1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petscdmda.h> 4 #include <petscsf.h> 5 6 /*@ 7 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 8 9 Collective on MPI_Comm 10 11 Input Parameters: 12 + comm - The communicator for the DM object 13 . dim - The spatial dimension 14 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 15 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 16 . refinementUniform - Flag for uniform parallel refinement 17 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 18 19 Output Parameter: 20 . dm - The DM object 21 22 Level: beginner 23 24 .keywords: DM, create 25 .seealso: DMSetType(), DMCreate() 26 @*/ 27 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 28 { 29 DM dm; 30 PetscInt p; 31 PetscMPIInt rank; 32 PetscErrorCode ierr; 33 34 PetscFunctionBegin; 35 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 36 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 37 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 38 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 39 switch (dim) { 40 case 2: 41 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 42 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 43 break; 44 case 3: 45 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 46 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 47 break; 48 default: 49 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 50 } 51 if (rank) { 52 PetscInt numPoints[2] = {0, 0}; 53 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 54 } else { 55 switch (dim) { 56 case 2: 57 if (simplex) { 58 PetscInt numPoints[2] = {4, 2}; 59 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 60 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 61 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 62 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 63 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 64 65 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 66 for (p = 0; p < 4; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 67 } else { 68 PetscInt numPoints[2] = {6, 2}; 69 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 70 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 71 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 72 PetscScalar vertexCoords[12] = {-1.0, -0.5, 0.0, -0.5, 0.0, 0.5, -1.0, 0.5, 1.0, -0.5, 1.0, 0.5}; 73 74 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 75 } 76 break; 77 case 3: 78 if (simplex) { 79 PetscInt numPoints[2] = {5, 2}; 80 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 81 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 82 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 83 PetscScalar vertexCoords[15] = {-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0}; 84 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 85 86 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 87 for (p = 0; p < 5; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 88 } else { 89 PetscInt numPoints[2] = {12, 2}; 90 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 91 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 92 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 93 PetscScalar vertexCoords[36] = {-1.0, -0.5, -0.5, -1.0, 0.5, -0.5, 0.0, 0.5, -0.5, 0.0, -0.5, -0.5, 94 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 95 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 96 97 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 98 } 99 break; 100 default: 101 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 102 } 103 } 104 *newdm = dm; 105 if (refinementLimit > 0.0) { 106 DM rdm; 107 const char *name; 108 109 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 110 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 111 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 112 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 113 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 114 ierr = DMDestroy(newdm);CHKERRQ(ierr); 115 *newdm = rdm; 116 } 117 if (interpolate) { 118 DM idm = NULL; 119 const char *name; 120 121 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 122 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 123 ierr = PetscObjectSetName((PetscObject) idm, name);CHKERRQ(ierr); 124 ierr = DMPlexCopyCoordinates(*newdm, idm);CHKERRQ(ierr); 125 ierr = DMCopyLabels(*newdm, idm);CHKERRQ(ierr); 126 ierr = DMDestroy(newdm);CHKERRQ(ierr); 127 *newdm = idm; 128 } 129 { 130 DM refinedMesh = NULL; 131 DM distributedMesh = NULL; 132 133 /* Distribute mesh over processes */ 134 ierr = DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);CHKERRQ(ierr); 135 if (distributedMesh) { 136 ierr = DMDestroy(newdm);CHKERRQ(ierr); 137 *newdm = distributedMesh; 138 } 139 if (refinementUniform) { 140 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 141 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 142 if (refinedMesh) { 143 ierr = DMDestroy(newdm);CHKERRQ(ierr); 144 *newdm = refinedMesh; 145 } 146 } 147 } 148 PetscFunctionReturn(0); 149 } 150 151 /*@ 152 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 153 154 Collective on MPI_Comm 155 156 Input Parameters: 157 + comm - The communicator for the DM object 158 . lower - The lower left corner coordinates 159 . upper - The upper right corner coordinates 160 - edges - The number of cells in each direction 161 162 Output Parameter: 163 . dm - The DM object 164 165 Note: Here is the numbering returned for 2 cells in each direction: 166 $ 18--5-17--4--16 167 $ | | | 168 $ 6 10 3 169 $ | | | 170 $ 19-11-20--9--15 171 $ | | | 172 $ 7 8 2 173 $ | | | 174 $ 12--0-13--1--14 175 176 Level: beginner 177 178 .keywords: DM, create 179 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 180 @*/ 181 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 182 { 183 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 184 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 185 PetscInt markerTop = 1; 186 PetscInt markerBottom = 1; 187 PetscInt markerRight = 1; 188 PetscInt markerLeft = 1; 189 PetscBool markerSeparate = PETSC_FALSE; 190 Vec coordinates; 191 PetscSection coordSection; 192 PetscScalar *coords; 193 PetscInt coordSize; 194 PetscMPIInt rank; 195 PetscInt v, vx, vy; 196 PetscErrorCode ierr; 197 198 PetscFunctionBegin; 199 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 200 if (markerSeparate) { 201 markerTop = 3; 202 markerBottom = 1; 203 markerRight = 2; 204 markerLeft = 4; 205 } 206 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 207 if (!rank) { 208 PetscInt e, ex, ey; 209 210 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 211 for (e = 0; e < numEdges; ++e) { 212 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 213 } 214 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 215 for (vx = 0; vx <= edges[0]; vx++) { 216 for (ey = 0; ey < edges[1]; ey++) { 217 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 218 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 219 PetscInt cone[2]; 220 221 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 222 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 223 if (vx == edges[0]) { 224 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 225 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 226 if (ey == edges[1]-1) { 227 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 228 } 229 } else if (vx == 0) { 230 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 231 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 232 if (ey == edges[1]-1) { 233 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 234 } 235 } 236 } 237 } 238 for (vy = 0; vy <= edges[1]; vy++) { 239 for (ex = 0; ex < edges[0]; ex++) { 240 PetscInt edge = vy*edges[0] + ex; 241 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 242 PetscInt cone[2]; 243 244 cone[0] = vertex; cone[1] = vertex+1; 245 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 246 if (vy == edges[1]) { 247 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 248 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 249 if (ex == edges[0]-1) { 250 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 251 } 252 } else if (vy == 0) { 253 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 254 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 255 if (ex == edges[0]-1) { 256 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 257 } 258 } 259 } 260 } 261 } 262 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 263 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 264 /* Build coordinates */ 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 the is the boundary of a cubic lattice. 295 296 Collective on MPI_Comm 297 298 Input Parameters: 299 + comm - The communicator for the DM object 300 . lower - The lower left front corner coordinates 301 . upper - The upper right back corner coordinates 302 - edges - The number of cells in each direction 303 304 Output Parameter: 305 . dm - The DM object 306 307 Level: beginner 308 309 .keywords: DM, create 310 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 311 @*/ 312 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 313 { 314 PetscInt vertices[3], numVertices; 315 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 316 Vec coordinates; 317 PetscSection coordSection; 318 PetscScalar *coords; 319 PetscInt coordSize; 320 PetscMPIInt rank; 321 PetscInt v, vx, vy, vz; 322 PetscInt voffset, iface=0, cone[4]; 323 PetscErrorCode ierr; 324 325 PetscFunctionBegin; 326 if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 327 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 328 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 329 numVertices = vertices[0]*vertices[1]*vertices[2]; 330 if (!rank) { 331 PetscInt f; 332 333 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 334 for (f = 0; f < numFaces; ++f) { 335 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 336 } 337 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 338 for (v = 0; v < numFaces+numVertices; ++v) { 339 ierr = DMSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr); 340 } 341 342 /* Side 0 (Top) */ 343 for (vy = 0; vy < faces[1]; vy++) { 344 for (vx = 0; vx < faces[0]; vx++) { 345 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 346 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 347 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 348 iface++; 349 } 350 } 351 352 /* Side 1 (Bottom) */ 353 for (vy = 0; vy < faces[1]; vy++) { 354 for (vx = 0; vx < faces[0]; vx++) { 355 voffset = numFaces + vy*(faces[0]+1) + vx; 356 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 357 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 358 iface++; 359 } 360 } 361 362 /* Side 2 (Front) */ 363 for (vz = 0; vz < faces[2]; vz++) { 364 for (vx = 0; vx < faces[0]; vx++) { 365 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 366 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 367 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 368 iface++; 369 } 370 } 371 372 /* Side 3 (Back) */ 373 for (vz = 0; vz < faces[2]; vz++) { 374 for (vx = 0; vx < faces[0]; vx++) { 375 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 376 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 377 cone[2] = voffset+1; cone[3] = voffset; 378 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 379 iface++; 380 } 381 } 382 383 /* Side 4 (Left) */ 384 for (vz = 0; vz < faces[2]; vz++) { 385 for (vy = 0; vy < faces[1]; vy++) { 386 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 387 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 388 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 389 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 390 iface++; 391 } 392 } 393 394 /* Side 5 (Right) */ 395 for (vz = 0; vz < faces[2]; vz++) { 396 for (vy = 0; vy < faces[1]; vy++) { 397 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + vx; 398 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 399 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 400 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 401 iface++; 402 } 403 } 404 } 405 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 406 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 407 /* Build coordinates */ 408 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 409 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 410 for (v = numFaces; v < numFaces+numVertices; ++v) { 411 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 412 } 413 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 414 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 415 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 416 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 417 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 418 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 419 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 420 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 421 for (vz = 0; vz <= faces[2]; ++vz) { 422 for (vy = 0; vy <= faces[1]; ++vy) { 423 for (vx = 0; vx <= faces[0]; ++vx) { 424 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 425 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 426 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 427 } 428 } 429 } 430 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 431 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 432 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 433 PetscFunctionReturn(0); 434 } 435 436 /*@ 437 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices. 438 439 Collective on MPI_Comm 440 441 Input Parameters: 442 + comm - The communicator for the DM object 443 . dim - The spatial dimension 444 . numFaces - Number of faces per dimension 445 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 446 447 Output Parameter: 448 . dm - The DM object 449 450 Level: beginner 451 452 .keywords: DM, create 453 .seealso: DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate() 454 @*/ 455 PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscInt numFaces, PetscBool interpolate, DM *dm) 456 { 457 DM boundary; 458 PetscErrorCode ierr; 459 460 PetscFunctionBegin; 461 PetscValidPointer(dm, 4); 462 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 463 PetscValidLogicalCollectiveInt(boundary,dim,2); 464 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 465 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 466 ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); 467 switch (dim) { 468 case 2: 469 { 470 PetscReal lower[2] = {0.0, 0.0}; 471 PetscReal upper[2] = {1.0, 1.0}; 472 PetscInt edges[2]; 473 474 edges[0] = numFaces; edges[1] = numFaces; 475 ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, edges);CHKERRQ(ierr); 476 break; 477 } 478 case 3: 479 { 480 PetscReal lower[3] = {0.0, 0.0, 0.0}; 481 PetscReal upper[3] = {1.0, 1.0, 1.0}; 482 PetscInt faces[3]; 483 484 faces[0] = numFaces; faces[1] = numFaces; faces[2] = numFaces; 485 ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr); 486 break; 487 } 488 default: 489 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 490 } 491 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 492 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 493 PetscFunctionReturn(0); 494 } 495 496 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 497 { 498 PetscInt markerTop = 1, faceMarkerTop = 1; 499 PetscInt markerBottom = 1, faceMarkerBottom = 1; 500 PetscInt markerFront = 1, faceMarkerFront = 1; 501 PetscInt markerBack = 1, faceMarkerBack = 1; 502 PetscInt markerRight = 1, faceMarkerRight = 1; 503 PetscInt markerLeft = 1, faceMarkerLeft = 1; 504 PetscInt dim; 505 PetscBool markerSeparate = PETSC_FALSE; 506 PetscMPIInt rank; 507 PetscErrorCode ierr; 508 509 PetscFunctionBegin; 510 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 511 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 512 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 513 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 514 switch (dim) { 515 case 2: 516 faceMarkerTop = 3; 517 faceMarkerBottom = 1; 518 faceMarkerRight = 2; 519 faceMarkerLeft = 4; 520 break; 521 case 3: 522 faceMarkerBottom = 1; 523 faceMarkerTop = 2; 524 faceMarkerFront = 3; 525 faceMarkerBack = 4; 526 faceMarkerRight = 5; 527 faceMarkerLeft = 6; 528 break; 529 default: 530 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %d not supported",dim); 531 break; 532 } 533 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 534 if (markerSeparate) { 535 markerBottom = faceMarkerBottom; 536 markerTop = faceMarkerTop; 537 markerFront = faceMarkerFront; 538 markerBack = faceMarkerBack; 539 markerRight = faceMarkerRight; 540 markerLeft = faceMarkerLeft; 541 } 542 { 543 const PetscInt numXEdges = !rank ? edges[0] : 0; 544 const PetscInt numYEdges = !rank ? edges[1] : 0; 545 const PetscInt numZEdges = !rank ? edges[2] : 0; 546 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 547 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 548 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 549 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 550 const PetscInt numXFaces = numYEdges*numZEdges; 551 const PetscInt numYFaces = numXEdges*numZEdges; 552 const PetscInt numZFaces = numXEdges*numYEdges; 553 const PetscInt numTotXFaces = numXVertices*numXFaces; 554 const PetscInt numTotYFaces = numYVertices*numYFaces; 555 const PetscInt numTotZFaces = numZVertices*numZFaces; 556 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 557 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 558 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 559 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 560 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 561 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 562 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 563 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 564 const PetscInt firstYFace = firstXFace + numTotXFaces; 565 const PetscInt firstZFace = firstYFace + numTotYFaces; 566 const PetscInt firstXEdge = numCells + numFaces + numVertices; 567 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 568 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 569 Vec coordinates; 570 PetscSection coordSection; 571 PetscScalar *coords; 572 PetscInt coordSize; 573 PetscInt v, vx, vy, vz; 574 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 575 576 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 577 for (c = 0; c < numCells; c++) { 578 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 579 } 580 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 581 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 582 } 583 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 584 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 585 } 586 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 587 /* Build cells */ 588 for (fz = 0; fz < numZEdges; ++fz) { 589 for (fy = 0; fy < numYEdges; ++fy) { 590 for (fx = 0; fx < numXEdges; ++fx) { 591 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 592 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 593 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 594 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 595 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 596 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 597 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 598 /* B, T, F, K, R, L */ 599 PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 600 PetscInt cone[6]; 601 602 /* no boundary twisting in 3D */ 603 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 604 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 605 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 606 } 607 } 608 } 609 /* Build x faces */ 610 for (fz = 0; fz < numZEdges; ++fz) { 611 for (fy = 0; fy < numYEdges; ++fy) { 612 for (fx = 0; fx < numXVertices; ++fx) { 613 PetscInt face = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 614 PetscInt edgeL = firstZEdge + ( fy* numXVertices+fx)*numZEdges + fz; 615 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 616 PetscInt edgeB = firstYEdge + ( fz* numXVertices+fx)*numYEdges + fy; 617 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 618 PetscInt ornt[4] = {0, 0, -2, -2}; 619 PetscInt cone[4]; 620 621 if (dim == 3) { 622 /* markers */ 623 if (bdX != DM_BOUNDARY_PERIODIC) { 624 if (fx == numXVertices-1) { 625 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 626 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 627 } 628 else if (fx == 0) { 629 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 630 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 631 } 632 } 633 } 634 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 635 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 636 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 637 } 638 } 639 } 640 /* Build y faces */ 641 for (fz = 0; fz < numZEdges; ++fz) { 642 for (fx = 0; fx < numXEdges; ++fx) { 643 for (fy = 0; fy < numYVertices; ++fy) { 644 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 645 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx )*numZEdges + fz; 646 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 647 PetscInt edgeB = firstXEdge + ( fz *numYVertices+fy)*numXEdges + fx; 648 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 649 PetscInt ornt[4] = {0, 0, -2, -2}; 650 PetscInt cone[4]; 651 652 if (dim == 3) { 653 /* markers */ 654 if (bdY != DM_BOUNDARY_PERIODIC) { 655 if (fy == numYVertices-1) { 656 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 657 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 658 } 659 else if (fy == 0) { 660 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 661 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 662 } 663 } 664 } 665 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 666 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 667 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 668 } 669 } 670 } 671 /* Build z faces */ 672 for (fy = 0; fy < numYEdges; ++fy) { 673 for (fx = 0; fx < numXEdges; ++fx) { 674 for (fz = 0; fz < numZVertices; fz++) { 675 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 676 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx )*numYEdges + fy; 677 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 678 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy )*numXEdges + fx; 679 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 680 PetscInt ornt[4] = {0, 0, -2, -2}; 681 PetscInt cone[4]; 682 683 if (dim == 2) { 684 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 685 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 686 } 687 else { 688 /* markers */ 689 if (bdZ != DM_BOUNDARY_PERIODIC) { 690 if (fz == numZVertices-1) { 691 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 692 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 693 } 694 else if (fz == 0) { 695 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 696 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 697 } 698 } 699 } 700 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 701 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 702 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 703 } 704 } 705 } 706 /* Build Z edges*/ 707 for (vy = 0; vy < numYVertices; vy++) { 708 for (vx = 0; vx < numXVertices; vx++) { 709 for (ez = 0; ez < numZEdges; ez++) { 710 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 711 const PetscInt vertexB = firstVertex + ( ez *numYVertices+vy)*numXVertices + vx; 712 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 713 PetscInt cone[2]; 714 715 if (dim == 3) { 716 if (bdX != DM_BOUNDARY_PERIODIC) { 717 if (vx == numXVertices-1) { 718 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 719 } 720 else if (vx == 0) { 721 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 722 } 723 } 724 if (bdY != DM_BOUNDARY_PERIODIC) { 725 if (vy == numYVertices-1) { 726 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 727 } 728 else if (vy == 0) { 729 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 730 } 731 } 732 } 733 cone[0] = vertexB; cone[1] = vertexT; 734 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 735 } 736 } 737 } 738 /* Build Y edges*/ 739 for (vz = 0; vz < numZVertices; vz++) { 740 for (vx = 0; vx < numXVertices; vx++) { 741 for (ey = 0; ey < numYEdges; ey++) { 742 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 743 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 744 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 745 const PetscInt vertexK = firstVertex + nextv; 746 PetscInt cone[2]; 747 748 cone[0] = vertexF; cone[1] = vertexK; 749 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 750 if (dim == 2) { 751 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 752 if (vx == numXVertices-1) { 753 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 754 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 755 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 756 if (ey == numYEdges-1) { 757 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 758 } 759 } 760 else if (vx == 0) { 761 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 762 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 763 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 764 if (ey == numYEdges-1) { 765 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 766 } 767 } 768 } 769 } 770 else { 771 if (bdX != DM_BOUNDARY_PERIODIC) { 772 if (vx == numXVertices-1) { 773 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 774 } 775 else if (vx == 0) { 776 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 777 } 778 } 779 if (bdZ != DM_BOUNDARY_PERIODIC) { 780 if (vz == numZVertices-1) { 781 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 782 } 783 else if (vz == 0) { 784 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 785 } 786 } 787 } 788 } 789 } 790 } 791 /* Build X edges*/ 792 for (vz = 0; vz < numZVertices; vz++) { 793 for (vy = 0; vy < numYVertices; vy++) { 794 for (ex = 0; ex < numXEdges; ex++) { 795 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 796 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 797 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 798 const PetscInt vertexR = firstVertex + nextv; 799 PetscInt cone[2]; 800 801 cone[0] = vertexL; cone[1] = vertexR; 802 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 803 if (dim == 2) { 804 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 805 if (vy == numYVertices-1) { 806 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 807 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 808 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 809 if (ex == numXEdges-1) { 810 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 811 } 812 } 813 else if (vy == 0) { 814 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 815 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 816 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 817 if (ex == numXEdges-1) { 818 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 819 } 820 } 821 } 822 } 823 else { 824 if (bdY != DM_BOUNDARY_PERIODIC) { 825 if (vy == numYVertices-1) { 826 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 827 } 828 else if (vy == 0) { 829 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 830 } 831 } 832 if (bdZ != DM_BOUNDARY_PERIODIC) { 833 if (vz == numZVertices-1) { 834 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 835 } 836 else if (vz == 0) { 837 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 838 } 839 } 840 } 841 } 842 } 843 } 844 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 845 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 846 /* Build coordinates */ 847 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 848 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 849 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 850 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 851 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 852 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 853 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 854 } 855 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 856 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 857 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 858 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 859 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 860 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 861 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 862 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 863 for (vz = 0; vz < numZVertices; ++vz) { 864 for (vy = 0; vy < numYVertices; ++vy) { 865 for (vx = 0; vx < numXVertices; ++vx) { 866 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 867 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 868 if (dim == 3) { 869 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 870 } 871 } 872 } 873 } 874 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 875 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 876 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 877 } 878 PetscFunctionReturn(0); 879 } 880 881 /*@ 882 DMPlexCreateHexBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using hexahedra. 883 884 Collective on MPI_Comm 885 886 Input Parameters: 887 + comm - The communicator for the DM object 888 . dim - The spatial dimension 889 . periodicX - The boundary type for the X direction 890 . periodicY - The boundary type for the Y direction 891 . periodicZ - The boundary type for the Z direction 892 - cells - The number of cells in each direction 893 894 Output Parameter: 895 . dm - The DM object 896 897 Note: Here is the numbering returned for 2 cells in each direction: 898 $ 22--8-23--9--24 899 $ | | | 900 $ 13 2 14 3 15 901 $ | | | 902 $ 19--6-20--7--21 903 $ | | | 904 $ 10 0 11 1 12 905 $ | | | 906 $ 16--4-17--5--18 907 908 Level: beginner 909 910 .keywords: DM, create 911 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 912 @*/ 913 PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DMBoundaryType periodicX, DMBoundaryType periodicY, DMBoundaryType periodicZ, DM *dm) 914 { 915 PetscInt i; 916 PetscErrorCode ierr; 917 918 PetscFunctionBegin; 919 PetscValidPointer(dm, 7); 920 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 921 PetscValidLogicalCollectiveInt(*dm,dim,2); 922 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 923 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 924 switch (dim) { 925 case 2: 926 { 927 PetscReal lower[3] = {0.0, 0.0, 0.0}; 928 PetscReal upper[3] = {1.0, 1.0, 0.0}; 929 PetscInt edges[3]; 930 931 edges[0] = cells[0]; 932 edges[1] = cells[1]; 933 edges[2] = 0; 934 935 ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, edges, periodicX, periodicY, DM_BOUNDARY_NONE);CHKERRQ(ierr); 936 if (periodicX == DM_BOUNDARY_PERIODIC || periodicX == DM_BOUNDARY_TWIST || 937 periodicY == DM_BOUNDARY_PERIODIC || periodicY == DM_BOUNDARY_TWIST) { 938 PetscReal L[2]; 939 PetscReal maxCell[2]; 940 DMBoundaryType bdType[2]; 941 942 bdType[0] = periodicX; 943 bdType[1] = periodicY; 944 for (i = 0; i < dim; i++) { 945 L[i] = upper[i] - lower[i]; 946 maxCell[i] = 1.1 * (L[i] / PetscMax(1,cells[i])); 947 } 948 949 ierr = DMSetPeriodicity(*dm,maxCell,L,bdType);CHKERRQ(ierr); 950 } 951 break; 952 } 953 case 3: 954 { 955 PetscReal lower[3] = {0.0, 0.0, 0.0}; 956 PetscReal upper[3] = {1.0, 1.0, 1.0}; 957 958 ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, cells, periodicX, periodicY, periodicZ);CHKERRQ(ierr); 959 if (periodicX == DM_BOUNDARY_PERIODIC || periodicX == DM_BOUNDARY_TWIST || 960 periodicY == DM_BOUNDARY_PERIODIC || periodicY == DM_BOUNDARY_TWIST || 961 periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 962 PetscReal L[3]; 963 PetscReal maxCell[3]; 964 DMBoundaryType bdType[3]; 965 966 bdType[0] = periodicX; 967 bdType[1] = periodicY; 968 bdType[2] = periodicZ; 969 for (i = 0; i < dim; i++) { 970 L[i] = upper[i] - lower[i]; 971 maxCell[i] = 1.1 * (L[i] / cells[i]); 972 } 973 974 ierr = DMSetPeriodicity(*dm,maxCell,L,bdType);CHKERRQ(ierr); 975 } 976 break; 977 } 978 default: 979 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 980 } 981 PetscFunctionReturn(0); 982 } 983 984 /*@C 985 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 986 987 Logically Collective on DM 988 989 Input Parameters: 990 + dm - the DM context 991 - prefix - the prefix to prepend to all option names 992 993 Notes: 994 A hyphen (-) must NOT be given at the beginning of the prefix name. 995 The first character of all runtime options is AUTOMATICALLY the hyphen. 996 997 Level: advanced 998 999 .seealso: SNESSetFromOptions() 1000 @*/ 1001 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1002 { 1003 DM_Plex *mesh = (DM_Plex *) dm->data; 1004 PetscErrorCode ierr; 1005 1006 PetscFunctionBegin; 1007 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1008 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1009 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1010 PetscFunctionReturn(0); 1011 } 1012 1013 /*@ 1014 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1015 1016 Collective on MPI_Comm 1017 1018 Input Parameters: 1019 + comm - The communicator for the DM object 1020 . numRefine - The number of regular refinements to the basic 5 cell structure 1021 - periodicZ - The boundary type for the Z direction 1022 1023 Output Parameter: 1024 . dm - The DM object 1025 1026 Note: Here is the output numbering looking from the bottom of the cylinder: 1027 $ 17-----14 1028 $ | | 1029 $ | 2 | 1030 $ | | 1031 $ 17-----8-----7-----14 1032 $ | | | | 1033 $ | 3 | 0 | 1 | 1034 $ | | | | 1035 $ 19-----5-----6-----13 1036 $ | | 1037 $ | 4 | 1038 $ | | 1039 $ 19-----13 1040 $ 1041 $ and up through the top 1042 $ 1043 $ 18-----16 1044 $ | | 1045 $ | 2 | 1046 $ | | 1047 $ 18----10----11-----16 1048 $ | | | | 1049 $ | 3 | 0 | 1 | 1050 $ | | | | 1051 $ 20-----9----12-----15 1052 $ | | 1053 $ | 4 | 1054 $ | | 1055 $ 20-----15 1056 1057 Level: beginner 1058 1059 .keywords: DM, create 1060 .seealso: DMPlexCreateHexBoxMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1061 @*/ 1062 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) 1063 { 1064 const PetscInt dim = 3; 1065 PetscInt numCells, numVertices, r; 1066 PetscErrorCode ierr; 1067 1068 PetscFunctionBegin; 1069 PetscValidPointer(dm, 4); 1070 if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); 1071 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1072 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1073 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1074 /* Create topology */ 1075 { 1076 PetscInt cone[8], c; 1077 1078 numCells = 5; 1079 numVertices = 16; 1080 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1081 numCells *= 3; 1082 numVertices = 24; 1083 } 1084 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1085 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} 1086 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1087 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1088 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1089 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1090 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1091 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1092 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1093 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1094 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1095 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1096 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1097 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1098 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1099 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1100 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1101 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1102 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1103 1104 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1105 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1106 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1107 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1108 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1109 ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); 1110 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1111 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1112 ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); 1113 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1114 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1115 ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); 1116 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1117 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1118 ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); 1119 1120 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1121 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1122 ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); 1123 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1124 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1125 ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); 1126 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1127 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1128 ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); 1129 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1130 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1131 ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); 1132 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1133 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1134 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1135 } else { 1136 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1137 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1138 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1139 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1140 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1141 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1142 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1143 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1144 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1145 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1146 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1147 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1148 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1149 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1150 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1151 } 1152 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1153 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1154 } 1155 /* Interpolate */ 1156 { 1157 DM idm = NULL; 1158 1159 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1160 ierr = DMDestroy(dm);CHKERRQ(ierr); 1161 *dm = idm; 1162 } 1163 /* Create cube geometry */ 1164 { 1165 Vec coordinates; 1166 PetscSection coordSection; 1167 PetscScalar *coords; 1168 PetscInt coordSize, v; 1169 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1170 const PetscReal ds2 = dis/2.0; 1171 1172 /* Build coordinates */ 1173 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1174 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1175 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1176 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1177 for (v = numCells; v < numCells+numVertices; ++v) { 1178 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1179 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1180 } 1181 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1182 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1183 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1184 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1185 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1186 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1187 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1188 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1189 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1190 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1191 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1192 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1193 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1194 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1195 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1196 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1197 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1198 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1199 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1200 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1201 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1202 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1203 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1204 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1205 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1206 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1207 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1208 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1209 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1210 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1211 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1212 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1213 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1214 } 1215 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1216 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1217 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1218 } 1219 /* Create periodicity */ 1220 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1221 PetscReal L[3]; 1222 PetscReal maxCell[3]; 1223 DMBoundaryType bdType[3]; 1224 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1225 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1226 PetscInt i, numZCells = 3; 1227 1228 bdType[0] = DM_BOUNDARY_NONE; 1229 bdType[1] = DM_BOUNDARY_NONE; 1230 bdType[2] = periodicZ; 1231 for (i = 0; i < dim; i++) { 1232 L[i] = upper[i] - lower[i]; 1233 maxCell[i] = 1.1 * (L[i] / numZCells); 1234 } 1235 ierr = DMSetPeriodicity(*dm, maxCell, L, bdType);CHKERRQ(ierr); 1236 } 1237 /* Refine topology */ 1238 for (r = 0; r < numRefine; ++r) { 1239 DM rdm = NULL; 1240 1241 ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); 1242 ierr = DMDestroy(dm);CHKERRQ(ierr); 1243 *dm = rdm; 1244 } 1245 /* Remap geometry to cylinder 1246 Interior square: Linear interpolation is correct 1247 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1248 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1249 1250 phi = arctan(y/x) 1251 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1252 d_far = sqrt(1/2 + sin^2(phi)) 1253 1254 so we remap them using 1255 1256 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1257 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1258 1259 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1260 */ 1261 { 1262 Vec coordinates; 1263 PetscSection coordSection; 1264 PetscScalar *coords; 1265 PetscInt vStart, vEnd, v; 1266 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1267 const PetscReal ds2 = 0.5*dis; 1268 1269 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1270 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1271 ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); 1272 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1273 for (v = vStart; v < vEnd; ++v) { 1274 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1275 PetscInt off; 1276 1277 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 1278 if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; 1279 x = PetscRealPart(coords[off]); 1280 y = PetscRealPart(coords[off+1]); 1281 phi = PetscAtan2Real(y, x); 1282 sinp = PetscSinReal(phi); 1283 cosp = PetscCosReal(phi); 1284 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1285 dc = PetscAbsReal(ds2/sinp); 1286 df = PetscAbsReal(dis/sinp); 1287 xc = ds2*x/PetscAbsScalar(y); 1288 yc = ds2*PetscSignReal(y); 1289 } else { 1290 dc = PetscAbsReal(ds2/cosp); 1291 df = PetscAbsReal(dis/cosp); 1292 xc = ds2*PetscSignReal(x); 1293 yc = ds2*y/PetscAbsScalar(x); 1294 } 1295 coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); 1296 coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); 1297 } 1298 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1299 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1300 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); 1301 } 1302 } 1303 PetscFunctionReturn(0); 1304 } 1305 1306 /* External function declarations here */ 1307 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 1308 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 1309 extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm); 1310 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 1311 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 1312 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 1313 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 1314 extern PetscErrorCode DMSetUp_Plex(DM dm); 1315 extern PetscErrorCode DMDestroy_Plex(DM dm); 1316 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 1317 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 1318 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm); 1319 1320 /* Replace dm with the contents of dmNew 1321 - Share the DM_Plex structure 1322 - Share the coordinates 1323 - Share the SF 1324 */ 1325 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 1326 { 1327 PetscSF sf; 1328 DM coordDM, coarseDM; 1329 Vec coords; 1330 const PetscReal *maxCell, *L; 1331 const DMBoundaryType *bd; 1332 PetscErrorCode ierr; 1333 1334 PetscFunctionBegin; 1335 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 1336 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 1337 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 1338 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 1339 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 1340 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 1341 ierr = DMGetPeriodicity(dm, &maxCell, &L, &bd);CHKERRQ(ierr); 1342 if (L) {ierr = DMSetPeriodicity(dmNew, maxCell, L, bd);CHKERRQ(ierr);} 1343 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 1344 dm->data = dmNew->data; 1345 ((DM_Plex *) dmNew->data)->refct++; 1346 dmNew->labels->refct++; 1347 if (!--(dm->labels->refct)) { 1348 DMLabelLink next = dm->labels->next; 1349 1350 /* destroy the labels */ 1351 while (next) { 1352 DMLabelLink tmp = next->next; 1353 1354 ierr = DMLabelDestroy(&next->label);CHKERRQ(ierr); 1355 ierr = PetscFree(next);CHKERRQ(ierr); 1356 next = tmp; 1357 } 1358 ierr = PetscFree(dm->labels);CHKERRQ(ierr); 1359 } 1360 dm->labels = dmNew->labels; 1361 dm->depthLabel = dmNew->depthLabel; 1362 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 1363 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 1364 PetscFunctionReturn(0); 1365 } 1366 1367 /* Swap dm with the contents of dmNew 1368 - Swap the DM_Plex structure 1369 - Swap the coordinates 1370 - Swap the point PetscSF 1371 */ 1372 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 1373 { 1374 DM coordDMA, coordDMB; 1375 Vec coordsA, coordsB; 1376 PetscSF sfA, sfB; 1377 void *tmp; 1378 DMLabelLinkList listTmp; 1379 DMLabel depthTmp; 1380 PetscErrorCode ierr; 1381 1382 PetscFunctionBegin; 1383 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 1384 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 1385 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 1386 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 1387 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 1388 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 1389 1390 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 1391 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 1392 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 1393 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 1394 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 1395 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 1396 1397 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 1398 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 1399 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 1400 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 1401 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 1402 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 1403 1404 tmp = dmA->data; 1405 dmA->data = dmB->data; 1406 dmB->data = tmp; 1407 listTmp = dmA->labels; 1408 dmA->labels = dmB->labels; 1409 dmB->labels = listTmp; 1410 depthTmp = dmA->depthLabel; 1411 dmA->depthLabel = dmB->depthLabel; 1412 dmB->depthLabel = depthTmp; 1413 PetscFunctionReturn(0); 1414 } 1415 1416 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 1417 { 1418 DM_Plex *mesh = (DM_Plex*) dm->data; 1419 PetscErrorCode ierr; 1420 1421 PetscFunctionBegin; 1422 /* Handle viewing */ 1423 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 1424 ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);CHKERRQ(ierr); 1425 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 1426 /* Point Location */ 1427 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMView", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 1428 /* Generation and remeshing */ 1429 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMView", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 1430 /* Projection behavior */ 1431 ierr = PetscOptionsInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL);CHKERRQ(ierr); 1432 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 1433 1434 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 1435 PetscFunctionReturn(0); 1436 } 1437 1438 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 1439 { 1440 PetscInt refine = 0, coarsen = 0, r; 1441 PetscBool isHierarchy; 1442 PetscErrorCode ierr; 1443 1444 PetscFunctionBegin; 1445 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1446 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 1447 /* Handle DMPlex refinement */ 1448 ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); 1449 ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); 1450 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 1451 if (refine && isHierarchy) { 1452 DM *dms, coarseDM; 1453 1454 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 1455 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 1456 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 1457 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 1458 /* Total hack since we do not pass in a pointer */ 1459 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 1460 if (refine == 1) { 1461 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 1462 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 1463 } else { 1464 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 1465 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 1466 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 1467 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 1468 } 1469 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 1470 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 1471 /* Free DMs */ 1472 for (r = 0; r < refine; ++r) { 1473 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 1474 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 1475 } 1476 ierr = PetscFree(dms);CHKERRQ(ierr); 1477 } else { 1478 for (r = 0; r < refine; ++r) { 1479 DM refinedMesh; 1480 1481 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1482 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 1483 /* Total hack since we do not pass in a pointer */ 1484 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 1485 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1486 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 1487 } 1488 } 1489 /* Handle DMPlex coarsening */ 1490 ierr = PetscOptionsInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL);CHKERRQ(ierr); 1491 ierr = PetscOptionsInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy);CHKERRQ(ierr); 1492 if (coarsen && isHierarchy) { 1493 DM *dms; 1494 1495 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 1496 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 1497 /* Free DMs */ 1498 for (r = 0; r < coarsen; ++r) { 1499 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 1500 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 1501 } 1502 ierr = PetscFree(dms);CHKERRQ(ierr); 1503 } else { 1504 for (r = 0; r < coarsen; ++r) { 1505 DM coarseMesh; 1506 1507 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1508 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 1509 /* Total hack since we do not pass in a pointer */ 1510 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 1511 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1512 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 1513 } 1514 } 1515 /* Handle */ 1516 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 1517 ierr = PetscOptionsTail();CHKERRQ(ierr); 1518 PetscFunctionReturn(0); 1519 } 1520 1521 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 1522 { 1523 PetscErrorCode ierr; 1524 1525 PetscFunctionBegin; 1526 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 1527 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 1528 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 1529 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 1530 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 1531 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 1532 PetscFunctionReturn(0); 1533 } 1534 1535 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 1536 { 1537 PetscErrorCode ierr; 1538 1539 PetscFunctionBegin; 1540 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 1541 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 1542 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 1543 PetscFunctionReturn(0); 1544 } 1545 1546 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 1547 { 1548 PetscInt depth, d; 1549 PetscErrorCode ierr; 1550 1551 PetscFunctionBegin; 1552 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1553 if (depth == 1) { 1554 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 1555 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 1556 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 1557 else {*pStart = 0; *pEnd = 0;} 1558 } else { 1559 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 1560 } 1561 PetscFunctionReturn(0); 1562 } 1563 1564 static PetscErrorCode DMGetNeighors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 1565 { 1566 PetscSF sf; 1567 PetscErrorCode ierr; 1568 1569 PetscFunctionBegin; 1570 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 1571 ierr = PetscSFGetRanks(sf, nranks, ranks, NULL, NULL, NULL);CHKERRQ(ierr); 1572 PetscFunctionReturn(0); 1573 } 1574 1575 static PetscErrorCode DMInitialize_Plex(DM dm) 1576 { 1577 PetscErrorCode ierr; 1578 1579 PetscFunctionBegin; 1580 dm->ops->view = DMView_Plex; 1581 dm->ops->load = DMLoad_Plex; 1582 dm->ops->setfromoptions = DMSetFromOptions_Plex; 1583 dm->ops->clone = DMClone_Plex; 1584 dm->ops->setup = DMSetUp_Plex; 1585 dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; 1586 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 1587 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 1588 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 1589 dm->ops->getlocaltoglobalmapping = NULL; 1590 dm->ops->createfieldis = NULL; 1591 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 1592 dm->ops->getcoloring = NULL; 1593 dm->ops->creatematrix = DMCreateMatrix_Plex; 1594 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 1595 dm->ops->getaggregates = NULL; 1596 dm->ops->getinjection = DMCreateInjection_Plex; 1597 dm->ops->refine = DMRefine_Plex; 1598 dm->ops->coarsen = DMCoarsen_Plex; 1599 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 1600 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 1601 dm->ops->globaltolocalbegin = NULL; 1602 dm->ops->globaltolocalend = NULL; 1603 dm->ops->localtoglobalbegin = NULL; 1604 dm->ops->localtoglobalend = NULL; 1605 dm->ops->destroy = DMDestroy_Plex; 1606 dm->ops->createsubdm = DMCreateSubDM_Plex; 1607 dm->ops->getdimpoints = DMGetDimPoints_Plex; 1608 dm->ops->locatepoints = DMLocatePoints_Plex; 1609 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 1610 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 1611 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 1612 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 1613 dm->ops->computel2diff = DMComputeL2Diff_Plex; 1614 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 1615 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 1616 dm->ops->getneighbors = DMGetNeighors_Plex; 1617 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMAdaptLabel_C",DMAdaptLabel_Plex);CHKERRQ(ierr); 1618 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 1619 PetscFunctionReturn(0); 1620 } 1621 1622 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 1623 { 1624 DM_Plex *mesh = (DM_Plex *) dm->data; 1625 PetscErrorCode ierr; 1626 1627 PetscFunctionBegin; 1628 mesh->refct++; 1629 (*newdm)->data = mesh; 1630 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 1631 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 1632 PetscFunctionReturn(0); 1633 } 1634 1635 /*MC 1636 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 1637 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 1638 specified by a PetscSection object. Ownership in the global representation is determined by 1639 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 1640 1641 Level: intermediate 1642 1643 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 1644 M*/ 1645 1646 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 1647 { 1648 DM_Plex *mesh; 1649 PetscInt unit, d; 1650 PetscErrorCode ierr; 1651 1652 PetscFunctionBegin; 1653 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1654 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 1655 dm->dim = 0; 1656 dm->data = mesh; 1657 1658 mesh->refct = 1; 1659 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 1660 mesh->maxConeSize = 0; 1661 mesh->cones = NULL; 1662 mesh->coneOrientations = NULL; 1663 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 1664 mesh->maxSupportSize = 0; 1665 mesh->supports = NULL; 1666 mesh->refinementUniform = PETSC_TRUE; 1667 mesh->refinementLimit = -1.0; 1668 1669 mesh->facesTmp = NULL; 1670 1671 mesh->tetgenOpts = NULL; 1672 mesh->triangleOpts = NULL; 1673 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 1674 mesh->remeshBd = PETSC_FALSE; 1675 1676 mesh->subpointMap = NULL; 1677 1678 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 1679 1680 mesh->regularRefinement = PETSC_FALSE; 1681 mesh->depthState = -1; 1682 mesh->globalVertexNumbers = NULL; 1683 mesh->globalCellNumbers = NULL; 1684 mesh->anchorSection = NULL; 1685 mesh->anchorIS = NULL; 1686 mesh->createanchors = NULL; 1687 mesh->computeanchormatrix = NULL; 1688 mesh->parentSection = NULL; 1689 mesh->parents = NULL; 1690 mesh->childIDs = NULL; 1691 mesh->childSection = NULL; 1692 mesh->children = NULL; 1693 mesh->referenceTree = NULL; 1694 mesh->getchildsymmetry = NULL; 1695 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 1696 mesh->vtkCellHeight = 0; 1697 mesh->useCone = PETSC_FALSE; 1698 mesh->useClosure = PETSC_TRUE; 1699 mesh->useAnchors = PETSC_FALSE; 1700 1701 mesh->maxProjectionHeight = 0; 1702 1703 mesh->printSetValues = PETSC_FALSE; 1704 mesh->printFEM = 0; 1705 mesh->printTol = 1.0e-10; 1706 1707 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 1708 PetscFunctionReturn(0); 1709 } 1710 1711 /*@ 1712 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 1713 1714 Collective on MPI_Comm 1715 1716 Input Parameter: 1717 . comm - The communicator for the DMPlex object 1718 1719 Output Parameter: 1720 . mesh - The DMPlex object 1721 1722 Level: beginner 1723 1724 .keywords: DMPlex, create 1725 @*/ 1726 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 1727 { 1728 PetscErrorCode ierr; 1729 1730 PetscFunctionBegin; 1731 PetscValidPointer(mesh,2); 1732 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 1733 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 1734 PetscFunctionReturn(0); 1735 } 1736 1737 /* 1738 This takes as input the common mesh generator output, a list of the vertices for each cell, but vertex numbers are global and an SF is built for them 1739 */ 1740 static PetscErrorCode DMPlexBuildFromCellList_Parallel_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[], PetscSF *sfVert) 1741 { 1742 PetscSF sfPoint; 1743 PetscLayout vLayout; 1744 PetscHashI vhash; 1745 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 1746 const PetscInt *vrange; 1747 PetscInt numVerticesAdj, off, *verticesAdj, numVerticesGhost = 0, *localVertex, *cone, c, p, v, g; 1748 PETSC_UNUSED PetscHashIIter ret, iter; 1749 PetscMPIInt rank, size; 1750 PetscErrorCode ierr; 1751 1752 PetscFunctionBegin; 1753 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 1754 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 1755 /* Partition vertices */ 1756 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 1757 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 1758 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 1759 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 1760 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 1761 /* Count vertices and map them to procs */ 1762 PetscHashICreate(vhash); 1763 for (c = 0; c < numCells; ++c) { 1764 for (p = 0; p < numCorners; ++p) { 1765 PetscHashIPut(vhash, cells[c*numCorners+p], ret, iter); 1766 } 1767 } 1768 PetscHashISize(vhash, numVerticesAdj); 1769 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 1770 off = 0; ierr = PetscHashIGetKeys(vhash, &off, verticesAdj);CHKERRQ(ierr); 1771 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 1772 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 1773 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 1774 for (v = 0; v < numVerticesAdj; ++v) { 1775 const PetscInt gv = verticesAdj[v]; 1776 PetscInt vrank; 1777 1778 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 1779 vrank = vrank < 0 ? -(vrank+2) : vrank; 1780 remoteVerticesAdj[v].index = gv - vrange[vrank]; 1781 remoteVerticesAdj[v].rank = vrank; 1782 } 1783 /* Create cones */ 1784 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 1785 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 1786 ierr = DMSetUp(dm);CHKERRQ(ierr); 1787 ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1788 for (c = 0; c < numCells; ++c) { 1789 for (p = 0; p < numCorners; ++p) { 1790 const PetscInt gv = cells[c*numCorners+p]; 1791 PetscInt lv; 1792 1793 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 1794 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 1795 cone[p] = lv+numCells; 1796 } 1797 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1798 } 1799 ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1800 /* Create SF for vertices */ 1801 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfVert);CHKERRQ(ierr); 1802 ierr = PetscObjectSetName((PetscObject) *sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 1803 ierr = PetscSFSetFromOptions(*sfVert);CHKERRQ(ierr); 1804 ierr = PetscSFSetGraph(*sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 1805 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 1806 /* Build pointSF */ 1807 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 1808 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 1809 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 1810 ierr = PetscSFReduceBegin(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 1811 ierr = PetscSFReduceEnd(*sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 1812 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); 1813 ierr = PetscSFBcastBegin(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 1814 ierr = PetscSFBcastEnd(*sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 1815 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 1816 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 1817 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 1818 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 1819 if (vertexLocal[v].rank != rank) { 1820 localVertex[g] = v+numCells; 1821 remoteVertex[g].index = vertexLocal[v].index; 1822 remoteVertex[g].rank = vertexLocal[v].rank; 1823 ++g; 1824 } 1825 } 1826 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 1827 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 1828 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1829 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 1830 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 1831 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 1832 PetscHashIDestroy(vhash); 1833 /* Fill in the rest of the topology structure */ 1834 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1835 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1836 PetscFunctionReturn(0); 1837 } 1838 1839 /* 1840 This takes as input the coordinates for each owned vertex 1841 */ 1842 static PetscErrorCode DMPlexBuildCoordinates_Parallel_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numV, PetscSF sfVert, const PetscReal vertexCoords[]) 1843 { 1844 PetscSection coordSection; 1845 Vec coordinates; 1846 PetscScalar *coords; 1847 PetscInt numVertices, numVerticesAdj, coordSize, v; 1848 PetscErrorCode ierr; 1849 1850 PetscFunctionBegin; 1851 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 1852 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1853 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1854 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 1855 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVerticesAdj);CHKERRQ(ierr); 1856 for (v = numCells; v < numCells+numVerticesAdj; ++v) { 1857 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 1858 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 1859 } 1860 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1861 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1862 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 1863 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 1864 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1865 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1866 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1867 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1868 { 1869 MPI_Datatype coordtype; 1870 1871 /* Need a temp buffer for coords if we have complex/single */ 1872 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 1873 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 1874 #if defined(PETSC_USE_COMPLEX) 1875 { 1876 PetscScalar *svertexCoords; 1877 PetscInt i; 1878 ierr = PetscMalloc1(numV*spaceDim,&svertexCoords);CHKERRQ(ierr); 1879 for (i=0; i<numV*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 1880 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 1881 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 1882 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 1883 } 1884 #else 1885 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 1886 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 1887 #endif 1888 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 1889 } 1890 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1891 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1892 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1893 PetscFunctionReturn(0); 1894 } 1895 1896 /*@C 1897 DMPlexCreateFromCellListParallel - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 1898 1899 Input Parameters: 1900 + comm - The communicator 1901 . dim - The topological dimension of the mesh 1902 . numCells - The number of cells owned by this process 1903 . numVertices - The number of vertices owned by this process 1904 . numCorners - The number of vertices for each cell 1905 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 1906 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 1907 . spaceDim - The spatial dimension used for coordinates 1908 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 1909 1910 Output Parameter: 1911 + dm - The DM 1912 - vertexSF - Optional, SF describing complete vertex ownership 1913 1914 Note: Two triangles sharing a face 1915 $ 1916 $ 2 1917 $ / | \ 1918 $ / | \ 1919 $ / | \ 1920 $ 0 0 | 1 3 1921 $ \ | / 1922 $ \ | / 1923 $ \ | / 1924 $ 1 1925 would have input 1926 $ numCells = 2, numVertices = 4 1927 $ cells = [0 1 2 1 3 2] 1928 $ 1929 which would result in the DMPlex 1930 $ 1931 $ 4 1932 $ / | \ 1933 $ / | \ 1934 $ / | \ 1935 $ 2 0 | 1 5 1936 $ \ | / 1937 $ \ | / 1938 $ \ | / 1939 $ 3 1940 1941 Level: beginner 1942 1943 .seealso: DMPlexCreateFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 1944 @*/ 1945 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) 1946 { 1947 PetscSF sfVert; 1948 PetscErrorCode ierr; 1949 1950 PetscFunctionBegin; 1951 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1952 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1953 PetscValidLogicalCollectiveInt(*dm, dim, 2); 1954 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 1955 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1956 ierr = DMPlexBuildFromCellList_Parallel_Private(*dm, numCells, numVertices, numCorners, cells, &sfVert);CHKERRQ(ierr); 1957 if (interpolate) { 1958 DM idm = NULL; 1959 1960 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1961 ierr = DMDestroy(dm);CHKERRQ(ierr); 1962 *dm = idm; 1963 } 1964 ierr = DMPlexBuildCoordinates_Parallel_Private(*dm, spaceDim, numCells, numVertices,sfVert, vertexCoords);CHKERRQ(ierr); 1965 if (vertexSF) *vertexSF = sfVert; 1966 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 1967 PetscFunctionReturn(0); 1968 } 1969 1970 /* 1971 This takes as input the common mesh generator output, a list of the vertices for each cell 1972 */ 1973 static PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]) 1974 { 1975 PetscInt *cone, c, p; 1976 PetscErrorCode ierr; 1977 1978 PetscFunctionBegin; 1979 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1980 for (c = 0; c < numCells; ++c) { 1981 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 1982 } 1983 ierr = DMSetUp(dm);CHKERRQ(ierr); 1984 ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1985 for (c = 0; c < numCells; ++c) { 1986 for (p = 0; p < numCorners; ++p) { 1987 cone[p] = cells[c*numCorners+p]+numCells; 1988 } 1989 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1990 } 1991 ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1992 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1993 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1994 PetscFunctionReturn(0); 1995 } 1996 1997 /* 1998 This takes as input the coordinates for each vertex 1999 */ 2000 static PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 2001 { 2002 PetscSection coordSection; 2003 Vec coordinates; 2004 DM cdm; 2005 PetscScalar *coords; 2006 PetscInt v, d; 2007 PetscErrorCode ierr; 2008 2009 PetscFunctionBegin; 2010 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2011 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2012 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 2013 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 2014 for (v = numCells; v < numCells+numVertices; ++v) { 2015 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 2016 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 2017 } 2018 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2019 2020 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 2021 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 2022 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 2023 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2024 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2025 for (v = 0; v < numVertices; ++v) { 2026 for (d = 0; d < spaceDim; ++d) { 2027 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 2028 } 2029 } 2030 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2031 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2032 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2033 PetscFunctionReturn(0); 2034 } 2035 2036 /*@C 2037 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 2038 2039 Input Parameters: 2040 + comm - The communicator 2041 . dim - The topological dimension of the mesh 2042 . numCells - The number of cells 2043 . numVertices - The number of vertices 2044 . numCorners - The number of vertices for each cell 2045 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 2046 . cells - An array of numCells*numCorners numbers, the vertices for each cell 2047 . spaceDim - The spatial dimension used for coordinates 2048 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2049 2050 Output Parameter: 2051 . dm - The DM 2052 2053 Note: Two triangles sharing a face 2054 $ 2055 $ 2 2056 $ / | \ 2057 $ / | \ 2058 $ / | \ 2059 $ 0 0 | 1 3 2060 $ \ | / 2061 $ \ | / 2062 $ \ | / 2063 $ 1 2064 would have input 2065 $ numCells = 2, numVertices = 4 2066 $ cells = [0 1 2 1 3 2] 2067 $ 2068 which would result in the DMPlex 2069 $ 2070 $ 4 2071 $ / | \ 2072 $ / | \ 2073 $ / | \ 2074 $ 2 0 | 1 5 2075 $ \ | / 2076 $ \ | / 2077 $ \ | / 2078 $ 3 2079 2080 Level: beginner 2081 2082 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 2083 @*/ 2084 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) 2085 { 2086 PetscErrorCode ierr; 2087 2088 PetscFunctionBegin; 2089 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2090 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2091 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 2092 ierr = DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 2093 if (interpolate) { 2094 DM idm = NULL; 2095 2096 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2097 ierr = DMDestroy(dm);CHKERRQ(ierr); 2098 *dm = idm; 2099 } 2100 ierr = DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 2101 PetscFunctionReturn(0); 2102 } 2103 2104 /*@ 2105 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 2106 2107 Input Parameters: 2108 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 2109 . depth - The depth of the DAG 2110 . numPoints - The number of points at each depth 2111 . coneSize - The cone size of each point 2112 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 2113 . coneOrientations - The orientation of each cone point 2114 - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex 2115 2116 Output Parameter: 2117 . dm - The DM 2118 2119 Note: Two triangles sharing a face would have input 2120 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 2121 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 2122 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 2123 $ 2124 which would result in the DMPlex 2125 $ 2126 $ 4 2127 $ / | \ 2128 $ / | \ 2129 $ / | \ 2130 $ 2 0 | 1 5 2131 $ \ | / 2132 $ \ | / 2133 $ \ | / 2134 $ 3 2135 $ 2136 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 2137 2138 Level: advanced 2139 2140 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 2141 @*/ 2142 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 2143 { 2144 Vec coordinates; 2145 PetscSection coordSection; 2146 PetscScalar *coords; 2147 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 2148 PetscErrorCode ierr; 2149 2150 PetscFunctionBegin; 2151 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2152 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 2153 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %d cannot be less than intrinsic dimension %d",dimEmbed,dim); 2154 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 2155 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 2156 for (p = pStart; p < pEnd; ++p) { 2157 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 2158 if (firstVertex < 0 && !coneSize[p - pStart]) { 2159 firstVertex = p - pStart; 2160 } 2161 } 2162 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %d vertices but could not find any", numPoints[0]); 2163 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 2164 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 2165 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 2166 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 2167 } 2168 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2169 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2170 /* Build coordinates */ 2171 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 2172 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2173 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 2174 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 2175 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 2176 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 2177 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 2178 } 2179 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2180 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2181 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2182 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2183 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2184 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 2185 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2186 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2187 for (v = 0; v < numPoints[0]; ++v) { 2188 PetscInt off; 2189 2190 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 2191 for (d = 0; d < dimEmbed; ++d) { 2192 coords[off+d] = vertexCoords[v*dimEmbed+d]; 2193 } 2194 } 2195 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2196 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 2197 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2198 PetscFunctionReturn(0); 2199 } 2200 2201 /*@C 2202 DMPlexCreateFromFile - This takes a filename and produces a DM 2203 2204 Input Parameters: 2205 + comm - The communicator 2206 . filename - A file name 2207 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 2208 2209 Output Parameter: 2210 . dm - The DM 2211 2212 Level: beginner 2213 2214 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellList(), DMPlexCreate() 2215 @*/ 2216 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 2217 { 2218 const char *extGmsh = ".msh"; 2219 const char *extCGNS = ".cgns"; 2220 const char *extExodus = ".exo"; 2221 const char *extFluent = ".cas"; 2222 const char *extHDF5 = ".h5"; 2223 const char *extMed = ".med"; 2224 size_t len; 2225 PetscBool isGmsh, isCGNS, isExodus, isFluent, isHDF5, isMed; 2226 PetscMPIInt rank; 2227 PetscErrorCode ierr; 2228 2229 PetscFunctionBegin; 2230 PetscValidPointer(filename, 2); 2231 PetscValidPointer(dm, 4); 2232 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 2233 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 2234 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 2235 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 2236 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 2237 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 2238 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 2239 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 2240 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 2241 if (isGmsh) { 2242 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2243 } else if (isCGNS) { 2244 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2245 } else if (isExodus) { 2246 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2247 } else if (isFluent) { 2248 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2249 } else if (isHDF5) { 2250 PetscViewer viewer; 2251 2252 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 2253 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 2254 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 2255 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 2256 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 2257 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 2258 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 2259 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 2260 } else if (isMed) { 2261 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 2262 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 2263 PetscFunctionReturn(0); 2264 } 2265 2266 /*@ 2267 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 2268 2269 Collective on comm 2270 2271 Input Parameters: 2272 + comm - The communicator 2273 . dim - The spatial dimension 2274 - simplex - Flag for simplex, otherwise use a tensor-product cell 2275 2276 Output Parameter: 2277 . refdm - The reference cell 2278 2279 Level: intermediate 2280 2281 .keywords: reference cell 2282 .seealso: 2283 @*/ 2284 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 2285 { 2286 DM rdm; 2287 Vec coords; 2288 PetscErrorCode ierr; 2289 2290 PetscFunctionBeginUser; 2291 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 2292 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 2293 ierr = DMSetDimension(rdm, dim);CHKERRQ(ierr); 2294 switch (dim) { 2295 case 0: 2296 { 2297 PetscInt numPoints[1] = {1}; 2298 PetscInt coneSize[1] = {0}; 2299 PetscInt cones[1] = {0}; 2300 PetscInt coneOrientations[1] = {0}; 2301 PetscScalar vertexCoords[1] = {0.0}; 2302 2303 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2304 } 2305 break; 2306 case 1: 2307 { 2308 PetscInt numPoints[2] = {2, 1}; 2309 PetscInt coneSize[3] = {2, 0, 0}; 2310 PetscInt cones[2] = {1, 2}; 2311 PetscInt coneOrientations[2] = {0, 0}; 2312 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 2313 2314 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2315 } 2316 break; 2317 case 2: 2318 if (simplex) { 2319 PetscInt numPoints[2] = {3, 1}; 2320 PetscInt coneSize[4] = {3, 0, 0, 0}; 2321 PetscInt cones[3] = {1, 2, 3}; 2322 PetscInt coneOrientations[3] = {0, 0, 0}; 2323 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 2324 2325 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2326 } else { 2327 PetscInt numPoints[2] = {4, 1}; 2328 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2329 PetscInt cones[4] = {1, 2, 3, 4}; 2330 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2331 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 2332 2333 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2334 } 2335 break; 2336 case 3: 2337 if (simplex) { 2338 PetscInt numPoints[2] = {4, 1}; 2339 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 2340 PetscInt cones[4] = {1, 3, 2, 4}; 2341 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 2342 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}; 2343 2344 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2345 } else { 2346 PetscInt numPoints[2] = {8, 1}; 2347 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 2348 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 2349 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 2350 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, 2351 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 2352 2353 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 2354 } 2355 break; 2356 default: 2357 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %d", dim); 2358 } 2359 *refdm = NULL; 2360 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 2361 if (rdm->coordinateDM) { 2362 DM ncdm; 2363 PetscSection cs; 2364 PetscInt pEnd = -1; 2365 2366 ierr = DMGetDefaultSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 2367 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 2368 if (pEnd >= 0) { 2369 ierr = DMClone(rdm->coordinateDM, &ncdm);CHKERRQ(ierr); 2370 ierr = DMSetDefaultSection(ncdm, cs);CHKERRQ(ierr); 2371 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 2372 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 2373 } 2374 } 2375 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 2376 if (coords) { 2377 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 2378 } else { 2379 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 2380 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 2381 } 2382 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 2383 PetscFunctionReturn(0); 2384 } 2385