQ(ierr); 1997 cone[0] = 6; cone[1] = 10; 1998 ierr = DMPlexSetCone(*dm, 20, cone);CHKERRQ(ierr); 1999 cone[0] = 12; cone[1] = 13; 2000 ierr = DMPlexSetCone(*dm, 21, cone);CHKERRQ(ierr); 2001 cone[0] = 13; cone[1] = 11; 2002 ierr = DMPlexSetCone(*dm, 22, cone);CHKERRQ(ierr); 2003 cone[0] = 10; cone[1] = 12; 2004 ierr = DMPlexSetCone(*dm, 23, cone);CHKERRQ(ierr); 2005 cone[0] = 13; cone[1] = 8; 2006 ierr = DMPlexSetCone(*dm, 24, cone);CHKERRQ(ierr); 2007 cone[0] = 12; cone[1] = 9; 2008 ierr = DMPlexSetCone(*dm, 25, cone);CHKERRQ(ierr); 2009 } 2010 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2011 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2012 /* Build coordinates */ 2013 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2014 if (!rank) { 2015 coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R; 2016 coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R; 2017 coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R; 2018 coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R; 2019 coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R; 2020 coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R; 2021 coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R; 2022 coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R; 2023 } 2024 } 2025 break; 2026 case 3: 2027 if (simplex) { 2028 DM idm; 2029 const PetscReal edgeLen = 1.0/PETSC_PHI; 2030 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2031 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2032 PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 2033 const PetscInt degree = 12; 2034 PetscInt s[4] = {1, 1, 1}; 2035 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}, 2036 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 2037 PetscInt cone[4]; 2038 PetscInt *graph, p, i, j, k, l; 2039 2040 vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R; 2041 vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R; 2042 vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R; 2043 numCells = !rank ? 600 : 0; 2044 numVerts = !rank ? 120 : 0; 2045 firstVertex = numCells; 2046 /* Use the 600-cell, which for a unit sphere has coordinates which are 2047 2048 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2049 (\pm 1, 0, 0, 0) all cyclic permutations 8 2050 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2051 2052 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2053 length is then given by 1/\phi = 0.61803. 2054 2055 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2056 http://mathworld.wolfram.com/600-Cell.html 2057 */ 2058 /* Construct vertices */ 2059 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2060 i = 0; 2061 if (!rank) { 2062 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2063 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2064 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2065 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2066 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2067 ++i; 2068 } 2069 } 2070 } 2071 } 2072 for (p = 0; p < embedDim; ++p) { 2073 s[1] = s[2] = s[3] = 1; 2074 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2075 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2076 ++i; 2077 } 2078 } 2079 for (p = 0; p < 12; ++p) { 2080 s[3] = 1; 2081 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2082 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2083 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2084 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2085 ++i; 2086 } 2087 } 2088 } 2089 } 2090 } 2091 if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2092 /* Construct graph */ 2093 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2094 for (i = 0; i < numVerts; ++i) { 2095 for (j = 0, k = 0; j < numVerts; ++j) { 2096 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2097 } 2098 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2099 } 2100 /* Build Topology */ 2101 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 2102 for (c = 0; c < numCells; c++) { 2103 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 2104 } 2105 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 2106 /* Cells */ 2107 if (!rank) { 2108 for (i = 0, c = 0; i < numVerts; ++i) { 2109 for (j = 0; j < i; ++j) { 2110 for (k = 0; k < j; ++k) { 2111 for (l = 0; l < k; ++l) { 2112 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2113 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2114 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2115 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2116 { 2117 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2118 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2119 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2120 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2121 2122 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2123 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2124 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2125 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2126 2127 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2128 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2129 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2130 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2131 2132 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2133 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2134 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2135 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2136 PetscReal normal[4]; 2137 PetscInt e, f, g; 2138 2139 for (d = 0; d < embedDim; ++d) { 2140 normal[d] = 0.0; 2141 for (e = 0; e < embedDim; ++e) { 2142 for (f = 0; f < embedDim; ++f) { 2143 for (g = 0; g < embedDim; ++g) { 2144 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]); 2145 } 2146 } 2147 } 2148 } 2149 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2150 } 2151 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 2152 } 2153 } 2154 } 2155 } 2156 } 2157 } 2158 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2159 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2160 ierr = PetscFree(graph);CHKERRQ(ierr); 2161 /* Interpolate mesh */ 2162 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2163 ierr = DMDestroy(dm);CHKERRQ(ierr); 2164 *dm = idm; 2165 break; 2166 } 2167 default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2168 } 2169 /* Create coordinates */ 2170 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 2171 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2172 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2173 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2174 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2175 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2176 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2177 } 2178 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2179 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2180 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2181 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2182 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2183 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2184 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2185 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2186 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2187 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2188 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 2189 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2190 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2191 /* Create coordinate function space */ 2192 { 2193 DM cdm; 2194 PetscDS cds; 2195 PetscFE fe; 2196 PetscScalar radius = R; 2197 PetscInt dT, dE; 2198 2199 ierr = DMGetCoordinateDM(*dm, &cdm);CHKERRQ(ierr); 2200 ierr = DMGetDimension(*dm, &dT);CHKERRQ(ierr); 2201 ierr = DMGetCoordinateDim(*dm, &dE);CHKERRQ(ierr); 2202 ierr = PetscFECreateLagrange(PETSC_COMM_SELF, dT, dE, simplex, 1, -1, &fe);CHKERRQ(ierr); 2203 ierr = DMSetField(cdm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); 2204 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 2205 ierr = DMCreateDS(cdm);CHKERRQ(ierr); 2206 2207 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2208 ierr = PetscDSSetConstants(cds, 1, &radius);CHKERRQ(ierr); 2209 } 2210 ((DM_Plex *) (*dm)->data)->coordFunc = snapToSphere; 2211 PetscFunctionReturn(0); 2212 } 2213 2214 /*@ 2215 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 2216 2217 Collective 2218 2219 Input Parameters: 2220 + comm - The communicator for the DM object 2221 . dim - The dimension 2222 - R - The radius 2223 2224 Output Parameter: 2225 . dm - The DM object 2226 2227 Options Database Keys: 2228 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 2229 2230 Level: beginner 2231 2232 .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2233 @*/ 2234 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 2235 { 2236 DM sdm; 2237 DMLabel bdlabel; 2238 PetscErrorCode ierr; 2239 2240 PetscFunctionBegin; 2241 ierr = DMPlexCreateSphereMesh(comm, dim-1, PETSC_TRUE, R, &sdm);CHKERRQ(ierr); 2242 ierr = PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");CHKERRQ(ierr); 2243 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 2244 ierr = DMPlexGenerate(sdm, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); 2245 ierr = DMDestroy(&sdm);CHKERRQ(ierr); 2246 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 2247 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 2248 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 2249 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 2250 PetscFunctionReturn(0); 2251 } 2252 2253 /* External function declarations here */ 2254 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 2255 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2256 extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2257 extern PetscErrorCode DMCreateLocalSection_Plex(DM dm); 2258 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 2259 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 2260 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 2261 extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field); 2262 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 2263 extern PetscErrorCode DMSetUp_Plex(DM dm); 2264 extern PetscErrorCode DMDestroy_Plex(DM dm); 2265 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 2266 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 2267 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm); 2268 extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm); 2269 static PetscErrorCode DMInitialize_Plex(DM dm); 2270 2271 /* Replace dm with the contents of dmNew 2272 - Share the DM_Plex structure 2273 - Share the coordinates 2274 - Share the SF 2275 */ 2276 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 2277 { 2278 PetscSF sf; 2279 DM coordDM, coarseDM; 2280 DMField coordField; 2281 Vec coords; 2282 PetscBool isper; 2283 const PetscReal *maxCell, *L; 2284 const DMBoundaryType *bd; 2285 PetscErrorCode ierr; 2286 2287 PetscFunctionBegin; 2288 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 2289 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 2290 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 2291 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 2292 ierr = DMGetCoordinateField(dmNew, &coordField);CHKERRQ(ierr); 2293 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 2294 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 2295 ierr = DMSetCoordinateField(dm, coordField);CHKERRQ(ierr); 2296 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 2297 ierr = DMSetPeriodicity(dmNew, isper, maxCell, L, bd);CHKERRQ(ierr); 2298 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 2299 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2300 dm->data = dmNew->data; 2301 ((DM_Plex *) dmNew->data)->refct++; 2302 ierr = DMDestroyLabelLinkList_Internal(dm);CHKERRQ(ierr); 2303 ierr = DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE);CHKERRQ(ierr); 2304 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 2305 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 2306 PetscFunctionReturn(0); 2307 } 2308 2309 /* Swap dm with the contents of dmNew 2310 - Swap the DM_Plex structure 2311 - Swap the coordinates 2312 - Swap the point PetscSF 2313 */ 2314 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 2315 { 2316 DM coordDMA, coordDMB; 2317 Vec coordsA, coordsB; 2318 PetscSF sfA, sfB; 2319 void *tmp; 2320 DMLabelLink listTmp; 2321 DMLabel depthTmp; 2322 PetscInt tmpI; 2323 PetscErrorCode ierr; 2324 2325 PetscFunctionBegin; 2326 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 2327 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 2328 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 2329 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 2330 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 2331 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 2332 2333 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 2334 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 2335 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 2336 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 2337 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 2338 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 2339 2340 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 2341 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 2342 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 2343 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 2344 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 2345 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 2346 2347 tmp = dmA->data; 2348 dmA->data = dmB->data; 2349 dmB->data = tmp; 2350 listTmp = dmA->labels; 2351 dmA->labels = dmB->labels; 2352 dmB->labels = listTmp; 2353 depthTmp = dmA->depthLabel; 2354 dmA->depthLabel = dmB->depthLabel; 2355 dmB->depthLabel = depthTmp; 2356 depthTmp = dmA->celltypeLabel; 2357 dmA->celltypeLabel = dmB->celltypeLabel; 2358 dmB->celltypeLabel = depthTmp; 2359 tmpI = dmA->levelup; 2360 dmA->levelup = dmB->levelup; 2361 dmB->levelup = tmpI; 2362 PetscFunctionReturn(0); 2363 } 2364 2365 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2366 { 2367 DM_Plex *mesh = (DM_Plex*) dm->data; 2368 PetscBool flg; 2369 PetscErrorCode ierr; 2370 2371 PetscFunctionBegin; 2372 /* Handle viewing */ 2373 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 2374 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 2375 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 2376 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 2377 ierr = DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);CHKERRQ(ierr); 2378 if (flg) {ierr = PetscLogDefaultBegin();CHKERRQ(ierr);} 2379 /* Point Location */ 2380 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 2381 /* Partitioning and distribution */ 2382 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 2383 /* Generation and remeshing */ 2384 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 2385 /* Projection behavior */ 2386 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 2387 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 2388 ierr = PetscOptionsEnum("-dm_plex_cell_refiner", "Strategy for cell refinment", "ex40.c", DMPlexCellRefinerTypes, (PetscEnum) mesh->cellRefiner, (PetscEnum *) &mesh->cellRefiner, NULL);CHKERRQ(ierr); 2389 /* Checking structure */ 2390 { 2391 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE; 2392 2393 ierr = PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);CHKERRQ(ierr); 2394 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2395 if (all || (flg && flg2)) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 2396 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); 2397 if (all || (flg && flg2)) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 2398 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); 2399 if (all || (flg && flg2)) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 2400 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2401 if (all || (flg && flg2)) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 2402 ierr = PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2403 if (all || (flg && flg2)) {ierr = DMPlexCheckPointSF(dm);CHKERRQ(ierr);} 2404 ierr = PetscOptionsBool("-dm_plex_check_interface_cones", "Check points on inter-partition interfaces have conforming order of cone points", "DMPlexCheckInterfaceCones", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2405 if (all || (flg && flg2)) {ierr = DMPlexCheckInterfaceCones(dm);CHKERRQ(ierr);} 2406 ierr = PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2407 if (flg && flg2) {ierr = DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);CHKERRQ(ierr);} 2408 } 2409 2410 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2411 PetscFunctionReturn(0); 2412 } 2413 2414 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2415 { 2416 PetscInt refine = 0, coarsen = 0, r; 2417 PetscBool isHierarchy; 2418 PetscErrorCode ierr; 2419 2420 PetscFunctionBegin; 2421 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2422 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2423 /* Handle DMPlex refinement */ 2424 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 2425 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 2426 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2427 if (refine && isHierarchy) { 2428 DM *dms, coarseDM; 2429 2430 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2431 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2432 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2433 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2434 /* Total hack since we do not pass in a pointer */ 2435 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2436 if (refine == 1) { 2437 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2438 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2439 } else { 2440 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2441 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2442 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2443 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2444 } 2445 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2446 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2447 /* Free DMs */ 2448 for (r = 0; r < refine; ++r) { 2449 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2450 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2451 } 2452 ierr = PetscFree(dms);CHKERRQ(ierr); 2453 } else { 2454 for (r = 0; r < refine; ++r) { 2455 DM refinedMesh; 2456 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 2457 2458 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2459 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 2460 /* Total hack since we do not pass in a pointer */ 2461 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 2462 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2463 if (coordFunc) { 2464 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 2465 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 2466 } 2467 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 2468 } 2469 } 2470 /* Handle DMPlex coarsening */ 2471 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 2472 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 2473 if (coarsen && isHierarchy) { 2474 DM *dms; 2475 2476 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2477 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2478 /* Free DMs */ 2479 for (r = 0; r < coarsen; ++r) { 2480 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2481 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2482 } 2483 ierr = PetscFree(dms);CHKERRQ(ierr); 2484 } else { 2485 for (r = 0; r < coarsen; ++r) { 2486 DM coarseMesh; 2487 2488 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2489 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 2490 /* Total hack since we do not pass in a pointer */ 2491 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 2492 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2493 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 2494 } 2495 } 2496 /* Handle */ 2497 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2498 ierr = PetscOptionsTail();CHKERRQ(ierr); 2499 PetscFunctionReturn(0); 2500 } 2501 2502 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2503 { 2504 PetscErrorCode ierr; 2505 2506 PetscFunctionBegin; 2507 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2508 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2509 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2510 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2511 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2512 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2513 PetscFunctionReturn(0); 2514 } 2515 2516 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2517 { 2518 PetscErrorCode ierr; 2519 2520 PetscFunctionBegin; 2521 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2522 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2523 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2524 PetscFunctionReturn(0); 2525 } 2526 2527 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2528 { 2529 PetscInt depth, d; 2530 PetscErrorCode ierr; 2531 2532 PetscFunctionBegin; 2533 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2534 if (depth == 1) { 2535 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2536 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2537 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2538 else {*pStart = 0; *pEnd = 0;} 2539 } else { 2540 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2541 } 2542 PetscFunctionReturn(0); 2543 } 2544 2545 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2546 { 2547 PetscSF sf; 2548 PetscInt niranks, njranks, n; 2549 const PetscMPIInt *iranks, *jranks; 2550 DM_Plex *data = (DM_Plex*) dm->data; 2551 PetscErrorCode ierr; 2552 2553 PetscFunctionBegin; 2554 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2555 if (!data->neighbors) { 2556 ierr = PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);CHKERRQ(ierr); 2557 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);CHKERRQ(ierr); 2558 ierr = PetscMalloc1(njranks + niranks + 1, &data->neighbors);CHKERRQ(ierr); 2559 ierr = PetscArraycpy(data->neighbors + 1, jranks, njranks);CHKERRQ(ierr); 2560 ierr = PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);CHKERRQ(ierr); 2561 n = njranks + niranks; 2562 ierr = PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);CHKERRQ(ierr); 2563 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 2564 ierr = PetscMPIIntCast(n, data->neighbors);CHKERRQ(ierr); 2565 } 2566 if (nranks) *nranks = data->neighbors[0]; 2567 if (ranks) { 2568 if (data->neighbors[0]) *ranks = data->neighbors + 1; 2569 else *ranks = NULL; 2570 } 2571 PetscFunctionReturn(0); 2572 } 2573 2574 static PetscErrorCode DMInitialize_Plex(DM dm) 2575 { 2576 PetscErrorCode ierr; 2577 2578 PetscFunctionBegin; 2579 dm->ops->view = DMView_Plex; 2580 dm->ops->load = DMLoad_Plex; 2581 dm->ops->setfromoptions = DMSetFromOptions_Plex; 2582 dm->ops->clone = DMClone_Plex; 2583 dm->ops->setup = DMSetUp_Plex; 2584 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 2585 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 2586 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 2587 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 2588 dm->ops->getlocaltoglobalmapping = NULL; 2589 dm->ops->createfieldis = NULL; 2590 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 2591 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 2592 dm->ops->getcoloring = NULL; 2593 dm->ops->creatematrix = DMCreateMatrix_Plex; 2594 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 2595 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 2596 dm->ops->createinjection = DMCreateInjection_Plex; 2597 dm->ops->refine = DMRefine_Plex; 2598 dm->ops->coarsen = DMCoarsen_Plex; 2599 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 2600 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 2601 dm->ops->adaptlabel = DMAdaptLabel_Plex; 2602 dm->ops->adaptmetric = DMAdaptMetric_Plex; 2603 dm->ops->globaltolocalbegin = NULL; 2604 dm->ops->globaltolocalend = NULL; 2605 dm->ops->localtoglobalbegin = NULL; 2606 dm->ops->localtoglobalend = NULL; 2607 dm->ops->destroy = DMDestroy_Plex; 2608 dm->ops->createsubdm = DMCreateSubDM_Plex; 2609 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 2610 dm->ops->getdimpoints = DMGetDimPoints_Plex; 2611 dm->ops->locatepoints = DMLocatePoints_Plex; 2612 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 2613 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 2614 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 2615 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 2616 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 2617 dm->ops->computel2diff = DMComputeL2Diff_Plex; 2618 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 2619 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 2620 dm->ops->getneighbors = DMGetNeighbors_Plex; 2621 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 2622 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);CHKERRQ(ierr); 2623 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 2624 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 2625 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 2626 PetscFunctionReturn(0); 2627 } 2628 2629 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 2630 { 2631 DM_Plex *mesh = (DM_Plex *) dm->data; 2632 PetscErrorCode ierr; 2633 2634 PetscFunctionBegin; 2635 mesh->refct++; 2636 (*newdm)->data = mesh; 2637 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 2638 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 2639 PetscFunctionReturn(0); 2640 } 2641 2642 /*MC 2643 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 2644 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 2645 specified by a PetscSection object. Ownership in the global representation is determined by 2646 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 2647 2648 Options Database Keys: 2649 + -dm_plex_hash_location - Use grid hashing for point location 2650 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 2651 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 2652 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 2653 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 2654 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 2655 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 2656 . -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 2657 . -dm_plex_check_geometry - Check that cells have positive volume 2658 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 2659 . -dm_plex_view_scale <num> - Scale the TikZ 2660 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 2661 2662 2663 Level: intermediate 2664 2665 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 2666 M*/ 2667 2668 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 2669 { 2670 DM_Plex *mesh; 2671 PetscInt unit; 2672 PetscErrorCode ierr; 2673 2674 PetscFunctionBegin; 2675 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2676 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 2677 dm->dim = 0; 2678 dm->data = mesh; 2679 2680 mesh->refct = 1; 2681 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 2682 mesh->maxConeSize = 0; 2683 mesh->cones = NULL; 2684 mesh->coneOrientations = NULL; 2685 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 2686 mesh->maxSupportSize = 0; 2687 mesh->supports = NULL; 2688 mesh->refinementUniform = PETSC_TRUE; 2689 mesh->refinementLimit = -1.0; 2690 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 2691 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 2692 2693 mesh->facesTmp = NULL; 2694 2695 mesh->tetgenOpts = NULL; 2696 mesh->triangleOpts = NULL; 2697 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 2698 mesh->remeshBd = PETSC_FALSE; 2699 2700 mesh->subpointMap = NULL; 2701 2702 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 2703 2704 mesh->regularRefinement = PETSC_FALSE; 2705 mesh->depthState = -1; 2706 mesh->celltypeState = -1; 2707 mesh->globalVertexNumbers = NULL; 2708 mesh->globalCellNumbers = NULL; 2709 mesh->anchorSection = NULL; 2710 mesh->anchorIS = NULL; 2711 mesh->createanchors = NULL; 2712 mesh->computeanchormatrix = NULL; 2713 mesh->parentSection = NULL; 2714 mesh->parents = NULL; 2715 mesh->childIDs = NULL; 2716 mesh->childSection = NULL; 2717 mesh->children = NULL; 2718 mesh->referenceTree = NULL; 2719 mesh->getchildsymmetry = NULL; 2720 mesh->vtkCellHeight = 0; 2721 mesh->useAnchors = PETSC_FALSE; 2722 2723 mesh->maxProjectionHeight = 0; 2724 2725 mesh->neighbors = NULL; 2726 2727 mesh->printSetValues = PETSC_FALSE; 2728 mesh->printFEM = 0; 2729 mesh->printTol = 1.0e-10; 2730 2731 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2732 PetscFunctionReturn(0); 2733 } 2734 2735 /*@ 2736 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 2737 2738 Collective 2739 2740 Input Parameter: 2741 . comm - The communicator for the DMPlex object 2742 2743 Output Parameter: 2744 . mesh - The DMPlex object 2745 2746 Level: beginner 2747 2748 @*/ 2749 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 2750 { 2751 PetscErrorCode ierr; 2752 2753 PetscFunctionBegin; 2754 PetscValidPointer(mesh,2); 2755 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 2756 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 2757 PetscFunctionReturn(0); 2758 } 2759 2760 /*@C 2761 DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output) 2762 2763 Input Parameters: 2764 + dm - The DM 2765 . numCells - The number of cells owned by this process 2766 . numVertices - The number of vertices owned by this process 2767 . numCorners - The number of vertices for each cell 2768 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2769 2770 Output Parameter: 2771 . vertexSF - (Optional) SF describing complete vertex ownership 2772 2773 Notes: 2774 Two triangles sharing a face 2775 $ 2776 $ 2 2777 $ / | \ 2778 $ / | \ 2779 $ / | \ 2780 $ 0 0 | 1 3 2781 $ \ | / 2782 $ \ | / 2783 $ \ | / 2784 $ 1 2785 would have input 2786 $ numCells = 2, numVertices = 4 2787 $ cells = [0 1 2 1 3 2] 2788 $ 2789 which would result in the DMPlex 2790 $ 2791 $ 4 2792 $ / | \ 2793 $ / | \ 2794 $ / | \ 2795 $ 2 0 | 1 5 2796 $ \ | / 2797 $ \ | / 2798 $ \ | / 2799 $ 3 2800 2801 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 2802 2803 Not currently supported in Fortran. 2804 2805 Level: advanced 2806 2807 .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel() 2808 @*/ 2809 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF) 2810 { 2811 PetscSF sfPoint, sfVert; 2812 PetscLayout vLayout; 2813 PetscHSetI vhash; 2814 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 2815 const PetscInt *vrange; 2816 PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cones, c, p, v, g, dim; 2817 PetscMPIInt rank, size; 2818 PetscErrorCode ierr; 2819 2820 PetscFunctionBegin; 2821 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 2822 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2823 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2824 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2825 /* Partition vertices */ 2826 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 2827 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 2828 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 2829 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 2830 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 2831 /* Count vertices and map them to procs */ 2832 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 2833 for (c = 0; c < numCells; ++c) { 2834 for (p = 0; p < numCorners; ++p) { 2835 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 2836 } 2837 } 2838 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 2839 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 2840 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 2841 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 2842 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 2843 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 2844 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 2845 for (v = 0; v < numVerticesAdj; ++v) { 2846 const PetscInt gv = verticesAdj[v]; 2847 PetscInt vrank; 2848 2849 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 2850 vrank = vrank < 0 ? -(vrank+2) : vrank; 2851 remoteVerticesAdj[v].index = gv - vrange[vrank]; 2852 remoteVerticesAdj[v].rank = vrank; 2853 } 2854 /* Create cones */ 2855 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 2856 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 2857 ierr = DMSetUp(dm);CHKERRQ(ierr); 2858 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 2859 for (c = 0; c < numCells; ++c) { 2860 for (p = 0; p < numCorners; ++p) { 2861 const PetscInt gv = cells[c*numCorners+p]; 2862 PetscInt lv; 2863 2864 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 2865 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 2866 cones[c*numCorners+p] = lv+numCells; 2867 } 2868 } 2869 /* Create SF for vertices */ 2870 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), &sfVert);CHKERRQ(ierr); 2871 ierr = PetscObjectSetName((PetscObject) sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 2872 ierr = PetscSFSetFromOptions(sfVert);CHKERRQ(ierr); 2873 ierr = PetscSFSetGraph(sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 2874 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 2875 /* Build pointSF */ 2876 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 2877 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 2878 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 2879 ierr = PetscSFReduceBegin(sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2880 ierr = PetscSFReduceEnd(sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2881 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); 2882 ierr = PetscSFBcastBegin(sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2883 ierr = PetscSFBcastEnd(sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2884 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 2885 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 2886 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 2887 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 2888 if (vertexLocal[v].rank != rank) { 2889 localVertex[g] = v+numCells; 2890 remoteVertex[g].index = vertexLocal[v].index; 2891 remoteVertex[g].rank = vertexLocal[v].rank; 2892 ++g; 2893 } 2894 } 2895 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 2896 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 2897 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2898 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 2899 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 2900 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 2901 /* Fill in the rest of the topology structure */ 2902 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2903 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2904 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 2905 if (vertexSF) *vertexSF = sfVert; 2906 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 2907 PetscFunctionReturn(0); 2908 } 2909 2910 /*@C 2911 DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 2912 2913 Input Parameters: 2914 + dm - The DM 2915 . spaceDim - The spatial dimension used for coordinates 2916 . sfVert - SF describing complete vertex ownership 2917 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2918 2919 Level: advanced 2920 2921 Notes: 2922 Not currently supported in Fortran. 2923 2924 .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel() 2925 @*/ 2926 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 2927 { 2928 PetscSection coordSection; 2929 Vec coordinates; 2930 PetscScalar *coords; 2931 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 2932 PetscErrorCode ierr; 2933 2934 PetscFunctionBegin; 2935 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 2936 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 2937 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 2938 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 2939 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 2940 if (vEnd - vStart != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Supplied sfVert has wrong number of leaves = %D != %D = vEnd - vStart",numVerticesAdj,vEnd - vStart); 2941 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2942 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2943 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2944 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 2945 for (v = vStart; v < vEnd; ++v) { 2946 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2947 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2948 } 2949 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2950 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2951 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 2952 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2953 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2954 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2955 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2956 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2957 { 2958 MPI_Datatype coordtype; 2959 2960 /* Need a temp buffer for coords if we have complex/single */ 2961 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 2962 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 2963 #if defined(PETSC_USE_COMPLEX) 2964 { 2965 PetscScalar *svertexCoords; 2966 PetscInt i; 2967 ierr = PetscMalloc1(numVertices*spaceDim,&svertexCoords);CHKERRQ(ierr); 2968 for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 2969 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2970 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 2971 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 2972 } 2973 #else 2974 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2975 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 2976 #endif 2977 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 2978 } 2979 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2980 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2981 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2982 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 2983 PetscFunctionReturn(0); 2984 } 2985 2986 /*@ 2987 DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output) 2988 2989 Input Parameters: 2990 + comm - The communicator 2991 . dim - The topological dimension of the mesh 2992 . numCells - The number of cells owned by this process 2993 . numVertices - The number of vertices owned by this process 2994 . numCorners - The number of vertices for each cell 2995 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2996 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2997 . spaceDim - The spatial dimension used for coordinates 2998 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2999 3000 Output Parameter: 3001 + dm - The DM 3002 - vertexSF - (Optional) SF describing complete vertex ownership 3003 3004 Notes: 3005 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), 3006 DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel() 3007 3008 Level: intermediate 3009 3010 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate() 3011 @*/ 3012 PetscErrorCode DMPlexCreateFromCellListParallelPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PetscSF *vertexSF, DM *dm) 3013 { 3014 PetscSF sfVert; 3015 PetscErrorCode ierr; 3016 3017 PetscFunctionBegin; 3018 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3019 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3020 PetscValidLogicalCollectiveInt(*dm, dim, 2); 3021 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 3022 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3023 ierr = DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, numCorners, cells, &sfVert);CHKERRQ(ierr); 3024 if (interpolate) { 3025 DM idm; 3026 3027 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3028 ierr = DMDestroy(dm);CHKERRQ(ierr); 3029 *dm = idm; 3030 } 3031 ierr = DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);CHKERRQ(ierr); 3032 if (vertexSF) *vertexSF = sfVert; 3033 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 3034 PetscFunctionReturn(0); 3035 } 3036 3037 3038 /*@ 3039 DMPlexCreateFromCellListParallel - Deprecated, use DMPlexCreateFromCellListParallelPetsc() 3040 3041 Level: deprecated 3042 3043 .seealso: DMPlexCreateFromCellListParallelPetsc() 3044 @*/ 3045 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) 3046 { 3047 PetscErrorCode ierr; 3048 PetscInt i; 3049 PetscInt *pintCells; 3050 3051 PetscFunctionBegin; 3052 if (sizeof(int) > sizeof(PetscInt)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of int %zd greater than size of PetscInt %zd. Reconfigure PETSc --with-64-bit-indices=1", sizeof(int), sizeof(PetscInt)); 3053 if (sizeof(int) == sizeof(PetscInt)) { 3054 pintCells = (PetscInt *) cells; 3055 } else { 3056 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3057 for (i = 0; i < numCells*numCorners; i++) { 3058 pintCells[i] = (PetscInt) cells[i]; 3059 } 3060 } 3061 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, vertexCoords, vertexSF, dm);CHKERRQ(ierr); 3062 if (sizeof(int) != sizeof(PetscInt)) { 3063 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3064 } 3065 PetscFunctionReturn(0); 3066 } 3067 3068 /*@C 3069 DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3070 3071 Input Parameters: 3072 + dm - The DM 3073 . numCells - The number of cells owned by this process 3074 . numVertices - The number of vertices owned by this process 3075 . numCorners - The number of vertices for each cell 3076 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3077 3078 Level: advanced 3079 3080 Notes: 3081 Two triangles sharing a face 3082 $ 3083 $ 2 3084 $ / | \ 3085 $ / | \ 3086 $ / | \ 3087 $ 0 0 | 1 3 3088 $ \ | / 3089 $ \ | / 3090 $ \ | / 3091 $ 1 3092 would have input 3093 $ numCells = 2, numVertices = 4 3094 $ cells = [0 1 2 1 3 2] 3095 $ 3096 which would result in the DMPlex 3097 $ 3098 $ 4 3099 $ / | \ 3100 $ / | \ 3101 $ / | \ 3102 $ 2 0 | 1 5 3103 $ \ | / 3104 $ \ | / 3105 $ \ | / 3106 $ 3 3107 3108 Not currently supported in Fortran. 3109 3110 .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc() 3111 @*/ 3112 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 3113 { 3114 PetscInt *cones, c, p, dim; 3115 PetscErrorCode ierr; 3116 3117 PetscFunctionBegin; 3118 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3119 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3120 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 3121 for (c = 0; c < numCells; ++c) { 3122 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 3123 } 3124 ierr = DMSetUp(dm);CHKERRQ(ierr); 3125 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3126 for (c = 0; c < numCells; ++c) { 3127 for (p = 0; p < numCorners; ++p) { 3128 cones[c*numCorners+p] = cells[c*numCorners+p]+numCells; 3129 } 3130 } 3131 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3132 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3133 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3134 PetscFunctionReturn(0); 3135 } 3136 3137 /*@C 3138 DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 3139 3140 Input Parameters: 3141 + dm - The DM 3142 . spaceDim - The spatial dimension used for coordinates 3143 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3144 3145 Level: advanced 3146 3147 Notes: 3148 Not currently supported in Fortran. 3149 3150 .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList() 3151 @*/ 3152 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 3153 { 3154 PetscSection coordSection; 3155 Vec coordinates; 3156 DM cdm; 3157 PetscScalar *coords; 3158 PetscInt v, vStart, vEnd, d; 3159 PetscErrorCode ierr; 3160 3161 PetscFunctionBegin; 3162 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3163 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3164 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3165 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3166 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3167 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3168 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3169 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3170 for (v = vStart; v < vEnd; ++v) { 3171 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3172 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3173 } 3174 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3175 3176 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3177 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 3178 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3179 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3180 ierr = VecGetArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3181 for (v = 0; v < vEnd-vStart; ++v) { 3182 for (d = 0; d < spaceDim; ++d) { 3183 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 3184 } 3185 } 3186 ierr = VecRestoreArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3187 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3188 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3189 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3190 PetscFunctionReturn(0); 3191 } 3192 3193 /*@ 3194 DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output) 3195 3196 Input Parameters: 3197 + comm - The communicator 3198 . dim - The topological dimension of the mesh 3199 . numCells - The number of cells 3200 . numVertices - The number of vertices 3201 . numCorners - The number of vertices for each cell 3202 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3203 . cells - An array of numCells*numCorners numbers, the vertices for each cell 3204 . spaceDim - The spatial dimension used for coordinates 3205 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3206 3207 Output Parameter: 3208 . dm - The DM 3209 3210 Notes: 3211 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(), 3212 DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList() 3213 3214 Level: intermediate 3215 3216 .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 3217 @*/ 3218 PetscErrorCode DMPlexCreateFromCellListPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], DM *dm) 3219 { 3220 PetscErrorCode ierr; 3221 3222 PetscFunctionBegin; 3223 if (!dim) SETERRQ(comm, PETSC_ERR_ARG_OUTOFRANGE, "This is not appropriate for 0-dimensional meshes. Consider either creating the DM using DMPlexCreateFromDAG(), by hand, or using DMSwarm."); 3224 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3225 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3226 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3227 ierr = DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 3228 if (interpolate) { 3229 DM idm; 3230 3231 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3232 ierr = DMDestroy(dm);CHKERRQ(ierr); 3233 *dm = idm; 3234 } 3235 ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);CHKERRQ(ierr); 3236 PetscFunctionReturn(0); 3237 } 3238 3239 /*@ 3240 DMPlexCreateFromCellList - Deprecated, use DMPlexCreateFromCellListPetsc() 3241 3242 Level: deprecated 3243 3244 .seealso: DMPlexCreateFromCellListPetsc() 3245 @*/ 3246 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) 3247 { 3248 PetscErrorCode ierr; 3249 PetscInt i; 3250 PetscInt *pintCells; 3251 PetscReal *prealVC; 3252 3253 PetscFunctionBegin; 3254 if (sizeof(int) > sizeof(PetscInt)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of int %zd greater than size of PetscInt %zd. Reconfigure PETSc --with-64-bit-indices=1", sizeof(int), sizeof(PetscInt)); 3255 if (sizeof(int) == sizeof(PetscInt)) { 3256 pintCells = (PetscInt *) cells; 3257 } else { 3258 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3259 for (i = 0; i < numCells*numCorners; i++) { 3260 pintCells[i] = (PetscInt) cells[i]; 3261 } 3262 } 3263 if (sizeof(double) > sizeof(PetscReal)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Size of double %zd greater than size of PetscReal %zd. Reconfigure PETSc --with-precision=<higher precision>.", sizeof(double), sizeof(PetscReal)); 3264 if (sizeof(double) == sizeof(PetscReal)) { 3265 prealVC = (PetscReal *) vertexCoords; 3266 } else { 3267 ierr = PetscMalloc1(numVertices*spaceDim, &prealVC);CHKERRQ(ierr); 3268 for (i = 0; i < numVertices*spaceDim; i++) { 3269 prealVC[i] = (PetscReal) vertexCoords[i]; 3270 } 3271 } 3272 ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, prealVC, dm);CHKERRQ(ierr); 3273 if (sizeof(int) != sizeof(PetscInt)) { 3274 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3275 } 3276 if (sizeof(double) != sizeof(PetscReal)) { 3277 ierr = PetscFree(prealVC);CHKERRQ(ierr); 3278 } 3279 PetscFunctionReturn(0); 3280 } 3281 3282 /*@ 3283 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 3284 3285 Input Parameters: 3286 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 3287 . depth - The depth of the DAG 3288 . numPoints - Array of size depth + 1 containing the number of points at each depth 3289 . coneSize - The cone size of each point 3290 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 3291 . coneOrientations - The orientation of each cone point 3292 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 3293 3294 Output Parameter: 3295 . dm - The DM 3296 3297 Note: Two triangles sharing a face would have input 3298 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 3299 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 3300 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 3301 $ 3302 which would result in the DMPlex 3303 $ 3304 $ 4 3305 $ / | \ 3306 $ / | \ 3307 $ / | \ 3308 $ 2 0 | 1 5 3309 $ \ | / 3310 $ \ | / 3311 $ \ | / 3312 $ 3 3313 $ 3314 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 3315 3316 Level: advanced 3317 3318 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3319 @*/ 3320 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3321 { 3322 Vec coordinates; 3323 PetscSection coordSection; 3324 PetscScalar *coords; 3325 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3326 PetscErrorCode ierr; 3327 3328 PetscFunctionBegin; 3329 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3330 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3331 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 3332 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3333 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3334 for (p = pStart; p < pEnd; ++p) { 3335 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3336 if (firstVertex < 0 && !coneSize[p - pStart]) { 3337 firstVertex = p - pStart; 3338 } 3339 } 3340 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 3341 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3342 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3343 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3344 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3345 } 3346 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3347 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3348 /* Build coordinates */ 3349 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3350 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3351 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3352 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3353 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3354 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3355 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3356 } 3357 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3358 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3359 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3360 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3361 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3362 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3363 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3364 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3365 for (v = 0; v < numPoints[0]; ++v) { 3366 PetscInt off; 3367 3368 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3369 for (d = 0; d < dimEmbed; ++d) { 3370 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3371 } 3372 } 3373 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3374 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3375 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3376 PetscFunctionReturn(0); 3377 } 3378 3379 /*@C 3380 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3381 3382 + comm - The MPI communicator 3383 . filename - Name of the .dat file 3384 - interpolate - Create faces and edges in the mesh 3385 3386 Output Parameter: 3387 . dm - The DM object representing the mesh 3388 3389 Note: The format is the simplest possible: 3390 $ Ne 3391 $ v0 v1 ... vk 3392 $ Nv 3393 $ x y z marker 3394 3395 Level: beginner 3396 3397 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3398 @*/ 3399 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3400 { 3401 DMLabel marker; 3402 PetscViewer viewer; 3403 Vec coordinates; 3404 PetscSection coordSection; 3405 PetscScalar *coords; 3406 char line[PETSC_MAX_PATH_LEN]; 3407 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 3408 PetscMPIInt rank; 3409 int snum, Nv, Nc; 3410 PetscErrorCode ierr; 3411 3412 PetscFunctionBegin; 3413 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3414 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3415 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 3416 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3417 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3418 if (!rank) { 3419 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 3420 snum = sscanf(line, "%d %d", &Nc, &Nv); 3421 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3422 } else { 3423 Nc = Nv = 0; 3424 } 3425 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3426 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3427 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 3428 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3429 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 3430 /* Read topology */ 3431 if (!rank) { 3432 PetscInt cone[8], corners = 8; 3433 int vbuf[8], v; 3434 3435 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 3436 ierr = DMSetUp(*dm);CHKERRQ(ierr); 3437 for (c = 0; c < Nc; ++c) { 3438 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 3439 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]); 3440 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3441 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 3442 /* Hexahedra are inverted */ 3443 { 3444 PetscInt tmp = cone[1]; 3445 cone[1] = cone[3]; 3446 cone[3] = tmp; 3447 } 3448 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 3449 } 3450 } 3451 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 3452 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 3453 /* Read coordinates */ 3454 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 3455 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3456 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 3457 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 3458 for (v = Nc; v < Nc+Nv; ++v) { 3459 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 3460 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 3461 } 3462 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3463 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3464 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3465 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3466 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3467 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 3468 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 3469 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3470 if (!rank) { 3471 double x[3]; 3472 int val; 3473 3474 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 3475 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 3476 for (v = 0; v < Nv; ++v) { 3477 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 3478 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 3479 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3480 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 3481 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 3482 } 3483 } 3484 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3485 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 3486 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3487 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3488 if (interpolate) { 3489 DM idm; 3490 DMLabel bdlabel; 3491 3492 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3493 ierr = DMDestroy(dm);CHKERRQ(ierr); 3494 *dm = idm; 3495 3496 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 3497 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 3498 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 3499 } 3500 PetscFunctionReturn(0); 3501 } 3502 3503 /*@C 3504 DMPlexCreateFromFile - This takes a filename and produces a DM 3505 3506 Input Parameters: 3507 + comm - The communicator 3508 . filename - A file name 3509 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 3510 3511 Output Parameter: 3512 . dm - The DM 3513 3514 Options Database Keys: 3515 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 3516 3517 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 3518 $ -dm_plex_create_viewer_hdf5_collective 3519 3520 Level: beginner 3521 3522 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3523 @*/ 3524 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3525 { 3526 const char *extGmsh = ".msh"; 3527 const char *extGmsh2 = ".msh2"; 3528 const char *extGmsh4 = ".msh4"; 3529 const char *extCGNS = ".cgns"; 3530 const char *extExodus = ".exo"; 3531 const char *extGenesis = ".gen"; 3532 const char *extFluent = ".cas"; 3533 const char *extHDF5 = ".h5"; 3534 const char *extMed = ".med"; 3535 const char *extPLY = ".ply"; 3536 const char *extCV = ".dat"; 3537 size_t len; 3538 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV; 3539 PetscMPIInt rank; 3540 PetscErrorCode ierr; 3541 3542 PetscFunctionBegin; 3543 PetscValidCharPointer(filename, 2); 3544 PetscValidPointer(dm, 4); 3545 ierr = DMInitializePackage();CHKERRQ(ierr); 3546 ierr = PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 3547 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3548 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 3549 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 3550 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 3551 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 3552 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 3553 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 3554 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 3555 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 3556 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 3557 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 3558 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 3559 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 3560 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 3561 if (isGmsh || isGmsh2 || isGmsh4) { 3562 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3563 } else if (isCGNS) { 3564 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3565 } else if (isExodus || isGenesis) { 3566 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3567 } else if (isFluent) { 3568 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3569 } else if (isHDF5) { 3570 PetscBool load_hdf5_xdmf = PETSC_FALSE; 3571 PetscViewer viewer; 3572 3573 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 3574 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 3575 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 3576 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3577 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 3578 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 3579 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 3580 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3581 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3582 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3583 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3584 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 3585 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 3586 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 3587 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3588 3589 if (interpolate) { 3590 DM idm; 3591 3592 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3593 ierr = DMDestroy(dm);CHKERRQ(ierr); 3594 *dm = idm; 3595 } 3596 } else if (isMed) { 3597 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3598 } else if (isPLY) { 3599 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3600 } else if (isCV) { 3601 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3602 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 3603 ierr = PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 3604 PetscFunctionReturn(0); 3605 } 3606 3607 /*@ 3608 DMPlexCreateReferenceCellByType - Create a DMPLEX with the appropriate FEM reference cell 3609 3610 Collective 3611 3612 Input Parameters: 3613 + comm - The communicator 3614 - ct - The cell type of the reference cell 3615 3616 Output Parameter: 3617 . refdm - The reference cell 3618 3619 Level: intermediate 3620 3621 .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh() 3622 @*/ 3623 PetscErrorCode DMPlexCreateReferenceCellByType(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3624 { 3625 DM rdm; 3626 Vec coords; 3627 PetscErrorCode ierr; 3628 3629 PetscFunctionBegin; 3630 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 3631 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 3632 switch (ct) { 3633 case DM_POLYTOPE_POINT: 3634 { 3635 PetscInt numPoints[1] = {1}; 3636 PetscInt coneSize[1] = {0}; 3637 PetscInt cones[1] = {0}; 3638 PetscInt coneOrientations[1] = {0}; 3639 PetscScalar vertexCoords[1] = {0.0}; 3640 3641 ierr = DMSetDimension(rdm, 0);CHKERRQ(ierr); 3642 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3643 } 3644 break; 3645 case DM_POLYTOPE_SEGMENT: 3646 { 3647 PetscInt numPoints[2] = {2, 1}; 3648 PetscInt coneSize[3] = {2, 0, 0}; 3649 PetscInt cones[2] = {1, 2}; 3650 PetscInt coneOrientations[2] = {0, 0}; 3651 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3652 3653 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 3654 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3655 } 3656 break; 3657 case DM_POLYTOPE_TRIANGLE: 3658 { 3659 PetscInt numPoints[2] = {3, 1}; 3660 PetscInt coneSize[4] = {3, 0, 0, 0}; 3661 PetscInt cones[3] = {1, 2, 3}; 3662 PetscInt coneOrientations[3] = {0, 0, 0}; 3663 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3664 3665 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3666 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3667 } 3668 break; 3669 case DM_POLYTOPE_QUADRILATERAL: 3670 { 3671 PetscInt numPoints[2] = {4, 1}; 3672 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3673 PetscInt cones[4] = {1, 2, 3, 4}; 3674 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3675 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3676 3677 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3678 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3679 } 3680 break; 3681 case DM_POLYTOPE_SEG_PRISM_TENSOR: 3682 { 3683 PetscInt numPoints[2] = {4, 1}; 3684 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3685 PetscInt cones[4] = {1, 2, 3, 4}; 3686 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3687 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 3688 3689 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3690 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3691 } 3692 break; 3693 case DM_POLYTOPE_TETRAHEDRON: 3694 { 3695 PetscInt numPoints[2] = {4, 1}; 3696 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3697 PetscInt cones[4] = {1, 3, 2, 4}; 3698 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3699 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}; 3700 3701 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3702 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3703 } 3704 break; 3705 case DM_POLYTOPE_HEXAHEDRON: 3706 { 3707 PetscInt numPoints[2] = {8, 1}; 3708 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3709 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 3710 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3711 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, 3712 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3713 3714 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3715 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3716 } 3717 break; 3718 case DM_POLYTOPE_TRI_PRISM: 3719 { 3720 PetscInt numPoints[2] = {6, 1}; 3721 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3722 PetscInt cones[6] = {1, 3, 2, 4, 5, 6}; 3723 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3724 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3725 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3726 3727 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3728 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3729 } 3730 break; 3731 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3732 { 3733 PetscInt numPoints[2] = {6, 1}; 3734 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3735 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3736 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3737 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3738 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3739 3740 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3741 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3742 } 3743 break; 3744 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 3745 { 3746 PetscInt numPoints[2] = {8, 1}; 3747 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3748 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3749 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3750 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, 3751 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3752 3753 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3754 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3755 } 3756 break; 3757 default: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3758 } 3759 { 3760 PetscInt Nv, v; 3761 3762 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3763 ierr = DMCreateLabel(rdm, "celltype");CHKERRQ(ierr); 3764 ierr = DMPlexSetCellType(rdm, 0, ct);CHKERRQ(ierr); 3765 ierr = DMPlexGetChart(rdm, NULL, &Nv);CHKERRQ(ierr); 3766 for (v = 1; v < Nv; ++v) {ierr = DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr);} 3767 } 3768 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 3769 if (rdm->coordinateDM) { 3770 DM ncdm; 3771 PetscSection cs; 3772 PetscInt pEnd = -1; 3773 3774 ierr = DMGetLocalSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 3775 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 3776 if (pEnd >= 0) { 3777 ierr = DMClone(*refdm, &ncdm);CHKERRQ(ierr); 3778 ierr = DMCopyDisc(rdm->coordinateDM, ncdm);CHKERRQ(ierr); 3779 ierr = DMSetLocalSection(ncdm, cs);CHKERRQ(ierr); 3780 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 3781 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 3782 } 3783 } 3784 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 3785 if (coords) { 3786 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 3787 } else { 3788 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 3789 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 3790 } 3791 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 3792 PetscFunctionReturn(0); 3793 } 3794 3795 /*@ 3796 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3797 3798 Collective 3799 3800 Input Parameters: 3801 + comm - The communicator 3802 . dim - The spatial dimension 3803 - simplex - Flag for simplex, otherwise use a tensor-product cell 3804 3805 Output Parameter: 3806 . refdm - The reference cell 3807 3808 Level: intermediate 3809 3810 .seealso: DMPlexCreateReferenceCellByType(), DMPlexCreateBoxMesh() 3811 @*/ 3812 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 3813 { 3814 PetscErrorCode ierr; 3815 3816 PetscFunctionBeginUser; 3817 switch (dim) { 3818 case 0: ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_POINT, refdm);CHKERRQ(ierr);break; 3819 case 1: ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_SEGMENT, refdm);CHKERRQ(ierr);break; 3820 case 2: 3821 if (simplex) {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_TRIANGLE, refdm);CHKERRQ(ierr);} 3822 else {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_QUADRILATERAL, refdm);CHKERRQ(ierr);} 3823 break; 3824 case 3: 3825 if (simplex) {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_TETRAHEDRON, refdm);CHKERRQ(ierr);} 3826 else {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_HEXAHEDRON, refdm);CHKERRQ(ierr);} 3827 break; 3828 default: 3829 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %D", dim); 3830 } 3831 PetscFunctionReturn(0); 3832 } 3833