1 #define PETSCDM_DLL 2 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 3 #include <petsc/private/hashseti.h> /*I "petscdmplex.h" I*/ 4 #include <petscsf.h> 5 6 PetscLogEvent DMPLEX_CreateFromFile, DMPLEX_BuildFromCellList, DMPLEX_BuildCoordinatesFromCellList; 7 8 /*@ 9 DMPlexCreateDoublet - Creates a mesh of two cells of the specified type, optionally with later refinement. 10 11 Collective 12 13 Input Parameters: 14 + comm - The communicator for the DM object 15 . dim - The spatial dimension 16 . simplex - Flag for simplicial cells, otherwise they are tensor product cells 17 . interpolate - Flag to create intermediate mesh pieces (edges, faces) 18 . refinementUniform - Flag for uniform parallel refinement 19 - refinementLimit - A nonzero number indicates the largest admissible volume for a refined cell 20 21 Output Parameter: 22 . dm - The DM object 23 24 Level: beginner 25 26 .seealso: DMSetType(), DMCreate() 27 @*/ 28 PetscErrorCode DMPlexCreateDoublet(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscBool interpolate, PetscBool refinementUniform, PetscReal refinementLimit, DM *newdm) 29 { 30 DM dm; 31 PetscInt p; 32 PetscMPIInt rank; 33 PetscErrorCode ierr; 34 35 PetscFunctionBegin; 36 ierr = DMCreate(comm, &dm);CHKERRQ(ierr); 37 ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr); 38 ierr = DMSetDimension(dm, dim);CHKERRQ(ierr); 39 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 40 switch (dim) { 41 case 2: 42 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "triangular");CHKERRQ(ierr);} 43 else {ierr = PetscObjectSetName((PetscObject) dm, "quadrilateral");CHKERRQ(ierr);} 44 break; 45 case 3: 46 if (simplex) {ierr = PetscObjectSetName((PetscObject) dm, "tetrahedral");CHKERRQ(ierr);} 47 else {ierr = PetscObjectSetName((PetscObject) dm, "hexahedral");CHKERRQ(ierr);} 48 break; 49 default: 50 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim); 51 } 52 if (rank) { 53 PetscInt numPoints[2] = {0, 0}; 54 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, NULL, NULL, NULL, NULL);CHKERRQ(ierr); 55 } else { 56 switch (dim) { 57 case 2: 58 if (simplex) { 59 PetscInt numPoints[2] = {4, 2}; 60 PetscInt coneSize[6] = {3, 3, 0, 0, 0, 0}; 61 PetscInt cones[6] = {2, 3, 4, 5, 4, 3}; 62 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 63 PetscScalar vertexCoords[8] = {-0.5, 0.5, 0.0, 0.0, 0.0, 1.0, 0.5, 0.5}; 64 PetscInt markerPoints[8] = {2, 1, 3, 1, 4, 1, 5, 1}; 65 66 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 67 for (p = 0; p < 4; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 68 } else { 69 PetscInt numPoints[2] = {6, 2}; 70 PetscInt coneSize[8] = {4, 4, 0, 0, 0, 0, 0, 0}; 71 PetscInt cones[8] = {2, 3, 4, 5, 3, 6, 7, 4}; 72 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 73 PetscScalar vertexCoords[12] = {-1.0, -0.5, 0.0, -0.5, 0.0, 0.5, -1.0, 0.5, 1.0, -0.5, 1.0, 0.5}; 74 75 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 76 } 77 break; 78 case 3: 79 if (simplex) { 80 PetscInt numPoints[2] = {5, 2}; 81 PetscInt coneSize[7] = {4, 4, 0, 0, 0, 0, 0}; 82 PetscInt cones[8] = {4, 3, 5, 2, 5, 3, 4, 6}; 83 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 84 PetscScalar vertexCoords[15] = {-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0}; 85 PetscInt markerPoints[10] = {2, 1, 3, 1, 4, 1, 5, 1, 6, 1}; 86 87 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 88 for (p = 0; p < 5; ++p) {ierr = DMSetLabelValue(dm, "marker", markerPoints[p*2], markerPoints[p*2+1]);CHKERRQ(ierr);} 89 } else { 90 PetscInt numPoints[2] = {12, 2}; 91 PetscInt coneSize[14] = {8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 92 PetscInt cones[16] = {2, 3, 4, 5, 6, 7, 8, 9, 5, 4, 10, 11, 7, 12, 13, 8}; 93 PetscInt coneOrientations[16] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; 94 PetscScalar vertexCoords[36] = {-1.0, -0.5, -0.5, -1.0, 0.5, -0.5, 0.0, 0.5, -0.5, 0.0, -0.5, -0.5, 95 -1.0, -0.5, 0.5, 0.0, -0.5, 0.5, 0.0, 0.5, 0.5, -1.0, 0.5, 0.5, 96 1.0, 0.5, -0.5, 1.0, -0.5, -0.5, 1.0, -0.5, 0.5, 1.0, 0.5, 0.5}; 97 98 ierr = DMPlexCreateFromDAG(dm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 99 } 100 break; 101 default: 102 SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Cannot make meshes for dimension %D", dim); 103 } 104 } 105 *newdm = dm; 106 if (refinementLimit > 0.0) { 107 DM rdm; 108 const char *name; 109 110 ierr = DMPlexSetRefinementUniform(*newdm, PETSC_FALSE);CHKERRQ(ierr); 111 ierr = DMPlexSetRefinementLimit(*newdm, refinementLimit);CHKERRQ(ierr); 112 ierr = DMRefine(*newdm, comm, &rdm);CHKERRQ(ierr); 113 ierr = PetscObjectGetName((PetscObject) *newdm, &name);CHKERRQ(ierr); 114 ierr = PetscObjectSetName((PetscObject) rdm, name);CHKERRQ(ierr); 115 ierr = DMDestroy(newdm);CHKERRQ(ierr); 116 *newdm = rdm; 117 } 118 if (interpolate) { 119 DM idm; 120 121 ierr = DMPlexInterpolate(*newdm, &idm);CHKERRQ(ierr); 122 ierr = DMDestroy(newdm);CHKERRQ(ierr); 123 *newdm = idm; 124 } 125 { 126 DM refinedMesh = NULL; 127 DM distributedMesh = NULL; 128 129 /* Distribute mesh over processes */ 130 ierr = DMPlexDistribute(*newdm, 0, NULL, &distributedMesh);CHKERRQ(ierr); 131 if (distributedMesh) { 132 ierr = DMDestroy(newdm);CHKERRQ(ierr); 133 *newdm = distributedMesh; 134 } 135 if (refinementUniform) { 136 ierr = DMPlexSetRefinementUniform(*newdm, refinementUniform);CHKERRQ(ierr); 137 ierr = DMRefine(*newdm, comm, &refinedMesh);CHKERRQ(ierr); 138 if (refinedMesh) { 139 ierr = DMDestroy(newdm);CHKERRQ(ierr); 140 *newdm = refinedMesh; 141 } 142 } 143 } 144 PetscFunctionReturn(0); 145 } 146 147 /*@ 148 DMPlexCreateSquareBoundary - Creates a 1D mesh the is the boundary of a square lattice. 149 150 Collective 151 152 Input Parameters: 153 + comm - The communicator for the DM object 154 . lower - The lower left corner coordinates 155 . upper - The upper right corner coordinates 156 - edges - The number of cells in each direction 157 158 Output Parameter: 159 . dm - The DM object 160 161 Note: Here is the numbering returned for 2 cells in each direction: 162 $ 18--5-17--4--16 163 $ | | | 164 $ 6 10 3 165 $ | | | 166 $ 19-11-20--9--15 167 $ | | | 168 $ 7 8 2 169 $ | | | 170 $ 12--0-13--1--14 171 172 Level: beginner 173 174 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateCubeBoundary(), DMSetType(), DMCreate() 175 @*/ 176 PetscErrorCode DMPlexCreateSquareBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[]) 177 { 178 const PetscInt numVertices = (edges[0]+1)*(edges[1]+1); 179 const PetscInt numEdges = edges[0]*(edges[1]+1) + (edges[0]+1)*edges[1]; 180 PetscInt markerTop = 1; 181 PetscInt markerBottom = 1; 182 PetscInt markerRight = 1; 183 PetscInt markerLeft = 1; 184 PetscBool markerSeparate = PETSC_FALSE; 185 Vec coordinates; 186 PetscSection coordSection; 187 PetscScalar *coords; 188 PetscInt coordSize; 189 PetscMPIInt rank; 190 PetscInt v, vx, vy; 191 PetscErrorCode ierr; 192 193 PetscFunctionBegin; 194 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 195 if (markerSeparate) { 196 markerTop = 3; 197 markerBottom = 1; 198 markerRight = 2; 199 markerLeft = 4; 200 } 201 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 202 if (!rank) { 203 PetscInt e, ex, ey; 204 205 ierr = DMPlexSetChart(dm, 0, numEdges+numVertices);CHKERRQ(ierr); 206 for (e = 0; e < numEdges; ++e) { 207 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 208 } 209 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 210 for (vx = 0; vx <= edges[0]; vx++) { 211 for (ey = 0; ey < edges[1]; ey++) { 212 PetscInt edge = vx*edges[1] + ey + edges[0]*(edges[1]+1); 213 PetscInt vertex = ey*(edges[0]+1) + vx + numEdges; 214 PetscInt cone[2]; 215 216 cone[0] = vertex; cone[1] = vertex+edges[0]+1; 217 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 218 if (vx == edges[0]) { 219 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 220 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 221 if (ey == edges[1]-1) { 222 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 223 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerRight);CHKERRQ(ierr); 224 } 225 } else if (vx == 0) { 226 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 227 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 228 if (ey == edges[1]-1) { 229 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 230 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerLeft);CHKERRQ(ierr); 231 } 232 } 233 } 234 } 235 for (vy = 0; vy <= edges[1]; vy++) { 236 for (ex = 0; ex < edges[0]; ex++) { 237 PetscInt edge = vy*edges[0] + ex; 238 PetscInt vertex = vy*(edges[0]+1) + ex + numEdges; 239 PetscInt cone[2]; 240 241 cone[0] = vertex; cone[1] = vertex+1; 242 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 243 if (vy == edges[1]) { 244 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 245 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 246 if (ex == edges[0]-1) { 247 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 248 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerTop);CHKERRQ(ierr); 249 } 250 } else if (vy == 0) { 251 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 252 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 253 if (ex == edges[0]-1) { 254 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 255 ierr = DMSetLabelValue(dm, "Face Sets", cone[1], markerBottom);CHKERRQ(ierr); 256 } 257 } 258 } 259 } 260 } 261 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 262 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 263 /* Build coordinates */ 264 ierr = DMSetCoordinateDim(dm, 2);CHKERRQ(ierr); 265 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 266 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 267 ierr = PetscSectionSetChart(coordSection, numEdges, numEdges + numVertices);CHKERRQ(ierr); 268 ierr = PetscSectionSetFieldComponents(coordSection, 0, 2);CHKERRQ(ierr); 269 for (v = numEdges; v < numEdges+numVertices; ++v) { 270 ierr = PetscSectionSetDof(coordSection, v, 2);CHKERRQ(ierr); 271 ierr = PetscSectionSetFieldDof(coordSection, v, 0, 2);CHKERRQ(ierr); 272 } 273 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 274 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 275 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 276 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 277 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 278 ierr = VecSetBlockSize(coordinates, 2);CHKERRQ(ierr); 279 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 280 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 281 for (vy = 0; vy <= edges[1]; ++vy) { 282 for (vx = 0; vx <= edges[0]; ++vx) { 283 coords[(vy*(edges[0]+1)+vx)*2+0] = lower[0] + ((upper[0] - lower[0])/edges[0])*vx; 284 coords[(vy*(edges[0]+1)+vx)*2+1] = lower[1] + ((upper[1] - lower[1])/edges[1])*vy; 285 } 286 } 287 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 288 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 289 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 290 PetscFunctionReturn(0); 291 } 292 293 /*@ 294 DMPlexCreateCubeBoundary - Creates a 2D mesh that is the boundary of a cubic lattice. 295 296 Collective 297 298 Input Parameters: 299 + comm - The communicator for the DM object 300 . lower - The lower left front corner coordinates 301 . upper - The upper right back corner coordinates 302 - faces - The number of faces in each direction (the same as the number of cells) 303 304 Output Parameter: 305 . dm - The DM object 306 307 Level: beginner 308 309 .seealso: DMPlexCreateBoxMesh(), DMPlexCreateSquareBoundary(), DMSetType(), DMCreate() 310 @*/ 311 PetscErrorCode DMPlexCreateCubeBoundary(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt faces[]) 312 { 313 PetscInt vertices[3], numVertices; 314 PetscInt numFaces = 2*faces[0]*faces[1] + 2*faces[1]*faces[2] + 2*faces[0]*faces[2]; 315 Vec coordinates; 316 PetscSection coordSection; 317 PetscScalar *coords; 318 PetscInt coordSize; 319 PetscMPIInt rank; 320 PetscInt v, vx, vy, vz; 321 PetscInt voffset, iface=0, cone[4]; 322 PetscErrorCode ierr; 323 324 PetscFunctionBegin; 325 if ((faces[0] < 1) || (faces[1] < 1) || (faces[2] < 1)) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Must have at least 1 face per side"); 326 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 327 vertices[0] = faces[0]+1; vertices[1] = faces[1]+1; vertices[2] = faces[2]+1; 328 numVertices = vertices[0]*vertices[1]*vertices[2]; 329 if (!rank) { 330 PetscInt f; 331 332 ierr = DMPlexSetChart(dm, 0, numFaces+numVertices);CHKERRQ(ierr); 333 for (f = 0; f < numFaces; ++f) { 334 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 335 } 336 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 337 338 /* Side 0 (Top) */ 339 for (vy = 0; vy < faces[1]; vy++) { 340 for (vx = 0; vx < faces[0]; vx++) { 341 voffset = numFaces + vertices[0]*vertices[1]*(vertices[2]-1) + vy*vertices[0] + vx; 342 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]+1; cone[3] = voffset+vertices[0]; 343 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 344 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 345 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 346 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 347 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 348 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 349 iface++; 350 } 351 } 352 353 /* Side 1 (Bottom) */ 354 for (vy = 0; vy < faces[1]; vy++) { 355 for (vx = 0; vx < faces[0]; vx++) { 356 voffset = numFaces + vy*(faces[0]+1) + vx; 357 cone[0] = voffset+1; cone[1] = voffset; cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]+1; 358 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 359 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 360 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 361 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 362 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 363 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+1, 1);CHKERRQ(ierr); 364 iface++; 365 } 366 } 367 368 /* Side 2 (Front) */ 369 for (vz = 0; vz < faces[2]; vz++) { 370 for (vx = 0; vx < faces[0]; vx++) { 371 voffset = numFaces + vz*vertices[0]*vertices[1] + vx; 372 cone[0] = voffset; cone[1] = voffset+1; cone[2] = voffset+vertices[0]*vertices[1]+1; cone[3] = voffset+vertices[0]*vertices[1]; 373 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 374 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 375 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 376 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 377 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 378 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 379 iface++; 380 } 381 } 382 383 /* Side 3 (Back) */ 384 for (vz = 0; vz < faces[2]; vz++) { 385 for (vx = 0; vx < faces[0]; vx++) { 386 voffset = numFaces + vz*vertices[0]*vertices[1] + vertices[0]*(vertices[1]-1) + vx; 387 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset+vertices[0]*vertices[1]+1; 388 cone[2] = voffset+1; cone[3] = voffset; 389 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 390 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 391 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 392 ierr = DMSetLabelValue(dm, "marker", voffset+1, 1);CHKERRQ(ierr); 393 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 394 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+1, 1);CHKERRQ(ierr); 395 iface++; 396 } 397 } 398 399 /* Side 4 (Left) */ 400 for (vz = 0; vz < faces[2]; vz++) { 401 for (vy = 0; vy < faces[1]; vy++) { 402 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0]; 403 cone[0] = voffset; cone[1] = voffset+vertices[0]*vertices[1]; 404 cone[2] = voffset+vertices[0]*vertices[1]+vertices[0]; cone[3] = voffset+vertices[0]; 405 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 406 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 407 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 408 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 409 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[1]+0, 1);CHKERRQ(ierr); 410 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 411 iface++; 412 } 413 } 414 415 /* Side 5 (Right) */ 416 for (vz = 0; vz < faces[2]; vz++) { 417 for (vy = 0; vy < faces[1]; vy++) { 418 voffset = numFaces + vz*vertices[0]*vertices[1] + vy*vertices[0] + faces[0]; 419 cone[0] = voffset+vertices[0]*vertices[1]; cone[1] = voffset; 420 cone[2] = voffset+vertices[0]; cone[3] = voffset+vertices[0]*vertices[1]+vertices[0]; 421 ierr = DMPlexSetCone(dm, iface, cone);CHKERRQ(ierr); 422 ierr = DMSetLabelValue(dm, "marker", iface, 1);CHKERRQ(ierr); 423 ierr = DMSetLabelValue(dm, "marker", voffset+0, 1);CHKERRQ(ierr); 424 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]+0, 1);CHKERRQ(ierr); 425 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+0, 1);CHKERRQ(ierr); 426 ierr = DMSetLabelValue(dm, "marker", voffset+vertices[0]*vertices[1]+vertices[0], 1);CHKERRQ(ierr); 427 iface++; 428 } 429 } 430 } 431 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 432 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 433 /* Build coordinates */ 434 ierr = DMSetCoordinateDim(dm, 3);CHKERRQ(ierr); 435 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 436 ierr = PetscSectionSetChart(coordSection, numFaces, numFaces + numVertices);CHKERRQ(ierr); 437 for (v = numFaces; v < numFaces+numVertices; ++v) { 438 ierr = PetscSectionSetDof(coordSection, v, 3);CHKERRQ(ierr); 439 } 440 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 441 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 442 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 443 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 444 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 445 ierr = VecSetBlockSize(coordinates, 3);CHKERRQ(ierr); 446 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 447 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 448 for (vz = 0; vz <= faces[2]; ++vz) { 449 for (vy = 0; vy <= faces[1]; ++vy) { 450 for (vx = 0; vx <= faces[0]; ++vx) { 451 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+0] = lower[0] + ((upper[0] - lower[0])/faces[0])*vx; 452 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+1] = lower[1] + ((upper[1] - lower[1])/faces[1])*vy; 453 coords[((vz*(faces[1]+1)+vy)*(faces[0]+1)+vx)*3+2] = lower[2] + ((upper[2] - lower[2])/faces[2])*vz; 454 } 455 } 456 } 457 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 458 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 459 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 460 PetscFunctionReturn(0); 461 } 462 463 static PetscErrorCode DMPlexCreateLineMesh_Internal(MPI_Comm comm,PetscInt segments,PetscReal lower,PetscReal upper,DMBoundaryType bd,DM *dm) 464 { 465 PetscInt i,fStart,fEnd,numCells = 0,numVerts = 0; 466 PetscInt numPoints[2],*coneSize,*cones,*coneOrientations; 467 PetscScalar *vertexCoords; 468 PetscReal L,maxCell; 469 PetscBool markerSeparate = PETSC_FALSE; 470 PetscInt markerLeft = 1, faceMarkerLeft = 1; 471 PetscInt markerRight = 1, faceMarkerRight = 2; 472 PetscBool wrap = (bd == DM_BOUNDARY_PERIODIC || bd == DM_BOUNDARY_TWIST) ? PETSC_TRUE : PETSC_FALSE; 473 PetscMPIInt rank; 474 PetscErrorCode ierr; 475 476 PetscFunctionBegin; 477 PetscValidPointer(dm,4); 478 479 ierr = DMCreate(comm,dm);CHKERRQ(ierr); 480 ierr = DMSetType(*dm,DMPLEX);CHKERRQ(ierr); 481 ierr = DMSetDimension(*dm,1);CHKERRQ(ierr); 482 ierr = DMCreateLabel(*dm,"marker");CHKERRQ(ierr); 483 ierr = DMCreateLabel(*dm,"Face Sets");CHKERRQ(ierr); 484 485 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 486 if (!rank) numCells = segments; 487 if (!rank) numVerts = segments + (wrap ? 0 : 1); 488 489 numPoints[0] = numVerts ; numPoints[1] = numCells; 490 ierr = PetscMalloc4(numCells+numVerts,&coneSize,numCells*2,&cones,numCells+numVerts,&coneOrientations,numVerts,&vertexCoords);CHKERRQ(ierr); 491 ierr = PetscArrayzero(coneOrientations,numCells+numVerts);CHKERRQ(ierr); 492 for (i = 0; i < numCells; ++i) { coneSize[i] = 2; } 493 for (i = 0; i < numVerts; ++i) { coneSize[numCells+i] = 0; } 494 for (i = 0; i < numCells; ++i) { cones[2*i] = numCells + i%numVerts; cones[2*i+1] = numCells + (i+1)%numVerts; } 495 for (i = 0; i < numVerts; ++i) { vertexCoords[i] = lower + (upper-lower)*((PetscReal)i/(PetscReal)numCells); } 496 ierr = DMPlexCreateFromDAG(*dm,1,numPoints,coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 497 ierr = PetscFree4(coneSize,cones,coneOrientations,vertexCoords);CHKERRQ(ierr); 498 499 ierr = PetscOptionsGetBool(((PetscObject)*dm)->options,((PetscObject)*dm)->prefix,"-dm_plex_separate_marker",&markerSeparate,NULL);CHKERRQ(ierr); 500 if (markerSeparate) { markerLeft = faceMarkerLeft; markerRight = faceMarkerRight;} 501 if (!wrap && !rank) { 502 ierr = DMPlexGetHeightStratum(*dm,1,&fStart,&fEnd);CHKERRQ(ierr); 503 ierr = DMSetLabelValue(*dm,"marker",fStart,markerLeft);CHKERRQ(ierr); 504 ierr = DMSetLabelValue(*dm,"marker",fEnd-1,markerRight);CHKERRQ(ierr); 505 ierr = DMSetLabelValue(*dm,"Face Sets",fStart,faceMarkerLeft);CHKERRQ(ierr); 506 ierr = DMSetLabelValue(*dm,"Face Sets",fEnd-1,faceMarkerRight);CHKERRQ(ierr); 507 } 508 if (wrap) { 509 L = upper - lower; 510 maxCell = (PetscReal)1.1*(L/(PetscReal)PetscMax(1,segments)); 511 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,&maxCell,&L,&bd);CHKERRQ(ierr); 512 } 513 PetscFunctionReturn(0); 514 } 515 516 static PetscErrorCode DMPlexCreateBoxMesh_Simplex_Internal(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm) 517 { 518 DM boundary; 519 PetscInt i; 520 PetscErrorCode ierr; 521 522 PetscFunctionBegin; 523 PetscValidPointer(dm, 4); 524 for (i = 0; i < dim; ++i) if (periodicity[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity is not supported for simplex meshes"); 525 ierr = DMCreate(comm, &boundary);CHKERRQ(ierr); 526 PetscValidLogicalCollectiveInt(boundary,dim,2); 527 ierr = DMSetType(boundary, DMPLEX);CHKERRQ(ierr); 528 ierr = DMSetDimension(boundary, dim-1);CHKERRQ(ierr); 529 ierr = DMSetCoordinateDim(boundary, dim);CHKERRQ(ierr); 530 switch (dim) { 531 case 2: ierr = DMPlexCreateSquareBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 532 case 3: ierr = DMPlexCreateCubeBoundary(boundary, lower, upper, faces);CHKERRQ(ierr);break; 533 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %D", dim); 534 } 535 ierr = DMPlexGenerate(boundary, NULL, interpolate, dm);CHKERRQ(ierr); 536 ierr = DMDestroy(&boundary);CHKERRQ(ierr); 537 PetscFunctionReturn(0); 538 } 539 540 static PetscErrorCode DMPlexCreateCubeMesh_Internal(DM dm, const PetscReal lower[], const PetscReal upper[], const PetscInt edges[], DMBoundaryType bdX, DMBoundaryType bdY, DMBoundaryType bdZ) 541 { 542 DMLabel cutLabel = NULL; 543 PetscInt markerTop = 1, faceMarkerTop = 1; 544 PetscInt markerBottom = 1, faceMarkerBottom = 1; 545 PetscInt markerFront = 1, faceMarkerFront = 1; 546 PetscInt markerBack = 1, faceMarkerBack = 1; 547 PetscInt markerRight = 1, faceMarkerRight = 1; 548 PetscInt markerLeft = 1, faceMarkerLeft = 1; 549 PetscInt dim; 550 PetscBool markerSeparate = PETSC_FALSE, cutMarker = PETSC_FALSE; 551 PetscMPIInt rank; 552 PetscErrorCode ierr; 553 554 PetscFunctionBegin; 555 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 556 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm), &rank);CHKERRQ(ierr); 557 ierr = DMCreateLabel(dm,"marker");CHKERRQ(ierr); 558 ierr = DMCreateLabel(dm,"Face Sets");CHKERRQ(ierr); 559 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_periodic_cut", &cutMarker, NULL);CHKERRQ(ierr); 560 if (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST || 561 bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST || 562 bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST) { 563 564 if (cutMarker) {ierr = DMCreateLabel(dm, "periodic_cut");CHKERRQ(ierr); ierr = DMGetLabel(dm, "periodic_cut", &cutLabel);CHKERRQ(ierr);} 565 } 566 switch (dim) { 567 case 2: 568 faceMarkerTop = 3; 569 faceMarkerBottom = 1; 570 faceMarkerRight = 2; 571 faceMarkerLeft = 4; 572 break; 573 case 3: 574 faceMarkerBottom = 1; 575 faceMarkerTop = 2; 576 faceMarkerFront = 3; 577 faceMarkerBack = 4; 578 faceMarkerRight = 5; 579 faceMarkerLeft = 6; 580 break; 581 default: 582 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Dimension %D not supported",dim); 583 break; 584 } 585 ierr = PetscOptionsGetBool(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-dm_plex_separate_marker", &markerSeparate, NULL);CHKERRQ(ierr); 586 if (markerSeparate) { 587 markerBottom = faceMarkerBottom; 588 markerTop = faceMarkerTop; 589 markerFront = faceMarkerFront; 590 markerBack = faceMarkerBack; 591 markerRight = faceMarkerRight; 592 markerLeft = faceMarkerLeft; 593 } 594 { 595 const PetscInt numXEdges = !rank ? edges[0] : 0; 596 const PetscInt numYEdges = !rank ? edges[1] : 0; 597 const PetscInt numZEdges = !rank ? edges[2] : 0; 598 const PetscInt numXVertices = !rank ? (bdX == DM_BOUNDARY_PERIODIC || bdX == DM_BOUNDARY_TWIST ? edges[0] : edges[0]+1) : 0; 599 const PetscInt numYVertices = !rank ? (bdY == DM_BOUNDARY_PERIODIC || bdY == DM_BOUNDARY_TWIST ? edges[1] : edges[1]+1) : 0; 600 const PetscInt numZVertices = !rank ? (bdZ == DM_BOUNDARY_PERIODIC || bdZ == DM_BOUNDARY_TWIST ? edges[2] : edges[2]+1) : 0; 601 const PetscInt numCells = numXEdges*numYEdges*numZEdges; 602 const PetscInt numXFaces = numYEdges*numZEdges; 603 const PetscInt numYFaces = numXEdges*numZEdges; 604 const PetscInt numZFaces = numXEdges*numYEdges; 605 const PetscInt numTotXFaces = numXVertices*numXFaces; 606 const PetscInt numTotYFaces = numYVertices*numYFaces; 607 const PetscInt numTotZFaces = numZVertices*numZFaces; 608 const PetscInt numFaces = numTotXFaces + numTotYFaces + numTotZFaces; 609 const PetscInt numTotXEdges = numXEdges*numYVertices*numZVertices; 610 const PetscInt numTotYEdges = numYEdges*numXVertices*numZVertices; 611 const PetscInt numTotZEdges = numZEdges*numXVertices*numYVertices; 612 const PetscInt numVertices = numXVertices*numYVertices*numZVertices; 613 const PetscInt numEdges = numTotXEdges + numTotYEdges + numTotZEdges; 614 const PetscInt firstVertex = (dim == 2) ? numFaces : numCells; 615 const PetscInt firstXFace = (dim == 2) ? 0 : numCells + numVertices; 616 const PetscInt firstYFace = firstXFace + numTotXFaces; 617 const PetscInt firstZFace = firstYFace + numTotYFaces; 618 const PetscInt firstXEdge = numCells + numFaces + numVertices; 619 const PetscInt firstYEdge = firstXEdge + numTotXEdges; 620 const PetscInt firstZEdge = firstYEdge + numTotYEdges; 621 Vec coordinates; 622 PetscSection coordSection; 623 PetscScalar *coords; 624 PetscInt coordSize; 625 PetscInt v, vx, vy, vz; 626 PetscInt c, f, fx, fy, fz, e, ex, ey, ez; 627 628 ierr = DMPlexSetChart(dm, 0, numCells+numFaces+numEdges+numVertices);CHKERRQ(ierr); 629 for (c = 0; c < numCells; c++) { 630 ierr = DMPlexSetConeSize(dm, c, 6);CHKERRQ(ierr); 631 } 632 for (f = firstXFace; f < firstXFace+numFaces; ++f) { 633 ierr = DMPlexSetConeSize(dm, f, 4);CHKERRQ(ierr); 634 } 635 for (e = firstXEdge; e < firstXEdge+numEdges; ++e) { 636 ierr = DMPlexSetConeSize(dm, e, 2);CHKERRQ(ierr); 637 } 638 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 639 /* Build cells */ 640 for (fz = 0; fz < numZEdges; ++fz) { 641 for (fy = 0; fy < numYEdges; ++fy) { 642 for (fx = 0; fx < numXEdges; ++fx) { 643 PetscInt cell = (fz*numYEdges + fy)*numXEdges + fx; 644 PetscInt faceB = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 645 PetscInt faceT = firstZFace + (fy*numXEdges+fx)*numZVertices + ((fz+1)%numZVertices); 646 PetscInt faceF = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 647 PetscInt faceK = firstYFace + (fz*numXEdges+fx)*numYVertices + ((fy+1)%numYVertices); 648 PetscInt faceL = firstXFace + (fz*numYEdges+fy)*numXVertices + fx; 649 PetscInt faceR = firstXFace + (fz*numYEdges+fy)*numXVertices + ((fx+1)%numXVertices); 650 /* B, T, F, K, R, L */ 651 PetscInt ornt[6] = {-4, 0, 0, -1, 0, -4}; /* ??? */ 652 PetscInt cone[6]; 653 654 /* no boundary twisting in 3D */ 655 cone[0] = faceB; cone[1] = faceT; cone[2] = faceF; cone[3] = faceK; cone[4] = faceR; cone[5] = faceL; 656 ierr = DMPlexSetCone(dm, cell, cone);CHKERRQ(ierr); 657 ierr = DMPlexSetConeOrientation(dm, cell, ornt);CHKERRQ(ierr); 658 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 659 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 660 if (bdZ != DM_BOUNDARY_NONE && fz == numZEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, cell, 2);CHKERRQ(ierr);} 661 } 662 } 663 } 664 /* Build x faces */ 665 for (fz = 0; fz < numZEdges; ++fz) { 666 for (fy = 0; fy < numYEdges; ++fy) { 667 for (fx = 0; fx < numXVertices; ++fx) { 668 PetscInt face = firstXFace + (fz*numYEdges+fy) *numXVertices+fx; 669 PetscInt edgeL = firstZEdge + (fy *numXVertices+fx)*numZEdges + fz; 670 PetscInt edgeR = firstZEdge + (((fy+1)%numYVertices)*numXVertices+fx)*numZEdges + fz; 671 PetscInt edgeB = firstYEdge + (fz *numXVertices+fx)*numYEdges + fy; 672 PetscInt edgeT = firstYEdge + (((fz+1)%numZVertices)*numXVertices+fx)*numYEdges + fy; 673 PetscInt ornt[4] = {0, 0, -2, -2}; 674 PetscInt cone[4]; 675 676 if (dim == 3) { 677 /* markers */ 678 if (bdX != DM_BOUNDARY_PERIODIC) { 679 if (fx == numXVertices-1) { 680 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerRight);CHKERRQ(ierr); 681 ierr = DMSetLabelValue(dm, "marker", face, markerRight);CHKERRQ(ierr); 682 } 683 else if (fx == 0) { 684 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerLeft);CHKERRQ(ierr); 685 ierr = DMSetLabelValue(dm, "marker", face, markerLeft);CHKERRQ(ierr); 686 } 687 } 688 } 689 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 690 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 691 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 692 } 693 } 694 } 695 /* Build y faces */ 696 for (fz = 0; fz < numZEdges; ++fz) { 697 for (fx = 0; fx < numXEdges; ++fx) { 698 for (fy = 0; fy < numYVertices; ++fy) { 699 PetscInt face = firstYFace + (fz*numXEdges+fx)*numYVertices + fy; 700 PetscInt edgeL = firstZEdge + (fy*numXVertices+ fx)*numZEdges + fz; 701 PetscInt edgeR = firstZEdge + (fy*numXVertices+((fx+1)%numXVertices))*numZEdges + fz; 702 PetscInt edgeB = firstXEdge + (fz *numYVertices+fy)*numXEdges + fx; 703 PetscInt edgeT = firstXEdge + (((fz+1)%numZVertices)*numYVertices+fy)*numXEdges + fx; 704 PetscInt ornt[4] = {0, 0, -2, -2}; 705 PetscInt cone[4]; 706 707 if (dim == 3) { 708 /* markers */ 709 if (bdY != DM_BOUNDARY_PERIODIC) { 710 if (fy == numYVertices-1) { 711 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBack);CHKERRQ(ierr); 712 ierr = DMSetLabelValue(dm, "marker", face, markerBack);CHKERRQ(ierr); 713 } 714 else if (fy == 0) { 715 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerFront);CHKERRQ(ierr); 716 ierr = DMSetLabelValue(dm, "marker", face, markerFront);CHKERRQ(ierr); 717 } 718 } 719 } 720 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 721 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 722 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 723 } 724 } 725 } 726 /* Build z faces */ 727 for (fy = 0; fy < numYEdges; ++fy) { 728 for (fx = 0; fx < numXEdges; ++fx) { 729 for (fz = 0; fz < numZVertices; fz++) { 730 PetscInt face = firstZFace + (fy*numXEdges+fx)*numZVertices + fz; 731 PetscInt edgeL = firstYEdge + (fz*numXVertices+ fx)*numYEdges + fy; 732 PetscInt edgeR = firstYEdge + (fz*numXVertices+((fx+1)%numXVertices))*numYEdges + fy; 733 PetscInt edgeB = firstXEdge + (fz*numYVertices+ fy)*numXEdges + fx; 734 PetscInt edgeT = firstXEdge + (fz*numYVertices+((fy+1)%numYVertices))*numXEdges + fx; 735 PetscInt ornt[4] = {0, 0, -2, -2}; 736 PetscInt cone[4]; 737 738 if (dim == 2) { 739 if (bdX == DM_BOUNDARY_TWIST && fx == numXEdges-1) {edgeR += numYEdges-1-2*fy; ornt[1] = -2;} 740 if (bdY == DM_BOUNDARY_TWIST && fy == numYEdges-1) {edgeT += numXEdges-1-2*fx; ornt[2] = 0;} 741 if (bdX != DM_BOUNDARY_NONE && fx == numXEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 742 if (bdY != DM_BOUNDARY_NONE && fy == numYEdges-1 && cutLabel) {ierr = DMLabelSetValue(cutLabel, face, 2);CHKERRQ(ierr);} 743 } else { 744 /* markers */ 745 if (bdZ != DM_BOUNDARY_PERIODIC) { 746 if (fz == numZVertices-1) { 747 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerTop);CHKERRQ(ierr); 748 ierr = DMSetLabelValue(dm, "marker", face, markerTop);CHKERRQ(ierr); 749 } 750 else if (fz == 0) { 751 ierr = DMSetLabelValue(dm, "Face Sets", face, faceMarkerBottom);CHKERRQ(ierr); 752 ierr = DMSetLabelValue(dm, "marker", face, markerBottom);CHKERRQ(ierr); 753 } 754 } 755 } 756 cone[0] = edgeB; cone[1] = edgeR; cone[2] = edgeT; cone[3] = edgeL; 757 ierr = DMPlexSetCone(dm, face, cone);CHKERRQ(ierr); 758 ierr = DMPlexSetConeOrientation(dm, face, ornt);CHKERRQ(ierr); 759 } 760 } 761 } 762 /* Build Z edges*/ 763 for (vy = 0; vy < numYVertices; vy++) { 764 for (vx = 0; vx < numXVertices; vx++) { 765 for (ez = 0; ez < numZEdges; ez++) { 766 const PetscInt edge = firstZEdge + (vy*numXVertices+vx)*numZEdges + ez; 767 const PetscInt vertexB = firstVertex + (ez *numYVertices+vy)*numXVertices + vx; 768 const PetscInt vertexT = firstVertex + (((ez+1)%numZVertices)*numYVertices+vy)*numXVertices + vx; 769 PetscInt cone[2]; 770 771 if (dim == 3) { 772 if (bdX != DM_BOUNDARY_PERIODIC) { 773 if (vx == numXVertices-1) { 774 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 775 } 776 else if (vx == 0) { 777 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 778 } 779 } 780 if (bdY != DM_BOUNDARY_PERIODIC) { 781 if (vy == numYVertices-1) { 782 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 783 } 784 else if (vy == 0) { 785 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 786 } 787 } 788 } 789 cone[0] = vertexB; cone[1] = vertexT; 790 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 791 } 792 } 793 } 794 /* Build Y edges*/ 795 for (vz = 0; vz < numZVertices; vz++) { 796 for (vx = 0; vx < numXVertices; vx++) { 797 for (ey = 0; ey < numYEdges; ey++) { 798 const PetscInt nextv = (dim == 2 && bdY == DM_BOUNDARY_TWIST && ey == numYEdges-1) ? (numXVertices-vx-1) : (vz*numYVertices+((ey+1)%numYVertices))*numXVertices + vx; 799 const PetscInt edge = firstYEdge + (vz*numXVertices+vx)*numYEdges + ey; 800 const PetscInt vertexF = firstVertex + (vz*numYVertices+ey)*numXVertices + vx; 801 const PetscInt vertexK = firstVertex + nextv; 802 PetscInt cone[2]; 803 804 cone[0] = vertexF; cone[1] = vertexK; 805 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 806 if (dim == 2) { 807 if ((bdX != DM_BOUNDARY_PERIODIC) && (bdX != DM_BOUNDARY_TWIST)) { 808 if (vx == numXVertices-1) { 809 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerRight);CHKERRQ(ierr); 810 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 811 ierr = DMSetLabelValue(dm, "marker", cone[0], markerRight);CHKERRQ(ierr); 812 if (ey == numYEdges-1) { 813 ierr = DMSetLabelValue(dm, "marker", cone[1], markerRight);CHKERRQ(ierr); 814 } 815 } else if (vx == 0) { 816 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerLeft);CHKERRQ(ierr); 817 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 818 ierr = DMSetLabelValue(dm, "marker", cone[0], markerLeft);CHKERRQ(ierr); 819 if (ey == numYEdges-1) { 820 ierr = DMSetLabelValue(dm, "marker", cone[1], markerLeft);CHKERRQ(ierr); 821 } 822 } 823 } else { 824 if (vx == 0 && cutLabel) { 825 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 826 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 827 if (ey == numYEdges-1) { 828 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 829 } 830 } 831 } 832 } else { 833 if (bdX != DM_BOUNDARY_PERIODIC) { 834 if (vx == numXVertices-1) { 835 ierr = DMSetLabelValue(dm, "marker", edge, markerRight);CHKERRQ(ierr); 836 } else if (vx == 0) { 837 ierr = DMSetLabelValue(dm, "marker", edge, markerLeft);CHKERRQ(ierr); 838 } 839 } 840 if (bdZ != DM_BOUNDARY_PERIODIC) { 841 if (vz == numZVertices-1) { 842 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 843 } else if (vz == 0) { 844 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 845 } 846 } 847 } 848 } 849 } 850 } 851 /* Build X edges*/ 852 for (vz = 0; vz < numZVertices; vz++) { 853 for (vy = 0; vy < numYVertices; vy++) { 854 for (ex = 0; ex < numXEdges; ex++) { 855 const PetscInt nextv = (dim == 2 && bdX == DM_BOUNDARY_TWIST && ex == numXEdges-1) ? (numYVertices-vy-1)*numXVertices : (vz*numYVertices+vy)*numXVertices + (ex+1)%numXVertices; 856 const PetscInt edge = firstXEdge + (vz*numYVertices+vy)*numXEdges + ex; 857 const PetscInt vertexL = firstVertex + (vz*numYVertices+vy)*numXVertices + ex; 858 const PetscInt vertexR = firstVertex + nextv; 859 PetscInt cone[2]; 860 861 cone[0] = vertexL; cone[1] = vertexR; 862 ierr = DMPlexSetCone(dm, edge, cone);CHKERRQ(ierr); 863 if (dim == 2) { 864 if ((bdY != DM_BOUNDARY_PERIODIC) && (bdY != DM_BOUNDARY_TWIST)) { 865 if (vy == numYVertices-1) { 866 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerTop);CHKERRQ(ierr); 867 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 868 ierr = DMSetLabelValue(dm, "marker", cone[0], markerTop);CHKERRQ(ierr); 869 if (ex == numXEdges-1) { 870 ierr = DMSetLabelValue(dm, "marker", cone[1], markerTop);CHKERRQ(ierr); 871 } 872 } else if (vy == 0) { 873 ierr = DMSetLabelValue(dm, "Face Sets", edge, faceMarkerBottom);CHKERRQ(ierr); 874 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 875 ierr = DMSetLabelValue(dm, "marker", cone[0], markerBottom);CHKERRQ(ierr); 876 if (ex == numXEdges-1) { 877 ierr = DMSetLabelValue(dm, "marker", cone[1], markerBottom);CHKERRQ(ierr); 878 } 879 } 880 } else { 881 if (vy == 0 && cutLabel) { 882 ierr = DMLabelSetValue(cutLabel, edge, 1);CHKERRQ(ierr); 883 ierr = DMLabelSetValue(cutLabel, cone[0], 1);CHKERRQ(ierr); 884 if (ex == numXEdges-1) { 885 ierr = DMLabelSetValue(cutLabel, cone[1], 1);CHKERRQ(ierr); 886 } 887 } 888 } 889 } else { 890 if (bdY != DM_BOUNDARY_PERIODIC) { 891 if (vy == numYVertices-1) { 892 ierr = DMSetLabelValue(dm, "marker", edge, markerBack);CHKERRQ(ierr); 893 } 894 else if (vy == 0) { 895 ierr = DMSetLabelValue(dm, "marker", edge, markerFront);CHKERRQ(ierr); 896 } 897 } 898 if (bdZ != DM_BOUNDARY_PERIODIC) { 899 if (vz == numZVertices-1) { 900 ierr = DMSetLabelValue(dm, "marker", edge, markerTop);CHKERRQ(ierr); 901 } 902 else if (vz == 0) { 903 ierr = DMSetLabelValue(dm, "marker", edge, markerBottom);CHKERRQ(ierr); 904 } 905 } 906 } 907 } 908 } 909 } 910 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 911 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 912 /* Build coordinates */ 913 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 914 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 915 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 916 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVertices);CHKERRQ(ierr); 917 for (v = firstVertex; v < firstVertex+numVertices; ++v) { 918 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 919 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 920 } 921 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 922 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 923 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 924 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 925 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 926 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 927 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 928 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 929 for (vz = 0; vz < numZVertices; ++vz) { 930 for (vy = 0; vy < numYVertices; ++vy) { 931 for (vx = 0; vx < numXVertices; ++vx) { 932 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+0] = lower[0] + ((upper[0] - lower[0])/numXEdges)*vx; 933 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+1] = lower[1] + ((upper[1] - lower[1])/numYEdges)*vy; 934 if (dim == 3) { 935 coords[((vz*numYVertices+vy)*numXVertices+vx)*dim+2] = lower[2] + ((upper[2] - lower[2])/numZEdges)*vz; 936 } 937 } 938 } 939 } 940 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 941 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 942 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 943 } 944 PetscFunctionReturn(0); 945 } 946 947 static PetscErrorCode DMPlexCreateBoxMesh_Tensor_Internal(MPI_Comm comm, PetscInt dim, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool interpolate, DM *dm) 948 { 949 PetscInt i; 950 PetscErrorCode ierr; 951 952 PetscFunctionBegin; 953 PetscValidPointer(dm, 7); 954 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 955 PetscValidLogicalCollectiveInt(*dm,dim,2); 956 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 957 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 958 switch (dim) { 959 case 2: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], DM_BOUNDARY_NONE);CHKERRQ(ierr);break;} 960 case 3: {ierr = DMPlexCreateCubeMesh_Internal(*dm, lower, upper, faces, periodicity[0], periodicity[1], periodicity[2]);CHKERRQ(ierr);break;} 961 default: SETERRQ1(comm, PETSC_ERR_SUP, "Dimension not supported: %D", dim); 962 } 963 if (periodicity[0] == DM_BOUNDARY_PERIODIC || periodicity[0] == DM_BOUNDARY_TWIST || 964 periodicity[1] == DM_BOUNDARY_PERIODIC || periodicity[1] == DM_BOUNDARY_TWIST || 965 (dim > 2 && (periodicity[2] == DM_BOUNDARY_PERIODIC || periodicity[2] == DM_BOUNDARY_TWIST))) { 966 PetscReal L[3]; 967 PetscReal maxCell[3]; 968 969 for (i = 0; i < dim; i++) { 970 L[i] = upper[i] - lower[i]; 971 maxCell[i] = 1.1 * (L[i] / PetscMax(1,faces[i])); 972 } 973 ierr = DMSetPeriodicity(*dm,PETSC_TRUE,maxCell,L,periodicity);CHKERRQ(ierr); 974 } 975 if (!interpolate) { 976 DM udm; 977 978 ierr = DMPlexUninterpolate(*dm, &udm);CHKERRQ(ierr); 979 ierr = DMPlexCopyCoordinates(*dm, udm);CHKERRQ(ierr); 980 ierr = DMDestroy(dm);CHKERRQ(ierr); 981 *dm = udm; 982 } 983 PetscFunctionReturn(0); 984 } 985 986 /*@C 987 DMPlexCreateBoxMesh - Creates a mesh on the tensor product of unit intervals (box) using simplices or tensor cells (hexahedra). 988 989 Collective 990 991 Input Parameters: 992 + comm - The communicator for the DM object 993 . dim - The spatial dimension 994 . simplex - PETSC_TRUE for simplices, PETSC_FALSE for tensor cells 995 . faces - Number of faces per dimension, or NULL for (1,) in 1D and (2, 2) in 2D and (1, 1, 1) in 3D 996 . lower - The lower left corner, or NULL for (0, 0, 0) 997 . upper - The upper right corner, or NULL for (1, 1, 1) 998 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 999 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1000 1001 Output Parameter: 1002 . dm - The DM object 1003 1004 Options Database Keys: 1005 These options override the hard-wired input values. 1006 + -dm_plex_box_dim <dim> - Set the topological dimension 1007 . -dm_plex_box_simplex <bool> - PETSC_TRUE for simplex elements, PETSC_FALSE for tensor elements 1008 . -dm_plex_box_lower <x,y,z> - Specify lower-left-bottom coordinates for the box 1009 . -dm_plex_box_upper <x,y,z> - Specify upper-right-top coordinates for the box 1010 - -dm_plex_box_faces <m,n,p> - Number of faces in each linear direction 1011 1012 1013 Notes: 1014 The options database keys above take lists of length d in d dimensions. 1015 1016 Here is the numbering returned for 2 faces in each direction for tensor cells: 1017 $ 10---17---11---18----12 1018 $ | | | 1019 $ | | | 1020 $ 20 2 22 3 24 1021 $ | | | 1022 $ | | | 1023 $ 7---15----8---16----9 1024 $ | | | 1025 $ | | | 1026 $ 19 0 21 1 23 1027 $ | | | 1028 $ | | | 1029 $ 4---13----5---14----6 1030 1031 and for simplicial cells 1032 1033 $ 14----8---15----9----16 1034 $ |\ 5 |\ 7 | 1035 $ | \ | \ | 1036 $ 13 2 14 3 15 1037 $ | 4 \ | 6 \ | 1038 $ | \ | \ | 1039 $ 11----6---12----7----13 1040 $ |\ |\ | 1041 $ | \ 1 | \ 3 | 1042 $ 10 0 11 1 12 1043 $ | 0 \ | 2 \ | 1044 $ | \ | \ | 1045 $ 8----4----9----5----10 1046 1047 Level: beginner 1048 1049 .seealso: DMPlexCreateFromFile(), DMPlexCreateHexCylinderMesh(), DMSetType(), DMCreate() 1050 @*/ 1051 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) 1052 { 1053 PetscInt fac[3] = {0, 0, 0}; 1054 PetscReal low[3] = {0, 0, 0}; 1055 PetscReal upp[3] = {1, 1, 1}; 1056 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1057 PetscInt i, n; 1058 PetscBool flg; 1059 PetscErrorCode ierr; 1060 1061 PetscFunctionBegin; 1062 ierr = PetscOptionsGetInt(NULL, NULL, "-dm_plex_box_dim", &dim, &flg);CHKERRQ(ierr); 1063 if ((dim < 0) || (dim > 3)) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Dimension %D should be in [1, 3]", dim); 1064 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_box_simplex", &simplex, &flg);CHKERRQ(ierr); 1065 n = 3; 1066 ierr = PetscOptionsGetIntArray(NULL, NULL, "-dm_plex_box_faces", fac, &n, &flg);CHKERRQ(ierr); 1067 for (i = 0; i < dim; ++i) fac[i] = faces ? faces[i] : (flg && i < n ? fac[i] : (dim == 1 ? 1 : 4-dim)); 1068 if (lower) for (i = 0; i < dim; ++i) low[i] = lower[i]; 1069 if (upper) for (i = 0; i < dim; ++i) upp[i] = upper[i]; 1070 if (periodicity) for (i = 0; i < dim; ++i) bdt[i] = periodicity[i]; 1071 /* Allow bounds to be specified from the command line */ 1072 n = 3; 1073 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_lower", low, &n, &flg);CHKERRQ(ierr); 1074 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Lower box point had %D values, should have been %D", n, dim); 1075 n = 3; 1076 ierr = PetscOptionsGetRealArray(NULL, NULL, "-dm_plex_box_upper", upp, &n, &flg);CHKERRQ(ierr); 1077 if (flg && (n != dim)) SETERRQ2(comm, PETSC_ERR_ARG_SIZ, "Upper box point had %D values, should have been %D", n, dim); 1078 1079 if (dim == 1) {ierr = DMPlexCreateLineMesh_Internal(comm, fac[0], low[0], upp[0], bdt[0], dm);CHKERRQ(ierr);} 1080 else if (simplex) {ierr = DMPlexCreateBoxMesh_Simplex_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1081 else {ierr = DMPlexCreateBoxMesh_Tensor_Internal(comm, dim, fac, low, upp, bdt, interpolate, dm);CHKERRQ(ierr);} 1082 PetscFunctionReturn(0); 1083 } 1084 1085 /*@ 1086 DMPlexCreateWedgeBoxMesh - Creates a 3-D mesh tesselating the (x,y) plane and extruding in the third direction using wedge cells. 1087 1088 Collective 1089 1090 Input Parameters: 1091 + comm - The communicator for the DM object 1092 . faces - Number of faces per dimension, or NULL for (1, 1, 1) 1093 . lower - The lower left corner, or NULL for (0, 0, 0) 1094 . upper - The upper right corner, or NULL for (1, 1, 1) 1095 . periodicity - The boundary type for the X,Y,Z direction, or NULL for DM_BOUNDARY_NONE 1096 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1097 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1098 1099 Output Parameter: 1100 . dm - The DM object 1101 1102 Level: beginner 1103 1104 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateWedgeCylinderMesh(), DMPlexExtrude(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1105 @*/ 1106 PetscErrorCode DMPlexCreateWedgeBoxMesh(MPI_Comm comm, const PetscInt faces[], const PetscReal lower[], const PetscReal upper[], const DMBoundaryType periodicity[], PetscBool orderHeight, PetscBool interpolate, DM *dm) 1107 { 1108 DM bdm, botdm; 1109 PetscInt i; 1110 PetscInt fac[3] = {0, 0, 0}; 1111 PetscReal low[3] = {0, 0, 0}; 1112 PetscReal upp[3] = {1, 1, 1}; 1113 DMBoundaryType bdt[3] = {DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE}; 1114 PetscErrorCode ierr; 1115 1116 PetscFunctionBegin; 1117 for (i = 0; i < 3; ++i) fac[i] = faces ? (faces[i] > 0 ? faces[i] : 1) : 1; 1118 if (lower) for (i = 0; i < 3; ++i) low[i] = lower[i]; 1119 if (upper) for (i = 0; i < 3; ++i) upp[i] = upper[i]; 1120 if (periodicity) for (i = 0; i < 3; ++i) bdt[i] = periodicity[i]; 1121 for (i = 0; i < 3; ++i) if (bdt[i] != DM_BOUNDARY_NONE) SETERRQ(comm, PETSC_ERR_SUP, "Periodicity not yet supported"); 1122 1123 ierr = DMCreate(comm, &bdm);CHKERRQ(ierr); 1124 ierr = DMSetType(bdm, DMPLEX);CHKERRQ(ierr); 1125 ierr = DMSetDimension(bdm, 1);CHKERRQ(ierr); 1126 ierr = DMSetCoordinateDim(bdm, 2);CHKERRQ(ierr); 1127 ierr = DMPlexCreateSquareBoundary(bdm, low, upp, fac);CHKERRQ(ierr); 1128 ierr = DMPlexGenerate(bdm, NULL, PETSC_FALSE, &botdm);CHKERRQ(ierr); 1129 ierr = DMDestroy(&bdm);CHKERRQ(ierr); 1130 ierr = DMPlexExtrude(botdm, fac[2], upp[2] - low[2], orderHeight, NULL, interpolate, dm);CHKERRQ(ierr); 1131 if (low[2] != 0.0) { 1132 Vec v; 1133 PetscScalar *x; 1134 PetscInt cDim, n; 1135 1136 ierr = DMGetCoordinatesLocal(*dm, &v);CHKERRQ(ierr); 1137 ierr = VecGetBlockSize(v, &cDim);CHKERRQ(ierr); 1138 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 1139 ierr = VecGetArray(v, &x);CHKERRQ(ierr); 1140 x += cDim; 1141 for (i=0; i<n; i+=cDim) x[i] += low[2]; 1142 ierr = VecRestoreArray(v,&x);CHKERRQ(ierr); 1143 ierr = DMSetCoordinatesLocal(*dm, v);CHKERRQ(ierr); 1144 } 1145 ierr = DMDestroy(&botdm);CHKERRQ(ierr); 1146 PetscFunctionReturn(0); 1147 } 1148 1149 /*@C 1150 DMPlexExtrude - Creates a (d+1)-D mesh by extruding a d-D mesh in the normal direction using prismatic cells. 1151 1152 Collective on idm 1153 1154 Input Parameters: 1155 + idm - The mesh to be extruded 1156 . layers - The number of layers, or PETSC_DETERMINE to use the default 1157 . height - The height of the extruded layer, or PETSC_DETERMINE to use the default 1158 . orderHeight - If PETSC_TRUE, orders the extruded cells in the height first. Otherwise, orders the cell on the layers first 1159 . extNormal - The normal direction in which the mesh should be extruded, or NULL to extrude using the surface normal 1160 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 1161 1162 Output Parameter: 1163 . dm - The DM object 1164 1165 Notes: 1166 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. 1167 1168 Options Database Keys: 1169 + -dm_plex_extrude_layers <k> - Sets the nubmer of layers k 1170 . -dm_plex_extrude_height <h> - Sets the height h of each layer 1171 . -dm_plex_extrude_order_height - If true, order cells by height first 1172 - -dm_plex_extrude_normal <n0,...,nd> - Sets the normal vector along which to extrude 1173 1174 Level: advanced 1175 1176 .seealso: DMPlexCreateWedgeCylinderMesh(), DMPlexCreateWedgeBoxMesh(), DMSetType(), DMCreate() 1177 @*/ 1178 PetscErrorCode DMPlexExtrude(DM idm, PetscInt layers, PetscReal height, PetscBool orderHeight, const PetscReal extNormal[], PetscBool interpolate, DM* dm) 1179 { 1180 PetscScalar *coordsB; 1181 const PetscScalar *coordsA; 1182 PetscReal *normals = NULL; 1183 PetscReal clNormal[3]; 1184 Vec coordinatesA, coordinatesB; 1185 PetscSection coordSectionA, coordSectionB; 1186 PetscInt dim, cDim, cDimB, c, l, v, coordSize, *newCone; 1187 PetscInt cStart, cEnd, vStart, vEnd, cellV, numCells, numVertices; 1188 const char *prefix; 1189 PetscBool haveCLNormal; 1190 PetscErrorCode ierr; 1191 1192 PetscFunctionBegin; 1193 PetscValidHeaderSpecific(idm, DM_CLASSID, 1); 1194 PetscValidLogicalCollectiveInt(idm, layers, 2); 1195 PetscValidLogicalCollectiveReal(idm, height, 3); 1196 PetscValidLogicalCollectiveBool(idm, interpolate, 4); 1197 ierr = DMGetDimension(idm, &dim);CHKERRQ(ierr); 1198 ierr = DMGetCoordinateDim(idm, &cDim);CHKERRQ(ierr); 1199 cDimB = cDim == dim ? cDim+1 : cDim; 1200 if (dim < 1 || dim > 3) SETERRQ1(PetscObjectComm((PetscObject)idm), PETSC_ERR_SUP, "Support for dimension %D not coded", dim); 1201 1202 ierr = PetscObjectGetOptionsPrefix((PetscObject) idm, &prefix);CHKERRQ(ierr); 1203 if (layers < 0) layers = 1; 1204 ierr = PetscOptionsGetInt(NULL, prefix, "-dm_plex_extrude_layers", &layers, NULL);CHKERRQ(ierr); 1205 if (layers <= 0) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Number of layers %D must be positive", layers); 1206 if (height < 0.) height = 1.; 1207 ierr = PetscOptionsGetReal(NULL, prefix, "-dm_plex_extrude_height", &height, NULL);CHKERRQ(ierr); 1208 if (height <= 0.) SETERRQ1(PetscObjectComm((PetscObject) idm), PETSC_ERR_ARG_OUTOFRANGE, "Height of layers %g must be positive", (double) height); 1209 ierr = PetscOptionsGetBool(NULL, prefix, "-dm_plex_extrude_order_height", &orderHeight, NULL);CHKERRQ(ierr); 1210 c = 3; 1211 ierr = PetscOptionsGetRealArray(NULL, prefix, "-dm_plex_extrude_normal", clNormal, &c, &haveCLNormal);CHKERRQ(ierr); 1212 if (haveCLNormal && c != cDimB) SETERRQ2(PetscObjectComm((PetscObject)idm), PETSC_ERR_ARG_SIZ, "Input normal has size %D != %D extruded coordinate dimension", c, cDimB); 1213 1214 ierr = DMPlexGetHeightStratum(idm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1215 ierr = DMPlexGetDepthStratum(idm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1216 numCells = (cEnd - cStart)*layers; 1217 numVertices = (vEnd - vStart)*(layers+1); 1218 ierr = DMCreate(PetscObjectComm((PetscObject)idm), dm);CHKERRQ(ierr); 1219 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1220 ierr = DMSetDimension(*dm, dim+1);CHKERRQ(ierr); 1221 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1222 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1223 ierr = DMCreateLabel(*dm, "celltype");CHKERRQ(ierr); 1224 for (c = cStart, cellV = 0; c < cEnd; ++c) { 1225 DMPolytopeType ct, nct; 1226 PetscInt *closure = NULL; 1227 PetscInt closureSize, numCorners = 0; 1228 1229 ierr = DMPlexGetCellType(idm, c, &ct);CHKERRQ(ierr); 1230 switch (ct) { 1231 case DM_POLYTOPE_SEGMENT: nct = DM_POLYTOPE_SEG_PRISM_TENSOR;break; 1232 case DM_POLYTOPE_TRIANGLE: nct = DM_POLYTOPE_TRI_PRISM_TENSOR;break; 1233 case DM_POLYTOPE_QUADRILATERAL: nct = DM_POLYTOPE_QUAD_PRISM_TENSOR;break; 1234 default: nct = DM_POLYTOPE_UNKNOWN; 1235 } 1236 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1237 for (v = 0; v < closureSize*2; v += 2) if ((closure[v] >= vStart) && (closure[v] < vEnd)) numCorners++; 1238 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1239 for (l = 0; l < layers; ++l) { 1240 const PetscInt cell = orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart; 1241 1242 ierr = DMPlexSetConeSize(*dm, cell, 2*numCorners);CHKERRQ(ierr); 1243 ierr = DMPlexSetCellType(*dm, cell, nct);CHKERRQ(ierr); 1244 } 1245 cellV = PetscMax(numCorners,cellV); 1246 } 1247 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1248 1249 if (dim != cDim && !(extNormal || haveCLNormal)) {ierr = PetscCalloc1(cDim*(vEnd - vStart), &normals);CHKERRQ(ierr);} 1250 ierr = PetscMalloc1(3*cellV,&newCone);CHKERRQ(ierr); 1251 for (c = cStart; c < cEnd; ++c) { 1252 PetscInt *closure = NULL; 1253 PetscInt closureSize, numCorners = 0, l; 1254 PetscReal normal[3] = {0, 0, 0}; 1255 1256 if (normals) {ierr = DMPlexComputeCellGeometryFVM(idm, c, NULL, NULL, normal);CHKERRQ(ierr);} 1257 ierr = DMPlexGetTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1258 for (v = 0; v < closureSize*2; v += 2) { 1259 if ((closure[v] >= vStart) && (closure[v] < vEnd)) { 1260 PetscInt d; 1261 1262 newCone[numCorners++] = closure[v] - vStart; 1263 if (normals) {for (d = 0; d < cDim; ++d) normals[cDim*(closure[v]-vStart)+d] += normal[d];} 1264 } 1265 } 1266 ierr = DMPlexRestoreTransitiveClosure(idm, c, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 1267 for (l = 0; l < layers; ++l) { 1268 PetscInt i; 1269 1270 for (i = 0; i < numCorners; ++i) { 1271 newCone[ numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + numCells : l*(vEnd - vStart) + newCone[i] + numCells; 1272 newCone[2*numCorners + i] = orderHeight ? (layers+1)*newCone[i] + l + 1 + numCells : (l+1)*(vEnd - vStart) + newCone[i] + numCells; 1273 } 1274 ierr = DMPlexSetCone(*dm, orderHeight ? layers*(c - cStart) + l : l*(cEnd - cStart) + c - cStart, newCone + numCorners);CHKERRQ(ierr); 1275 } 1276 } 1277 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1278 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1279 ierr = PetscFree(newCone);CHKERRQ(ierr); 1280 1281 ierr = DMGetCoordinateSection(*dm, &coordSectionB);CHKERRQ(ierr); 1282 ierr = PetscSectionSetNumFields(coordSectionB, 1);CHKERRQ(ierr); 1283 ierr = PetscSectionSetFieldComponents(coordSectionB, 0, cDimB);CHKERRQ(ierr); 1284 ierr = PetscSectionSetChart(coordSectionB, numCells, numCells+numVertices);CHKERRQ(ierr); 1285 for (v = numCells; v < numCells+numVertices; ++v) { 1286 ierr = PetscSectionSetDof(coordSectionB, v, cDimB);CHKERRQ(ierr); 1287 ierr = PetscSectionSetFieldDof(coordSectionB, v, 0, cDimB);CHKERRQ(ierr); 1288 ierr = DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1289 } 1290 ierr = PetscSectionSetUp(coordSectionB);CHKERRQ(ierr); 1291 ierr = PetscSectionGetStorageSize(coordSectionB, &coordSize);CHKERRQ(ierr); 1292 ierr = VecCreate(PETSC_COMM_SELF, &coordinatesB);CHKERRQ(ierr); 1293 ierr = PetscObjectSetName((PetscObject) coordinatesB, "coordinates");CHKERRQ(ierr); 1294 ierr = VecSetSizes(coordinatesB, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1295 ierr = VecSetBlockSize(coordinatesB, cDimB);CHKERRQ(ierr); 1296 ierr = VecSetType(coordinatesB,VECSTANDARD);CHKERRQ(ierr); 1297 1298 ierr = DMGetCoordinateSection(idm, &coordSectionA);CHKERRQ(ierr); 1299 ierr = DMGetCoordinatesLocal(idm, &coordinatesA);CHKERRQ(ierr); 1300 ierr = VecGetArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1301 ierr = VecGetArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1302 for (v = vStart; v < vEnd; ++v) { 1303 const PetscScalar *cptr; 1304 PetscReal ones2[2] = { 0., 1.}, ones3[3] = { 0., 0., 1.}; 1305 PetscReal normal[3]; 1306 PetscReal norm, h = height/layers; 1307 PetscInt offA, d, cDimA = cDim; 1308 1309 if (normals) {for (d = 0; d < cDimB; ++d) normal[d] = normals[cDimB*(v - vStart)+d];} 1310 else if (haveCLNormal) {for (d = 0; d < cDimB; ++d) normal[d] = clNormal[d];} 1311 else if (extNormal) {for (d = 0; d < cDimB; ++d) normal[d] = extNormal[d];} 1312 else if (cDimB == 2) {for (d = 0; d < cDimB; ++d) normal[d] = ones2[d];} 1313 else if (cDimB == 3) {for (d = 0; d < cDimB; ++d) normal[d] = ones3[d];} 1314 else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unable to determine normal for extrusion"); 1315 for (d = 0, norm = 0.0; d < cDimB; ++d) norm += normal[d]*normal[d]; 1316 for (d = 0; d < cDimB; ++d) normal[d] *= 1./PetscSqrtReal(norm); 1317 1318 ierr = PetscSectionGetOffset(coordSectionA, v, &offA);CHKERRQ(ierr); 1319 cptr = coordsA + offA; 1320 for (l = 0; l < layers+1; ++l) { 1321 PetscInt offB, d, newV; 1322 1323 newV = orderHeight ? (layers+1)*(v -vStart) + l + numCells : (vEnd -vStart)*l + (v -vStart) + numCells; 1324 ierr = PetscSectionGetOffset(coordSectionB, newV, &offB);CHKERRQ(ierr); 1325 for (d = 0; d < cDimA; ++d) { coordsB[offB+d] = cptr[d]; } 1326 for (d = 0; d < cDimB; ++d) { coordsB[offB+d] += l ? normal[d]*h : 0.0; } 1327 cptr = coordsB + offB; 1328 cDimA = cDimB; 1329 } 1330 } 1331 ierr = VecRestoreArrayRead(coordinatesA, &coordsA);CHKERRQ(ierr); 1332 ierr = VecRestoreArray(coordinatesB, &coordsB);CHKERRQ(ierr); 1333 ierr = DMSetCoordinatesLocal(*dm, coordinatesB);CHKERRQ(ierr); 1334 ierr = VecDestroy(&coordinatesB);CHKERRQ(ierr); 1335 ierr = PetscFree(normals);CHKERRQ(ierr); 1336 if (interpolate) { 1337 DM idm; 1338 1339 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1340 ierr = DMPlexCopyCoordinates(*dm, idm);CHKERRQ(ierr); 1341 ierr = DMDestroy(dm);CHKERRQ(ierr); 1342 *dm = idm; 1343 } 1344 PetscFunctionReturn(0); 1345 } 1346 1347 /*@C 1348 DMPlexSetOptionsPrefix - Sets the prefix used for searching for all DM options in the database. 1349 1350 Logically Collective on dm 1351 1352 Input Parameters: 1353 + dm - the DM context 1354 - prefix - the prefix to prepend to all option names 1355 1356 Notes: 1357 A hyphen (-) must NOT be given at the beginning of the prefix name. 1358 The first character of all runtime options is AUTOMATICALLY the hyphen. 1359 1360 Level: advanced 1361 1362 .seealso: SNESSetFromOptions() 1363 @*/ 1364 PetscErrorCode DMPlexSetOptionsPrefix(DM dm, const char prefix[]) 1365 { 1366 DM_Plex *mesh = (DM_Plex *) dm->data; 1367 PetscErrorCode ierr; 1368 1369 PetscFunctionBegin; 1370 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1371 ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, prefix);CHKERRQ(ierr); 1372 ierr = PetscObjectSetOptionsPrefix((PetscObject) mesh->partitioner, prefix);CHKERRQ(ierr); 1373 PetscFunctionReturn(0); 1374 } 1375 1376 /*@ 1377 DMPlexCreateHexCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using hexahedra. 1378 1379 Collective 1380 1381 Input Parameters: 1382 + comm - The communicator for the DM object 1383 . numRefine - The number of regular refinements to the basic 5 cell structure 1384 - periodicZ - The boundary type for the Z direction 1385 1386 Output Parameter: 1387 . dm - The DM object 1388 1389 Note: Here is the output numbering looking from the bottom of the cylinder: 1390 $ 17-----14 1391 $ | | 1392 $ | 2 | 1393 $ | | 1394 $ 17-----8-----7-----14 1395 $ | | | | 1396 $ | 3 | 0 | 1 | 1397 $ | | | | 1398 $ 19-----5-----6-----13 1399 $ | | 1400 $ | 4 | 1401 $ | | 1402 $ 19-----13 1403 $ 1404 $ and up through the top 1405 $ 1406 $ 18-----16 1407 $ | | 1408 $ | 2 | 1409 $ | | 1410 $ 18----10----11-----16 1411 $ | | | | 1412 $ | 3 | 0 | 1 | 1413 $ | | | | 1414 $ 20-----9----12-----15 1415 $ | | 1416 $ | 4 | 1417 $ | | 1418 $ 20-----15 1419 1420 Level: beginner 1421 1422 .seealso: DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1423 @*/ 1424 PetscErrorCode DMPlexCreateHexCylinderMesh(MPI_Comm comm, PetscInt numRefine, DMBoundaryType periodicZ, DM *dm) 1425 { 1426 const PetscInt dim = 3; 1427 PetscInt numCells, numVertices, r; 1428 PetscMPIInt rank; 1429 PetscErrorCode ierr; 1430 1431 PetscFunctionBegin; 1432 PetscValidPointer(dm, 4); 1433 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1434 if (numRefine < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of refinements %D cannot be negative", numRefine); 1435 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1436 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1437 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1438 /* Create topology */ 1439 { 1440 PetscInt cone[8], c; 1441 1442 numCells = !rank ? 5 : 0; 1443 numVertices = !rank ? 16 : 0; 1444 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1445 numCells *= 3; 1446 numVertices = !rank ? 24 : 0; 1447 } 1448 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1449 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 8);CHKERRQ(ierr);} 1450 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1451 if (!rank) { 1452 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1453 cone[0] = 15; cone[1] = 18; cone[2] = 17; cone[3] = 16; 1454 cone[4] = 31; cone[5] = 32; cone[6] = 33; cone[7] = 34; 1455 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1456 cone[0] = 16; cone[1] = 17; cone[2] = 24; cone[3] = 23; 1457 cone[4] = 32; cone[5] = 36; cone[6] = 37; cone[7] = 33; /* 22 25 26 21 */ 1458 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1459 cone[0] = 18; cone[1] = 27; cone[2] = 24; cone[3] = 17; 1460 cone[4] = 34; cone[5] = 33; cone[6] = 37; cone[7] = 38; 1461 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1462 cone[0] = 29; cone[1] = 27; cone[2] = 18; cone[3] = 15; 1463 cone[4] = 35; cone[5] = 31; cone[6] = 34; cone[7] = 38; 1464 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1465 cone[0] = 29; cone[1] = 15; cone[2] = 16; cone[3] = 23; 1466 cone[4] = 35; cone[5] = 36; cone[6] = 32; cone[7] = 31; 1467 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1468 1469 cone[0] = 31; cone[1] = 34; cone[2] = 33; cone[3] = 32; 1470 cone[4] = 19; cone[5] = 22; cone[6] = 21; cone[7] = 20; 1471 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1472 cone[0] = 32; cone[1] = 33; cone[2] = 37; cone[3] = 36; 1473 cone[4] = 22; cone[5] = 25; cone[6] = 26; cone[7] = 21; 1474 ierr = DMPlexSetCone(*dm, 6, cone);CHKERRQ(ierr); 1475 cone[0] = 34; cone[1] = 38; cone[2] = 37; cone[3] = 33; 1476 cone[4] = 20; cone[5] = 21; cone[6] = 26; cone[7] = 28; 1477 ierr = DMPlexSetCone(*dm, 7, cone);CHKERRQ(ierr); 1478 cone[0] = 35; cone[1] = 38; cone[2] = 34; cone[3] = 31; 1479 cone[4] = 30; cone[5] = 19; cone[6] = 20; cone[7] = 28; 1480 ierr = DMPlexSetCone(*dm, 8, cone);CHKERRQ(ierr); 1481 cone[0] = 35; cone[1] = 31; cone[2] = 32; cone[3] = 36; 1482 cone[4] = 30; cone[5] = 25; cone[6] = 22; cone[7] = 19; 1483 ierr = DMPlexSetCone(*dm, 9, cone);CHKERRQ(ierr); 1484 1485 cone[0] = 19; cone[1] = 20; cone[2] = 21; cone[3] = 22; 1486 cone[4] = 15; cone[5] = 16; cone[6] = 17; cone[7] = 18; 1487 ierr = DMPlexSetCone(*dm, 10, cone);CHKERRQ(ierr); 1488 cone[0] = 22; cone[1] = 21; cone[2] = 26; cone[3] = 25; 1489 cone[4] = 16; cone[5] = 23; cone[6] = 24; cone[7] = 17; 1490 ierr = DMPlexSetCone(*dm, 11, cone);CHKERRQ(ierr); 1491 cone[0] = 20; cone[1] = 28; cone[2] = 26; cone[3] = 21; 1492 cone[4] = 18; cone[5] = 17; cone[6] = 24; cone[7] = 27; 1493 ierr = DMPlexSetCone(*dm, 12, cone);CHKERRQ(ierr); 1494 cone[0] = 30; cone[1] = 28; cone[2] = 20; cone[3] = 19; 1495 cone[4] = 29; cone[5] = 15; cone[6] = 18; cone[7] = 27; 1496 ierr = DMPlexSetCone(*dm, 13, cone);CHKERRQ(ierr); 1497 cone[0] = 30; cone[1] = 19; cone[2] = 22; cone[3] = 25; 1498 cone[4] = 29; cone[5] = 23; cone[6] = 16; cone[7] = 15; 1499 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1500 } else { 1501 cone[0] = 5; cone[1] = 8; cone[2] = 7; cone[3] = 6; 1502 cone[4] = 9; cone[5] = 12; cone[6] = 11; cone[7] = 10; 1503 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1504 cone[0] = 6; cone[1] = 7; cone[2] = 14; cone[3] = 13; 1505 cone[4] = 12; cone[5] = 15; cone[6] = 16; cone[7] = 11; 1506 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1507 cone[0] = 8; cone[1] = 17; cone[2] = 14; cone[3] = 7; 1508 cone[4] = 10; cone[5] = 11; cone[6] = 16; cone[7] = 18; 1509 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1510 cone[0] = 19; cone[1] = 17; cone[2] = 8; cone[3] = 5; 1511 cone[4] = 20; cone[5] = 9; cone[6] = 10; cone[7] = 18; 1512 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1513 cone[0] = 19; cone[1] = 5; cone[2] = 6; cone[3] = 13; 1514 cone[4] = 20; cone[5] = 15; cone[6] = 12; cone[7] = 9; 1515 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1516 } 1517 } 1518 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1519 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1520 } 1521 /* Interpolate */ 1522 { 1523 DM idm; 1524 1525 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1526 ierr = DMDestroy(dm);CHKERRQ(ierr); 1527 *dm = idm; 1528 } 1529 /* Create cube geometry */ 1530 { 1531 Vec coordinates; 1532 PetscSection coordSection; 1533 PetscScalar *coords; 1534 PetscInt coordSize, v; 1535 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1536 const PetscReal ds2 = dis/2.0; 1537 1538 /* Build coordinates */ 1539 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1540 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1541 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1542 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1543 for (v = numCells; v < numCells+numVertices; ++v) { 1544 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1545 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1546 } 1547 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1548 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1549 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1550 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1551 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1552 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1553 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1554 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1555 if (!rank) { 1556 coords[0*dim+0] = -ds2; coords[0*dim+1] = -ds2; coords[0*dim+2] = 0.0; 1557 coords[1*dim+0] = ds2; coords[1*dim+1] = -ds2; coords[1*dim+2] = 0.0; 1558 coords[2*dim+0] = ds2; coords[2*dim+1] = ds2; coords[2*dim+2] = 0.0; 1559 coords[3*dim+0] = -ds2; coords[3*dim+1] = ds2; coords[3*dim+2] = 0.0; 1560 coords[4*dim+0] = -ds2; coords[4*dim+1] = -ds2; coords[4*dim+2] = 1.0; 1561 coords[5*dim+0] = -ds2; coords[5*dim+1] = ds2; coords[5*dim+2] = 1.0; 1562 coords[6*dim+0] = ds2; coords[6*dim+1] = ds2; coords[6*dim+2] = 1.0; 1563 coords[7*dim+0] = ds2; coords[7*dim+1] = -ds2; coords[7*dim+2] = 1.0; 1564 coords[ 8*dim+0] = dis; coords[ 8*dim+1] = -dis; coords[ 8*dim+2] = 0.0; 1565 coords[ 9*dim+0] = dis; coords[ 9*dim+1] = dis; coords[ 9*dim+2] = 0.0; 1566 coords[10*dim+0] = dis; coords[10*dim+1] = -dis; coords[10*dim+2] = 1.0; 1567 coords[11*dim+0] = dis; coords[11*dim+1] = dis; coords[11*dim+2] = 1.0; 1568 coords[12*dim+0] = -dis; coords[12*dim+1] = dis; coords[12*dim+2] = 0.0; 1569 coords[13*dim+0] = -dis; coords[13*dim+1] = dis; coords[13*dim+2] = 1.0; 1570 coords[14*dim+0] = -dis; coords[14*dim+1] = -dis; coords[14*dim+2] = 0.0; 1571 coords[15*dim+0] = -dis; coords[15*dim+1] = -dis; coords[15*dim+2] = 1.0; 1572 if (periodicZ == DM_BOUNDARY_PERIODIC) { 1573 /* 15 31 19 */ coords[16*dim+0] = -ds2; coords[16*dim+1] = -ds2; coords[16*dim+2] = 0.5; 1574 /* 16 32 22 */ coords[17*dim+0] = ds2; coords[17*dim+1] = -ds2; coords[17*dim+2] = 0.5; 1575 /* 17 33 21 */ coords[18*dim+0] = ds2; coords[18*dim+1] = ds2; coords[18*dim+2] = 0.5; 1576 /* 18 34 20 */ coords[19*dim+0] = -ds2; coords[19*dim+1] = ds2; coords[19*dim+2] = 0.5; 1577 /* 29 35 30 */ coords[20*dim+0] = -dis; coords[20*dim+1] = -dis; coords[20*dim+2] = 0.5; 1578 /* 23 36 25 */ coords[21*dim+0] = dis; coords[21*dim+1] = -dis; coords[21*dim+2] = 0.5; 1579 /* 24 37 26 */ coords[22*dim+0] = dis; coords[22*dim+1] = dis; coords[22*dim+2] = 0.5; 1580 /* 27 38 28 */ coords[23*dim+0] = -dis; coords[23*dim+1] = dis; coords[23*dim+2] = 0.5; 1581 } 1582 } 1583 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1584 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1585 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1586 } 1587 /* Create periodicity */ 1588 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1589 PetscReal L[3]; 1590 PetscReal maxCell[3]; 1591 DMBoundaryType bdType[3]; 1592 PetscReal lower[3] = {0.0, 0.0, 0.0}; 1593 PetscReal upper[3] = {1.0, 1.0, 1.5}; 1594 PetscInt i, numZCells = 3; 1595 1596 bdType[0] = DM_BOUNDARY_NONE; 1597 bdType[1] = DM_BOUNDARY_NONE; 1598 bdType[2] = periodicZ; 1599 for (i = 0; i < dim; i++) { 1600 L[i] = upper[i] - lower[i]; 1601 maxCell[i] = 1.1 * (L[i] / numZCells); 1602 } 1603 ierr = DMSetPeriodicity(*dm, PETSC_TRUE, maxCell, L, bdType);CHKERRQ(ierr); 1604 } 1605 /* Refine topology */ 1606 for (r = 0; r < numRefine; ++r) { 1607 DM rdm = NULL; 1608 1609 ierr = DMRefine(*dm, comm, &rdm);CHKERRQ(ierr); 1610 ierr = DMDestroy(dm);CHKERRQ(ierr); 1611 *dm = rdm; 1612 } 1613 /* Remap geometry to cylinder 1614 Interior square: Linear interpolation is correct 1615 The other cells all have vertices on rays from the origin. We want to uniformly expand the spacing 1616 such that the last vertex is on the unit circle. So the closest and farthest vertices are at distance 1617 1618 phi = arctan(y/x) 1619 d_close = sqrt(1/8 + 1/4 sin^2(phi)) 1620 d_far = sqrt(1/2 + sin^2(phi)) 1621 1622 so we remap them using 1623 1624 x_new = x_close + (x - x_close) (1 - d_close) / (d_far - d_close) 1625 y_new = y_close + (y - y_close) (1 - d_close) / (d_far - d_close) 1626 1627 If pi/4 < phi < 3pi/4 or -3pi/4 < phi < -pi/4, then we switch x and y. 1628 */ 1629 { 1630 Vec coordinates; 1631 PetscSection coordSection; 1632 PetscScalar *coords; 1633 PetscInt vStart, vEnd, v; 1634 const PetscReal dis = 1.0/PetscSqrtReal(2.0); 1635 const PetscReal ds2 = 0.5*dis; 1636 1637 ierr = DMPlexGetDepthStratum(*dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 1638 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1639 ierr = DMGetCoordinatesLocal(*dm, &coordinates);CHKERRQ(ierr); 1640 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1641 for (v = vStart; v < vEnd; ++v) { 1642 PetscReal phi, sinp, cosp, dc, df, x, y, xc, yc; 1643 PetscInt off; 1644 1645 ierr = PetscSectionGetOffset(coordSection, v, &off);CHKERRQ(ierr); 1646 if ((PetscAbsScalar(coords[off+0]) <= ds2) && (PetscAbsScalar(coords[off+1]) <= ds2)) continue; 1647 x = PetscRealPart(coords[off]); 1648 y = PetscRealPart(coords[off+1]); 1649 phi = PetscAtan2Real(y, x); 1650 sinp = PetscSinReal(phi); 1651 cosp = PetscCosReal(phi); 1652 if ((PetscAbsReal(phi) > PETSC_PI/4.0) && (PetscAbsReal(phi) < 3.0*PETSC_PI/4.0)) { 1653 dc = PetscAbsReal(ds2/sinp); 1654 df = PetscAbsReal(dis/sinp); 1655 xc = ds2*x/PetscAbsReal(y); 1656 yc = ds2*PetscSignReal(y); 1657 } else { 1658 dc = PetscAbsReal(ds2/cosp); 1659 df = PetscAbsReal(dis/cosp); 1660 xc = ds2*PetscSignReal(x); 1661 yc = ds2*y/PetscAbsReal(x); 1662 } 1663 coords[off+0] = xc + (coords[off+0] - xc)*(1.0 - dc)/(df - dc); 1664 coords[off+1] = yc + (coords[off+1] - yc)*(1.0 - dc)/(df - dc); 1665 } 1666 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1667 if (periodicZ == DM_BOUNDARY_PERIODIC || periodicZ == DM_BOUNDARY_TWIST) { 1668 ierr = DMLocalizeCoordinates(*dm);CHKERRQ(ierr); 1669 } 1670 } 1671 PetscFunctionReturn(0); 1672 } 1673 1674 /*@ 1675 DMPlexCreateWedgeCylinderMesh - Creates a mesh on the tensor product of the unit interval with the circle (cylinder) using wedges. 1676 1677 Collective 1678 1679 Input Parameters: 1680 + comm - The communicator for the DM object 1681 . n - The number of wedges around the origin 1682 - interpolate - Create edges and faces 1683 1684 Output Parameter: 1685 . dm - The DM object 1686 1687 Level: beginner 1688 1689 .seealso: DMPlexCreateHexCylinderMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1690 @*/ 1691 PetscErrorCode DMPlexCreateWedgeCylinderMesh(MPI_Comm comm, PetscInt n, PetscBool interpolate, DM *dm) 1692 { 1693 const PetscInt dim = 3; 1694 PetscInt numCells, numVertices, v; 1695 PetscMPIInt rank; 1696 PetscErrorCode ierr; 1697 1698 PetscFunctionBegin; 1699 PetscValidPointer(dm, 3); 1700 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1701 if (n < 0) SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Number of wedges %D cannot be negative", n); 1702 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1703 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1704 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1705 /* Must create the celltype label here so that we do not automatically try to compute the types */ 1706 ierr = DMCreateLabel(*dm, "celltype");CHKERRQ(ierr); 1707 /* Create topology */ 1708 { 1709 PetscInt cone[6], c; 1710 1711 numCells = !rank ? n : 0; 1712 numVertices = !rank ? 2*(n+1) : 0; 1713 ierr = DMPlexSetChart(*dm, 0, numCells+numVertices);CHKERRQ(ierr); 1714 for (c = 0; c < numCells; c++) {ierr = DMPlexSetConeSize(*dm, c, 6);CHKERRQ(ierr);} 1715 ierr = DMSetUp(*dm);CHKERRQ(ierr); 1716 for (c = 0; c < numCells; c++) { 1717 cone[0] = c+n*1; cone[1] = (c+1)%n+n*1; cone[2] = 0+3*n; 1718 cone[3] = c+n*2; cone[4] = (c+1)%n+n*2; cone[5] = 1+3*n; 1719 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 1720 ierr = DMPlexSetCellType(*dm, c, DM_POLYTOPE_TRI_PRISM_TENSOR);CHKERRQ(ierr); 1721 } 1722 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1723 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1724 } 1725 for (v = numCells; v < numCells+numVertices; ++v) { 1726 ierr = DMPlexSetCellType(*dm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr); 1727 } 1728 /* Interpolate */ 1729 if (interpolate) { 1730 DM idm; 1731 1732 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1733 ierr = DMDestroy(dm);CHKERRQ(ierr); 1734 *dm = idm; 1735 } 1736 /* Create cylinder geometry */ 1737 { 1738 Vec coordinates; 1739 PetscSection coordSection; 1740 PetscScalar *coords; 1741 PetscInt coordSize, c; 1742 1743 /* Build coordinates */ 1744 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 1745 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 1746 ierr = PetscSectionSetFieldComponents(coordSection, 0, dim);CHKERRQ(ierr); 1747 ierr = PetscSectionSetChart(coordSection, numCells, numCells+numVertices);CHKERRQ(ierr); 1748 for (v = numCells; v < numCells+numVertices; ++v) { 1749 ierr = PetscSectionSetDof(coordSection, v, dim);CHKERRQ(ierr); 1750 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dim);CHKERRQ(ierr); 1751 } 1752 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 1753 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 1754 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 1755 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 1756 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 1757 ierr = VecSetBlockSize(coordinates, dim);CHKERRQ(ierr); 1758 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 1759 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 1760 for (c = 0; c < numCells; c++) { 1761 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; 1762 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; 1763 } 1764 if (!rank) { 1765 coords[(2*n+0)*dim+0] = 0.0; coords[(2*n+0)*dim+1] = 0.0; coords[(2*n+0)*dim+2] = 1.0; 1766 coords[(2*n+1)*dim+0] = 0.0; coords[(2*n+1)*dim+1] = 0.0; coords[(2*n+1)*dim+2] = 0.0; 1767 } 1768 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 1769 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 1770 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 1771 } 1772 PetscFunctionReturn(0); 1773 } 1774 1775 PETSC_STATIC_INLINE PetscReal DiffNormReal(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 += PetscSqr(x[i] - y[i]); 1780 return PetscSqrtReal(prod); 1781 } 1782 PETSC_STATIC_INLINE PetscReal DotReal(PetscInt dim, const PetscReal x[], const PetscReal y[]) 1783 { 1784 PetscReal prod = 0.0; 1785 PetscInt i; 1786 for (i = 0; i < dim; ++i) prod += x[i]*y[i]; 1787 return prod; 1788 } 1789 1790 /* The first constant is the sphere radius */ 1791 static void snapToSphere(PetscInt dim, PetscInt Nf, PetscInt NfAux, 1792 const PetscInt uOff[], const PetscInt uOff_x[], const PetscScalar u[], const PetscScalar u_t[], const PetscScalar u_x[], 1793 const PetscInt aOff[], const PetscInt aOff_x[], const PetscScalar a[], const PetscScalar a_t[], const PetscScalar a_x[], 1794 PetscReal t, const PetscReal x[], PetscInt numConstants, const PetscScalar constants[], PetscScalar f0[]) 1795 { 1796 PetscReal r = PetscRealPart(constants[0]); 1797 PetscReal norm2 = 0.0, fac; 1798 PetscInt n = uOff[1] - uOff[0], d; 1799 1800 for (d = 0; d < n; ++d) norm2 += PetscSqr(PetscRealPart(u[d])); 1801 fac = r/PetscSqrtReal(norm2); 1802 for (d = 0; d < n; ++d) f0[d] = u[d]*fac; 1803 } 1804 1805 /*@ 1806 DMPlexCreateSphereMesh - Creates a mesh on the d-dimensional sphere, S^d. 1807 1808 Collective 1809 1810 Input Parameters: 1811 + comm - The communicator for the DM object 1812 . dim - The dimension 1813 . simplex - Use simplices, or tensor product cells 1814 - R - The radius 1815 1816 Output Parameter: 1817 . dm - The DM object 1818 1819 Level: beginner 1820 1821 .seealso: DMPlexCreateBallMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 1822 @*/ 1823 PetscErrorCode DMPlexCreateSphereMesh(MPI_Comm comm, PetscInt dim, PetscBool simplex, PetscReal R, DM *dm) 1824 { 1825 const PetscInt embedDim = dim+1; 1826 PetscSection coordSection; 1827 Vec coordinates; 1828 PetscScalar *coords; 1829 PetscReal *coordsIn; 1830 PetscInt numCells, numEdges, numVerts, firstVertex, v, firstEdge, coordSize, d, c, e; 1831 PetscMPIInt rank; 1832 PetscErrorCode ierr; 1833 1834 PetscFunctionBegin; 1835 PetscValidPointer(dm, 4); 1836 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 1837 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 1838 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 1839 ierr = DMSetCoordinateDim(*dm, dim+1);CHKERRQ(ierr); 1840 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) *dm), &rank);CHKERRQ(ierr); 1841 switch (dim) { 1842 case 2: 1843 if (simplex) { 1844 DM idm; 1845 const PetscReal radius = PetscSqrtReal(1 + PETSC_PHI*PETSC_PHI)/(1.0 + PETSC_PHI); 1846 const PetscReal edgeLen = 2.0/(1.0 + PETSC_PHI) * (R/radius); 1847 const PetscInt degree = 5; 1848 PetscReal vertex[3] = {0.0, 1.0/(1.0 + PETSC_PHI), PETSC_PHI/(1.0 + PETSC_PHI)}; 1849 PetscInt s[3] = {1, 1, 1}; 1850 PetscInt cone[3]; 1851 PetscInt *graph, p, i, j, k; 1852 1853 vertex[0] *= R/radius; vertex[1] *= R/radius; vertex[2] *= R/radius; 1854 numCells = !rank ? 20 : 0; 1855 numVerts = !rank ? 12 : 0; 1856 firstVertex = numCells; 1857 /* Use icosahedron, which for a R-sphere has coordinates which are all cyclic permutations of 1858 1859 (0, \pm 1/\phi+1, \pm \phi/\phi+1) 1860 1861 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 1862 length is then given by 2/(1+\phi) = 2 * 0.38197 = 0.76393. 1863 */ 1864 /* Construct vertices */ 1865 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 1866 if (!rank) { 1867 for (p = 0, i = 0; p < embedDim; ++p) { 1868 for (s[1] = -1; s[1] < 2; s[1] += 2) { 1869 for (s[2] = -1; s[2] < 2; s[2] += 2) { 1870 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertex[(d+p)%embedDim]; 1871 ++i; 1872 } 1873 } 1874 } 1875 } 1876 /* Construct graph */ 1877 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 1878 for (i = 0; i < numVerts; ++i) { 1879 for (j = 0, k = 0; j < numVerts; ++j) { 1880 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 1881 } 1882 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid icosahedron, vertex %D degree %D != %D", i, k, degree); 1883 } 1884 /* Build Topology */ 1885 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 1886 for (c = 0; c < numCells; c++) { 1887 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 1888 } 1889 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1890 /* Cells */ 1891 for (i = 0, c = 0; i < numVerts; ++i) { 1892 for (j = 0; j < i; ++j) { 1893 for (k = 0; k < j; ++k) { 1894 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i]) { 1895 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; 1896 /* Check orientation */ 1897 { 1898 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}}}; 1899 PetscReal normal[3]; 1900 PetscInt e, f; 1901 1902 for (d = 0; d < embedDim; ++d) { 1903 normal[d] = 0.0; 1904 for (e = 0; e < embedDim; ++e) { 1905 for (f = 0; f < embedDim; ++f) { 1906 normal[d] += epsilon[d][e][f]*(coordsIn[j*embedDim+e] - coordsIn[i*embedDim+e])*(coordsIn[k*embedDim+f] - coordsIn[i*embedDim+f]); 1907 } 1908 } 1909 } 1910 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 1911 } 1912 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 1913 } 1914 } 1915 } 1916 } 1917 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 1918 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 1919 ierr = PetscFree(graph);CHKERRQ(ierr); 1920 /* Interpolate mesh */ 1921 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 1922 ierr = DMDestroy(dm);CHKERRQ(ierr); 1923 *dm = idm; 1924 } else { 1925 /* 1926 12-21--13 1927 | | 1928 25 4 24 1929 | | 1930 12-25--9-16--8-24--13 1931 | | | | 1932 23 5 17 0 15 3 22 1933 | | | | 1934 10-20--6-14--7-19--11 1935 | | 1936 20 1 19 1937 | | 1938 10-18--11 1939 | | 1940 23 2 22 1941 | | 1942 12-21--13 1943 */ 1944 PetscInt cone[4], ornt[4]; 1945 1946 numCells = !rank ? 6 : 0; 1947 numEdges = !rank ? 12 : 0; 1948 numVerts = !rank ? 8 : 0; 1949 firstVertex = numCells; 1950 firstEdge = numCells + numVerts; 1951 /* Build Topology */ 1952 ierr = DMPlexSetChart(*dm, 0, numCells+numEdges+numVerts);CHKERRQ(ierr); 1953 for (c = 0; c < numCells; c++) { 1954 ierr = DMPlexSetConeSize(*dm, c, 4);CHKERRQ(ierr); 1955 } 1956 for (e = firstEdge; e < firstEdge+numEdges; ++e) { 1957 ierr = DMPlexSetConeSize(*dm, e, 2);CHKERRQ(ierr); 1958 } 1959 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 1960 if (!rank) { 1961 /* Cell 0 */ 1962 cone[0] = 14; cone[1] = 15; cone[2] = 16; cone[3] = 17; 1963 ierr = DMPlexSetCone(*dm, 0, cone);CHKERRQ(ierr); 1964 ornt[0] = 0; ornt[1] = 0; ornt[2] = 0; ornt[3] = 0; 1965 ierr = DMPlexSetConeOrientation(*dm, 0, ornt);CHKERRQ(ierr); 1966 /* Cell 1 */ 1967 cone[0] = 18; cone[1] = 19; cone[2] = 14; cone[3] = 20; 1968 ierr = DMPlexSetCone(*dm, 1, cone);CHKERRQ(ierr); 1969 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1970 ierr = DMPlexSetConeOrientation(*dm, 1, ornt);CHKERRQ(ierr); 1971 /* Cell 2 */ 1972 cone[0] = 21; cone[1] = 22; cone[2] = 18; cone[3] = 23; 1973 ierr = DMPlexSetCone(*dm, 2, cone);CHKERRQ(ierr); 1974 ornt[0] = 0; ornt[1] = 0; ornt[2] = -2; ornt[3] = 0; 1975 ierr = DMPlexSetConeOrientation(*dm, 2, ornt);CHKERRQ(ierr); 1976 /* Cell 3 */ 1977 cone[0] = 19; cone[1] = 22; cone[2] = 24; cone[3] = 15; 1978 ierr = DMPlexSetCone(*dm, 3, cone);CHKERRQ(ierr); 1979 ornt[0] = -2; ornt[1] = -2; ornt[2] = 0; ornt[3] = -2; 1980 ierr = DMPlexSetConeOrientation(*dm, 3, ornt);CHKERRQ(ierr); 1981 /* Cell 4 */ 1982 cone[0] = 16; cone[1] = 24; cone[2] = 21; cone[3] = 25; 1983 ierr = DMPlexSetCone(*dm, 4, cone);CHKERRQ(ierr); 1984 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = 0; 1985 ierr = DMPlexSetConeOrientation(*dm, 4, ornt);CHKERRQ(ierr); 1986 /* Cell 5 */ 1987 cone[0] = 20; cone[1] = 17; cone[2] = 25; cone[3] = 23; 1988 ierr = DMPlexSetCone(*dm, 5, cone);CHKERRQ(ierr); 1989 ornt[0] = -2; ornt[1] = -2; ornt[2] = -2; ornt[3] = -2; 1990 ierr = DMPlexSetConeOrientation(*dm, 5, ornt);CHKERRQ(ierr); 1991 /* Edges */ 1992 cone[0] = 6; cone[1] = 7; 1993 ierr = DMPlexSetCone(*dm, 14, cone);CHKERRQ(ierr); 1994 cone[0] = 7; cone[1] = 8; 1995 ierr = DMPlexSetCone(*dm, 15, cone);CHKERRQ(ierr); 1996 cone[0] = 8; cone[1] = 9; 1997 ierr = DMPlexSetCone(*dm, 16, cone);CHKERRQ(ierr); 1998 cone[0] = 9; cone[1] = 6; 1999 ierr = DMPlexSetCone(*dm, 17, cone);CHKERRQ(ierr); 2000 cone[0] = 10; cone[1] = 11; 2001 ierr = DMPlexSetCone(*dm, 18, cone);CHKERRQ(ierr); 2002 cone[0] = 11; cone[1] = 7; 2003 ierr = DMPlexSetCone(*dm, 19, cone);CHKERRQ(ierr); 2004 cone[0] = 6; cone[1] = 10; 2005 ierr = DMPlexSetCone(*dm, 20, cone);CHKERRQ(ierr); 2006 cone[0] = 12; cone[1] = 13; 2007 ierr = DMPlexSetCone(*dm, 21, cone);CHKERRQ(ierr); 2008 cone[0] = 13; cone[1] = 11; 2009 ierr = DMPlexSetCone(*dm, 22, cone);CHKERRQ(ierr); 2010 cone[0] = 10; cone[1] = 12; 2011 ierr = DMPlexSetCone(*dm, 23, cone);CHKERRQ(ierr); 2012 cone[0] = 13; cone[1] = 8; 2013 ierr = DMPlexSetCone(*dm, 24, cone);CHKERRQ(ierr); 2014 cone[0] = 12; cone[1] = 9; 2015 ierr = DMPlexSetCone(*dm, 25, cone);CHKERRQ(ierr); 2016 } 2017 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2018 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2019 /* Build coordinates */ 2020 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2021 if (!rank) { 2022 coordsIn[0*embedDim+0] = -R; coordsIn[0*embedDim+1] = R; coordsIn[0*embedDim+2] = -R; 2023 coordsIn[1*embedDim+0] = R; coordsIn[1*embedDim+1] = R; coordsIn[1*embedDim+2] = -R; 2024 coordsIn[2*embedDim+0] = R; coordsIn[2*embedDim+1] = -R; coordsIn[2*embedDim+2] = -R; 2025 coordsIn[3*embedDim+0] = -R; coordsIn[3*embedDim+1] = -R; coordsIn[3*embedDim+2] = -R; 2026 coordsIn[4*embedDim+0] = -R; coordsIn[4*embedDim+1] = R; coordsIn[4*embedDim+2] = R; 2027 coordsIn[5*embedDim+0] = R; coordsIn[5*embedDim+1] = R; coordsIn[5*embedDim+2] = R; 2028 coordsIn[6*embedDim+0] = -R; coordsIn[6*embedDim+1] = -R; coordsIn[6*embedDim+2] = R; 2029 coordsIn[7*embedDim+0] = R; coordsIn[7*embedDim+1] = -R; coordsIn[7*embedDim+2] = R; 2030 } 2031 } 2032 break; 2033 case 3: 2034 if (simplex) { 2035 DM idm; 2036 const PetscReal edgeLen = 1.0/PETSC_PHI; 2037 PetscReal vertexA[4] = {0.5, 0.5, 0.5, 0.5}; 2038 PetscReal vertexB[4] = {1.0, 0.0, 0.0, 0.0}; 2039 PetscReal vertexC[4] = {0.5, 0.5*PETSC_PHI, 0.5/PETSC_PHI, 0.0}; 2040 const PetscInt degree = 12; 2041 PetscInt s[4] = {1, 1, 1}; 2042 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}, 2043 {2, 0, 1, 3}, {2, 1, 3, 0}, {2, 3, 0, 1}, {3, 0, 2, 1}, {3, 1, 0, 2}, {3, 2, 1, 0}}; 2044 PetscInt cone[4]; 2045 PetscInt *graph, p, i, j, k, l; 2046 2047 vertexA[0] *= R; vertexA[1] *= R; vertexA[2] *= R; vertexA[3] *= R; 2048 vertexB[0] *= R; vertexB[1] *= R; vertexB[2] *= R; vertexB[3] *= R; 2049 vertexC[0] *= R; vertexC[1] *= R; vertexC[2] *= R; vertexC[3] *= R; 2050 numCells = !rank ? 600 : 0; 2051 numVerts = !rank ? 120 : 0; 2052 firstVertex = numCells; 2053 /* Use the 600-cell, which for a unit sphere has coordinates which are 2054 2055 1/2 (\pm 1, \pm 1, \pm 1, \pm 1) 16 2056 (\pm 1, 0, 0, 0) all cyclic permutations 8 2057 1/2 (\pm 1, \pm phi, \pm 1/phi, 0) all even permutations 96 2058 2059 where \phi^2 - \phi - 1 = 0, meaning \phi is the golden ratio \frac{1 + \sqrt{5}}{2}. The edge 2060 length is then given by 1/\phi = 0.61803. 2061 2062 http://buzzard.pugetsound.edu/sage-practice/ch03s03.html 2063 http://mathworld.wolfram.com/600-Cell.html 2064 */ 2065 /* Construct vertices */ 2066 ierr = PetscCalloc1(numVerts * embedDim, &coordsIn);CHKERRQ(ierr); 2067 i = 0; 2068 if (!rank) { 2069 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2070 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2071 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2072 for (s[3] = -1; s[3] < 2; s[3] += 2) { 2073 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[d]*vertexA[d]; 2074 ++i; 2075 } 2076 } 2077 } 2078 } 2079 for (p = 0; p < embedDim; ++p) { 2080 s[1] = s[2] = s[3] = 1; 2081 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2082 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[(d+p)%embedDim]*vertexB[(d+p)%embedDim]; 2083 ++i; 2084 } 2085 } 2086 for (p = 0; p < 12; ++p) { 2087 s[3] = 1; 2088 for (s[0] = -1; s[0] < 2; s[0] += 2) { 2089 for (s[1] = -1; s[1] < 2; s[1] += 2) { 2090 for (s[2] = -1; s[2] < 2; s[2] += 2) { 2091 for (d = 0; d < embedDim; ++d) coordsIn[i*embedDim+d] = s[evenPerm[p][d]]*vertexC[evenPerm[p][d]]; 2092 ++i; 2093 } 2094 } 2095 } 2096 } 2097 } 2098 if (i != numVerts) SETERRQ2(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertices %D != %D", i, numVerts); 2099 /* Construct graph */ 2100 ierr = PetscCalloc1(numVerts * numVerts, &graph);CHKERRQ(ierr); 2101 for (i = 0; i < numVerts; ++i) { 2102 for (j = 0, k = 0; j < numVerts; ++j) { 2103 if (PetscAbsReal(DiffNormReal(embedDim, &coordsIn[i*embedDim], &coordsIn[j*embedDim]) - edgeLen) < PETSC_SMALL) {graph[i*numVerts+j] = 1; ++k;} 2104 } 2105 if (k != degree) SETERRQ3(comm, PETSC_ERR_PLIB, "Invalid 600-cell, vertex %D degree %D != %D", i, k, degree); 2106 } 2107 /* Build Topology */ 2108 ierr = DMPlexSetChart(*dm, 0, numCells+numVerts);CHKERRQ(ierr); 2109 for (c = 0; c < numCells; c++) { 2110 ierr = DMPlexSetConeSize(*dm, c, embedDim);CHKERRQ(ierr); 2111 } 2112 ierr = DMSetUp(*dm);CHKERRQ(ierr); /* Allocate space for cones */ 2113 /* Cells */ 2114 if (!rank) { 2115 for (i = 0, c = 0; i < numVerts; ++i) { 2116 for (j = 0; j < i; ++j) { 2117 for (k = 0; k < j; ++k) { 2118 for (l = 0; l < k; ++l) { 2119 if (graph[i*numVerts+j] && graph[j*numVerts+k] && graph[k*numVerts+i] && 2120 graph[l*numVerts+i] && graph[l*numVerts+j] && graph[l*numVerts+k]) { 2121 cone[0] = firstVertex+i; cone[1] = firstVertex+j; cone[2] = firstVertex+k; cone[3] = firstVertex+l; 2122 /* Check orientation: https://ef.gy/linear-algebra:normal-vectors-in-higher-dimensional-spaces */ 2123 { 2124 const PetscInt epsilon[4][4][4][4] = {{{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2125 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, -1, 0}}, 2126 {{0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 1, 0, 0}}, 2127 {{0, 0, 0, 0}, { 0, 0, 1, 0}, { 0, -1, 0, 0}, { 0, 0, 0, 0}}}, 2128 2129 {{{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, -1}, { 0, 0, 1, 0}}, 2130 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2131 {{0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}}, 2132 {{0, 0, -1, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}}}, 2133 2134 {{{0, 0, 0, 0}, { 0, 0, 0, 1}, { 0, 0, 0, 0}, { 0, -1, 0, 0}}, 2135 {{0, 0, 0, -1}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 1, 0, 0, 0}}, 2136 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2137 {{0, 1, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}, 2138 2139 {{{0, 0, 0, 0}, { 0, 0, -1, 0}, { 0, 1, 0, 0}, { 0, 0, 0, 0}}, 2140 {{0, 0, 1, 0}, { 0, 0, 0, 0}, {-1, 0, 0, 0}, { 0, 0, 0, 0}}, 2141 {{0, -1, 0, 0}, { 1, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}, 2142 {{0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}, { 0, 0, 0, 0}}}}; 2143 PetscReal normal[4]; 2144 PetscInt e, f, g; 2145 2146 for (d = 0; d < embedDim; ++d) { 2147 normal[d] = 0.0; 2148 for (e = 0; e < embedDim; ++e) { 2149 for (f = 0; f < embedDim; ++f) { 2150 for (g = 0; g < embedDim; ++g) { 2151 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]); 2152 } 2153 } 2154 } 2155 } 2156 if (DotReal(embedDim, normal, &coordsIn[i*embedDim]) < 0) {PetscInt tmp = cone[1]; cone[1] = cone[2]; cone[2] = tmp;} 2157 } 2158 ierr = DMPlexSetCone(*dm, c++, cone);CHKERRQ(ierr); 2159 } 2160 } 2161 } 2162 } 2163 } 2164 } 2165 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 2166 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 2167 ierr = PetscFree(graph);CHKERRQ(ierr); 2168 /* Interpolate mesh */ 2169 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 2170 ierr = DMDestroy(dm);CHKERRQ(ierr); 2171 *dm = idm; 2172 break; 2173 } 2174 default: SETERRQ1(comm, PETSC_ERR_SUP, "Unsupported dimension for sphere: %D", dim); 2175 } 2176 /* Create coordinates */ 2177 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 2178 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 2179 ierr = PetscSectionSetFieldComponents(coordSection, 0, embedDim);CHKERRQ(ierr); 2180 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numVerts);CHKERRQ(ierr); 2181 for (v = firstVertex; v < firstVertex+numVerts; ++v) { 2182 ierr = PetscSectionSetDof(coordSection, v, embedDim);CHKERRQ(ierr); 2183 ierr = PetscSectionSetFieldDof(coordSection, v, 0, embedDim);CHKERRQ(ierr); 2184 } 2185 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 2186 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 2187 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 2188 ierr = VecSetBlockSize(coordinates, embedDim);CHKERRQ(ierr); 2189 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 2190 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 2191 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 2192 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 2193 for (v = 0; v < numVerts; ++v) for (d = 0; d < embedDim; ++d) {coords[v*embedDim+d] = coordsIn[v*embedDim+d];} 2194 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 2195 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 2196 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 2197 ierr = PetscFree(coordsIn);CHKERRQ(ierr); 2198 /* Create coordinate function space */ 2199 { 2200 DM cdm; 2201 PetscDS cds; 2202 PetscFE fe; 2203 PetscScalar radius = R; 2204 PetscInt dT, dE; 2205 2206 ierr = DMGetCoordinateDM(*dm, &cdm);CHKERRQ(ierr); 2207 ierr = DMGetDimension(*dm, &dT);CHKERRQ(ierr); 2208 ierr = DMGetCoordinateDim(*dm, &dE);CHKERRQ(ierr); 2209 ierr = PetscFECreateLagrange(PETSC_COMM_SELF, dT, dE, simplex, 1, -1, &fe);CHKERRQ(ierr); 2210 ierr = DMSetField(cdm, 0, NULL, (PetscObject) fe);CHKERRQ(ierr); 2211 ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); 2212 ierr = DMCreateDS(cdm);CHKERRQ(ierr); 2213 2214 ierr = DMGetDS(cdm, &cds);CHKERRQ(ierr); 2215 ierr = PetscDSSetConstants(cds, 1, &radius);CHKERRQ(ierr); 2216 } 2217 ((DM_Plex *) (*dm)->data)->coordFunc = snapToSphere; 2218 PetscFunctionReturn(0); 2219 } 2220 2221 /*@ 2222 DMPlexCreateBallMesh - Creates a simplex mesh on the d-dimensional ball, B^d. 2223 2224 Collective 2225 2226 Input Parameters: 2227 + comm - The communicator for the DM object 2228 . dim - The dimension 2229 - R - The radius 2230 2231 Output Parameter: 2232 . dm - The DM object 2233 2234 Options Database Keys: 2235 - bd_dm_refine - This will refine the surface mesh preserving the sphere geometry 2236 2237 Level: beginner 2238 2239 .seealso: DMPlexCreateSphereMesh(), DMPlexCreateBoxMesh(), DMSetType(), DMCreate() 2240 @*/ 2241 PetscErrorCode DMPlexCreateBallMesh(MPI_Comm comm, PetscInt dim, PetscReal R, DM *dm) 2242 { 2243 DM sdm; 2244 DMLabel bdlabel; 2245 PetscErrorCode ierr; 2246 2247 PetscFunctionBegin; 2248 ierr = DMPlexCreateSphereMesh(comm, dim-1, PETSC_TRUE, R, &sdm);CHKERRQ(ierr); 2249 ierr = PetscObjectSetOptionsPrefix((PetscObject) sdm, "bd_");CHKERRQ(ierr); 2250 ierr = DMSetFromOptions(sdm);CHKERRQ(ierr); 2251 ierr = DMPlexGenerate(sdm, NULL, PETSC_TRUE, dm);CHKERRQ(ierr); 2252 ierr = DMDestroy(&sdm);CHKERRQ(ierr); 2253 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 2254 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 2255 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 2256 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 2257 PetscFunctionReturn(0); 2258 } 2259 2260 /* External function declarations here */ 2261 extern PetscErrorCode DMCreateInterpolation_Plex(DM dmCoarse, DM dmFine, Mat *interpolation, Vec *scaling); 2262 extern PetscErrorCode DMCreateInjection_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2263 extern PetscErrorCode DMCreateMassMatrix_Plex(DM dmCoarse, DM dmFine, Mat *mat); 2264 extern PetscErrorCode DMCreateLocalSection_Plex(DM dm); 2265 extern PetscErrorCode DMCreateDefaultConstraints_Plex(DM dm); 2266 extern PetscErrorCode DMCreateMatrix_Plex(DM dm, Mat *J); 2267 extern PetscErrorCode DMCreateCoordinateDM_Plex(DM dm, DM *cdm); 2268 extern PetscErrorCode DMCreateCoordinateField_Plex(DM dm, DMField *field); 2269 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm); 2270 extern PetscErrorCode DMSetUp_Plex(DM dm); 2271 extern PetscErrorCode DMDestroy_Plex(DM dm); 2272 extern PetscErrorCode DMView_Plex(DM dm, PetscViewer viewer); 2273 extern PetscErrorCode DMLoad_Plex(DM dm, PetscViewer viewer); 2274 extern PetscErrorCode DMCreateSubDM_Plex(DM dm, PetscInt numFields, const PetscInt fields[], IS *is, DM *subdm); 2275 extern PetscErrorCode DMCreateSuperDM_Plex(DM dms[], PetscInt len, IS **is, DM *superdm); 2276 static PetscErrorCode DMInitialize_Plex(DM dm); 2277 2278 /* Replace dm with the contents of dmNew 2279 - Share the DM_Plex structure 2280 - Share the coordinates 2281 - Share the SF 2282 */ 2283 static PetscErrorCode DMPlexReplace_Static(DM dm, DM dmNew) 2284 { 2285 PetscSF sf; 2286 DM coordDM, coarseDM; 2287 DMField coordField; 2288 Vec coords; 2289 PetscBool isper; 2290 const PetscReal *maxCell, *L; 2291 const DMBoundaryType *bd; 2292 PetscErrorCode ierr; 2293 2294 PetscFunctionBegin; 2295 ierr = DMGetPointSF(dmNew, &sf);CHKERRQ(ierr); 2296 ierr = DMSetPointSF(dm, sf);CHKERRQ(ierr); 2297 ierr = DMGetCoordinateDM(dmNew, &coordDM);CHKERRQ(ierr); 2298 ierr = DMGetCoordinatesLocal(dmNew, &coords);CHKERRQ(ierr); 2299 ierr = DMGetCoordinateField(dmNew, &coordField);CHKERRQ(ierr); 2300 ierr = DMSetCoordinateDM(dm, coordDM);CHKERRQ(ierr); 2301 ierr = DMSetCoordinatesLocal(dm, coords);CHKERRQ(ierr); 2302 ierr = DMSetCoordinateField(dm, coordField);CHKERRQ(ierr); 2303 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 2304 ierr = DMSetPeriodicity(dmNew, isper, maxCell, L, bd);CHKERRQ(ierr); 2305 ierr = DMDestroy_Plex(dm);CHKERRQ(ierr); 2306 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2307 dm->data = dmNew->data; 2308 ((DM_Plex *) dmNew->data)->refct++; 2309 ierr = DMDestroyLabelLinkList_Internal(dm);CHKERRQ(ierr); 2310 ierr = DMCopyLabels(dmNew, dm, PETSC_OWN_POINTER, PETSC_TRUE);CHKERRQ(ierr); 2311 ierr = DMGetCoarseDM(dmNew,&coarseDM);CHKERRQ(ierr); 2312 ierr = DMSetCoarseDM(dm,coarseDM);CHKERRQ(ierr); 2313 PetscFunctionReturn(0); 2314 } 2315 2316 /* Swap dm with the contents of dmNew 2317 - Swap the DM_Plex structure 2318 - Swap the coordinates 2319 - Swap the point PetscSF 2320 */ 2321 static PetscErrorCode DMPlexSwap_Static(DM dmA, DM dmB) 2322 { 2323 DM coordDMA, coordDMB; 2324 Vec coordsA, coordsB; 2325 PetscSF sfA, sfB; 2326 void *tmp; 2327 DMLabelLink listTmp; 2328 DMLabel depthTmp; 2329 PetscInt tmpI; 2330 PetscErrorCode ierr; 2331 2332 PetscFunctionBegin; 2333 ierr = DMGetPointSF(dmA, &sfA);CHKERRQ(ierr); 2334 ierr = DMGetPointSF(dmB, &sfB);CHKERRQ(ierr); 2335 ierr = PetscObjectReference((PetscObject) sfA);CHKERRQ(ierr); 2336 ierr = DMSetPointSF(dmA, sfB);CHKERRQ(ierr); 2337 ierr = DMSetPointSF(dmB, sfA);CHKERRQ(ierr); 2338 ierr = PetscObjectDereference((PetscObject) sfA);CHKERRQ(ierr); 2339 2340 ierr = DMGetCoordinateDM(dmA, &coordDMA);CHKERRQ(ierr); 2341 ierr = DMGetCoordinateDM(dmB, &coordDMB);CHKERRQ(ierr); 2342 ierr = PetscObjectReference((PetscObject) coordDMA);CHKERRQ(ierr); 2343 ierr = DMSetCoordinateDM(dmA, coordDMB);CHKERRQ(ierr); 2344 ierr = DMSetCoordinateDM(dmB, coordDMA);CHKERRQ(ierr); 2345 ierr = PetscObjectDereference((PetscObject) coordDMA);CHKERRQ(ierr); 2346 2347 ierr = DMGetCoordinatesLocal(dmA, &coordsA);CHKERRQ(ierr); 2348 ierr = DMGetCoordinatesLocal(dmB, &coordsB);CHKERRQ(ierr); 2349 ierr = PetscObjectReference((PetscObject) coordsA);CHKERRQ(ierr); 2350 ierr = DMSetCoordinatesLocal(dmA, coordsB);CHKERRQ(ierr); 2351 ierr = DMSetCoordinatesLocal(dmB, coordsA);CHKERRQ(ierr); 2352 ierr = PetscObjectDereference((PetscObject) coordsA);CHKERRQ(ierr); 2353 2354 tmp = dmA->data; 2355 dmA->data = dmB->data; 2356 dmB->data = tmp; 2357 listTmp = dmA->labels; 2358 dmA->labels = dmB->labels; 2359 dmB->labels = listTmp; 2360 depthTmp = dmA->depthLabel; 2361 dmA->depthLabel = dmB->depthLabel; 2362 dmB->depthLabel = depthTmp; 2363 depthTmp = dmA->celltypeLabel; 2364 dmA->celltypeLabel = dmB->celltypeLabel; 2365 dmB->celltypeLabel = depthTmp; 2366 tmpI = dmA->levelup; 2367 dmA->levelup = dmB->levelup; 2368 dmB->levelup = tmpI; 2369 PetscFunctionReturn(0); 2370 } 2371 2372 PetscErrorCode DMSetFromOptions_NonRefinement_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2373 { 2374 DM_Plex *mesh = (DM_Plex*) dm->data; 2375 PetscBool flg; 2376 PetscErrorCode ierr; 2377 2378 PetscFunctionBegin; 2379 /* Handle viewing */ 2380 ierr = PetscOptionsBool("-dm_plex_print_set_values", "Output all set values info", "DMPlexMatSetClosure", PETSC_FALSE, &mesh->printSetValues, NULL);CHKERRQ(ierr); 2381 ierr = PetscOptionsBoundedInt("-dm_plex_print_fem", "Debug output level all fem computations", "DMPlexSNESComputeResidualFEM", 0, &mesh->printFEM, NULL,0);CHKERRQ(ierr); 2382 ierr = PetscOptionsReal("-dm_plex_print_tol", "Tolerance for FEM output", "DMPlexSNESComputeResidualFEM", mesh->printTol, &mesh->printTol, NULL);CHKERRQ(ierr); 2383 ierr = PetscOptionsBoundedInt("-dm_plex_print_l2", "Debug output level all L2 diff computations", "DMComputeL2Diff", 0, &mesh->printL2, NULL,0);CHKERRQ(ierr); 2384 ierr = DMMonitorSetFromOptions(dm, "-dm_plex_monitor_throughput", "Monitor the simulation throughput", "DMPlexMonitorThroughput", DMPlexMonitorThroughput, NULL, &flg);CHKERRQ(ierr); 2385 if (flg) {ierr = PetscLogDefaultBegin();CHKERRQ(ierr);} 2386 /* Point Location */ 2387 ierr = PetscOptionsBool("-dm_plex_hash_location", "Use grid hashing for point location", "DMInterpolate", PETSC_FALSE, &mesh->useHashLocation, NULL);CHKERRQ(ierr); 2388 /* Partitioning and distribution */ 2389 ierr = PetscOptionsBool("-dm_plex_partition_balance", "Attempt to evenly divide points on partition boundary between processes", "DMPlexSetPartitionBalance", PETSC_FALSE, &mesh->partitionBalance, NULL);CHKERRQ(ierr); 2390 /* Generation and remeshing */ 2391 ierr = PetscOptionsBool("-dm_plex_remesh_bd", "Allow changes to the boundary on remeshing", "DMAdapt", PETSC_FALSE, &mesh->remeshBd, NULL);CHKERRQ(ierr); 2392 /* Projection behavior */ 2393 ierr = PetscOptionsBoundedInt("-dm_plex_max_projection_height", "Maxmimum mesh point height used to project locally", "DMPlexSetMaxProjectionHeight", 0, &mesh->maxProjectionHeight, NULL,0);CHKERRQ(ierr); 2394 ierr = PetscOptionsBool("-dm_plex_regular_refinement", "Use special nested projection algorithm for regular refinement", "DMPlexSetRegularRefinement", mesh->regularRefinement, &mesh->regularRefinement, NULL);CHKERRQ(ierr); 2395 ierr = PetscOptionsEnum("-dm_plex_cell_refiner", "Strategy for cell refinment", "ex40.c", DMPlexCellRefinerTypes, (PetscEnum) mesh->cellRefiner, (PetscEnum *) &mesh->cellRefiner, NULL);CHKERRQ(ierr); 2396 /* Checking structure */ 2397 { 2398 PetscBool flg = PETSC_FALSE, flg2 = PETSC_FALSE, all = PETSC_FALSE; 2399 2400 ierr = PetscOptionsBool("-dm_plex_check_all", "Perform all checks", NULL, PETSC_FALSE, &all, &flg2);CHKERRQ(ierr); 2401 ierr = PetscOptionsBool("-dm_plex_check_symmetry", "Check that the adjacency information in the mesh is symmetric", "DMPlexCheckSymmetry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2402 if (all || (flg && flg2)) {ierr = DMPlexCheckSymmetry(dm);CHKERRQ(ierr);} 2403 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); 2404 if (all || (flg && flg2)) {ierr = DMPlexCheckSkeleton(dm, 0);CHKERRQ(ierr);} 2405 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); 2406 if (all || (flg && flg2)) {ierr = DMPlexCheckFaces(dm, 0);CHKERRQ(ierr);} 2407 ierr = PetscOptionsBool("-dm_plex_check_geometry", "Check that cells have positive volume", "DMPlexCheckGeometry", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2408 if (all || (flg && flg2)) {ierr = DMPlexCheckGeometry(dm);CHKERRQ(ierr);} 2409 ierr = PetscOptionsBool("-dm_plex_check_pointsf", "Check some necessary conditions for PointSF", "DMPlexCheckPointSF", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2410 if (all || (flg && flg2)) {ierr = DMPlexCheckPointSF(dm);CHKERRQ(ierr);} 2411 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); 2412 if (all || (flg && flg2)) {ierr = DMPlexCheckInterfaceCones(dm);CHKERRQ(ierr);} 2413 ierr = PetscOptionsBool("-dm_plex_check_cell_shape", "Check cell shape", "DMPlexCheckCellShape", PETSC_FALSE, &flg, &flg2);CHKERRQ(ierr); 2414 if (flg && flg2) {ierr = DMPlexCheckCellShape(dm, PETSC_TRUE, PETSC_DETERMINE);CHKERRQ(ierr);} 2415 } 2416 2417 ierr = PetscPartitionerSetFromOptions(mesh->partitioner);CHKERRQ(ierr); 2418 PetscFunctionReturn(0); 2419 } 2420 2421 static PetscErrorCode DMSetFromOptions_Plex(PetscOptionItems *PetscOptionsObject,DM dm) 2422 { 2423 PetscInt prerefine = 0, refine = 0, r, coarsen = 0, overlap = 0; 2424 PetscBool distribute = PETSC_FALSE, isHierarchy; 2425 PetscErrorCode ierr; 2426 2427 PetscFunctionBegin; 2428 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2429 ierr = PetscOptionsHead(PetscOptionsObject,"DMPlex Options");CHKERRQ(ierr); 2430 /* Handle DMPlex refinement before distribution */ 2431 ierr = PetscOptionsBoundedInt("-dm_refine_pre", "The number of uniform refinements before distribution", "DMCreate", prerefine, &prerefine, NULL,0);CHKERRQ(ierr); 2432 if (prerefine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2433 for (r = 0; r < prerefine; ++r) { 2434 DM rdm; 2435 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 2436 2437 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2438 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &rdm);CHKERRQ(ierr); 2439 /* Total hack since we do not pass in a pointer */ 2440 ierr = DMPlexReplace_Static(dm, rdm);CHKERRQ(ierr); 2441 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2442 if (coordFunc) { 2443 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 2444 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 2445 } 2446 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 2447 } 2448 /* Handle DMPlex distribution */ 2449 ierr = PetscOptionsBool("-dm_distribute", "Flag to redistribute a mesh among processes", "DMCreate", distribute, &distribute, NULL);CHKERRQ(ierr); 2450 ierr = PetscOptionsBoundedInt("-dm_distribute_overlap", "The size of the overlap halo", "DMCreate", overlap, &overlap, NULL, 0);CHKERRQ(ierr); 2451 if (distribute) { 2452 DM pdm = NULL; 2453 PetscPartitioner part; 2454 2455 ierr = DMPlexGetPartitioner(dm, &part);CHKERRQ(ierr); 2456 ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr); 2457 ierr = DMPlexDistribute(dm, overlap, NULL, &pdm);CHKERRQ(ierr); 2458 if (pdm) { 2459 ierr = DMPlexReplace_Static(dm, pdm);CHKERRQ(ierr); 2460 ierr = DMDestroy(&pdm);CHKERRQ(ierr); 2461 } 2462 } 2463 /* Handle DMPlex refinement */ 2464 ierr = PetscOptionsBoundedInt("-dm_refine", "The number of uniform refinements", "DMCreate", refine, &refine, NULL,0);CHKERRQ(ierr); 2465 ierr = PetscOptionsBoundedInt("-dm_refine_hierarchy", "The number of uniform refinements", "DMCreate", refine, &refine, &isHierarchy,0);CHKERRQ(ierr); 2466 if (refine) {ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);} 2467 if (refine && isHierarchy) { 2468 DM *dms, coarseDM; 2469 2470 ierr = DMGetCoarseDM(dm, &coarseDM);CHKERRQ(ierr); 2471 ierr = PetscObjectReference((PetscObject)coarseDM);CHKERRQ(ierr); 2472 ierr = PetscMalloc1(refine,&dms);CHKERRQ(ierr); 2473 ierr = DMRefineHierarchy(dm, refine, dms);CHKERRQ(ierr); 2474 /* Total hack since we do not pass in a pointer */ 2475 ierr = DMPlexSwap_Static(dm, dms[refine-1]);CHKERRQ(ierr); 2476 if (refine == 1) { 2477 ierr = DMSetCoarseDM(dm, dms[0]);CHKERRQ(ierr); 2478 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2479 } else { 2480 ierr = DMSetCoarseDM(dm, dms[refine-2]);CHKERRQ(ierr); 2481 ierr = DMPlexSetRegularRefinement(dm, PETSC_TRUE);CHKERRQ(ierr); 2482 ierr = DMSetCoarseDM(dms[0], dms[refine-1]);CHKERRQ(ierr); 2483 ierr = DMPlexSetRegularRefinement(dms[0], PETSC_TRUE);CHKERRQ(ierr); 2484 } 2485 ierr = DMSetCoarseDM(dms[refine-1], coarseDM);CHKERRQ(ierr); 2486 ierr = PetscObjectDereference((PetscObject)coarseDM);CHKERRQ(ierr); 2487 /* Free DMs */ 2488 for (r = 0; r < refine; ++r) { 2489 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2490 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2491 } 2492 ierr = PetscFree(dms);CHKERRQ(ierr); 2493 } else { 2494 for (r = 0; r < refine; ++r) { 2495 DM refinedMesh; 2496 PetscPointFunc coordFunc = ((DM_Plex*) dm->data)->coordFunc; 2497 2498 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2499 ierr = DMRefine(dm, PetscObjectComm((PetscObject) dm), &refinedMesh);CHKERRQ(ierr); 2500 /* Total hack since we do not pass in a pointer */ 2501 ierr = DMPlexReplace_Static(dm, refinedMesh);CHKERRQ(ierr); 2502 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2503 if (coordFunc) { 2504 ierr = DMPlexRemapGeometry(dm, 0.0, coordFunc);CHKERRQ(ierr); 2505 ((DM_Plex*) dm->data)->coordFunc = coordFunc; 2506 } 2507 ierr = DMDestroy(&refinedMesh);CHKERRQ(ierr); 2508 } 2509 } 2510 /* Handle DMPlex coarsening */ 2511 ierr = PetscOptionsBoundedInt("-dm_coarsen", "Coarsen the mesh", "DMCreate", coarsen, &coarsen, NULL,0);CHKERRQ(ierr); 2512 ierr = PetscOptionsBoundedInt("-dm_coarsen_hierarchy", "The number of coarsenings", "DMCreate", coarsen, &coarsen, &isHierarchy,0);CHKERRQ(ierr); 2513 if (coarsen && isHierarchy) { 2514 DM *dms; 2515 2516 ierr = PetscMalloc1(coarsen, &dms);CHKERRQ(ierr); 2517 ierr = DMCoarsenHierarchy(dm, coarsen, dms);CHKERRQ(ierr); 2518 /* Free DMs */ 2519 for (r = 0; r < coarsen; ++r) { 2520 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dms[r]);CHKERRQ(ierr); 2521 ierr = DMDestroy(&dms[r]);CHKERRQ(ierr); 2522 } 2523 ierr = PetscFree(dms);CHKERRQ(ierr); 2524 } else { 2525 for (r = 0; r < coarsen; ++r) { 2526 DM coarseMesh; 2527 2528 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2529 ierr = DMCoarsen(dm, PetscObjectComm((PetscObject) dm), &coarseMesh);CHKERRQ(ierr); 2530 /* Total hack since we do not pass in a pointer */ 2531 ierr = DMPlexReplace_Static(dm, coarseMesh);CHKERRQ(ierr); 2532 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2533 ierr = DMDestroy(&coarseMesh);CHKERRQ(ierr); 2534 } 2535 } 2536 /* Handle */ 2537 ierr = DMSetFromOptions_NonRefinement_Plex(PetscOptionsObject, dm);CHKERRQ(ierr); 2538 ierr = PetscOptionsTail();CHKERRQ(ierr); 2539 PetscFunctionReturn(0); 2540 } 2541 2542 static PetscErrorCode DMCreateGlobalVector_Plex(DM dm,Vec *vec) 2543 { 2544 PetscErrorCode ierr; 2545 2546 PetscFunctionBegin; 2547 ierr = DMCreateGlobalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2548 /* ierr = VecSetOperation(*vec, VECOP_DUPLICATE, (void(*)(void)) VecDuplicate_MPI_DM);CHKERRQ(ierr); */ 2549 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex);CHKERRQ(ierr); 2550 ierr = VecSetOperation(*vec, VECOP_VIEWNATIVE, (void (*)(void)) VecView_Plex_Native);CHKERRQ(ierr); 2551 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex);CHKERRQ(ierr); 2552 ierr = VecSetOperation(*vec, VECOP_LOADNATIVE, (void (*)(void)) VecLoad_Plex_Native);CHKERRQ(ierr); 2553 PetscFunctionReturn(0); 2554 } 2555 2556 static PetscErrorCode DMCreateLocalVector_Plex(DM dm,Vec *vec) 2557 { 2558 PetscErrorCode ierr; 2559 2560 PetscFunctionBegin; 2561 ierr = DMCreateLocalVector_Section_Private(dm,vec);CHKERRQ(ierr); 2562 ierr = VecSetOperation(*vec, VECOP_VIEW, (void (*)(void)) VecView_Plex_Local);CHKERRQ(ierr); 2563 ierr = VecSetOperation(*vec, VECOP_LOAD, (void (*)(void)) VecLoad_Plex_Local);CHKERRQ(ierr); 2564 PetscFunctionReturn(0); 2565 } 2566 2567 static PetscErrorCode DMGetDimPoints_Plex(DM dm, PetscInt dim, PetscInt *pStart, PetscInt *pEnd) 2568 { 2569 PetscInt depth, d; 2570 PetscErrorCode ierr; 2571 2572 PetscFunctionBegin; 2573 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 2574 if (depth == 1) { 2575 ierr = DMGetDimension(dm, &d);CHKERRQ(ierr); 2576 if (dim == 0) {ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr);} 2577 else if (dim == d) {ierr = DMPlexGetDepthStratum(dm, 1, pStart, pEnd);CHKERRQ(ierr);} 2578 else {*pStart = 0; *pEnd = 0;} 2579 } else { 2580 ierr = DMPlexGetDepthStratum(dm, dim, pStart, pEnd);CHKERRQ(ierr); 2581 } 2582 PetscFunctionReturn(0); 2583 } 2584 2585 static PetscErrorCode DMGetNeighbors_Plex(DM dm, PetscInt *nranks, const PetscMPIInt *ranks[]) 2586 { 2587 PetscSF sf; 2588 PetscInt niranks, njranks, n; 2589 const PetscMPIInt *iranks, *jranks; 2590 DM_Plex *data = (DM_Plex*) dm->data; 2591 PetscErrorCode ierr; 2592 2593 PetscFunctionBegin; 2594 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 2595 if (!data->neighbors) { 2596 ierr = PetscSFGetRootRanks(sf, &njranks, &jranks, NULL, NULL, NULL);CHKERRQ(ierr); 2597 ierr = PetscSFGetLeafRanks(sf, &niranks, &iranks, NULL, NULL);CHKERRQ(ierr); 2598 ierr = PetscMalloc1(njranks + niranks + 1, &data->neighbors);CHKERRQ(ierr); 2599 ierr = PetscArraycpy(data->neighbors + 1, jranks, njranks);CHKERRQ(ierr); 2600 ierr = PetscArraycpy(data->neighbors + njranks + 1, iranks, niranks);CHKERRQ(ierr); 2601 n = njranks + niranks; 2602 ierr = PetscSortRemoveDupsMPIInt(&n, data->neighbors + 1);CHKERRQ(ierr); 2603 /* The following cast should never fail: can't have more neighbors than PETSC_MPI_INT_MAX */ 2604 ierr = PetscMPIIntCast(n, data->neighbors);CHKERRQ(ierr); 2605 } 2606 if (nranks) *nranks = data->neighbors[0]; 2607 if (ranks) { 2608 if (data->neighbors[0]) *ranks = data->neighbors + 1; 2609 else *ranks = NULL; 2610 } 2611 PetscFunctionReturn(0); 2612 } 2613 2614 static PetscErrorCode DMInitialize_Plex(DM dm) 2615 { 2616 PetscErrorCode ierr; 2617 2618 PetscFunctionBegin; 2619 dm->ops->view = DMView_Plex; 2620 dm->ops->load = DMLoad_Plex; 2621 dm->ops->setfromoptions = DMSetFromOptions_Plex; 2622 dm->ops->clone = DMClone_Plex; 2623 dm->ops->setup = DMSetUp_Plex; 2624 dm->ops->createlocalsection = DMCreateLocalSection_Plex; 2625 dm->ops->createdefaultconstraints = DMCreateDefaultConstraints_Plex; 2626 dm->ops->createglobalvector = DMCreateGlobalVector_Plex; 2627 dm->ops->createlocalvector = DMCreateLocalVector_Plex; 2628 dm->ops->getlocaltoglobalmapping = NULL; 2629 dm->ops->createfieldis = NULL; 2630 dm->ops->createcoordinatedm = DMCreateCoordinateDM_Plex; 2631 dm->ops->createcoordinatefield = DMCreateCoordinateField_Plex; 2632 dm->ops->getcoloring = NULL; 2633 dm->ops->creatematrix = DMCreateMatrix_Plex; 2634 dm->ops->createinterpolation = DMCreateInterpolation_Plex; 2635 dm->ops->createmassmatrix = DMCreateMassMatrix_Plex; 2636 dm->ops->createinjection = DMCreateInjection_Plex; 2637 dm->ops->refine = DMRefine_Plex; 2638 dm->ops->coarsen = DMCoarsen_Plex; 2639 dm->ops->refinehierarchy = DMRefineHierarchy_Plex; 2640 dm->ops->coarsenhierarchy = DMCoarsenHierarchy_Plex; 2641 dm->ops->adaptlabel = DMAdaptLabel_Plex; 2642 dm->ops->adaptmetric = DMAdaptMetric_Plex; 2643 dm->ops->globaltolocalbegin = NULL; 2644 dm->ops->globaltolocalend = NULL; 2645 dm->ops->localtoglobalbegin = NULL; 2646 dm->ops->localtoglobalend = NULL; 2647 dm->ops->destroy = DMDestroy_Plex; 2648 dm->ops->createsubdm = DMCreateSubDM_Plex; 2649 dm->ops->createsuperdm = DMCreateSuperDM_Plex; 2650 dm->ops->getdimpoints = DMGetDimPoints_Plex; 2651 dm->ops->locatepoints = DMLocatePoints_Plex; 2652 dm->ops->projectfunctionlocal = DMProjectFunctionLocal_Plex; 2653 dm->ops->projectfunctionlabellocal = DMProjectFunctionLabelLocal_Plex; 2654 dm->ops->projectfieldlocal = DMProjectFieldLocal_Plex; 2655 dm->ops->projectfieldlabellocal = DMProjectFieldLabelLocal_Plex; 2656 dm->ops->projectbdfieldlabellocal = DMProjectBdFieldLabelLocal_Plex; 2657 dm->ops->computel2diff = DMComputeL2Diff_Plex; 2658 dm->ops->computel2gradientdiff = DMComputeL2GradientDiff_Plex; 2659 dm->ops->computel2fielddiff = DMComputeL2FieldDiff_Plex; 2660 dm->ops->getneighbors = DMGetNeighbors_Plex; 2661 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertBoundaryValues_C",DMPlexInsertBoundaryValues_Plex);CHKERRQ(ierr); 2662 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexInsertTimeDerviativeBoundaryValues_C",DMPlexInsertTimeDerivativeBoundaryValues_Plex);CHKERRQ(ierr); 2663 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMSetUpGLVisViewer_C",DMSetUpGLVisViewer_Plex);CHKERRQ(ierr); 2664 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMCreateNeumannOverlap_C",DMCreateNeumannOverlap_Plex);CHKERRQ(ierr); 2665 ierr = PetscObjectComposeFunction((PetscObject)dm,"DMPlexGetOverlap_C",DMPlexGetOverlap_Plex);CHKERRQ(ierr); 2666 PetscFunctionReturn(0); 2667 } 2668 2669 PETSC_INTERN PetscErrorCode DMClone_Plex(DM dm, DM *newdm) 2670 { 2671 DM_Plex *mesh = (DM_Plex *) dm->data; 2672 PetscErrorCode ierr; 2673 2674 PetscFunctionBegin; 2675 mesh->refct++; 2676 (*newdm)->data = mesh; 2677 ierr = PetscObjectChangeTypeName((PetscObject) *newdm, DMPLEX);CHKERRQ(ierr); 2678 ierr = DMInitialize_Plex(*newdm);CHKERRQ(ierr); 2679 PetscFunctionReturn(0); 2680 } 2681 2682 /*MC 2683 DMPLEX = "plex" - A DM object that encapsulates an unstructured mesh, or CW Complex, which can be expressed using a Hasse Diagram. 2684 In the local representation, Vecs contain all unknowns in the interior and shared boundary. This is 2685 specified by a PetscSection object. Ownership in the global representation is determined by 2686 ownership of the underlying DMPlex points. This is specified by another PetscSection object. 2687 2688 Options Database Keys: 2689 + -dm_plex_hash_location - Use grid hashing for point location 2690 . -dm_plex_partition_balance - Attempt to evenly divide points on partition boundary between processes 2691 . -dm_plex_remesh_bd - Allow changes to the boundary on remeshing 2692 . -dm_plex_max_projection_height - Maxmimum mesh point height used to project locally 2693 . -dm_plex_regular_refinement - Use special nested projection algorithm for regular refinement 2694 . -dm_plex_check_symmetry - Check that the adjacency information in the mesh is symmetric 2695 . -dm_plex_check_skeleton <celltype> - Check that each cell has the correct number of vertices 2696 . -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 2697 . -dm_plex_check_geometry - Check that cells have positive volume 2698 . -dm_view :mesh.tex:ascii_latex - View the mesh in LaTeX/TikZ 2699 . -dm_plex_view_scale <num> - Scale the TikZ 2700 - -dm_plex_print_fem <num> - View FEM assembly information, such as element vectors and matrices 2701 2702 2703 Level: intermediate 2704 2705 .seealso: DMType, DMPlexCreate(), DMCreate(), DMSetType() 2706 M*/ 2707 2708 PETSC_EXTERN PetscErrorCode DMCreate_Plex(DM dm) 2709 { 2710 DM_Plex *mesh; 2711 PetscInt unit; 2712 PetscErrorCode ierr; 2713 2714 PetscFunctionBegin; 2715 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2716 ierr = PetscNewLog(dm,&mesh);CHKERRQ(ierr); 2717 dm->dim = 0; 2718 dm->data = mesh; 2719 2720 mesh->refct = 1; 2721 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->coneSection);CHKERRQ(ierr); 2722 mesh->maxConeSize = 0; 2723 mesh->cones = NULL; 2724 mesh->coneOrientations = NULL; 2725 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm), &mesh->supportSection);CHKERRQ(ierr); 2726 mesh->maxSupportSize = 0; 2727 mesh->supports = NULL; 2728 mesh->refinementUniform = PETSC_TRUE; 2729 mesh->refinementLimit = -1.0; 2730 mesh->interpolated = DMPLEX_INTERPOLATED_INVALID; 2731 mesh->interpolatedCollective = DMPLEX_INTERPOLATED_INVALID; 2732 2733 mesh->facesTmp = NULL; 2734 2735 mesh->tetgenOpts = NULL; 2736 mesh->triangleOpts = NULL; 2737 ierr = PetscPartitionerCreate(PetscObjectComm((PetscObject)dm), &mesh->partitioner);CHKERRQ(ierr); 2738 mesh->remeshBd = PETSC_FALSE; 2739 2740 mesh->subpointMap = NULL; 2741 2742 for (unit = 0; unit < NUM_PETSC_UNITS; ++unit) mesh->scale[unit] = 1.0; 2743 2744 mesh->regularRefinement = PETSC_FALSE; 2745 mesh->depthState = -1; 2746 mesh->celltypeState = -1; 2747 mesh->globalVertexNumbers = NULL; 2748 mesh->globalCellNumbers = NULL; 2749 mesh->anchorSection = NULL; 2750 mesh->anchorIS = NULL; 2751 mesh->createanchors = NULL; 2752 mesh->computeanchormatrix = NULL; 2753 mesh->parentSection = NULL; 2754 mesh->parents = NULL; 2755 mesh->childIDs = NULL; 2756 mesh->childSection = NULL; 2757 mesh->children = NULL; 2758 mesh->referenceTree = NULL; 2759 mesh->getchildsymmetry = NULL; 2760 mesh->vtkCellHeight = 0; 2761 mesh->useAnchors = PETSC_FALSE; 2762 2763 mesh->maxProjectionHeight = 0; 2764 2765 mesh->neighbors = NULL; 2766 2767 mesh->printSetValues = PETSC_FALSE; 2768 mesh->printFEM = 0; 2769 mesh->printTol = 1.0e-10; 2770 2771 ierr = DMInitialize_Plex(dm);CHKERRQ(ierr); 2772 PetscFunctionReturn(0); 2773 } 2774 2775 /*@ 2776 DMPlexCreate - Creates a DMPlex object, which encapsulates an unstructured mesh, or CW complex, which can be expressed using a Hasse Diagram. 2777 2778 Collective 2779 2780 Input Parameter: 2781 . comm - The communicator for the DMPlex object 2782 2783 Output Parameter: 2784 . mesh - The DMPlex object 2785 2786 Level: beginner 2787 2788 @*/ 2789 PetscErrorCode DMPlexCreate(MPI_Comm comm, DM *mesh) 2790 { 2791 PetscErrorCode ierr; 2792 2793 PetscFunctionBegin; 2794 PetscValidPointer(mesh,2); 2795 ierr = DMCreate(comm, mesh);CHKERRQ(ierr); 2796 ierr = DMSetType(*mesh, DMPLEX);CHKERRQ(ierr); 2797 PetscFunctionReturn(0); 2798 } 2799 2800 /*@C 2801 DMPlexBuildFromCellListParallel - Build distributed DMPLEX topology from a list of vertices for each cell (common mesh generator output) 2802 2803 Input Parameters: 2804 + dm - The DM 2805 . numCells - The number of cells owned by this process 2806 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 2807 . NVertices - The global number of vertices, or PETSC_DECIDE 2808 . numCorners - The number of vertices for each cell 2809 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 2810 2811 Output Parameter: 2812 . vertexSF - (Optional) SF describing complete vertex ownership 2813 2814 Notes: 2815 Two triangles sharing a face 2816 $ 2817 $ 2 2818 $ / | \ 2819 $ / | \ 2820 $ / | \ 2821 $ 0 0 | 1 3 2822 $ \ | / 2823 $ \ | / 2824 $ \ | / 2825 $ 1 2826 would have input 2827 $ numCells = 2, numVertices = 4 2828 $ cells = [0 1 2 1 3 2] 2829 $ 2830 which would result in the DMPlex 2831 $ 2832 $ 4 2833 $ / | \ 2834 $ / | \ 2835 $ / | \ 2836 $ 2 0 | 1 5 2837 $ \ | / 2838 $ \ | / 2839 $ \ | / 2840 $ 3 2841 2842 Vertices are implicitly numbered consecutively 0,...,NVertices. 2843 Each rank owns a chunk of numVertices consecutive vertices. 2844 If numVertices is PETSC_DECIDE, PETSc will distribute them as evenly as possible using PetscLayout. 2845 If both NVertices and numVertices are PETSC_DECIDE, NVertices is computed by PETSc as the maximum vertex index in cells + 1. 2846 If only NVertices is PETSC_DECIDE, it is computed as the sum of numVertices over all ranks. 2847 2848 The cell distribution is arbitrary non-overlapping, independent of the vertex distribution. 2849 2850 Not currently supported in Fortran. 2851 2852 Level: advanced 2853 2854 .seealso: DMPlexBuildFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildCoordinatesFromCellListParallel() 2855 @*/ 2856 PetscErrorCode DMPlexBuildFromCellListParallel(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, const PetscInt cells[], PetscSF *vertexSF) 2857 { 2858 PetscSF sfPoint, sfVert; 2859 PetscLayout vLayout; 2860 PetscHSetI vhash; 2861 PetscSFNode *remoteVerticesAdj, *vertexLocal, *vertexOwner, *remoteVertex; 2862 const PetscInt *vrange; 2863 PetscInt numVerticesAdj, off = 0, *verticesAdj, numVerticesGhost = 0, *localVertex, *cones, c, p, v, g, dim; 2864 PetscMPIInt rank, size; 2865 PetscErrorCode ierr; 2866 2867 PetscFunctionBegin; 2868 PetscValidLogicalCollectiveInt(dm,NVertices,4); 2869 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 2870 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 2871 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 2872 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2873 /* Get/check global number of vertices */ 2874 { 2875 PetscInt NVerticesInCells, i; 2876 const PetscInt len = numCells * numCorners; 2877 2878 /* NVerticesInCells = max(cells) + 1 */ 2879 NVerticesInCells = PETSC_MIN_INT; 2880 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 2881 ++NVerticesInCells; 2882 ierr = MPI_Allreduce(MPI_IN_PLACE, &NVerticesInCells, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 2883 2884 if (numVertices == PETSC_DECIDE && NVertices == PETSC_DECIDE) NVertices = NVerticesInCells; 2885 else if (NVertices != PETSC_DECIDE && NVertices < NVerticesInCells) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Specified global number of vertices %D must be greater than or equal to the number of vertices in cells %D",NVertices,NVerticesInCells); 2886 } 2887 /* Partition vertices */ 2888 ierr = PetscLayoutCreate(PetscObjectComm((PetscObject) dm), &vLayout);CHKERRQ(ierr); 2889 ierr = PetscLayoutSetLocalSize(vLayout, numVertices);CHKERRQ(ierr); 2890 ierr = PetscLayoutSetSize(vLayout, NVertices);CHKERRQ(ierr); 2891 ierr = PetscLayoutSetBlockSize(vLayout, 1);CHKERRQ(ierr); 2892 ierr = PetscLayoutSetUp(vLayout);CHKERRQ(ierr); 2893 ierr = PetscLayoutGetRanges(vLayout, &vrange);CHKERRQ(ierr); 2894 /* Count vertices and map them to procs */ 2895 ierr = PetscHSetICreate(&vhash);CHKERRQ(ierr); 2896 for (c = 0; c < numCells; ++c) { 2897 for (p = 0; p < numCorners; ++p) { 2898 ierr = PetscHSetIAdd(vhash, cells[c*numCorners+p]);CHKERRQ(ierr); 2899 } 2900 } 2901 ierr = PetscHSetIGetSize(vhash, &numVerticesAdj);CHKERRQ(ierr); 2902 ierr = PetscMalloc1(numVerticesAdj, &verticesAdj);CHKERRQ(ierr); 2903 ierr = PetscHSetIGetElems(vhash, &off, verticesAdj);CHKERRQ(ierr); 2904 ierr = PetscHSetIDestroy(&vhash);CHKERRQ(ierr); 2905 if (off != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid number of local vertices %D should be %D", off, numVerticesAdj); 2906 ierr = PetscSortInt(numVerticesAdj, verticesAdj);CHKERRQ(ierr); 2907 ierr = PetscMalloc1(numVerticesAdj, &remoteVerticesAdj);CHKERRQ(ierr); 2908 for (v = 0; v < numVerticesAdj; ++v) { 2909 const PetscInt gv = verticesAdj[v]; 2910 PetscInt vrank; 2911 2912 ierr = PetscFindInt(gv, size+1, vrange, &vrank);CHKERRQ(ierr); 2913 vrank = vrank < 0 ? -(vrank+2) : vrank; 2914 remoteVerticesAdj[v].index = gv - vrange[vrank]; 2915 remoteVerticesAdj[v].rank = vrank; 2916 } 2917 /* Create cones */ 2918 ierr = DMPlexSetChart(dm, 0, numCells+numVerticesAdj);CHKERRQ(ierr); 2919 for (c = 0; c < numCells; ++c) {ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr);} 2920 ierr = DMSetUp(dm);CHKERRQ(ierr); 2921 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 2922 for (c = 0; c < numCells; ++c) { 2923 for (p = 0; p < numCorners; ++p) { 2924 const PetscInt gv = cells[c*numCorners+p]; 2925 PetscInt lv; 2926 2927 ierr = PetscFindInt(gv, numVerticesAdj, verticesAdj, &lv);CHKERRQ(ierr); 2928 if (lv < 0) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Could not find global vertex %D in local connectivity", gv); 2929 cones[c*numCorners+p] = lv+numCells; 2930 } 2931 } 2932 /* Create SF for vertices */ 2933 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), &sfVert);CHKERRQ(ierr); 2934 ierr = PetscObjectSetName((PetscObject) sfVert, "Vertex Ownership SF");CHKERRQ(ierr); 2935 ierr = PetscSFSetFromOptions(sfVert);CHKERRQ(ierr); 2936 ierr = PetscSFSetGraph(sfVert, numVertices, numVerticesAdj, NULL, PETSC_OWN_POINTER, remoteVerticesAdj, PETSC_OWN_POINTER);CHKERRQ(ierr); 2937 ierr = PetscFree(verticesAdj);CHKERRQ(ierr); 2938 /* Build pointSF */ 2939 ierr = PetscMalloc2(numVerticesAdj, &vertexLocal, numVertices, &vertexOwner);CHKERRQ(ierr); 2940 for (v = 0; v < numVerticesAdj; ++v) {vertexLocal[v].index = v+numCells; vertexLocal[v].rank = rank;} 2941 for (v = 0; v < numVertices; ++v) {vertexOwner[v].index = -1; vertexOwner[v].rank = -1;} 2942 ierr = PetscSFReduceBegin(sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2943 ierr = PetscSFReduceEnd(sfVert, MPIU_2INT, vertexLocal, vertexOwner, MPI_MAXLOC);CHKERRQ(ierr); 2944 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); 2945 ierr = PetscSFBcastBegin(sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2946 ierr = PetscSFBcastEnd(sfVert, MPIU_2INT, vertexOwner, vertexLocal);CHKERRQ(ierr); 2947 for (v = 0; v < numVerticesAdj; ++v) if (vertexLocal[v].rank != rank) ++numVerticesGhost; 2948 ierr = PetscMalloc1(numVerticesGhost, &localVertex);CHKERRQ(ierr); 2949 ierr = PetscMalloc1(numVerticesGhost, &remoteVertex);CHKERRQ(ierr); 2950 for (v = 0, g = 0; v < numVerticesAdj; ++v) { 2951 if (vertexLocal[v].rank != rank) { 2952 localVertex[g] = v+numCells; 2953 remoteVertex[g].index = vertexLocal[v].index; 2954 remoteVertex[g].rank = vertexLocal[v].rank; 2955 ++g; 2956 } 2957 } 2958 ierr = PetscFree2(vertexLocal, vertexOwner);CHKERRQ(ierr); 2959 if (g != numVerticesGhost) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of vertex ghosts %D should be %D", g, numVerticesGhost); 2960 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 2961 ierr = PetscObjectSetName((PetscObject) sfPoint, "point SF");CHKERRQ(ierr); 2962 ierr = PetscSFSetGraph(sfPoint, numCells+numVerticesAdj, numVerticesGhost, localVertex, PETSC_OWN_POINTER, remoteVertex, PETSC_OWN_POINTER);CHKERRQ(ierr); 2963 ierr = PetscLayoutDestroy(&vLayout);CHKERRQ(ierr); 2964 /* Fill in the rest of the topology structure */ 2965 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 2966 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 2967 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 2968 if (vertexSF) *vertexSF = sfVert; 2969 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 2970 PetscFunctionReturn(0); 2971 } 2972 2973 /*@C 2974 DMPlexBuildCoordinatesFromCellListParallel - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 2975 2976 Input Parameters: 2977 + dm - The DM 2978 . spaceDim - The spatial dimension used for coordinates 2979 . sfVert - SF describing complete vertex ownership 2980 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 2981 2982 Level: advanced 2983 2984 Notes: 2985 Not currently supported in Fortran. 2986 2987 .seealso: DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellListParallel() 2988 @*/ 2989 PetscErrorCode DMPlexBuildCoordinatesFromCellListParallel(DM dm, PetscInt spaceDim, PetscSF sfVert, const PetscReal vertexCoords[]) 2990 { 2991 PetscSection coordSection; 2992 Vec coordinates; 2993 PetscScalar *coords; 2994 PetscInt numVertices, numVerticesAdj, coordSize, v, vStart, vEnd; 2995 PetscErrorCode ierr; 2996 2997 PetscFunctionBegin; 2998 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 2999 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3000 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3001 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3002 ierr = PetscSFGetGraph(sfVert, &numVertices, &numVerticesAdj, NULL, NULL);CHKERRQ(ierr); 3003 if (vEnd - vStart != numVerticesAdj) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Supplied sfVert has wrong number of leaves = %D != %D = vEnd - vStart",numVerticesAdj,vEnd - vStart); 3004 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3005 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3006 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3007 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3008 for (v = vStart; v < vEnd; ++v) { 3009 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3010 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3011 } 3012 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3013 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3014 ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr); 3015 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3016 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3017 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3018 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3019 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3020 { 3021 MPI_Datatype coordtype; 3022 3023 /* Need a temp buffer for coords if we have complex/single */ 3024 ierr = MPI_Type_contiguous(spaceDim, MPIU_SCALAR, &coordtype);CHKERRQ(ierr); 3025 ierr = MPI_Type_commit(&coordtype);CHKERRQ(ierr); 3026 #if defined(PETSC_USE_COMPLEX) 3027 { 3028 PetscScalar *svertexCoords; 3029 PetscInt i; 3030 ierr = PetscMalloc1(numVertices*spaceDim,&svertexCoords);CHKERRQ(ierr); 3031 for (i=0; i<numVertices*spaceDim; i++) svertexCoords[i] = vertexCoords[i]; 3032 ierr = PetscSFBcastBegin(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 3033 ierr = PetscSFBcastEnd(sfVert, coordtype, svertexCoords, coords);CHKERRQ(ierr); 3034 ierr = PetscFree(svertexCoords);CHKERRQ(ierr); 3035 } 3036 #else 3037 ierr = PetscSFBcastBegin(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 3038 ierr = PetscSFBcastEnd(sfVert, coordtype, vertexCoords, coords);CHKERRQ(ierr); 3039 #endif 3040 ierr = MPI_Type_free(&coordtype);CHKERRQ(ierr); 3041 } 3042 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3043 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3044 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3045 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3046 PetscFunctionReturn(0); 3047 } 3048 3049 /*@ 3050 DMPlexCreateFromCellListParallelPetsc - Create distributed DMPLEX from a list of vertices for each cell (common mesh generator output) 3051 3052 Input Parameters: 3053 + comm - The communicator 3054 . dim - The topological dimension of the mesh 3055 . numCells - The number of cells owned by this process 3056 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3057 . NVertices - The global number of vertices, or PETSC_DECIDE 3058 . numCorners - The number of vertices for each cell 3059 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3060 . cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3061 . spaceDim - The spatial dimension used for coordinates 3062 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3063 3064 Output Parameter: 3065 + dm - The DM 3066 - vertexSF - (Optional) SF describing complete vertex ownership 3067 3068 Notes: 3069 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), 3070 DMPlexBuildFromCellListParallel(), DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellListParallel() 3071 3072 See DMPlexBuildFromCellListParallel() for an example and details about the topology-related parameters. 3073 See DMPlexBuildCoordinatesFromCellListParallel() for details about the geometry-related parameters. 3074 3075 Level: intermediate 3076 3077 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromDAG(), DMPlexCreate() 3078 @*/ 3079 PetscErrorCode DMPlexCreateFromCellListParallelPetsc(MPI_Comm comm, PetscInt dim, PetscInt numCells, PetscInt numVertices, PetscInt NVertices, PetscInt numCorners, PetscBool interpolate, const PetscInt cells[], PetscInt spaceDim, const PetscReal vertexCoords[], PetscSF *vertexSF, DM *dm) 3080 { 3081 PetscSF sfVert; 3082 PetscErrorCode ierr; 3083 3084 PetscFunctionBegin; 3085 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3086 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3087 PetscValidLogicalCollectiveInt(*dm, dim, 2); 3088 PetscValidLogicalCollectiveInt(*dm, spaceDim, 8); 3089 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3090 ierr = DMPlexBuildFromCellListParallel(*dm, numCells, numVertices, NVertices, numCorners, cells, &sfVert);CHKERRQ(ierr); 3091 if (interpolate) { 3092 DM idm; 3093 3094 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3095 ierr = DMDestroy(dm);CHKERRQ(ierr); 3096 *dm = idm; 3097 } 3098 ierr = DMPlexBuildCoordinatesFromCellListParallel(*dm, spaceDim, sfVert, vertexCoords);CHKERRQ(ierr); 3099 if (vertexSF) *vertexSF = sfVert; 3100 else {ierr = PetscSFDestroy(&sfVert);CHKERRQ(ierr);} 3101 PetscFunctionReturn(0); 3102 } 3103 3104 3105 /*@ 3106 DMPlexCreateFromCellListParallel - Deprecated, use DMPlexCreateFromCellListParallelPetsc() 3107 3108 Level: deprecated 3109 3110 .seealso: DMPlexCreateFromCellListParallelPetsc() 3111 @*/ 3112 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) 3113 { 3114 PetscErrorCode ierr; 3115 PetscInt i; 3116 PetscInt *pintCells; 3117 3118 PetscFunctionBegin; 3119 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)); 3120 if (sizeof(int) == sizeof(PetscInt)) { 3121 pintCells = (PetscInt *) cells; 3122 } else { 3123 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3124 for (i = 0; i < numCells*numCorners; i++) { 3125 pintCells[i] = (PetscInt) cells[i]; 3126 } 3127 } 3128 ierr = DMPlexCreateFromCellListParallelPetsc(comm, dim, numCells, numVertices, PETSC_DECIDE, numCorners, interpolate, pintCells, spaceDim, vertexCoords, vertexSF, dm);CHKERRQ(ierr); 3129 if (sizeof(int) != sizeof(PetscInt)) { 3130 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3131 } 3132 PetscFunctionReturn(0); 3133 } 3134 3135 /*@C 3136 DMPlexBuildFromCellList - Build DMPLEX topology from a list of vertices for each cell (common mesh generator output) 3137 3138 Input Parameters: 3139 + dm - The DM 3140 . numCells - The number of cells owned by this process 3141 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3142 . numCorners - The number of vertices for each cell 3143 - cells - An array of numCells*numCorners numbers, the global vertex numbers for each cell 3144 3145 Level: advanced 3146 3147 Notes: 3148 Two triangles sharing a face 3149 $ 3150 $ 2 3151 $ / | \ 3152 $ / | \ 3153 $ / | \ 3154 $ 0 0 | 1 3 3155 $ \ | / 3156 $ \ | / 3157 $ \ | / 3158 $ 1 3159 would have input 3160 $ numCells = 2, numVertices = 4 3161 $ cells = [0 1 2 1 3 2] 3162 $ 3163 which would result in the DMPlex 3164 $ 3165 $ 4 3166 $ / | \ 3167 $ / | \ 3168 $ / | \ 3169 $ 2 0 | 1 5 3170 $ \ | / 3171 $ \ | / 3172 $ \ | / 3173 $ 3 3174 3175 If numVertices is PETSC_DECIDE, it is computed by PETSc as the maximum vertex index in cells + 1. 3176 3177 Not currently supported in Fortran. 3178 3179 .seealso: DMPlexBuildFromCellListParallel(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromCellListPetsc() 3180 @*/ 3181 PetscErrorCode DMPlexBuildFromCellList(DM dm, PetscInt numCells, PetscInt numVertices, PetscInt numCorners, const PetscInt cells[]) 3182 { 3183 PetscInt *cones, c, p, dim; 3184 PetscErrorCode ierr; 3185 3186 PetscFunctionBegin; 3187 ierr = PetscLogEventBegin(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3188 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3189 /* Get/check global number of vertices */ 3190 { 3191 PetscInt NVerticesInCells, i; 3192 const PetscInt len = numCells * numCorners; 3193 3194 /* NVerticesInCells = max(cells) + 1 */ 3195 NVerticesInCells = PETSC_MIN_INT; 3196 for (i=0; i<len; i++) if (cells[i] > NVerticesInCells) NVerticesInCells = cells[i]; 3197 ++NVerticesInCells; 3198 3199 if (numVertices == PETSC_DECIDE) numVertices = NVerticesInCells; 3200 else if (numVertices < NVerticesInCells) SETERRQ2(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Specified number of vertices %D must be greater than or equal to the number of vertices in cells %D",numVertices,NVerticesInCells); 3201 } 3202 ierr = DMPlexSetChart(dm, 0, numCells+numVertices);CHKERRQ(ierr); 3203 for (c = 0; c < numCells; ++c) { 3204 ierr = DMPlexSetConeSize(dm, c, numCorners);CHKERRQ(ierr); 3205 } 3206 ierr = DMSetUp(dm);CHKERRQ(ierr); 3207 ierr = DMPlexGetCones(dm,&cones);CHKERRQ(ierr); 3208 for (c = 0; c < numCells; ++c) { 3209 for (p = 0; p < numCorners; ++p) { 3210 cones[c*numCorners+p] = cells[c*numCorners+p]+numCells; 3211 } 3212 } 3213 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3214 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3215 ierr = PetscLogEventEnd(DMPLEX_BuildFromCellList,dm,0,0,0);CHKERRQ(ierr); 3216 PetscFunctionReturn(0); 3217 } 3218 3219 /*@C 3220 DMPlexBuildCoordinatesFromCellList - Build DM coordinates from a list of coordinates for each owned vertex (common mesh generator output) 3221 3222 Input Parameters: 3223 + dm - The DM 3224 . spaceDim - The spatial dimension used for coordinates 3225 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3226 3227 Level: advanced 3228 3229 Notes: 3230 Not currently supported in Fortran. 3231 3232 .seealso: DMPlexBuildCoordinatesFromCellListParallel(), DMPlexCreateFromCellListPetsc(), DMPlexBuildFromCellList() 3233 @*/ 3234 PetscErrorCode DMPlexBuildCoordinatesFromCellList(DM dm, PetscInt spaceDim, const PetscReal vertexCoords[]) 3235 { 3236 PetscSection coordSection; 3237 Vec coordinates; 3238 DM cdm; 3239 PetscScalar *coords; 3240 PetscInt v, vStart, vEnd, d; 3241 PetscErrorCode ierr; 3242 3243 PetscFunctionBegin; 3244 ierr = PetscLogEventBegin(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3245 ierr = DMPlexGetDepthStratum(dm, 0, &vStart, &vEnd);CHKERRQ(ierr); 3246 if (vStart < 0 || vEnd < 0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "DM is not set up properly. DMPlexBuildFromCellList() should be called first."); 3247 ierr = DMSetCoordinateDim(dm, spaceDim);CHKERRQ(ierr); 3248 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3249 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3250 ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr); 3251 ierr = PetscSectionSetChart(coordSection, vStart, vEnd);CHKERRQ(ierr); 3252 for (v = vStart; v < vEnd; ++v) { 3253 ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr); 3254 ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr); 3255 } 3256 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3257 3258 ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); 3259 ierr = DMCreateLocalVector(cdm, &coordinates);CHKERRQ(ierr); 3260 ierr = VecSetBlockSize(coordinates, spaceDim);CHKERRQ(ierr); 3261 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3262 ierr = VecGetArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3263 for (v = 0; v < vEnd-vStart; ++v) { 3264 for (d = 0; d < spaceDim; ++d) { 3265 coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d]; 3266 } 3267 } 3268 ierr = VecRestoreArrayWrite(coordinates, &coords);CHKERRQ(ierr); 3269 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3270 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3271 ierr = PetscLogEventEnd(DMPLEX_BuildCoordinatesFromCellList,dm,0,0,0);CHKERRQ(ierr); 3272 PetscFunctionReturn(0); 3273 } 3274 3275 /*@ 3276 DMPlexCreateFromCellListPetsc - Create DMPLEX from a list of vertices for each cell (common mesh generator output) 3277 3278 Input Parameters: 3279 + comm - The communicator 3280 . dim - The topological dimension of the mesh 3281 . numCells - The number of cells 3282 . numVertices - The number of vertices owned by this process, or PETSC_DECIDE 3283 . numCorners - The number of vertices for each cell 3284 . interpolate - Flag indicating that intermediate mesh entities (faces, edges) should be created automatically 3285 . cells - An array of numCells*numCorners numbers, the vertices for each cell 3286 . spaceDim - The spatial dimension used for coordinates 3287 - vertexCoords - An array of numVertices*spaceDim numbers, the coordinates of each vertex 3288 3289 Output Parameter: 3290 . dm - The DM 3291 3292 Notes: 3293 This function is just a convenient sequence of DMCreate(), DMSetType(), DMSetDimension(), DMPlexBuildFromCellList(), 3294 DMPlexInterpolate(), DMPlexBuildCoordinatesFromCellList() 3295 3296 See DMPlexBuildFromCellList() for an example and details about the topology-related parameters. 3297 See DMPlexBuildCoordinatesFromCellList() for details about the geometry-related parameters. 3298 3299 Level: intermediate 3300 3301 .seealso: DMPlexCreateFromCellListParallelPetsc(), DMPlexBuildFromCellList(), DMPlexBuildCoordinatesFromCellList(), DMPlexCreateFromDAG(), DMPlexCreate() 3302 @*/ 3303 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) 3304 { 3305 PetscErrorCode ierr; 3306 3307 PetscFunctionBegin; 3308 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."); 3309 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3310 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3311 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3312 ierr = DMPlexBuildFromCellList(*dm, numCells, numVertices, numCorners, cells);CHKERRQ(ierr); 3313 if (interpolate) { 3314 DM idm; 3315 3316 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3317 ierr = DMDestroy(dm);CHKERRQ(ierr); 3318 *dm = idm; 3319 } 3320 ierr = DMPlexBuildCoordinatesFromCellList(*dm, spaceDim, vertexCoords);CHKERRQ(ierr); 3321 PetscFunctionReturn(0); 3322 } 3323 3324 /*@ 3325 DMPlexCreateFromCellList - Deprecated, use DMPlexCreateFromCellListPetsc() 3326 3327 Level: deprecated 3328 3329 .seealso: DMPlexCreateFromCellListPetsc() 3330 @*/ 3331 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) 3332 { 3333 PetscErrorCode ierr; 3334 PetscInt i; 3335 PetscInt *pintCells; 3336 PetscReal *prealVC; 3337 3338 PetscFunctionBegin; 3339 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)); 3340 if (sizeof(int) == sizeof(PetscInt)) { 3341 pintCells = (PetscInt *) cells; 3342 } else { 3343 ierr = PetscMalloc1(numCells*numCorners, &pintCells);CHKERRQ(ierr); 3344 for (i = 0; i < numCells*numCorners; i++) { 3345 pintCells[i] = (PetscInt) cells[i]; 3346 } 3347 } 3348 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)); 3349 if (sizeof(double) == sizeof(PetscReal)) { 3350 prealVC = (PetscReal *) vertexCoords; 3351 } else { 3352 ierr = PetscMalloc1(numVertices*spaceDim, &prealVC);CHKERRQ(ierr); 3353 for (i = 0; i < numVertices*spaceDim; i++) { 3354 prealVC[i] = (PetscReal) vertexCoords[i]; 3355 } 3356 } 3357 ierr = DMPlexCreateFromCellListPetsc(comm, dim, numCells, numVertices, numCorners, interpolate, pintCells, spaceDim, prealVC, dm);CHKERRQ(ierr); 3358 if (sizeof(int) != sizeof(PetscInt)) { 3359 ierr = PetscFree(pintCells);CHKERRQ(ierr); 3360 } 3361 if (sizeof(double) != sizeof(PetscReal)) { 3362 ierr = PetscFree(prealVC);CHKERRQ(ierr); 3363 } 3364 PetscFunctionReturn(0); 3365 } 3366 3367 /*@ 3368 DMPlexCreateFromDAG - This takes as input the adjacency-list representation of the Directed Acyclic Graph (Hasse Diagram) encoding a mesh, and produces a DM 3369 3370 Input Parameters: 3371 + dm - The empty DM object, usually from DMCreate() and DMSetDimension() 3372 . depth - The depth of the DAG 3373 . numPoints - Array of size depth + 1 containing the number of points at each depth 3374 . coneSize - The cone size of each point 3375 . cones - The concatenation of the cone points for each point, the cone list must be oriented correctly for each point 3376 . coneOrientations - The orientation of each cone point 3377 - vertexCoords - An array of numPoints[0]*spacedim numbers representing the coordinates of each vertex, with spacedim the value set via DMSetCoordinateDim() 3378 3379 Output Parameter: 3380 . dm - The DM 3381 3382 Note: Two triangles sharing a face would have input 3383 $ depth = 1, numPoints = [4 2], coneSize = [3 3 0 0 0 0] 3384 $ cones = [2 3 4 3 5 4], coneOrientations = [0 0 0 0 0 0] 3385 $ vertexCoords = [-1.0 0.0 0.0 -1.0 0.0 1.0 1.0 0.0] 3386 $ 3387 which would result in the DMPlex 3388 $ 3389 $ 4 3390 $ / | \ 3391 $ / | \ 3392 $ / | \ 3393 $ 2 0 | 1 5 3394 $ \ | / 3395 $ \ | / 3396 $ \ | / 3397 $ 3 3398 $ 3399 $ Notice that all points are numbered consecutively, unlike DMPlexCreateFromCellListPetsc() 3400 3401 Level: advanced 3402 3403 .seealso: DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3404 @*/ 3405 PetscErrorCode DMPlexCreateFromDAG(DM dm, PetscInt depth, const PetscInt numPoints[], const PetscInt coneSize[], const PetscInt cones[], const PetscInt coneOrientations[], const PetscScalar vertexCoords[]) 3406 { 3407 Vec coordinates; 3408 PetscSection coordSection; 3409 PetscScalar *coords; 3410 PetscInt coordSize, firstVertex = -1, pStart = 0, pEnd = 0, p, v, dim, dimEmbed, d, off; 3411 PetscErrorCode ierr; 3412 3413 PetscFunctionBegin; 3414 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 3415 ierr = DMGetCoordinateDim(dm, &dimEmbed);CHKERRQ(ierr); 3416 if (dimEmbed < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Embedding dimension %D cannot be less than intrinsic dimension %d",dimEmbed,dim); 3417 for (d = 0; d <= depth; ++d) pEnd += numPoints[d]; 3418 ierr = DMPlexSetChart(dm, pStart, pEnd);CHKERRQ(ierr); 3419 for (p = pStart; p < pEnd; ++p) { 3420 ierr = DMPlexSetConeSize(dm, p, coneSize[p-pStart]);CHKERRQ(ierr); 3421 if (firstVertex < 0 && !coneSize[p - pStart]) { 3422 firstVertex = p - pStart; 3423 } 3424 } 3425 if (firstVertex < 0 && numPoints[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Expected %D vertices but could not find any", numPoints[0]); 3426 ierr = DMSetUp(dm);CHKERRQ(ierr); /* Allocate space for cones */ 3427 for (p = pStart, off = 0; p < pEnd; off += coneSize[p-pStart], ++p) { 3428 ierr = DMPlexSetCone(dm, p, &cones[off]);CHKERRQ(ierr); 3429 ierr = DMPlexSetConeOrientation(dm, p, &coneOrientations[off]);CHKERRQ(ierr); 3430 } 3431 ierr = DMPlexSymmetrize(dm);CHKERRQ(ierr); 3432 ierr = DMPlexStratify(dm);CHKERRQ(ierr); 3433 /* Build coordinates */ 3434 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 3435 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3436 ierr = PetscSectionSetFieldComponents(coordSection, 0, dimEmbed);CHKERRQ(ierr); 3437 ierr = PetscSectionSetChart(coordSection, firstVertex, firstVertex+numPoints[0]);CHKERRQ(ierr); 3438 for (v = firstVertex; v < firstVertex+numPoints[0]; ++v) { 3439 ierr = PetscSectionSetDof(coordSection, v, dimEmbed);CHKERRQ(ierr); 3440 ierr = PetscSectionSetFieldDof(coordSection, v, 0, dimEmbed);CHKERRQ(ierr); 3441 } 3442 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3443 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3444 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3445 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3446 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3447 ierr = VecSetBlockSize(coordinates, dimEmbed);CHKERRQ(ierr); 3448 ierr = VecSetType(coordinates,VECSTANDARD);CHKERRQ(ierr); 3449 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3450 for (v = 0; v < numPoints[0]; ++v) { 3451 PetscInt off; 3452 3453 ierr = PetscSectionGetOffset(coordSection, v+firstVertex, &off);CHKERRQ(ierr); 3454 for (d = 0; d < dimEmbed; ++d) { 3455 coords[off+d] = vertexCoords[v*dimEmbed+d]; 3456 } 3457 } 3458 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3459 ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr); 3460 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3461 PetscFunctionReturn(0); 3462 } 3463 3464 /*@C 3465 DMPlexCreateCellVertexFromFile - Create a DMPlex mesh from a simple cell-vertex file. 3466 3467 + comm - The MPI communicator 3468 . filename - Name of the .dat file 3469 - interpolate - Create faces and edges in the mesh 3470 3471 Output Parameter: 3472 . dm - The DM object representing the mesh 3473 3474 Note: The format is the simplest possible: 3475 $ Ne 3476 $ v0 v1 ... vk 3477 $ Nv 3478 $ x y z marker 3479 3480 Level: beginner 3481 3482 .seealso: DMPlexCreateFromFile(), DMPlexCreateMedFromFile(), DMPlexCreateGmsh(), DMPlexCreate() 3483 @*/ 3484 PetscErrorCode DMPlexCreateCellVertexFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3485 { 3486 DMLabel marker; 3487 PetscViewer viewer; 3488 Vec coordinates; 3489 PetscSection coordSection; 3490 PetscScalar *coords; 3491 char line[PETSC_MAX_PATH_LEN]; 3492 PetscInt dim = 3, cdim = 3, coordSize, v, c, d; 3493 PetscMPIInt rank; 3494 int snum, Nv, Nc; 3495 PetscErrorCode ierr; 3496 3497 PetscFunctionBegin; 3498 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3499 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3500 ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr); 3501 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3502 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3503 if (!rank) { 3504 ierr = PetscViewerRead(viewer, line, 2, NULL, PETSC_STRING);CHKERRQ(ierr); 3505 snum = sscanf(line, "%d %d", &Nc, &Nv); 3506 if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3507 } else { 3508 Nc = Nv = 0; 3509 } 3510 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3511 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3512 ierr = DMPlexSetChart(*dm, 0, Nc+Nv);CHKERRQ(ierr); 3513 ierr = DMSetDimension(*dm, dim);CHKERRQ(ierr); 3514 ierr = DMSetCoordinateDim(*dm, cdim);CHKERRQ(ierr); 3515 /* Read topology */ 3516 if (!rank) { 3517 PetscInt cone[8], corners = 8; 3518 int vbuf[8], v; 3519 3520 for (c = 0; c < Nc; ++c) {ierr = DMPlexSetConeSize(*dm, c, corners);CHKERRQ(ierr);} 3521 ierr = DMSetUp(*dm);CHKERRQ(ierr); 3522 for (c = 0; c < Nc; ++c) { 3523 ierr = PetscViewerRead(viewer, line, corners, NULL, PETSC_STRING);CHKERRQ(ierr); 3524 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]); 3525 if (snum != corners) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3526 for (v = 0; v < corners; ++v) cone[v] = vbuf[v] + Nc; 3527 /* Hexahedra are inverted */ 3528 { 3529 PetscInt tmp = cone[1]; 3530 cone[1] = cone[3]; 3531 cone[3] = tmp; 3532 } 3533 ierr = DMPlexSetCone(*dm, c, cone);CHKERRQ(ierr); 3534 } 3535 } 3536 ierr = DMPlexSymmetrize(*dm);CHKERRQ(ierr); 3537 ierr = DMPlexStratify(*dm);CHKERRQ(ierr); 3538 /* Read coordinates */ 3539 ierr = DMGetCoordinateSection(*dm, &coordSection);CHKERRQ(ierr); 3540 ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr); 3541 ierr = PetscSectionSetFieldComponents(coordSection, 0, cdim);CHKERRQ(ierr); 3542 ierr = PetscSectionSetChart(coordSection, Nc, Nc + Nv);CHKERRQ(ierr); 3543 for (v = Nc; v < Nc+Nv; ++v) { 3544 ierr = PetscSectionSetDof(coordSection, v, cdim);CHKERRQ(ierr); 3545 ierr = PetscSectionSetFieldDof(coordSection, v, 0, cdim);CHKERRQ(ierr); 3546 } 3547 ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr); 3548 ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr); 3549 ierr = VecCreate(PETSC_COMM_SELF, &coordinates);CHKERRQ(ierr); 3550 ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr); 3551 ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr); 3552 ierr = VecSetBlockSize(coordinates, cdim);CHKERRQ(ierr); 3553 ierr = VecSetType(coordinates, VECSTANDARD);CHKERRQ(ierr); 3554 ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr); 3555 if (!rank) { 3556 double x[3]; 3557 int val; 3558 3559 ierr = DMCreateLabel(*dm, "marker");CHKERRQ(ierr); 3560 ierr = DMGetLabel(*dm, "marker", &marker);CHKERRQ(ierr); 3561 for (v = 0; v < Nv; ++v) { 3562 ierr = PetscViewerRead(viewer, line, 4, NULL, PETSC_STRING);CHKERRQ(ierr); 3563 snum = sscanf(line, "%lg %lg %lg %d", &x[0], &x[1], &x[2], &val); 3564 if (snum != 4) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse cell-vertex file: %s", line); 3565 for (d = 0; d < cdim; ++d) coords[v*cdim+d] = x[d]; 3566 if (val) {ierr = DMLabelSetValue(marker, v+Nc, val);CHKERRQ(ierr);} 3567 } 3568 } 3569 ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr); 3570 ierr = DMSetCoordinatesLocal(*dm, coordinates);CHKERRQ(ierr); 3571 ierr = VecDestroy(&coordinates);CHKERRQ(ierr); 3572 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3573 if (interpolate) { 3574 DM idm; 3575 DMLabel bdlabel; 3576 3577 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3578 ierr = DMDestroy(dm);CHKERRQ(ierr); 3579 *dm = idm; 3580 3581 ierr = DMGetLabel(*dm, "marker", &bdlabel);CHKERRQ(ierr); 3582 ierr = DMPlexMarkBoundaryFaces(*dm, PETSC_DETERMINE, bdlabel);CHKERRQ(ierr); 3583 ierr = DMPlexLabelComplete(*dm, bdlabel);CHKERRQ(ierr); 3584 } 3585 PetscFunctionReturn(0); 3586 } 3587 3588 /*@C 3589 DMPlexCreateFromFile - This takes a filename and produces a DM 3590 3591 Input Parameters: 3592 + comm - The communicator 3593 . filename - A file name 3594 - interpolate - Flag to create intermediate mesh pieces (edges, faces) 3595 3596 Output Parameter: 3597 . dm - The DM 3598 3599 Options Database Keys: 3600 . -dm_plex_create_from_hdf5_xdmf - use the PETSC_VIEWER_HDF5_XDMF format for reading HDF5 3601 3602 Use -dm_plex_create_ prefix to pass options to the internal PetscViewer, e.g. 3603 $ -dm_plex_create_viewer_hdf5_collective 3604 3605 Level: beginner 3606 3607 .seealso: DMPlexCreateFromDAG(), DMPlexCreateFromCellListPetsc(), DMPlexCreate() 3608 @*/ 3609 PetscErrorCode DMPlexCreateFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm) 3610 { 3611 const char *extGmsh = ".msh"; 3612 const char *extGmsh2 = ".msh2"; 3613 const char *extGmsh4 = ".msh4"; 3614 const char *extCGNS = ".cgns"; 3615 const char *extExodus = ".exo"; 3616 const char *extGenesis = ".gen"; 3617 const char *extFluent = ".cas"; 3618 const char *extHDF5 = ".h5"; 3619 const char *extMed = ".med"; 3620 const char *extPLY = ".ply"; 3621 const char *extCV = ".dat"; 3622 size_t len; 3623 PetscBool isGmsh, isGmsh2, isGmsh4, isCGNS, isExodus, isGenesis, isFluent, isHDF5, isMed, isPLY, isCV; 3624 PetscMPIInt rank; 3625 PetscErrorCode ierr; 3626 3627 PetscFunctionBegin; 3628 PetscValidCharPointer(filename, 2); 3629 PetscValidPointer(dm, 4); 3630 ierr = DMInitializePackage();CHKERRQ(ierr); 3631 ierr = PetscLogEventBegin(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 3632 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 3633 ierr = PetscStrlen(filename, &len);CHKERRQ(ierr); 3634 if (!len) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Filename must be a valid path"); 3635 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGmsh, 4, &isGmsh);CHKERRQ(ierr); 3636 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh2, 5, &isGmsh2);CHKERRQ(ierr); 3637 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extGmsh4, 5, &isGmsh4);CHKERRQ(ierr); 3638 ierr = PetscStrncmp(&filename[PetscMax(0,len-5)], extCGNS, 5, &isCGNS);CHKERRQ(ierr); 3639 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extExodus, 4, &isExodus);CHKERRQ(ierr); 3640 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extGenesis, 4, &isGenesis);CHKERRQ(ierr); 3641 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extFluent, 4, &isFluent);CHKERRQ(ierr); 3642 ierr = PetscStrncmp(&filename[PetscMax(0,len-3)], extHDF5, 3, &isHDF5);CHKERRQ(ierr); 3643 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extMed, 4, &isMed);CHKERRQ(ierr); 3644 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extPLY, 4, &isPLY);CHKERRQ(ierr); 3645 ierr = PetscStrncmp(&filename[PetscMax(0,len-4)], extCV, 4, &isCV);CHKERRQ(ierr); 3646 if (isGmsh || isGmsh2 || isGmsh4) { 3647 ierr = DMPlexCreateGmshFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3648 } else if (isCGNS) { 3649 ierr = DMPlexCreateCGNSFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3650 } else if (isExodus || isGenesis) { 3651 ierr = DMPlexCreateExodusFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3652 } else if (isFluent) { 3653 ierr = DMPlexCreateFluentFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3654 } else if (isHDF5) { 3655 PetscBool load_hdf5_xdmf = PETSC_FALSE; 3656 PetscViewer viewer; 3657 3658 /* PETSC_VIEWER_HDF5_XDMF is used if the filename ends with .xdmf.h5, or if -dm_plex_create_from_hdf5_xdmf option is present */ 3659 ierr = PetscStrncmp(&filename[PetscMax(0,len-8)], ".xdmf", 5, &load_hdf5_xdmf);CHKERRQ(ierr); 3660 ierr = PetscOptionsGetBool(NULL, NULL, "-dm_plex_create_from_hdf5_xdmf", &load_hdf5_xdmf, NULL);CHKERRQ(ierr); 3661 ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr); 3662 ierr = PetscViewerSetType(viewer, PETSCVIEWERHDF5);CHKERRQ(ierr); 3663 ierr = PetscViewerSetOptionsPrefix(viewer, "dm_plex_create_");CHKERRQ(ierr); 3664 ierr = PetscViewerSetFromOptions(viewer);CHKERRQ(ierr); 3665 ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr); 3666 ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr); 3667 ierr = DMCreate(comm, dm);CHKERRQ(ierr); 3668 ierr = DMSetType(*dm, DMPLEX);CHKERRQ(ierr); 3669 if (load_hdf5_xdmf) {ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_XDMF);CHKERRQ(ierr);} 3670 ierr = DMLoad(*dm, viewer);CHKERRQ(ierr); 3671 if (load_hdf5_xdmf) {ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);} 3672 ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); 3673 3674 if (interpolate) { 3675 DM idm; 3676 3677 ierr = DMPlexInterpolate(*dm, &idm);CHKERRQ(ierr); 3678 ierr = DMDestroy(dm);CHKERRQ(ierr); 3679 *dm = idm; 3680 } 3681 } else if (isMed) { 3682 ierr = DMPlexCreateMedFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3683 } else if (isPLY) { 3684 ierr = DMPlexCreatePLYFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3685 } else if (isCV) { 3686 ierr = DMPlexCreateCellVertexFromFile(comm, filename, interpolate, dm);CHKERRQ(ierr); 3687 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Cannot load file %s: unrecognized extension", filename); 3688 ierr = PetscLogEventEnd(DMPLEX_CreateFromFile,0,0,0,0);CHKERRQ(ierr); 3689 PetscFunctionReturn(0); 3690 } 3691 3692 /*@ 3693 DMPlexCreateReferenceCellByType - Create a DMPLEX with the appropriate FEM reference cell 3694 3695 Collective 3696 3697 Input Parameters: 3698 + comm - The communicator 3699 - ct - The cell type of the reference cell 3700 3701 Output Parameter: 3702 . refdm - The reference cell 3703 3704 Level: intermediate 3705 3706 .seealso: DMPlexCreateReferenceCell(), DMPlexCreateBoxMesh() 3707 @*/ 3708 PetscErrorCode DMPlexCreateReferenceCellByType(MPI_Comm comm, DMPolytopeType ct, DM *refdm) 3709 { 3710 DM rdm; 3711 Vec coords; 3712 PetscErrorCode ierr; 3713 3714 PetscFunctionBegin; 3715 ierr = DMCreate(comm, &rdm);CHKERRQ(ierr); 3716 ierr = DMSetType(rdm, DMPLEX);CHKERRQ(ierr); 3717 switch (ct) { 3718 case DM_POLYTOPE_POINT: 3719 { 3720 PetscInt numPoints[1] = {1}; 3721 PetscInt coneSize[1] = {0}; 3722 PetscInt cones[1] = {0}; 3723 PetscInt coneOrientations[1] = {0}; 3724 PetscScalar vertexCoords[1] = {0.0}; 3725 3726 ierr = DMSetDimension(rdm, 0);CHKERRQ(ierr); 3727 ierr = DMPlexCreateFromDAG(rdm, 0, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3728 } 3729 break; 3730 case DM_POLYTOPE_SEGMENT: 3731 { 3732 PetscInt numPoints[2] = {2, 1}; 3733 PetscInt coneSize[3] = {2, 0, 0}; 3734 PetscInt cones[2] = {1, 2}; 3735 PetscInt coneOrientations[2] = {0, 0}; 3736 PetscScalar vertexCoords[2] = {-1.0, 1.0}; 3737 3738 ierr = DMSetDimension(rdm, 1);CHKERRQ(ierr); 3739 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3740 } 3741 break; 3742 case DM_POLYTOPE_TRIANGLE: 3743 { 3744 PetscInt numPoints[2] = {3, 1}; 3745 PetscInt coneSize[4] = {3, 0, 0, 0}; 3746 PetscInt cones[3] = {1, 2, 3}; 3747 PetscInt coneOrientations[3] = {0, 0, 0}; 3748 PetscScalar vertexCoords[6] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0}; 3749 3750 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3751 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3752 } 3753 break; 3754 case DM_POLYTOPE_QUADRILATERAL: 3755 { 3756 PetscInt numPoints[2] = {4, 1}; 3757 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3758 PetscInt cones[4] = {1, 2, 3, 4}; 3759 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3760 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0}; 3761 3762 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3763 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3764 } 3765 break; 3766 case DM_POLYTOPE_SEG_PRISM_TENSOR: 3767 { 3768 PetscInt numPoints[2] = {4, 1}; 3769 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3770 PetscInt cones[4] = {1, 2, 3, 4}; 3771 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3772 PetscScalar vertexCoords[8] = {-1.0, -1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0}; 3773 3774 ierr = DMSetDimension(rdm, 2);CHKERRQ(ierr); 3775 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3776 } 3777 break; 3778 case DM_POLYTOPE_TETRAHEDRON: 3779 { 3780 PetscInt numPoints[2] = {4, 1}; 3781 PetscInt coneSize[5] = {4, 0, 0, 0, 0}; 3782 PetscInt cones[4] = {1, 3, 2, 4}; 3783 PetscInt coneOrientations[4] = {0, 0, 0, 0}; 3784 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}; 3785 3786 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3787 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3788 } 3789 break; 3790 case DM_POLYTOPE_HEXAHEDRON: 3791 { 3792 PetscInt numPoints[2] = {8, 1}; 3793 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3794 PetscInt cones[8] = {1, 4, 3, 2, 5, 6, 7, 8}; 3795 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3796 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, 3797 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3798 3799 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3800 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3801 } 3802 break; 3803 case DM_POLYTOPE_TRI_PRISM: 3804 { 3805 PetscInt numPoints[2] = {6, 1}; 3806 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3807 PetscInt cones[6] = {1, 3, 2, 4, 5, 6}; 3808 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3809 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3810 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3811 3812 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3813 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3814 } 3815 break; 3816 case DM_POLYTOPE_TRI_PRISM_TENSOR: 3817 { 3818 PetscInt numPoints[2] = {6, 1}; 3819 PetscInt coneSize[7] = {6, 0, 0, 0, 0, 0, 0}; 3820 PetscInt cones[6] = {1, 2, 3, 4, 5, 6}; 3821 PetscInt coneOrientations[6] = {0, 0, 0, 0, 0, 0}; 3822 PetscScalar vertexCoords[18] = {-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 3823 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, 1.0, 1.0}; 3824 3825 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3826 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3827 } 3828 break; 3829 case DM_POLYTOPE_QUAD_PRISM_TENSOR: 3830 { 3831 PetscInt numPoints[2] = {8, 1}; 3832 PetscInt coneSize[9] = {8, 0, 0, 0, 0, 0, 0, 0, 0}; 3833 PetscInt cones[8] = {1, 2, 3, 4, 5, 6, 7, 8}; 3834 PetscInt coneOrientations[8] = {0, 0, 0, 0, 0, 0, 0, 0}; 3835 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, 3836 -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0}; 3837 3838 ierr = DMSetDimension(rdm, 3);CHKERRQ(ierr); 3839 ierr = DMPlexCreateFromDAG(rdm, 1, numPoints, coneSize, cones, coneOrientations, vertexCoords);CHKERRQ(ierr); 3840 } 3841 break; 3842 default: SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for cell type %s", DMPolytopeTypes[ct]); 3843 } 3844 { 3845 PetscInt Nv, v; 3846 3847 /* Must create the celltype label here so that we do not automatically try to compute the types */ 3848 ierr = DMCreateLabel(rdm, "celltype");CHKERRQ(ierr); 3849 ierr = DMPlexSetCellType(rdm, 0, ct);CHKERRQ(ierr); 3850 ierr = DMPlexGetChart(rdm, NULL, &Nv);CHKERRQ(ierr); 3851 for (v = 1; v < Nv; ++v) {ierr = DMPlexSetCellType(rdm, v, DM_POLYTOPE_POINT);CHKERRQ(ierr);} 3852 } 3853 ierr = DMPlexInterpolate(rdm, refdm);CHKERRQ(ierr); 3854 if (rdm->coordinateDM) { 3855 DM ncdm; 3856 PetscSection cs; 3857 PetscInt pEnd = -1; 3858 3859 ierr = DMGetLocalSection(rdm->coordinateDM, &cs);CHKERRQ(ierr); 3860 if (cs) {ierr = PetscSectionGetChart(cs, NULL, &pEnd);CHKERRQ(ierr);} 3861 if (pEnd >= 0) { 3862 ierr = DMClone(*refdm, &ncdm);CHKERRQ(ierr); 3863 ierr = DMCopyDisc(rdm->coordinateDM, ncdm);CHKERRQ(ierr); 3864 ierr = DMSetLocalSection(ncdm, cs);CHKERRQ(ierr); 3865 ierr = DMSetCoordinateDM(*refdm, ncdm);CHKERRQ(ierr); 3866 ierr = DMDestroy(&ncdm);CHKERRQ(ierr); 3867 } 3868 } 3869 ierr = DMGetCoordinatesLocal(rdm, &coords);CHKERRQ(ierr); 3870 if (coords) { 3871 ierr = DMSetCoordinatesLocal(*refdm, coords);CHKERRQ(ierr); 3872 } else { 3873 ierr = DMGetCoordinates(rdm, &coords);CHKERRQ(ierr); 3874 if (coords) {ierr = DMSetCoordinates(*refdm, coords);CHKERRQ(ierr);} 3875 } 3876 ierr = DMDestroy(&rdm);CHKERRQ(ierr); 3877 PetscFunctionReturn(0); 3878 } 3879 3880 /*@ 3881 DMPlexCreateReferenceCell - Create a DMPLEX with the appropriate FEM reference cell 3882 3883 Collective 3884 3885 Input Parameters: 3886 + comm - The communicator 3887 . dim - The spatial dimension 3888 - simplex - Flag for simplex, otherwise use a tensor-product cell 3889 3890 Output Parameter: 3891 . refdm - The reference cell 3892 3893 Level: intermediate 3894 3895 .seealso: DMPlexCreateReferenceCellByType(), DMPlexCreateBoxMesh() 3896 @*/ 3897 PetscErrorCode DMPlexCreateReferenceCell(MPI_Comm comm, PetscInt dim, PetscBool simplex, DM *refdm) 3898 { 3899 PetscErrorCode ierr; 3900 3901 PetscFunctionBeginUser; 3902 switch (dim) { 3903 case 0: ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_POINT, refdm);CHKERRQ(ierr);break; 3904 case 1: ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_SEGMENT, refdm);CHKERRQ(ierr);break; 3905 case 2: 3906 if (simplex) {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_TRIANGLE, refdm);CHKERRQ(ierr);} 3907 else {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_QUADRILATERAL, refdm);CHKERRQ(ierr);} 3908 break; 3909 case 3: 3910 if (simplex) {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_TETRAHEDRON, refdm);CHKERRQ(ierr);} 3911 else {ierr = DMPlexCreateReferenceCellByType(comm, DM_POLYTOPE_HEXAHEDRON, refdm);CHKERRQ(ierr);} 3912 break; 3913 default: 3914 SETERRQ1(comm, PETSC_ERR_ARG_WRONG, "Cannot create reference cell for dimension %D", dim); 3915 } 3916 PetscFunctionReturn(0); 3917 } 3918