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