1 #define PETSCDM_DLL 2 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petscdmda.h> 4 #include <petscsf.h> 5 6 #undef __FUNCT__ 7 #define __FUNCT__ "DMPlexCreateDoublet" 8 /*@ 9 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 10 11 Collective on MPI_Comm 12 13 Input Parameters: 14 + comm - The communicator for the DM object 15 . dim - The spatial dimension 16 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 17 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 18 . refinementUniform - Flag for uniform parallel refinement 19 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 20 21 Output Parameter: 22 . dm - The DM object 23 24 Level: beginner 25 26 .keywords: DM, create 27 .seealso: DMSetType(), DMCreate() 28 @*/ 29 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 30 { 31 DM dm; 32 PetscInt p; 33 PetscMPIInt rank; 34 PetscErrorCode ierr; 35 36 PetscFunctionBegin; 37 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 38 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 39 ierr = DMPlexSetDimension(dm, dim);CHKERRQ(ierr); 40 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 41 switch (dim) { 42 case 2: 43 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 44 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 45 break; 46 case 3: 47 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 48 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 49 break; 50 default: 51 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 52 } 53 if (rank) { 54 PetscInt numPoints[2] = {0, 0}; 55 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 56 } else { 57 switch (dim) { 58 case 2: 59 if (simplex) { 60 PetscInt numPoints[2] = {4, 2}; 61 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 62 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 63 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 64 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 65 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 66 67 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 68 for (p = 0; p < 4; ++p) {ierr = DMPlexSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 69 } else { 70 PetscInt numPoints[2] = {6, 2}; 71 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 72 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 73 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 74 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}; 75 76 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 77 } 78 break; 79 case 3: 80 if (simplex) { 81 PetscInt numPoints[2] = {5, 2}; 82 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 83 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 84 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 85 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}; 86 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 87 88 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 89 for (p = 0; p < 5; ++p) {ierr = DMPlexSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 90 } else { 91 PetscInt numPoints[2] = {12, 2}; 92 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 93 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 94 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 95 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, 96 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 97 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 98 99 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 100 } 101 break; 102 default: 103 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %d", dim); 104 } 105 } 106 *newdm = dm; 107 if (refinementLimit > 0.0) { 108 DM rdm; 109 const char *name; 110 111 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 112 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 113 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 114 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 115 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 116 ierr = DMDestroy(newdm);CHKERRQ(ierr); 117 *newdm = rdm; 118 } 119 if (interpolate) { 120 DM idm = NULL; 121 const char *name; 122 123 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 124 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 125 ierr = PetscObjectSetName((PetscObject) idm, name);CHKERRQ(ierr); 126 ierr = DMPlexCopyCoordinates(*newdm, idm);CHKERRQ(ierr); 127 ierr = DMPlexCopyLabels(*newdm, idm);CHKERRQ(ierr); 128 ierr = DMDestroy(newdm);CHKERRQ(ierr); 129 *newdm = idm; 130 } 131 { 132 DM refinedMesh = NULL; 133 DM distributedMesh = NULL; 134 135 /* Distribute mesh over processes */ 136 ierr = DMPlexDistribute(*newdm, NULL, 0, NULL, &distributedMesh);CHKERRQ(ierr); 137 if (distributedMesh) { 138 ierr = DMDestroy(newdm);CHKERRQ(ierr); 139 *newdm = distributedMesh; 140 } 141 if (refinementUniform) { 142 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 143 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 144 if (refinedMesh) { 145 ierr = DMDestroy(newdm);CHKERRQ(ierr); 146 *newdm = refinedMesh; 147 } 148 } 149 } 150 PetscFunctionReturn(0); 151 } 152 153 #undef __FUNCT__ 154 #define __FUNCT__ "DMPlexCreateSquareBoundary" 155 /*@ 156 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 157 158 Collective on MPI_Comm 159 160 Input Parameters: 161 + comm - The communicator for the DM object 162 . lower - The lower left corner coordinates 163 . upper - The upper right corner coordinates 164 - edges - The number of cells in each direction 165 166 Output Parameter: 167 . dm - The DM object 168 169 Note: Here is the numbering returned for 2 cells in each direction: 170 $ 18--5-17--4--16 171 $ | | | 172 $ 6 10 3 173 $ | | | 174 $ 19-11-20--9--15 175 $ | | | 176 $ 7 8 2 177 $ | | | 178 $ 12--0-13--1--14 179 180 Level: beginner 181 182 .keywords: DM, create 183 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 184 @*/ 185 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 186 { 187 PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 188 PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 189 PetscInt markerTop = 1; 190 PetscInt markerBottom = 1; 191 PetscInt markerRight = 1; 192 PetscInt markerLeft = 1; 193 PetscBool markerSeparate = PETSC_FALSE; 194 Vec coordinates; 195 PetscSection coordSection; 196 PetscScalar *coords; 197 PetscInt coordSize; 198 PetscMPIInt rank; 199 PetscInt v, vx, vy; 200 PetscErrorCode ierr; 201 202 PetscFunctionBegin; 203 ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 204 if (markerSeparate) { 205 markerTop = 1; 206 markerBottom = 0; 207 markerRight = 0; 208 markerLeft = 0; 209 } 210 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 211 if (!rank) { 212 PetscInt e, ex, ey; 213 214 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 215 for (e = 0; e < numEdges; ++e) { 216 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 217 } 218 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 219 for (vx = 0; vx <= edges[0]; vx++) { 220 for (ey = 0; ey < edges[1]; ey++) { 221 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 222 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 223 PetscInt cone[2]; 224 225 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 226 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 227 if (vx == edges[0]) { 228 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 229 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 230 if (ey == edges[1]-1) { 231 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 232 } 233 } else if (vx == 0) { 234 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 235 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 236 if (ey == edges[1]-1) { 237 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 238 } 239 } 240 } 241 } 242 for (vy = 0; vy <= edges[1]; vy++) { 243 for (ex = 0; ex < edges[0]; ex++) { 244 PetscInt edge = vy*edges[0] + ex; 245 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 246 PetscInt cone[2]; 247 248 cone[0] = vertex; cone[1] = vertex+1; 249 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 250 if (vy == edges[1]) { 251 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 252 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 253 if (ex == edges[0]-1) { 254 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 255 } 256 } else if (vy == 0) { 257 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 258 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 259 if (ex == edges[0]-1) { 260 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 261 } 262 } 263 } 264 } 265 } 266 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 267 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 268 /* Build coordinates */ 269 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 270 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 271 for (v = numEdges; v < numEdges+numVertices; ++v) { 272 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 273 } 274 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 275 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 276 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 277 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 278 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);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 #undef __FUNCT__ 294 #define __FUNCT__ "DMPlexCreateCubeBoundary" 295 /*@ 296 DMPlexCreateCubeBoundary - Creates a 2D mesh the is the boundary of a cubic lattice. 297 298 Collective on MPI_Comm 299 300 Input Parameters: 301 + comm - The communicator for the DM object 302 . lower - The lower left front corner coordinates 303 . upper - The upper right back corner coordinates 304 - edges - The number of cells in each direction 305 306 Output Parameter: 307 . dm - The DM object 308 309 Level: beginner 310 311 .keywords: DM, create 312 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 313 @*/ 314 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 315 { 316 PetscInt vertices[3], numVertices; 317 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 318 Vec coordinates; 319 PetscSection coordSection; 320 PetscScalar *coords; 321 PetscInt coordSize; 322 PetscMPIInt rank; 323 PetscInt v, vx, vy, vz; 324 PetscInt voffset, iface=0, cone[4]; 325 PetscErrorCode ierr; 326 327 PetscFunctionBegin; 328 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"); 329 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 330 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 331 numVertices = vertices[0]*vertices[1]*vertices[2]; 332 if (!rank) { 333 PetscInt f; 334 335 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 336 for (f = 0; f < numFaces; ++f) { 337 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 338 } 339 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 340 for (v = 0; v < numFaces+numVertices; ++v) { 341 ierr = DMPlexSetLabelValue(dm, "marker", v, 1);CHKERRQ(ierr); 342 } 343 344 /* Side 0 (Top) */ 345 for (vy = 0; vy < faces[1]; vy++) { 346 for (vx = 0; vx < faces[0]; vx++) { 347 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 348 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 349 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 350 iface++; 351 } 352 } 353 354 /* Side 1 (Bottom) */ 355 for (vy = 0; vy < faces[1]; vy++) { 356 for (vx = 0; vx < faces[0]; vx++) { 357 voffset = numFaces + vy*(faces[0]+1) + vx; 358 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 359 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 360 iface++; 361 } 362 } 363 364 /* Side 2 (Front) */ 365 for (vz = 0; vz < faces[2]; vz++) { 366 for (vx = 0; vx < faces[0]; vx++) { 367 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 368 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 369 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 370 iface++; 371 } 372 } 373 374 /* Side 3 (Back) */ 375 for (vz = 0; vz < faces[2]; vz++) { 376 for (vx = 0; vx < faces[0]; vx++) { 377 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 378 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 379 cone[2] = voffset+1; cone[3] = voffset; 380 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 381 iface++; 382 } 383 } 384 385 /* Side 4 (Left) */ 386 for (vz = 0; vz < faces[2]; vz++) { 387 for (vy = 0; vy < faces[1]; vy++) { 388 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 389 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 390 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 391 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 392 iface++; 393 } 394 } 395 396 /* Side 5 (Right) */ 397 for (vz = 0; vz < faces[2]; vz++) { 398 for (vy = 0; vy < faces[1]; vy++) { 399 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + vx; 400 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 401 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 402 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 403 iface++; 404 } 405 } 406 } 407 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 408 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 409 /* Build coordinates */ 410 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 411 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 412 for (v = numFaces; v < numFaces+numVertices; ++v) { 413 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 414 } 415 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 416 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 417 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 418 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 419 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 420 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 421 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 422 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 423 for (vz = 0; vz <= faces[2]; ++vz) { 424 for (vy = 0; vy <= faces[1]; ++vy) { 425 for (vx = 0; vx <= faces[0]; ++vx) { 426 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 427 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 428 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 429 } 430 } 431 } 432 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 433 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 434 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 435 PetscFunctionReturn(0); 436 } 437 438 #undef __FUNCT__ 439 #define __FUNCT__ "DMPlexCreateSquareMesh" 440 /*@ 441 DMPlexCreateSquareMesh - Creates a 2D mesh for a square lattice. 442 443 Collective on MPI_Comm 444 445 Input Parameters: 446 + comm - The communicator for the DM object 447 . lower - The lower left corner coordinates 448 . upper - The upper right corner coordinates 449 . edges - The number of cells in each direction 450 . bdX - The boundary type for the X direction 451 - bdY - The boundary type for the Y direction 452 453 Output Parameter: 454 . dm - The DM object 455 456 Note: Here is the numbering returned for 2 cells in each direction: 457 $ 22--8-23--9--24 458 $ | | | 459 $ 13 2 14 3 15 460 $ | | | 461 $ 19--6-20--7--21 462 $ | | | 463 $ 10 0 11 1 12 464 $ | | | 465 $ 16--4-17--5--18 466 467 Level: beginner 468 469 .keywords: DM, create 470 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 471 @*/ 472 PetscErrorCode DMPlexCreateSquareMesh(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY) 473 { 474 PetscInt markerTop = 1; 475 PetscInt markerBottom = 1; 476 PetscInt markerRight = 1; 477 PetscInt markerLeft = 1; 478 PetscBool markerSeparate = PETSC_FALSE; 479 PetscMPIInt rank; 480 PetscErrorCode ierr; 481 482 PetscFunctionBegin; 483 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 484 ierr = PetscOptionsGetBool(((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 485 if (markerSeparate) { 486 markerTop = 3; 487 markerBottom = 1; 488 markerRight = 2; 489 markerLeft = 4; 490 } 491 { 492 const PetscInt numXEdges = !rank ? edges[0] : 0; 493 const PetscInt numYEdges = !rank ? edges[1] : 0; 494 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 495 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 496 const PetscInt numTotXEdges = numXEdges*numYVertices; 497 const PetscInt numTotYEdges = numYEdges*numXVertices; 498 const PetscInt numVertices = numXVertices*numYVertices; 499 const PetscInt numEdges = numTotXEdges + numTotYEdges; 500 const PetscInt numFaces = numXEdges*numYEdges; 501 const PetscInt firstVertex = numFaces; 502 const PetscInt firstXEdge = numFaces + numVertices; 503 const PetscInt firstYEdge = numFaces + numVertices + numTotXEdges; 504 Vec coordinates; 505 PetscSection coordSection; 506 PetscScalar *coords; 507 PetscInt coordSize; 508 PetscInt v, vx, vy; 509 PetscInt f, fx, fy, e, ex, ey; 510 511 ierr = DMPlexSetChart(dm, 0, numFaces+numEdges+numVertices);CHKERRQ(ierr); 512 for (f = 0; f < numFaces; ++f) { 513 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 514 } 515 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 516 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 517 } 518 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 519 /* Build faces */ 520 for (fy = 0; fy < numYEdges; fy++) { 521 for (fx = 0; fx < numXEdges; fx++) { 522 const PetscInt face = fy*numXEdges + fx; 523 const PetscInt edgeL = firstYEdge + fx *numYEdges + fy; 524 const PetscInt edgeR = firstYEdge + ((fx+1)%numXVertices)*numYEdges + fy; 525 const PetscInt edgeB = firstXEdge + fy *numXEdges + fx; 526 const PetscInt edgeT = firstXEdge + ((fy+1)%numYVertices)*numXEdges + fx; 527 const PetscInt ornt[4] = {0, 0, -2, -2}; 528 PetscInt cone[4]; 529 530 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 531 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 532 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 533 } 534 } 535 /* Build Y edges*/ 536 for (vx = 0; vx < numXVertices; vx++) { 537 for (ey = 0; ey < numYEdges; ey++) { 538 const PetscInt nextv = (bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : ((ey+1)%numYVertices)*numXVertices + vx; 539 const PetscInt edge = firstYEdge + vx*numYEdges + ey; 540 const PetscInt vertexB = firstVertex + ey*numXVertices + vx; 541 const PetscInt vertexT = firstVertex + nextv; 542 PetscInt cone[2]; 543 544 cone[0] = vertexB; cone[1] = vertexT; 545 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 546 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 547 if (vx == numXVertices-1) { 548 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 549 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 550 if (ey == numYEdges-1) { 551 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 552 } 553 } else if (vx == 0) { 554 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 555 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 556 if (ey == numYEdges-1) { 557 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 558 } 559 } 560 } 561 } 562 } 563 /* Build X edges*/ 564 for (vy = 0; vy < numYVertices; vy++) { 565 for (ex = 0; ex < numXEdges; ex++) { 566 const PetscInt nextv = (bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : vy*numXVertices + (ex+1)%numXVertices; 567 const PetscInt edge = firstXEdge + vy*numXEdges + ex; 568 const PetscInt vertexL = firstVertex + vy*numXVertices + ex; 569 const PetscInt vertexR = firstVertex + nextv; 570 PetscInt cone[2]; 571 572 cone[0] = vertexL; cone[1] = vertexR; 573 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 574 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 575 if (vy == numYVertices-1) { 576 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 577 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 578 if (ex == numXEdges-1) { 579 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 580 } 581 } else if (vy == 0) { 582 ierr = DMPlexSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 583 ierr = DMPlexSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 584 if (ex == numXEdges-1) { 585 ierr = DMPlexSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 586 } 587 } 588 } 589 } 590 } 591 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 592 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 593 /* Build coordinates */ 594 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 595 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 596 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 597 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 598 } 599 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 600 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 601 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 602 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 603 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 604 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 605 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 606 for (vy = 0; vy < numYVertices; ++vy) { 607 for (vx = 0; vx < numXVertices; ++vx) { 608 coords[(vy*numXVertices+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 609 coords[(vy*numXVertices+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 610 } 611 } 612 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 613 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 614 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 615 } 616 PetscFunctionReturn(0); 617 } 618 619 #undef __FUNCT__ 620 #define __FUNCT__ "DMPlexCreateBoxMesh" 621 /*@ 622 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices. 623 624 Collective on MPI_Comm 625 626 Input Parameters: 627 + comm - The communicator for the DM object 628 . dim - The spatial dimension 629 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 630 631 Output Parameter: 632 . dm - The DM object 633 634 Level: beginner 635 636 .keywords: DM, create 637 .seealso: DMPlexCreateHexBoxMesh(), DMSetType(), DMCreate() 638 @*/ 639 PetscErrorCode DMPlexCreateBoxMesh(MPI_Comm comm, PetscInt dim, PetscBool interpolate, DM *dm) 640 { 641 DM boundary; 642 PetscErrorCode ierr; 643 644 PetscFunctionBegin; 645 PetscValidPointer(dm, 4); 646 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 647 PetscValidLogicalCollectiveInt(boundary,dim,2); 648 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 649 ierr = DMPlexSetDimension(boundary, dim-1);CHKERRQ(ierr); 650 switch (dim) { 651 case 2: 652 { 653 PetscReal lower[2] = {0.0, 0.0}; 654 PetscReal upper[2] = {1.0, 1.0}; 655 PetscInt edges[2] = {2, 2}; 656 657 ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, edges);CHKERRQ(ierr); 658 break; 659 } 660 case 3: 661 { 662 PetscReal lower[3] = {0.0, 0.0, 0.0}; 663 PetscReal upper[3] = {1.0, 1.0, 1.0}; 664 PetscInt faces[3] = {1, 1, 1}; 665 666 ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr); 667 break; 668 } 669 default: 670 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 671 } 672 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 673 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 674 PetscFunctionReturn(0); 675 } 676 677 #undef __FUNCT__ 678 #define __FUNCT__ "DMPlexCreateHexBoxMesh" 679 /*@ 680 DMPlexCreateHexBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using hexahedra. 681 682 Collective on MPI_Comm 683 684 Input Parameters: 685 + comm - The communicator for the DM object 686 . dim - The spatial dimension 687 . periodicX - The boundary type for the X direction 688 . periodicY - The boundary type for the Y direction 689 . periodicZ - The boundary type for the Z direction 690 - cells - The number of cells in each direction 691 692 Output Parameter: 693 . dm - The DM object 694 695 Level: beginner 696 697 .keywords: DM, create 698 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 699 @*/ 700 PetscErrorCode DMPlexCreateHexBoxMesh(MPI_Comm comm, PetscInt dim, const PetscInt cells[], DMBoundaryType periodicX, DMBoundaryType periodicY, DMBoundaryType periodicZ, DM *dm) 701 { 702 PetscErrorCode ierr; 703 704 PetscFunctionBegin; 705 PetscValidPointer(dm, 4); 706 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 707 PetscValidLogicalCollectiveInt(*dm,dim,2); 708 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 709 ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); 710 switch (dim) { 711 case 2: 712 { 713 PetscReal lower[2] = {0.0, 0.0}; 714 PetscReal upper[2] = {1.0, 1.0}; 715 716 ierr = DMPlexCreateSquareMesh(*dm, lower, upper, cells, periodicX, periodicY);CHKERRQ(ierr); 717 break; 718 } 719 #if 0 720 case 3: 721 { 722 PetscReal lower[3] = {0.0, 0.0, 0.0}; 723 PetscReal upper[3] = {1.0, 1.0, 1.0}; 724 725 ierr = DMPlexCreateCubeMesh(boundary, lower, upper, cells, periodicX, periodicY, periodicZ);CHKERRQ(ierr); 726 break; 727 } 728 #endif 729 default: 730 SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %d", dim); 731 } 732 PetscFunctionReturn(0); 733 } 734 735 /* External function declarations here */ 736 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 737 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, VecScatter *ctx); 738 extern PetscErrorCode DMCreateDefaultSection_Plex(DM dm); 739 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 740 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 741 extern PetscErrorCode DMRefine_Plex(DM dm, MPI_Comm comm, DM *dmRefined); 742 extern PetscErrorCode DMCoarsen_Plex(DM dm, MPI_Comm comm, DM *dmCoarsened); 743 extern PetscErrorCode DMRefineHierarchy_Plex(DM dm, PetscInt nlevels, DM dmRefined[]); 744 extern PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 745 extern PetscErrorCode DMSetUp_Plex(DM dm); 746 extern PetscErrorCode DMDestroy_Plex(DM dm); 747 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 748 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 749 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, PetscInt fields[], IS *is, DM *subdm); 750 extern PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, IS *cellIS); 751 752 #undef __FUNCT__ 753 #define __FUNCT__ "DMPlexReplace_Static" 754 /* Replace dm with the contents of dmNew 755 - Share the DM_Plex structure 756 - Share the coordinates 757 */ 758 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 759 { 760 PetscSection coordSection; 761 Vec coords; 762 PetscErrorCode ierr; 763 764 PetscFunctionBegin; 765 ierr = DMGetCoordinateSection(dmNew, &coordSection);CHKERRQ(ierr); 766 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 767 ierr = DMSetCoordinateSection(dm, coordSection);CHKERRQ(ierr); 768 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 769 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 770 dm->data = dmNew->data; 771 ((DM_Plex *) dmNew->data)->refct++; 772 PetscFunctionReturn(0); 773 } 774 775 #undef __FUNCT__ 776 #define __FUNCT__ "DMPlexSwap_Static" 777 /* Swap dm with the contents of dmNew 778 - Swap the DM_Plex structure 779 - Swap the coordinates 780 */ 781 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 782 { 783 DM coordDMA, coordDMB; 784 Vec coordsA, coordsB; 785 void *tmp; 786 PetscErrorCode ierr; 787 788 PetscFunctionBegin; 789 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 790 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 791 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 792 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 793 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 794 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 795 796 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 797 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 798 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 799 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 800 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 801 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 802 tmp = dmA->data; 803 dmA->data = dmB->data; 804 dmB->data = tmp; 805 PetscFunctionReturn(0); 806 } 807 808 #undef __FUNCT__ 809 #define __FUNCT__ "DMSetFromOptions_NonRefinement_Plex" 810 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(DM dm) 811 { 812 DM_Plex *mesh = (DM_Plex*) dm->data; 813 DMBoundary b; 814 PetscErrorCode ierr; 815 816 PetscFunctionBegin; 817 /* Handle boundary conditions */ 818 ierr = PetscOptionsBegin(PetscObjectComm((PetscObject) dm), NULL, "Boundary condition options", "");CHKERRQ(ierr); 819 for (b = mesh->boundary; b; b = b->next) { 820 char optname[1024]; 821 PetscInt ids[1024], len = 1024, i; 822 PetscBool flg; 823 824 ierr = PetscSNPrintf(optname, sizeof(optname), "-bc_%s", b->name);CHKERRQ(ierr); 825 ierr = PetscMemzero(ids, sizeof(ids));CHKERRQ(ierr); 826 ierr = PetscOptionsIntArray(optname, "List of boundary IDs", "", ids, &len, &flg);CHKERRQ(ierr); 827 if (flg) { 828 DMLabel label; 829 830 ierr = DMPlexGetLabel(dm, b->name, &label);CHKERRQ(ierr); 831 for (i = 0; i < len; ++i) { 832 PetscBool has; 833 834 ierr = DMLabelHasValue(label, ids[i], &has);CHKERRQ(ierr); 835 if (!has) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Boundary id %D is not present in the label %s", ids[i], b->name); 836 } 837 b->numids = len; 838 ierr = PetscFree(b->ids);CHKERRQ(ierr); 839 ierr = PetscMalloc1(len, &b->ids);CHKERRQ(ierr); 840 ierr = PetscMemcpy(b->ids, ids, len*sizeof(PetscInt));CHKERRQ(ierr); 841 } 842 } 843 ierr = PetscOptionsEnd();CHKERRQ(ierr); 844 /* Handle viewing */ 845 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMView", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 846 ierr = PetscOptionsInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMView", 0, &mesh->printFEM, NULL);CHKERRQ(ierr); 847 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMView", PETSC_FALSE, &mesh->printTol, NULL);CHKERRQ(ierr); 848 PetscFunctionReturn(0); 849 } 850 851 #undef __FUNCT__ 852 #define __FUNCT__ "DMSetFromOptions_Plex" 853 PetscErrorCode DMSetFromOptions_Plex(DM dm) 854 { 855 PetscInt refine = 0, r; 856 PetscBool isHierarchy; 857 PetscErrorCode ierr; 858 859 PetscFunctionBegin; 860 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 861 ierr = PetscOptionsHead("DMPlex Options");CHKERRQ(ierr); 862 /* Handle DMPlex refinement */ 863 ierr = PetscOptionsInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL);CHKERRQ(ierr); 864 ierr = PetscOptionsInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy);CHKERRQ(ierr); 865 ierr = DMPlexSetRefinementUniform(dm, refine ? PETSC_TRUE : PETSC_FALSE);CHKERRQ(ierr); 866 if (refine && isHierarchy) { 867 DM *dms; 868 869 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 870 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 871 /* Total hack since we do not pass in a pointer */ 872 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 873 if (refine == 1) { 874 ierr = DMPlexSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 875 } else { 876 ierr = DMPlexSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 877 ierr = DMPlexSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 878 } 879 /* Free DMs */ 880 for (r = 0; r < refine; ++r) { 881 ierr = DMSetFromOptions_NonRefinement_Plex(dm);CHKERRQ(ierr); 882 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 883 } 884 ierr = PetscFree(dms);CHKERRQ(ierr); 885 } else { 886 for (r = 0; r < refine; ++r) { 887 DM refinedMesh; 888 889 ierr = DMSetFromOptions_NonRefinement_Plex(dm);CHKERRQ(ierr); 890 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 891 /* Total hack since we do not pass in a pointer */ 892 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 893 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 894 } 895 } 896 ierr = DMSetFromOptions_NonRefinement_Plex(dm);CHKERRQ(ierr); 897 ierr = PetscOptionsTail();CHKERRQ(ierr); 898 PetscFunctionReturn(0); 899 } 900 901 #undef __FUNCT__ 902 #define __FUNCT__ "DMCreateGlobalVector_Plex" 903 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 904 { 905 PetscErrorCode ierr; 906 907 PetscFunctionBegin; 908 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 909 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 910 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 911 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 912 PetscFunctionReturn(0); 913 } 914 915 #undef __FUNCT__ 916 #define __FUNCT__ "DMCreateLocalVector_Plex" 917 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 918 { 919 PetscErrorCode ierr; 920 921 PetscFunctionBegin; 922 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 923 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 924 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 925 PetscFunctionReturn(0); 926 } 927 928 #undef __FUNCT__ 929 #define __FUNCT__ "DMInitialize_Plex" 930 PetscErrorCode DMInitialize_Plex(DM dm) 931 { 932 PetscFunctionBegin; 933 dm->ops->view = DMView_Plex; 934 dm->ops->load = DMLoad_Plex; 935 dm->ops->setfromoptions = DMSetFromOptions_Plex; 936 dm->ops->clone = DMClone_Plex; 937 dm->ops->setup = DMSetUp_Plex; 938 dm->ops->createdefaultsection = DMCreateDefaultSection_Plex; 939 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 940 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 941 dm->ops->getlocaltoglobalmapping = NULL; 942 dm->ops->getlocaltoglobalmappingblock = NULL; 943 dm->ops->createfieldis = NULL; 944 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 945 dm->ops->getcoloring = NULL; 946 dm->ops->creatematrix = DMCreateMatrix_Plex; 947 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 948 dm->ops->getaggregates = NULL; 949 dm->ops->getinjection = DMCreateInjection_Plex; 950 dm->ops->refine = DMRefine_Plex; 951 dm->ops->coarsen = DMCoarsen_Plex; 952 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 953 dm->ops->coarsenhierarchy = NULL; 954 dm->ops->globaltolocalbegin = NULL; 955 dm->ops->globaltolocalend = NULL; 956 dm->ops->localtoglobalbegin = NULL; 957 dm->ops->localtoglobalend = NULL; 958 dm->ops->destroy = DMDestroy_Plex; 959 dm->ops->createsubdm = DMCreateSubDM_Plex; 960 dm->ops->locatepoints = DMLocatePoints_Plex; 961 PetscFunctionReturn(0); 962 } 963 964 #undef __FUNCT__ 965 #define __FUNCT__ "DMClone_Plex" 966 PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 967 { 968 DM_Plex *mesh = (DM_Plex *) dm->data; 969 PetscErrorCode ierr; 970 971 PetscFunctionBegin; 972 mesh->refct++; 973 (*newdm)->data = mesh; 974 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 975 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 976 PetscFunctionReturn(0); 977 } 978 979 /*MC 980 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 981 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 982 specified by a PetscSection object. Ownership in the global representation is determined by 983 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 984 985 Level: intermediate 986 987 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 988 M*/ 989 990 #undef __FUNCT__ 991 #define __FUNCT__ "DMCreate_Plex" 992 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 993 { 994 DM_Plex *mesh; 995 PetscInt unit, d; 996 PetscErrorCode ierr; 997 998 PetscFunctionBegin; 999 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1000 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 1001 dm->data = mesh; 1002 1003 mesh->refct = 1; 1004 mesh->dim = 0; 1005 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 1006 mesh->maxConeSize = 0; 1007 mesh->cones = NULL; 1008 mesh->coneOrientations = NULL; 1009 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 1010 mesh->maxSupportSize = 0; 1011 mesh->supports = NULL; 1012 mesh->refinementUniform = PETSC_TRUE; 1013 mesh->refinementLimit = -1.0; 1014 1015 mesh->facesTmp = NULL; 1016 1017 mesh->subpointMap = NULL; 1018 1019 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 1020 1021 mesh->labels = NULL; 1022 mesh->depthLabel = NULL; 1023 mesh->globalVertexNumbers = NULL; 1024 mesh->globalCellNumbers = NULL; 1025 for (d = 0; d < 8; ++d) mesh->hybridPointMax[d] = PETSC_DETERMINE; 1026 mesh->vtkCellHeight = 0; 1027 mesh->useCone = PETSC_FALSE; 1028 mesh->useClosure = PETSC_TRUE; 1029 1030 mesh->printSetValues = PETSC_FALSE; 1031 mesh->printFEM = 0; 1032 mesh->printTol = 1.0e-10; 1033 1034 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 1035 PetscFunctionReturn(0); 1036 } 1037 1038 #undef __FUNCT__ 1039 #define __FUNCT__ "DMPlexCreate" 1040 /*@ 1041 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 1042 1043 Collective on MPI_Comm 1044 1045 Input Parameter: 1046 . comm - The communicator for the DMPlex object 1047 1048 Output Parameter: 1049 . mesh - The DMPlex object 1050 1051 Level: beginner 1052 1053 .keywords: DMPlex, create 1054 @*/ 1055 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 1056 { 1057 PetscErrorCode ierr; 1058 1059 PetscFunctionBegin; 1060 PetscValidPointer(mesh,2); 1061 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 1062 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 1063 PetscFunctionReturn(0); 1064 } 1065 1066 #undef __FUNCT__ 1067 #define __FUNCT__ "DMPlexBuildFromCellList_Private" 1068 /* 1069 This takes as input the common mesh generator output, a list of the vertices for each cell 1070 */ 1071 PetscErrorCode DMPlexBuildFromCellList_Private(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const int cells[]) 1072 { 1073 PetscInt *cone, c, p; 1074 PetscErrorCode ierr; 1075 1076 PetscFunctionBegin; 1077 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 1078 for (c = 0; c < numCells; ++c) { 1079 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 1080 } 1081 ierr = DMSetUp(dm);CHKERRQ(ierr); 1082 ierr = DMGetWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1083 for (c = 0; c < numCells; ++c) { 1084 for (p = 0; p < numCorners; ++p) { 1085 cone[p] = cells[c*numCorners+p]+numCells; 1086 } 1087 ierr = DMPlexSetCone(dm, c, cone);CHKERRQ(ierr); 1088 } 1089 ierr = DMRestoreWorkArray(dm, numCorners, PETSC_INT, &cone);CHKERRQ(ierr); 1090 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1091 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1092 PetscFunctionReturn(0); 1093 } 1094 1095 #undef __FUNCT__ 1096 #define __FUNCT__ "DMPlexBuildCoordinates_Private" 1097 /* 1098 This takes as input the coordinates for each vertex 1099 */ 1100 PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[]) 1101 { 1102 PetscSection coordSection; 1103 Vec coordinates; 1104 PetscScalar *coords; 1105 PetscInt coordSize, v, d; 1106 PetscErrorCode ierr; 1107 1108 PetscFunctionBegin; 1109 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1110 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1111 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 1112 ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr); 1113 for (v = numCells; v < numCells+numVertices; ++v) { 1114 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 1115 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 1116 } 1117 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1118 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1119 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 1120 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 1121 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1122 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1123 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1124 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1125 for (v = 0; v < numVertices; ++v) { 1126 for (d = 0; d < spaceDim; ++d) { 1127 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 1128 } 1129 } 1130 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1131 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1132 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1133 PetscFunctionReturn(0); 1134 } 1135 1136 #undef __FUNCT__ 1137 #define __FUNCT__ "DMPlexCreateFromCellList" 1138 /*@C 1139 DMPlexCreateFromCellList - This takes as input common mesh generator output, a list of the vertices for each cell, and produces a DM 1140 1141 Input Parameters: 1142 + comm - The communicator 1143 . dim - The topological dimension of the mesh 1144 . numCells - The number of cells 1145 . numVertices - The number of vertices 1146 . numCorners - The number of vertices for each cell 1147 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 1148 . cells - An array of numCells*numCorners numbers, the vertices for each cell 1149 . spaceDim - The spatial dimension used for coordinates 1150 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 1151 1152 Output Parameter: 1153 . dm - The DM 1154 1155 Note: Two triangles sharing a face 1156 $ 1157 $ 2 1158 $ / | \ 1159 $ / | \ 1160 $ / | \ 1161 $ 0 0 | 1 3 1162 $ \ | / 1163 $ \ | / 1164 $ \ | / 1165 $ 1 1166 would have input 1167 $ numCells = 2, numVertices = 4 1168 $ cells = [0 1 2 1 3 2] 1169 $ 1170 which would result in the DMPlex 1171 $ 1172 $ 4 1173 $ / | \ 1174 $ / | \ 1175 $ / | \ 1176 $ 2 0 | 1 5 1177 $ \ | / 1178 $ \ | / 1179 $ \ | / 1180 $ 3 1181 1182 Level: beginner 1183 1184 .seealso: DMPlexCreateFromDAG(), DMPlexCreate() 1185 @*/ 1186 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) 1187 { 1188 PetscErrorCode ierr; 1189 1190 PetscFunctionBegin; 1191 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1192 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1193 ierr = DMPlexSetDimension(*dm, dim);CHKERRQ(ierr); 1194 ierr = DMPlexBuildFromCellList_Private(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 1195 if (interpolate) { 1196 DM idm = NULL; 1197 1198 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1199 ierr = DMDestroy(dm);CHKERRQ(ierr); 1200 *dm = idm; 1201 } 1202 ierr = DMPlexBuildCoordinates_Private(*dm, spaceDim, numCells, numVertices, vertexCoords);CHKERRQ(ierr); 1203 PetscFunctionReturn(0); 1204 } 1205 1206 #undef __FUNCT__ 1207 #define __FUNCT__ "DMPlexCreateFromDAG" 1208 /*@ 1209 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 1210 1211 Input Parameters: 1212 + dm - The empty DM object, usually from DMCreate() and DMPlexSetDimension() 1213 . depth - The depth of the DAG 1214 . numPoints - The number of points at each depth 1215 . coneSize - The cone size of each point 1216 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 1217 . coneOrientations - The orientation of each cone point 1218 - vertexCoords - An array of numVertices*dim numbers, the coordinates of each vertex 1219 1220 Output Parameter: 1221 . dm - The DM 1222 1223 Note: Two triangles sharing a face would have input 1224 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 1225 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 1226 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 1227 $ 1228 which would result in the DMPlex 1229 $ 1230 $ 4 1231 $ / | \ 1232 $ / | \ 1233 $ / | \ 1234 $ 2 0 | 1 5 1235 $ \ | / 1236 $ \ | / 1237 $ \ | / 1238 $ 3 1239 $ 1240 $ Notice that all points are numbered consecutively, unlikely DMPlexCreateFromCellList() 1241 1242 Level: advanced 1243 1244 .seealso: DMPlexCreateFromCellList(), DMPlexCreate() 1245 @*/ 1246 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 1247 { 1248 Vec coordinates; 1249 PetscSection coordSection; 1250 PetscScalar *coords; 1251 PetscInt coordSize, firstVertex = numPoints[depth], pStart = 0, pEnd = 0, p, v, dim, d, off; 1252 PetscErrorCode ierr; 1253 1254 PetscFunctionBegin; 1255 ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr); 1256 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 1257 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 1258 for (p = pStart; p < pEnd; ++p) { 1259 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 1260 } 1261 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 1262 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 1263 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 1264 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 1265 } 1266 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 1267 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 1268 /* Build coordinates */ 1269 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1270 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1271 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1272 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 1273 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 1274 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1275 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1276 } 1277 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1278 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1279 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 1280 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1281 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1282 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1283 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1284 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1285 for (v = 0; v < numPoints[0]; ++v) { 1286 PetscInt off; 1287 1288 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 1289 for (d = 0; d < dim; ++d) { 1290 coords[off+d] = vertexCoords[v*dim+d]; 1291 } 1292 } 1293 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1294 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 1295 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1296 PetscFunctionReturn(0); 1297 } 1298