1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 3 #undef __FUNCT__ 4 #define __FUNCT__ "DMPlexGetLineIntersection_2D_Internal" 5 static PetscErrorCode DMPlexGetLineIntersection_2D_Internal(const PetscReal segmentA[], const PetscReal segmentB[], PetscReal intersection[], PetscBool *hasIntersection) 6 { 7 const PetscReal p0_x = segmentA[0*2+0]; 8 const PetscReal p0_y = segmentA[0*2+1]; 9 const PetscReal p1_x = segmentA[1*2+0]; 10 const PetscReal p1_y = segmentA[1*2+1]; 11 const PetscReal p2_x = segmentB[0*2+0]; 12 const PetscReal p2_y = segmentB[0*2+1]; 13 const PetscReal p3_x = segmentB[1*2+0]; 14 const PetscReal p3_y = segmentB[1*2+1]; 15 const PetscReal s1_x = p1_x - p0_x; 16 const PetscReal s1_y = p1_y - p0_y; 17 const PetscReal s2_x = p3_x - p2_x; 18 const PetscReal s2_y = p3_y - p2_y; 19 const PetscReal denom = (-s2_x * s1_y + s1_x * s2_y); 20 21 PetscFunctionBegin; 22 *hasIntersection = PETSC_FALSE; 23 /* Non-parallel lines */ 24 if (denom != 0.0) { 25 const PetscReal s = (-s1_y * (p0_x - p2_x) + s1_x * (p0_y - p2_y)) / denom; 26 const PetscReal t = ( s2_x * (p0_y - p2_y) - s2_y * (p0_x - p2_x)) / denom; 27 28 if (s >= 0 && s <= 1 && t >= 0 && t <= 1) { 29 *hasIntersection = PETSC_TRUE; 30 if (intersection) { 31 intersection[0] = p0_x + (t * s1_x); 32 intersection[1] = p0_y + (t * s1_y); 33 } 34 } 35 } 36 PetscFunctionReturn(0); 37 } 38 39 #undef __FUNCT__ 40 #define __FUNCT__ "DMPlexLocatePoint_Simplex_2D_Internal" 41 static PetscErrorCode DMPlexLocatePoint_Simplex_2D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) 42 { 43 const PetscInt embedDim = 2; 44 const PetscReal eps = PETSC_SQRT_MACHINE_EPSILON; 45 PetscReal x = PetscRealPart(point[0]); 46 PetscReal y = PetscRealPart(point[1]); 47 PetscReal v0[2], J[4], invJ[4], detJ; 48 PetscReal xi, eta; 49 PetscErrorCode ierr; 50 51 PetscFunctionBegin; 52 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 53 xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]); 54 eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]); 55 56 if ((xi >= -eps) && (eta >= -eps) && (xi + eta <= 2.0+eps)) *cell = c; 57 else *cell = DMLOCATEPOINT_POINT_NOT_FOUND; 58 PetscFunctionReturn(0); 59 } 60 61 #undef __FUNCT__ 62 #define __FUNCT__ "DMPlexClosestPoint_Simplex_2D_Internal" 63 static PetscErrorCode DMPlexClosestPoint_Simplex_2D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscReal cpoint[]) 64 { 65 const PetscInt embedDim = 2; 66 PetscReal x = PetscRealPart(point[0]); 67 PetscReal y = PetscRealPart(point[1]); 68 PetscReal v0[2], J[4], invJ[4], detJ; 69 PetscReal xi, eta, r; 70 PetscErrorCode ierr; 71 72 PetscFunctionBegin; 73 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 74 xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]); 75 eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]); 76 77 xi = PetscMax(xi, 0.0); 78 eta = PetscMax(eta, 0.0); 79 r = (xi + eta)/2.0; 80 if (xi + eta > 2.0) { 81 r = (xi + eta)/2.0; 82 xi /= r; 83 eta /= r; 84 } 85 cpoint[0] = J[0*embedDim+0]*xi + J[0*embedDim+1]*eta + v0[0]; 86 cpoint[1] = J[1*embedDim+0]*xi + J[1*embedDim+1]*eta + v0[1]; 87 PetscFunctionReturn(0); 88 } 89 90 #undef __FUNCT__ 91 #define __FUNCT__ "DMPlexLocatePoint_General_2D_Internal" 92 static PetscErrorCode DMPlexLocatePoint_General_2D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) 93 { 94 PetscSection coordSection; 95 Vec coordsLocal; 96 PetscScalar *coords = NULL; 97 const PetscInt faces[8] = {0, 1, 1, 2, 2, 3, 3, 0}; 98 PetscReal x = PetscRealPart(point[0]); 99 PetscReal y = PetscRealPart(point[1]); 100 PetscInt crossings = 0, f; 101 PetscErrorCode ierr; 102 103 PetscFunctionBegin; 104 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 105 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 106 ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); 107 for (f = 0; f < 4; ++f) { 108 PetscReal x_i = PetscRealPart(coords[faces[2*f+0]*2+0]); 109 PetscReal y_i = PetscRealPart(coords[faces[2*f+0]*2+1]); 110 PetscReal x_j = PetscRealPart(coords[faces[2*f+1]*2+0]); 111 PetscReal y_j = PetscRealPart(coords[faces[2*f+1]*2+1]); 112 PetscReal slope = (y_j - y_i) / (x_j - x_i); 113 PetscBool cond1 = (x_i <= x) && (x < x_j) ? PETSC_TRUE : PETSC_FALSE; 114 PetscBool cond2 = (x_j <= x) && (x < x_i) ? PETSC_TRUE : PETSC_FALSE; 115 PetscBool above = (y < slope * (x - x_i) + y_i) ? PETSC_TRUE : PETSC_FALSE; 116 if ((cond1 || cond2) && above) ++crossings; 117 } 118 if (crossings % 2) *cell = c; 119 else *cell = DMLOCATEPOINT_POINT_NOT_FOUND; 120 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); 121 PetscFunctionReturn(0); 122 } 123 124 #undef __FUNCT__ 125 #define __FUNCT__ "DMPlexLocatePoint_Simplex_3D_Internal" 126 static PetscErrorCode DMPlexLocatePoint_Simplex_3D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) 127 { 128 const PetscInt embedDim = 3; 129 PetscReal v0[3], J[9], invJ[9], detJ; 130 PetscReal x = PetscRealPart(point[0]); 131 PetscReal y = PetscRealPart(point[1]); 132 PetscReal z = PetscRealPart(point[2]); 133 PetscReal xi, eta, zeta; 134 PetscErrorCode ierr; 135 136 PetscFunctionBegin; 137 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 138 xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]) + invJ[0*embedDim+2]*(z - v0[2]); 139 eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]) + invJ[1*embedDim+2]*(z - v0[2]); 140 zeta = invJ[2*embedDim+0]*(x - v0[0]) + invJ[2*embedDim+1]*(y - v0[1]) + invJ[2*embedDim+2]*(z - v0[2]); 141 142 if ((xi >= 0.0) && (eta >= 0.0) && (zeta >= 0.0) && (xi + eta + zeta <= 2.0)) *cell = c; 143 else *cell = DMLOCATEPOINT_POINT_NOT_FOUND; 144 PetscFunctionReturn(0); 145 } 146 147 #undef __FUNCT__ 148 #define __FUNCT__ "DMPlexLocatePoint_General_3D_Internal" 149 static PetscErrorCode DMPlexLocatePoint_General_3D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) 150 { 151 PetscSection coordSection; 152 Vec coordsLocal; 153 PetscScalar *coords; 154 const PetscInt faces[24] = {0, 3, 2, 1, 5, 4, 7, 6, 3, 0, 4, 5, 155 1, 2, 6, 7, 3, 5, 6, 2, 0, 1, 7, 4}; 156 PetscBool found = PETSC_TRUE; 157 PetscInt f; 158 PetscErrorCode ierr; 159 160 PetscFunctionBegin; 161 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 162 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 163 ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); 164 for (f = 0; f < 6; ++f) { 165 /* Check the point is under plane */ 166 /* Get face normal */ 167 PetscReal v_i[3]; 168 PetscReal v_j[3]; 169 PetscReal normal[3]; 170 PetscReal pp[3]; 171 PetscReal dot; 172 173 v_i[0] = PetscRealPart(coords[faces[f*4+3]*3+0]-coords[faces[f*4+0]*3+0]); 174 v_i[1] = PetscRealPart(coords[faces[f*4+3]*3+1]-coords[faces[f*4+0]*3+1]); 175 v_i[2] = PetscRealPart(coords[faces[f*4+3]*3+2]-coords[faces[f*4+0]*3+2]); 176 v_j[0] = PetscRealPart(coords[faces[f*4+1]*3+0]-coords[faces[f*4+0]*3+0]); 177 v_j[1] = PetscRealPart(coords[faces[f*4+1]*3+1]-coords[faces[f*4+0]*3+1]); 178 v_j[2] = PetscRealPart(coords[faces[f*4+1]*3+2]-coords[faces[f*4+0]*3+2]); 179 normal[0] = v_i[1]*v_j[2] - v_i[2]*v_j[1]; 180 normal[1] = v_i[2]*v_j[0] - v_i[0]*v_j[2]; 181 normal[2] = v_i[0]*v_j[1] - v_i[1]*v_j[0]; 182 pp[0] = PetscRealPart(coords[faces[f*4+0]*3+0] - point[0]); 183 pp[1] = PetscRealPart(coords[faces[f*4+0]*3+1] - point[1]); 184 pp[2] = PetscRealPart(coords[faces[f*4+0]*3+2] - point[2]); 185 dot = normal[0]*pp[0] + normal[1]*pp[1] + normal[2]*pp[2]; 186 187 /* Check that projected point is in face (2D location problem) */ 188 if (dot < 0.0) { 189 found = PETSC_FALSE; 190 break; 191 } 192 } 193 if (found) *cell = c; 194 else *cell = DMLOCATEPOINT_POINT_NOT_FOUND; 195 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); 196 PetscFunctionReturn(0); 197 } 198 199 #undef __FUNCT__ 200 #define __FUNCT__ "PetscGridHashInitialize_Internal" 201 static PetscErrorCode PetscGridHashInitialize_Internal(PetscGridHash box, PetscInt dim, const PetscScalar point[]) 202 { 203 PetscInt d; 204 205 PetscFunctionBegin; 206 box->dim = dim; 207 for (d = 0; d < dim; ++d) box->lower[d] = box->upper[d] = PetscRealPart(point[d]); 208 PetscFunctionReturn(0); 209 } 210 211 #undef __FUNCT__ 212 #define __FUNCT__ "PetscGridHashCreate" 213 PetscErrorCode PetscGridHashCreate(MPI_Comm comm, PetscInt dim, const PetscScalar point[], PetscGridHash *box) 214 { 215 PetscErrorCode ierr; 216 217 PetscFunctionBegin; 218 ierr = PetscMalloc1(1, box);CHKERRQ(ierr); 219 ierr = PetscGridHashInitialize_Internal(*box, dim, point);CHKERRQ(ierr); 220 PetscFunctionReturn(0); 221 } 222 223 #undef __FUNCT__ 224 #define __FUNCT__ "PetscGridHashEnlarge" 225 PetscErrorCode PetscGridHashEnlarge(PetscGridHash box, const PetscScalar point[]) 226 { 227 PetscInt d; 228 229 PetscFunctionBegin; 230 for (d = 0; d < box->dim; ++d) { 231 box->lower[d] = PetscMin(box->lower[d], PetscRealPart(point[d])); 232 box->upper[d] = PetscMax(box->upper[d], PetscRealPart(point[d])); 233 } 234 PetscFunctionReturn(0); 235 } 236 237 #undef __FUNCT__ 238 #define __FUNCT__ "PetscGridHashSetGrid" 239 /* 240 PetscGridHashSetGrid - Divide the grid into boxes 241 242 Not collective 243 244 Input Parameters: 245 + box - The grid hash object 246 . n - The number of boxes in each dimension, or PETSC_DETERMINE 247 - h - The box size in each dimension, only used if n[d] == PETSC_DETERMINE 248 249 Level: developer 250 251 .seealso: PetscGridHashCreate() 252 */ 253 PetscErrorCode PetscGridHashSetGrid(PetscGridHash box, const PetscInt n[], const PetscReal h[]) 254 { 255 PetscInt d; 256 257 PetscFunctionBegin; 258 for (d = 0; d < box->dim; ++d) { 259 box->extent[d] = box->upper[d] - box->lower[d]; 260 if (n[d] == PETSC_DETERMINE) { 261 box->h[d] = h[d]; 262 box->n[d] = PetscCeilReal(box->extent[d]/h[d]); 263 } else { 264 box->n[d] = n[d]; 265 box->h[d] = box->extent[d]/n[d]; 266 } 267 } 268 PetscFunctionReturn(0); 269 } 270 271 #undef __FUNCT__ 272 #define __FUNCT__ "PetscGridHashGetEnclosingBox" 273 /* 274 PetscGridHashGetEnclosingBox - Find the grid boxes containing each input point 275 276 Not collective 277 278 Input Parameters: 279 + box - The grid hash object 280 . numPoints - The number of input points 281 - points - The input point coordinates 282 283 Output Parameters: 284 + dboxes - An array of numPoints*dim integers expressing the enclosing box as (i_0, i_1, ..., i_dim) 285 - boxes - An array of numPoints integers expressing the enclosing box as single number, or NULL 286 287 Level: developer 288 289 .seealso: PetscGridHashCreate() 290 */ 291 PetscErrorCode PetscGridHashGetEnclosingBox(PetscGridHash box, PetscInt numPoints, const PetscScalar points[], PetscInt dboxes[], PetscInt boxes[]) 292 { 293 const PetscReal *lower = box->lower; 294 const PetscReal *upper = box->upper; 295 const PetscReal *h = box->h; 296 const PetscInt *n = box->n; 297 const PetscInt dim = box->dim; 298 PetscInt d, p; 299 300 PetscFunctionBegin; 301 for (p = 0; p < numPoints; ++p) { 302 for (d = 0; d < dim; ++d) { 303 PetscInt dbox = PetscFloorReal((PetscRealPart(points[p*dim+d]) - lower[d])/h[d]); 304 305 if (dbox == n[d] && PetscAbsReal(PetscRealPart(points[p*dim+d]) - upper[d]) < 1.0e-9) dbox = n[d]-1; 306 if (dbox < 0 || dbox >= n[d]) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Input point %d (%g, %g, %g) is outside of our bounding box", 307 p, PetscRealPart(points[p*dim+0]), dim > 1 ? PetscRealPart(points[p*dim+1]) : 0.0, dim > 2 ? PetscRealPart(points[p*dim+2]) : 0.0); 308 dboxes[p*dim+d] = dbox; 309 } 310 if (boxes) for (d = 1, boxes[p] = dboxes[p*dim]; d < dim; ++d) boxes[p] += dboxes[p*dim+d]*n[d-1]; 311 } 312 PetscFunctionReturn(0); 313 } 314 315 #undef __FUNCT__ 316 #define __FUNCT__ "PetscGridHashDestroy" 317 PetscErrorCode PetscGridHashDestroy(PetscGridHash *box) 318 { 319 PetscErrorCode ierr; 320 321 PetscFunctionBegin; 322 if (*box) { 323 ierr = PetscSectionDestroy(&(*box)->cellSection);CHKERRQ(ierr); 324 ierr = ISDestroy(&(*box)->cells);CHKERRQ(ierr); 325 ierr = DMLabelDestroy(&(*box)->cellsSparse);CHKERRQ(ierr); 326 } 327 ierr = PetscFree(*box);CHKERRQ(ierr); 328 PetscFunctionReturn(0); 329 } 330 331 #undef __FUNCT__ 332 #define __FUNCT__ "DMPlexLocatePoint_Internal" 333 PetscErrorCode DMPlexLocatePoint_Internal(DM dm, PetscInt dim, const PetscScalar point[], PetscInt cellStart, PetscInt *cell) 334 { 335 PetscInt coneSize; 336 PetscErrorCode ierr; 337 338 PetscFunctionBegin; 339 switch (dim) { 340 case 2: 341 ierr = DMPlexGetConeSize(dm, cellStart, &coneSize);CHKERRQ(ierr); 342 switch (coneSize) { 343 case 3: 344 ierr = DMPlexLocatePoint_Simplex_2D_Internal(dm, point, cellStart, cell);CHKERRQ(ierr); 345 break; 346 case 4: 347 ierr = DMPlexLocatePoint_General_2D_Internal(dm, point, cellStart, cell);CHKERRQ(ierr); 348 break; 349 default: 350 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for cell with cone size %D", coneSize); 351 } 352 break; 353 case 3: 354 ierr = DMPlexGetConeSize(dm, cellStart, &coneSize);CHKERRQ(ierr); 355 switch (coneSize) { 356 case 4: 357 ierr = DMPlexLocatePoint_Simplex_3D_Internal(dm, point, cellStart, cell);CHKERRQ(ierr); 358 break; 359 case 6: 360 ierr = DMPlexLocatePoint_General_3D_Internal(dm, point, cellStart, cell);CHKERRQ(ierr); 361 break; 362 default: 363 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for cell with cone size %D", coneSize); 364 } 365 break; 366 default: 367 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for mesh dimension %D", dim); 368 } 369 PetscFunctionReturn(0); 370 } 371 372 #undef __FUNCT__ 373 #define __FUNCT__ "DMPlexClosestPoint_Internal" 374 /* 375 DMPlexClosestPoint_Internal - Returns the closest point in the cell to the given point 376 */ 377 PetscErrorCode DMPlexClosestPoint_Internal(DM dm, PetscInt dim, const PetscScalar point[], PetscInt cell, PetscReal cpoint[]) 378 { 379 PetscInt coneSize; 380 PetscErrorCode ierr; 381 382 PetscFunctionBegin; 383 switch (dim) { 384 case 2: 385 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 386 switch (coneSize) { 387 case 3: 388 ierr = DMPlexClosestPoint_Simplex_2D_Internal(dm, point, cell, cpoint);CHKERRQ(ierr); 389 break; 390 #if 0 391 case 4: 392 ierr = DMPlexClosestPoint_General_2D_Internal(dm, point, cell, cpoint);CHKERRQ(ierr); 393 break; 394 #endif 395 default: 396 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No closest point location for cell with cone size %D", coneSize); 397 } 398 break; 399 #if 0 400 case 3: 401 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 402 switch (coneSize) { 403 case 4: 404 ierr = DMPlexClosestPoint_Simplex_3D_Internal(dm, point, cell, cpoint);CHKERRQ(ierr); 405 break; 406 case 6: 407 ierr = DMPlexClosestPoint_General_3D_Internal(dm, point, cell, cpoint);CHKERRQ(ierr); 408 break; 409 default: 410 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No closest point location for cell with cone size %D", coneSize); 411 } 412 break; 413 #endif 414 default: 415 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No closest point location for mesh dimension %D", dim); 416 } 417 PetscFunctionReturn(0); 418 } 419 420 #undef __FUNCT__ 421 #define __FUNCT__ "DMPlexComputeGridHash_Internal" 422 /* 423 DMPlexComputeGridHash_Internal - Create a grid hash structure covering the Plex 424 425 Collective on DM 426 427 Input Parameter: 428 . dm - The Plex 429 430 Output Parameter: 431 . localBox - The grid hash object 432 433 Level: developer 434 435 .seealso: PetscGridHashCreate(), PetscGridHashGetEnclosingBox() 436 */ 437 PetscErrorCode DMPlexComputeGridHash_Internal(DM dm, PetscGridHash *localBox) 438 { 439 MPI_Comm comm; 440 PetscGridHash lbox; 441 Vec coordinates; 442 PetscSection coordSection; 443 Vec coordsLocal; 444 const PetscScalar *coords; 445 PetscInt *dboxes, *boxes; 446 PetscInt n[3] = {10, 10, 10}; 447 PetscInt dim, N, cStart, cEnd, cMax, c, i; 448 PetscErrorCode ierr; 449 450 PetscFunctionBegin; 451 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 452 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 453 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 454 if (dim != 2) SETERRQ(comm, PETSC_ERR_SUP, "I have only coded this for 2D"); 455 ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr); 456 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 457 ierr = PetscGridHashCreate(comm, dim, coords, &lbox);CHKERRQ(ierr); 458 for (i = 0; i < N; i += dim) {ierr = PetscGridHashEnlarge(lbox, &coords[i]);CHKERRQ(ierr);} 459 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 460 ierr = PetscGridHashSetGrid(lbox, n, NULL);CHKERRQ(ierr); 461 #if 0 462 /* Could define a custom reduction to merge these */ 463 ierr = MPIU_Allreduce(lbox->lower, gbox->lower, 3, MPIU_REAL, MPI_MIN, comm);CHKERRQ(ierr); 464 ierr = MPIU_Allreduce(lbox->upper, gbox->upper, 3, MPIU_REAL, MPI_MAX, comm);CHKERRQ(ierr); 465 #endif 466 /* Is there a reason to snap the local bounding box to a division of the global box? */ 467 /* Should we compute all overlaps of local boxes? We could do this with a rendevouz scheme partitioning the global box */ 468 /* Create label */ 469 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 470 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 471 if (cMax >= 0) cEnd = PetscMin(cEnd, cMax); 472 ierr = DMLabelCreate("cells", &lbox->cellsSparse);CHKERRQ(ierr); 473 ierr = DMLabelCreateIndex(lbox->cellsSparse, cStart, cEnd);CHKERRQ(ierr); 474 /* Compute boxes which overlap each cell: http://stackoverflow.com/questions/13790208/triangle-square-intersection-test-in-2d */ 475 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 476 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 477 ierr = PetscCalloc2(16 * dim, &dboxes, 16, &boxes);CHKERRQ(ierr); 478 for (c = cStart; c < cEnd; ++c) { 479 const PetscReal *h = lbox->h; 480 PetscScalar *ccoords = NULL; 481 PetscInt csize = 0; 482 PetscScalar point[3]; 483 PetscInt dlim[6], d, e, i, j, k; 484 485 /* Find boxes enclosing each vertex */ 486 ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, &csize, &ccoords);CHKERRQ(ierr); 487 ierr = PetscGridHashGetEnclosingBox(lbox, csize/dim, ccoords, dboxes, boxes);CHKERRQ(ierr); 488 /* Mark cells containing the vertices */ 489 for (e = 0; e < csize/dim; ++e) {ierr = DMLabelSetValue(lbox->cellsSparse, c, boxes[e]);CHKERRQ(ierr);} 490 /* Get grid of boxes containing these */ 491 for (d = 0; d < dim; ++d) {dlim[d*2+0] = dlim[d*2+1] = dboxes[d];} 492 for (d = dim; d < 3; ++d) {dlim[d*2+0] = dlim[d*2+1] = 0;} 493 for (e = 1; e < dim+1; ++e) { 494 for (d = 0; d < dim; ++d) { 495 dlim[d*2+0] = PetscMin(dlim[d*2+0], dboxes[e*dim+d]); 496 dlim[d*2+1] = PetscMax(dlim[d*2+1], dboxes[e*dim+d]); 497 } 498 } 499 /* Check for intersection of box with cell */ 500 for (k = dlim[2*2+0], point[2] = lbox->lower[2] + k*h[2]; k <= dlim[2*2+1]; ++k, point[2] += h[2]) { 501 for (j = dlim[1*2+0], point[1] = lbox->lower[1] + j*h[1]; j <= dlim[1*2+1]; ++j, point[1] += h[1]) { 502 for (i = dlim[0*2+0], point[0] = lbox->lower[0] + i*h[0]; i <= dlim[0*2+1]; ++i, point[0] += h[0]) { 503 const PetscInt box = (k*lbox->n[1] + j)*lbox->n[0] + i; 504 PetscScalar cpoint[3]; 505 PetscInt cell, edge, ii, jj, kk; 506 507 /* Check whether cell contains any vertex of these subboxes TODO vectorize this */ 508 for (kk = 0, cpoint[2] = point[2]; kk < (dim > 2 ? 2 : 1); ++kk, cpoint[2] += h[2]) { 509 for (jj = 0, cpoint[1] = point[1]; jj < (dim > 1 ? 2 : 1); ++jj, cpoint[1] += h[1]) { 510 for (ii = 0, cpoint[0] = point[0]; ii < 2; ++ii, cpoint[0] += h[0]) { 511 512 ierr = DMPlexLocatePoint_Internal(dm, dim, cpoint, c, &cell);CHKERRQ(ierr); 513 if (cell >= 0) {DMLabelSetValue(lbox->cellsSparse, c, box);CHKERRQ(ierr); ii = jj = kk = 2;} 514 } 515 } 516 } 517 /* Check whether cell edge intersects any edge of these subboxes TODO vectorize this */ 518 for (edge = 0; edge < dim+1; ++edge) { 519 PetscReal segA[6], segB[6]; 520 521 for (d = 0; d < dim; ++d) {segA[d] = PetscRealPart(ccoords[edge*dim+d]); segA[dim+d] = PetscRealPart(ccoords[((edge+1)%(dim+1))*dim+d]);} 522 for (kk = 0; kk < (dim > 2 ? 2 : 1); ++kk) { 523 if (dim > 2) {segB[2] = PetscRealPart(point[2]); 524 segB[dim+2] = PetscRealPart(point[2]) + kk*h[2];} 525 for (jj = 0; jj < (dim > 1 ? 2 : 1); ++jj) { 526 if (dim > 1) {segB[1] = PetscRealPart(point[1]); 527 segB[dim+1] = PetscRealPart(point[1]) + jj*h[1];} 528 for (ii = 0; ii < 2; ++ii) { 529 PetscBool intersects; 530 531 segB[0] = PetscRealPart(point[0]); 532 segB[dim+0] = PetscRealPart(point[0]) + ii*h[0]; 533 ierr = DMPlexGetLineIntersection_2D_Internal(segA, segB, NULL, &intersects);CHKERRQ(ierr); 534 if (intersects) {DMLabelSetValue(lbox->cellsSparse, c, box);CHKERRQ(ierr); edge = ii = jj = kk = dim+1;} 535 } 536 } 537 } 538 } 539 } 540 } 541 } 542 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, NULL, &ccoords);CHKERRQ(ierr); 543 } 544 ierr = PetscFree2(dboxes, boxes);CHKERRQ(ierr); 545 ierr = DMLabelConvertToSection(lbox->cellsSparse, &lbox->cellSection, &lbox->cells);CHKERRQ(ierr); 546 ierr = DMLabelDestroy(&lbox->cellsSparse);CHKERRQ(ierr); 547 *localBox = lbox; 548 PetscFunctionReturn(0); 549 } 550 551 #undef __FUNCT__ 552 #define __FUNCT__ "DMLocatePoints_Plex" 553 PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, DMPointLocationType ltype, PetscSF cellSF) 554 { 555 DM_Plex *mesh = (DM_Plex *) dm->data; 556 PetscBool hash = mesh->useHashLocation; 557 PetscInt bs, numPoints, p, numFound, *found = NULL; 558 PetscInt dim, cStart, cEnd, cMax, numCells, c; 559 const PetscInt *boxCells; 560 PetscSFNode *cells; 561 PetscScalar *a; 562 PetscMPIInt result; 563 PetscErrorCode ierr; 564 565 PetscFunctionBegin; 566 if (ltype == DM_POINTLOCATION_NEAREST && !hash) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Nearest point location only supported with grid hashing."); 567 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 568 ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr); 569 ierr = MPI_Comm_compare(PetscObjectComm((PetscObject)cellSF),PETSC_COMM_SELF,&result);CHKERRQ(ierr); 570 if (result != MPI_IDENT && result != MPI_CONGRUENT) SETERRQ(PetscObjectComm((PetscObject)cellSF),PETSC_ERR_SUP, "Trying parallel point location: only local point location supported"); 571 if (bs != dim) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Block size for point vector %D must be the mesh coordinate dimension %D", bs, dim); 572 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 573 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 574 if (cMax >= 0) cEnd = PetscMin(cEnd, cMax); 575 ierr = VecGetLocalSize(v, &numPoints);CHKERRQ(ierr); 576 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 577 numPoints /= bs; 578 ierr = PetscMalloc1(numPoints, &cells);CHKERRQ(ierr); 579 if (hash) { 580 if (!mesh->lbox) {ierr = PetscInfo(dm, "Initializing grid hashing");CHKERRQ(ierr);ierr = DMPlexComputeGridHash_Internal(dm, &mesh->lbox);CHKERRQ(ierr);} 581 /* Designate the local box for each point */ 582 /* Send points to correct process */ 583 /* Search cells that lie in each subbox */ 584 /* Should we bin points before doing search? */ 585 ierr = ISGetIndices(mesh->lbox->cells, &boxCells);CHKERRQ(ierr); 586 } 587 for (p = 0, numFound = 0; p < numPoints; ++p) { 588 const PetscScalar *point = &a[p*bs]; 589 PetscInt dbin[3], bin, cell = -1, cellOffset; 590 591 cells[p].rank = 0; 592 cells[p].index = DMLOCATEPOINT_POINT_NOT_FOUND; 593 if (hash) { 594 ierr = PetscGridHashGetEnclosingBox(mesh->lbox, 1, point, dbin, &bin);CHKERRQ(ierr); 595 /* TODO Lay an interface over this so we can switch between Section (dense) and Label (sparse) */ 596 ierr = PetscSectionGetDof(mesh->lbox->cellSection, bin, &numCells);CHKERRQ(ierr); 597 ierr = PetscSectionGetOffset(mesh->lbox->cellSection, bin, &cellOffset);CHKERRQ(ierr); 598 for (c = cellOffset; c < cellOffset + numCells; ++c) { 599 ierr = DMPlexLocatePoint_Internal(dm, dim, point, boxCells[c], &cell);CHKERRQ(ierr); 600 if (cell >= 0) { 601 cells[p].rank = 0; 602 cells[p].index = cell; 603 numFound++; 604 break; 605 } 606 } 607 } else { 608 for (c = cStart; c < cEnd; ++c) { 609 ierr = DMPlexLocatePoint_Internal(dm, dim, point, c, &cell);CHKERRQ(ierr); 610 if (cell >= 0) { 611 cells[p].rank = 0; 612 cells[p].index = cell; 613 numFound++; 614 break; 615 } 616 } 617 } 618 } 619 if (hash) {ierr = ISRestoreIndices(mesh->lbox->cells, &boxCells);CHKERRQ(ierr);} 620 if (ltype == DM_POINTLOCATION_NEAREST && hash && numFound < numPoints) { 621 for (p = 0; p < numPoints; p++) { 622 const PetscScalar *point = &a[p*bs]; 623 PetscReal cpoint[3], diff[3], dist, distMax = PETSC_MAX_REAL; 624 PetscInt dbin[3], bin, cellOffset, d; 625 626 if (cells[p].index < 0) { 627 ++numFound; 628 ierr = PetscGridHashGetEnclosingBox(mesh->lbox, 1, point, dbin, &bin);CHKERRQ(ierr); 629 ierr = PetscSectionGetDof(mesh->lbox->cellSection, bin, &numCells);CHKERRQ(ierr); 630 ierr = PetscSectionGetOffset(mesh->lbox->cellSection, bin, &cellOffset);CHKERRQ(ierr); 631 for (c = cellOffset; c < cellOffset + numCells; ++c) { 632 ierr = DMPlexClosestPoint_Internal(dm, dim, point, boxCells[c], cpoint);CHKERRQ(ierr); 633 for (d = 0; d < dim; ++d) diff[d] = cpoint[d] - PetscRealPart(point[d]); 634 dist = DMPlex_NormD_Internal(dim, diff); 635 if (dist < distMax) { 636 for (d = 0; d < dim; ++d) a[p*bs+d] = cpoint[d]; 637 cells[p].rank = 0; 638 cells[p].index = boxCells[c]; 639 distMax = dist; 640 break; 641 } 642 } 643 } 644 } 645 } 646 /* This code is only be relevant when interfaced to parallel point location */ 647 /* Check for highest numbered proc that claims a point (do we care?) */ 648 if (ltype == DM_POINTLOCATION_REMOVE && numFound < numPoints) { 649 ierr = PetscMalloc1(numFound,&found);CHKERRQ(ierr); 650 for (p = 0, numFound = 0; p < numPoints; p++) { 651 if (cells[p].rank >= 0 && cells[p].index >= 0) { 652 if (numFound < p) { 653 cells[numFound] = cells[p]; 654 } 655 found[numFound++] = p; 656 } 657 } 658 } 659 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 660 ierr = PetscSFSetGraph(cellSF, cEnd - cStart, numFound, found, PETSC_OWN_POINTER, cells, PETSC_OWN_POINTER);CHKERRQ(ierr); 661 PetscFunctionReturn(0); 662 } 663 664 #undef __FUNCT__ 665 #define __FUNCT__ "DMPlexComputeProjection2Dto1D_Internal" 666 /* 667 DMPlexComputeProjection2Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 2D 668 */ 669 PetscErrorCode DMPlexComputeProjection2Dto1D_Internal(PetscScalar coords[], PetscReal R[]) 670 { 671 const PetscReal x = PetscRealPart(coords[2] - coords[0]); 672 const PetscReal y = PetscRealPart(coords[3] - coords[1]); 673 const PetscReal r = PetscSqrtReal(x*x + y*y), c = x/r, s = y/r; 674 675 PetscFunctionBegin; 676 R[0] = c; R[1] = -s; 677 R[2] = s; R[3] = c; 678 coords[0] = 0.0; 679 coords[1] = r; 680 PetscFunctionReturn(0); 681 } 682 683 #undef __FUNCT__ 684 #define __FUNCT__ "DMPlexComputeProjection3Dto1D_Internal" 685 /* 686 DMPlexComputeProjection3Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 3D 687 688 This uses the basis completion described by Frisvad, 689 690 http://www.imm.dtu.dk/~jerf/papers/abstracts/onb.html 691 DOI:10.1080/2165347X.2012.689606 692 */ 693 PetscErrorCode DMPlexComputeProjection3Dto1D_Internal(PetscScalar coords[], PetscReal R[]) 694 { 695 PetscReal x = PetscRealPart(coords[3] - coords[0]); 696 PetscReal y = PetscRealPart(coords[4] - coords[1]); 697 PetscReal z = PetscRealPart(coords[5] - coords[2]); 698 PetscReal r = PetscSqrtReal(x*x + y*y + z*z); 699 PetscReal rinv = 1. / r; 700 PetscFunctionBegin; 701 702 x *= rinv; y *= rinv; z *= rinv; 703 if (x > 0.) { 704 PetscReal inv1pX = 1./ (1. + x); 705 706 R[0] = x; R[1] = -y; R[2] = -z; 707 R[3] = y; R[4] = 1. - y*y*inv1pX; R[5] = -y*z*inv1pX; 708 R[6] = z; R[7] = -y*z*inv1pX; R[8] = 1. - z*z*inv1pX; 709 } 710 else { 711 PetscReal inv1mX = 1./ (1. - x); 712 713 R[0] = x; R[1] = z; R[2] = y; 714 R[3] = y; R[4] = -y*z*inv1mX; R[5] = 1. - y*y*inv1mX; 715 R[6] = z; R[7] = 1. - z*z*inv1mX; R[8] = -y*z*inv1mX; 716 } 717 coords[0] = 0.0; 718 coords[1] = r; 719 PetscFunctionReturn(0); 720 } 721 722 #undef __FUNCT__ 723 #define __FUNCT__ "DMPlexComputeProjection3Dto2D_Internal" 724 /* 725 DMPlexComputeProjection3Dto2D_Internal - Rewrite coordinates to be the 2D projection of the 3D 726 */ 727 PetscErrorCode DMPlexComputeProjection3Dto2D_Internal(PetscInt coordSize, PetscScalar coords[], PetscReal R[]) 728 { 729 PetscReal x1[3], x2[3], n[3], norm; 730 PetscReal x1p[3], x2p[3], xnp[3]; 731 PetscReal sqrtz, alpha; 732 const PetscInt dim = 3; 733 PetscInt d, e, p; 734 735 PetscFunctionBegin; 736 /* 0) Calculate normal vector */ 737 for (d = 0; d < dim; ++d) { 738 x1[d] = PetscRealPart(coords[1*dim+d] - coords[0*dim+d]); 739 x2[d] = PetscRealPart(coords[2*dim+d] - coords[0*dim+d]); 740 } 741 n[0] = x1[1]*x2[2] - x1[2]*x2[1]; 742 n[1] = x1[2]*x2[0] - x1[0]*x2[2]; 743 n[2] = x1[0]*x2[1] - x1[1]*x2[0]; 744 norm = PetscSqrtReal(n[0]*n[0] + n[1]*n[1] + n[2]*n[2]); 745 n[0] /= norm; 746 n[1] /= norm; 747 n[2] /= norm; 748 /* 1) Take the normal vector and rotate until it is \hat z 749 750 Let the normal vector be <nx, ny, nz> and alpha = 1/sqrt(1 - nz^2), then 751 752 R = / alpha nx nz alpha ny nz -1/alpha \ 753 | -alpha ny alpha nx 0 | 754 \ nx ny nz / 755 756 will rotate the normal vector to \hat z 757 */ 758 sqrtz = PetscSqrtReal(1.0 - n[2]*n[2]); 759 /* Check for n = z */ 760 if (sqrtz < 1.0e-10) { 761 const PetscInt s = PetscSign(n[2]); 762 /* If nz < 0, rotate 180 degrees around x-axis */ 763 for (p = 3; p < coordSize/3; ++p) { 764 coords[p*2+0] = PetscRealPart(coords[p*dim+0] - coords[0*dim+0]); 765 coords[p*2+1] = (PetscRealPart(coords[p*dim+1] - coords[0*dim+1])) * s; 766 } 767 coords[0] = 0.0; 768 coords[1] = 0.0; 769 coords[2] = x1[0]; 770 coords[3] = x1[1] * s; 771 coords[4] = x2[0]; 772 coords[5] = x2[1] * s; 773 R[0] = 1.0; R[1] = 0.0; R[2] = 0.0; 774 R[3] = 0.0; R[4] = 1.0 * s; R[5] = 0.0; 775 R[6] = 0.0; R[7] = 0.0; R[8] = 1.0 * s; 776 PetscFunctionReturn(0); 777 } 778 alpha = 1.0/sqrtz; 779 R[0] = alpha*n[0]*n[2]; R[1] = alpha*n[1]*n[2]; R[2] = -sqrtz; 780 R[3] = -alpha*n[1]; R[4] = alpha*n[0]; R[5] = 0.0; 781 R[6] = n[0]; R[7] = n[1]; R[8] = n[2]; 782 for (d = 0; d < dim; ++d) { 783 x1p[d] = 0.0; 784 x2p[d] = 0.0; 785 for (e = 0; e < dim; ++e) { 786 x1p[d] += R[d*dim+e]*x1[e]; 787 x2p[d] += R[d*dim+e]*x2[e]; 788 } 789 } 790 if (PetscAbsReal(x1p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); 791 if (PetscAbsReal(x2p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); 792 /* 2) Project to (x, y) */ 793 for (p = 3; p < coordSize/3; ++p) { 794 for (d = 0; d < dim; ++d) { 795 xnp[d] = 0.0; 796 for (e = 0; e < dim; ++e) { 797 xnp[d] += R[d*dim+e]*PetscRealPart(coords[p*dim+e] - coords[0*dim+e]); 798 } 799 if (d < dim-1) coords[p*2+d] = xnp[d]; 800 } 801 } 802 coords[0] = 0.0; 803 coords[1] = 0.0; 804 coords[2] = x1p[0]; 805 coords[3] = x1p[1]; 806 coords[4] = x2p[0]; 807 coords[5] = x2p[1]; 808 /* Output R^T which rotates \hat z to the input normal */ 809 for (d = 0; d < dim; ++d) { 810 for (e = d+1; e < dim; ++e) { 811 PetscReal tmp; 812 813 tmp = R[d*dim+e]; 814 R[d*dim+e] = R[e*dim+d]; 815 R[e*dim+d] = tmp; 816 } 817 } 818 PetscFunctionReturn(0); 819 } 820 821 #undef __FUNCT__ 822 #define __FUNCT__ "Volume_Triangle_Internal" 823 PETSC_UNUSED 824 PETSC_STATIC_INLINE void Volume_Triangle_Internal(PetscReal *vol, PetscReal coords[]) 825 { 826 /* Signed volume is 1/2 the determinant 827 828 | 1 1 1 | 829 | x0 x1 x2 | 830 | y0 y1 y2 | 831 832 but if x0,y0 is the origin, we have 833 834 | x1 x2 | 835 | y1 y2 | 836 */ 837 const PetscReal x1 = coords[2] - coords[0], y1 = coords[3] - coords[1]; 838 const PetscReal x2 = coords[4] - coords[0], y2 = coords[5] - coords[1]; 839 PetscReal M[4], detM; 840 M[0] = x1; M[1] = x2; 841 M[2] = y1; M[3] = y2; 842 DMPlex_Det2D_Internal(&detM, M); 843 *vol = 0.5*detM; 844 (void)PetscLogFlops(5.0); 845 } 846 847 #undef __FUNCT__ 848 #define __FUNCT__ "Volume_Triangle_Origin_Internal" 849 PETSC_STATIC_INLINE void Volume_Triangle_Origin_Internal(PetscReal *vol, PetscReal coords[]) 850 { 851 DMPlex_Det2D_Internal(vol, coords); 852 *vol *= 0.5; 853 } 854 855 #undef __FUNCT__ 856 #define __FUNCT__ "Volume_Tetrahedron_Internal" 857 PETSC_UNUSED 858 PETSC_STATIC_INLINE void Volume_Tetrahedron_Internal(PetscReal *vol, PetscReal coords[]) 859 { 860 /* Signed volume is 1/6th of the determinant 861 862 | 1 1 1 1 | 863 | x0 x1 x2 x3 | 864 | y0 y1 y2 y3 | 865 | z0 z1 z2 z3 | 866 867 but if x0,y0,z0 is the origin, we have 868 869 | x1 x2 x3 | 870 | y1 y2 y3 | 871 | z1 z2 z3 | 872 */ 873 const PetscReal x1 = coords[3] - coords[0], y1 = coords[4] - coords[1], z1 = coords[5] - coords[2]; 874 const PetscReal x2 = coords[6] - coords[0], y2 = coords[7] - coords[1], z2 = coords[8] - coords[2]; 875 const PetscReal x3 = coords[9] - coords[0], y3 = coords[10] - coords[1], z3 = coords[11] - coords[2]; 876 PetscReal M[9], detM; 877 M[0] = x1; M[1] = x2; M[2] = x3; 878 M[3] = y1; M[4] = y2; M[5] = y3; 879 M[6] = z1; M[7] = z2; M[8] = z3; 880 DMPlex_Det3D_Internal(&detM, M); 881 *vol = -0.16666666666666666666666*detM; 882 (void)PetscLogFlops(10.0); 883 } 884 885 #undef __FUNCT__ 886 #define __FUNCT__ "Volume_Tetrahedron_Origin_Internal" 887 PETSC_STATIC_INLINE void Volume_Tetrahedron_Origin_Internal(PetscReal *vol, PetscReal coords[]) 888 { 889 DMPlex_Det3D_Internal(vol, coords); 890 *vol *= -0.16666666666666666666666; 891 } 892 893 #undef __FUNCT__ 894 #define __FUNCT__ "DMPlexComputeLineGeometry_Internal" 895 static PetscErrorCode DMPlexComputeLineGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 896 { 897 PetscSection coordSection; 898 Vec coordinates; 899 PetscScalar *coords = NULL; 900 PetscInt numCoords, d, pStart, pEnd, numSelfCoords = 0; 901 PetscErrorCode ierr; 902 903 PetscFunctionBegin; 904 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 905 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 906 ierr = PetscSectionGetChart(coordSection,&pStart,&pEnd);CHKERRQ(ierr); 907 if (e >= pStart && e < pEnd) {ierr = PetscSectionGetDof(coordSection,e,&numSelfCoords);CHKERRQ(ierr);} 908 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 909 numCoords = numSelfCoords ? numSelfCoords : numCoords; 910 if (invJ && !J) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "In order to compute invJ, J must not be NULL"); 911 *detJ = 0.0; 912 if (numCoords == 6) { 913 const PetscInt dim = 3; 914 PetscReal R[9], J0; 915 916 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 917 ierr = DMPlexComputeProjection3Dto1D_Internal(coords, R);CHKERRQ(ierr); 918 if (J) { 919 J0 = 0.5*PetscRealPart(coords[1]); 920 J[0] = R[0]*J0; J[1] = R[1]; J[2] = R[2]; 921 J[3] = R[3]*J0; J[4] = R[4]; J[5] = R[5]; 922 J[6] = R[6]*J0; J[7] = R[7]; J[8] = R[8]; 923 DMPlex_Det3D_Internal(detJ, J); 924 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 925 } 926 } else if (numCoords == 4) { 927 const PetscInt dim = 2; 928 PetscReal R[4], J0; 929 930 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 931 ierr = DMPlexComputeProjection2Dto1D_Internal(coords, R);CHKERRQ(ierr); 932 if (J) { 933 J0 = 0.5*PetscRealPart(coords[1]); 934 J[0] = R[0]*J0; J[1] = R[1]; 935 J[2] = R[2]*J0; J[3] = R[3]; 936 DMPlex_Det2D_Internal(detJ, J); 937 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 938 } 939 } else if (numCoords == 2) { 940 const PetscInt dim = 1; 941 942 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 943 if (J) { 944 J[0] = 0.5*(PetscRealPart(coords[1]) - PetscRealPart(coords[0])); 945 *detJ = J[0]; 946 ierr = PetscLogFlops(2.0);CHKERRQ(ierr); 947 if (invJ) {invJ[0] = 1.0/J[0]; ierr = PetscLogFlops(1.0);CHKERRQ(ierr);} 948 } 949 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this segment is %D != 2", numCoords); 950 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 951 PetscFunctionReturn(0); 952 } 953 954 #undef __FUNCT__ 955 #define __FUNCT__ "DMPlexComputeTriangleGeometry_Internal" 956 static PetscErrorCode DMPlexComputeTriangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 957 { 958 PetscSection coordSection; 959 Vec coordinates; 960 PetscScalar *coords = NULL; 961 PetscInt numCoords, d, f, g; 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 966 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 967 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 968 *detJ = 0.0; 969 if (numCoords == 9) { 970 const PetscInt dim = 3; 971 PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; 972 973 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 974 ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); 975 if (J) { 976 const PetscInt pdim = 2; 977 978 for (d = 0; d < pdim; d++) { 979 for (f = 0; f < pdim; f++) { 980 J0[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 981 } 982 } 983 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 984 DMPlex_Det3D_Internal(detJ, J0); 985 for (d = 0; d < dim; d++) { 986 for (f = 0; f < dim; f++) { 987 J[d*dim+f] = 0.0; 988 for (g = 0; g < dim; g++) { 989 J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; 990 } 991 } 992 } 993 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 994 } 995 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 996 } else if (numCoords == 6) { 997 const PetscInt dim = 2; 998 999 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1000 if (J) { 1001 for (d = 0; d < dim; d++) { 1002 for (f = 0; f < dim; f++) { 1003 J[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); 1004 } 1005 } 1006 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 1007 DMPlex_Det2D_Internal(detJ, J); 1008 } 1009 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 1010 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this triangle is %D != 6 or 9", numCoords); 1011 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 1012 PetscFunctionReturn(0); 1013 } 1014 1015 #undef __FUNCT__ 1016 #define __FUNCT__ "DMPlexComputeRectangleGeometry_Internal" 1017 static PetscErrorCode DMPlexComputeRectangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1018 { 1019 PetscSection coordSection; 1020 Vec coordinates; 1021 PetscScalar *coords = NULL; 1022 PetscInt numCoords, numSelfCoords = 0, d, f, g, pStart, pEnd; 1023 PetscErrorCode ierr; 1024 1025 PetscFunctionBegin; 1026 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1027 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1028 ierr = PetscSectionGetChart(coordSection,&pStart,&pEnd);CHKERRQ(ierr); 1029 if (e >= pStart && e < pEnd) {ierr = PetscSectionGetDof(coordSection,e,&numSelfCoords);CHKERRQ(ierr);} 1030 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 1031 numCoords = numSelfCoords ? numSelfCoords : numCoords; 1032 *detJ = 0.0; 1033 if (numCoords == 12) { 1034 const PetscInt dim = 3; 1035 PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; 1036 1037 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1038 ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); 1039 if (J) { 1040 const PetscInt pdim = 2; 1041 1042 for (d = 0; d < pdim; d++) { 1043 J0[d*dim+0] = 0.5*(PetscRealPart(coords[1*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 1044 J0[d*dim+1] = 0.5*(PetscRealPart(coords[3*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 1045 } 1046 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 1047 DMPlex_Det3D_Internal(detJ, J0); 1048 for (d = 0; d < dim; d++) { 1049 for (f = 0; f < dim; f++) { 1050 J[d*dim+f] = 0.0; 1051 for (g = 0; g < dim; g++) { 1052 J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; 1053 } 1054 } 1055 } 1056 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 1057 } 1058 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1059 } else if (numCoords == 8) { 1060 const PetscInt dim = 2; 1061 1062 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1063 if (J) { 1064 for (d = 0; d < dim; d++) { 1065 J[d*dim+0] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 1066 J[d*dim+1] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 1067 } 1068 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 1069 DMPlex_Det2D_Internal(detJ, J); 1070 } 1071 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 1072 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this quadrilateral is %D != 8 or 12", numCoords); 1073 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 1074 PetscFunctionReturn(0); 1075 } 1076 1077 #undef __FUNCT__ 1078 #define __FUNCT__ "DMPlexComputeTetrahedronGeometry_Internal" 1079 static PetscErrorCode DMPlexComputeTetrahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1080 { 1081 PetscSection coordSection; 1082 Vec coordinates; 1083 PetscScalar *coords = NULL; 1084 const PetscInt dim = 3; 1085 PetscInt d; 1086 PetscErrorCode ierr; 1087 1088 PetscFunctionBegin; 1089 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1090 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1091 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 1092 *detJ = 0.0; 1093 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1094 if (J) { 1095 for (d = 0; d < dim; d++) { 1096 /* I orient with outward face normals */ 1097 J[d*dim+0] = 0.5*(PetscRealPart(coords[2*dim+d]) - PetscRealPart(coords[0*dim+d])); 1098 J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 1099 J[d*dim+2] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 1100 } 1101 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 1102 DMPlex_Det3D_Internal(detJ, J); 1103 } 1104 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1105 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 1106 PetscFunctionReturn(0); 1107 } 1108 1109 #undef __FUNCT__ 1110 #define __FUNCT__ "DMPlexComputeHexahedronGeometry_Internal" 1111 static PetscErrorCode DMPlexComputeHexahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1112 { 1113 PetscSection coordSection; 1114 Vec coordinates; 1115 PetscScalar *coords = NULL; 1116 const PetscInt dim = 3; 1117 PetscInt d; 1118 PetscErrorCode ierr; 1119 1120 PetscFunctionBegin; 1121 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1122 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1123 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 1124 *detJ = 0.0; 1125 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1126 if (J) { 1127 for (d = 0; d < dim; d++) { 1128 J[d*dim+0] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 1129 J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 1130 J[d*dim+2] = 0.5*(PetscRealPart(coords[4*dim+d]) - PetscRealPart(coords[0*dim+d])); 1131 } 1132 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 1133 DMPlex_Det3D_Internal(detJ, J); 1134 } 1135 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1136 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 1137 PetscFunctionReturn(0); 1138 } 1139 1140 #undef __FUNCT__ 1141 #define __FUNCT__ "DMPlexComputeCellGeometryAffineFEM" 1142 /*@C 1143 DMPlexComputeCellGeometryAffineFEM - Assuming an affine map, compute the Jacobian, inverse Jacobian, and Jacobian determinant for a given cell 1144 1145 Collective on DM 1146 1147 Input Arguments: 1148 + dm - the DM 1149 - cell - the cell 1150 1151 Output Arguments: 1152 + v0 - the translation part of this affine transform 1153 . J - the Jacobian of the transform from the reference element 1154 . invJ - the inverse of the Jacobian 1155 - detJ - the Jacobian determinant 1156 1157 Level: advanced 1158 1159 Fortran Notes: 1160 Since it returns arrays, this routine is only available in Fortran 90, and you must 1161 include petsc.h90 in your code. 1162 1163 .seealso: DMPlexComputeCellGeometryFEM(), DMGetCoordinateSection(), DMGetCoordinateVec() 1164 @*/ 1165 PetscErrorCode DMPlexComputeCellGeometryAffineFEM(DM dm, PetscInt cell, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) 1166 { 1167 PetscInt depth, dim, coneSize; 1168 PetscErrorCode ierr; 1169 1170 PetscFunctionBegin; 1171 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1172 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1173 if (depth == 1) { 1174 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1175 } else { 1176 DMLabel depth; 1177 1178 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1179 ierr = DMLabelGetValue(depth, cell, &dim);CHKERRQ(ierr); 1180 } 1181 switch (dim) { 1182 case 1: 1183 ierr = DMPlexComputeLineGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1184 break; 1185 case 2: 1186 switch (coneSize) { 1187 case 3: 1188 ierr = DMPlexComputeTriangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1189 break; 1190 case 4: 1191 ierr = DMPlexComputeRectangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1192 break; 1193 default: 1194 SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of faces %D in cell %D for element geometry computation", coneSize, cell); 1195 } 1196 break; 1197 case 3: 1198 switch (coneSize) { 1199 case 4: 1200 ierr = DMPlexComputeTetrahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1201 break; 1202 case 6: /* Faces */ 1203 case 8: /* Vertices */ 1204 ierr = DMPlexComputeHexahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1205 break; 1206 default: 1207 SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of faces %D in cell %D for element geometry computation", coneSize, cell); 1208 } 1209 break; 1210 default: 1211 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); 1212 } 1213 PetscFunctionReturn(0); 1214 } 1215 1216 #undef __FUNCT__ 1217 #define __FUNCT__ "DMPlexComputeIsoparametricGeometry_Internal" 1218 static PetscErrorCode DMPlexComputeIsoparametricGeometry_Internal(DM dm, PetscFE fe, PetscInt point, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1219 { 1220 PetscQuadrature quad; 1221 PetscSection coordSection; 1222 Vec coordinates; 1223 PetscScalar *coords = NULL; 1224 const PetscReal *quadPoints; 1225 PetscReal *basisDer; 1226 PetscInt dim, cdim, pdim, qdim, Nq, numCoords, d, q; 1227 PetscErrorCode ierr; 1228 1229 PetscFunctionBegin; 1230 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1231 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1232 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, point, &numCoords, &coords);CHKERRQ(ierr); 1233 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1234 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 1235 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1236 ierr = PetscFEGetDimension(fe, &pdim);CHKERRQ(ierr); 1237 ierr = PetscQuadratureGetData(quad, &qdim, &Nq, &quadPoints, NULL);CHKERRQ(ierr); 1238 ierr = PetscFEGetDefaultTabulation(fe, NULL, &basisDer, NULL);CHKERRQ(ierr); 1239 *detJ = 0.0; 1240 if (qdim != dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Point dimension %d != quadrature dimension %d", dim, qdim); 1241 if (numCoords != pdim*cdim) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "There are %d coordinates for point %d != %d*%d", numCoords, point, pdim, cdim); 1242 if (v0) {for (d = 0; d < cdim; d++) v0[d] = PetscRealPart(coords[d]);} 1243 if (J) { 1244 ierr = PetscMemzero(J, Nq*cdim*dim*sizeof(PetscReal));CHKERRQ(ierr); 1245 for (q = 0; q < Nq; ++q) { 1246 PetscInt i, j, k, c, r; 1247 1248 /* J = dx_i/d\xi_j = sum[k=0,n-1] dN_k/d\xi_j * x_i(k) */ 1249 for (k = 0; k < pdim; ++k) 1250 for (j = 0; j < dim; ++j) 1251 for (i = 0; i < cdim; ++i) 1252 J[(q*cdim + i)*dim + j] += basisDer[(q*pdim + k)*dim + j] * PetscRealPart(coords[k*cdim + i]); 1253 ierr = PetscLogFlops(2.0*pdim*dim*cdim);CHKERRQ(ierr); 1254 if (cdim > dim) { 1255 for (c = dim; c < cdim; ++c) 1256 for (r = 0; r < cdim; ++r) 1257 J[r*cdim+c] = r == c ? 1.0 : 0.0; 1258 } 1259 switch (cdim) { 1260 case 3: 1261 DMPlex_Det3D_Internal(detJ, J); 1262 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1263 break; 1264 case 2: 1265 DMPlex_Det2D_Internal(detJ, J); 1266 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 1267 break; 1268 case 1: 1269 *detJ = J[0]; 1270 if (invJ) invJ[0] = 1.0/J[0]; 1271 } 1272 } 1273 } 1274 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, point, &numCoords, &coords);CHKERRQ(ierr); 1275 PetscFunctionReturn(0); 1276 } 1277 1278 #undef __FUNCT__ 1279 #define __FUNCT__ "DMPlexComputeCellGeometryFEM" 1280 /*@C 1281 DMPlexComputeCellGeometryFEM - Compute the Jacobian, inverse Jacobian, and Jacobian determinant at each quadrature point in the given cell 1282 1283 Collective on DM 1284 1285 Input Arguments: 1286 + dm - the DM 1287 . cell - the cell 1288 - fe - the finite element containing the quadrature 1289 1290 Output Arguments: 1291 + v0 - the translation part of this transform 1292 . J - the Jacobian of the transform from the reference element at each quadrature point 1293 . invJ - the inverse of the Jacobian at each quadrature point 1294 - detJ - the Jacobian determinant at each quadrature point 1295 1296 Level: advanced 1297 1298 Fortran Notes: 1299 Since it returns arrays, this routine is only available in Fortran 90, and you must 1300 include petsc.h90 in your code. 1301 1302 .seealso: DMGetCoordinateSection(), DMGetCoordinateVec() 1303 @*/ 1304 PetscErrorCode DMPlexComputeCellGeometryFEM(DM dm, PetscInt cell, PetscFE fe, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) 1305 { 1306 PetscErrorCode ierr; 1307 1308 PetscFunctionBegin; 1309 if (!fe) {ierr = DMPlexComputeCellGeometryAffineFEM(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr);} 1310 else {ierr = DMPlexComputeIsoparametricGeometry_Internal(dm, fe, cell, v0, J, invJ, detJ);CHKERRQ(ierr);} 1311 PetscFunctionReturn(0); 1312 } 1313 1314 #undef __FUNCT__ 1315 #define __FUNCT__ "DMPlexComputeGeometryFVM_1D_Internal" 1316 static PetscErrorCode DMPlexComputeGeometryFVM_1D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1317 { 1318 PetscSection coordSection; 1319 Vec coordinates; 1320 PetscScalar *coords = NULL; 1321 PetscScalar tmp[2]; 1322 PetscInt coordSize; 1323 PetscErrorCode ierr; 1324 1325 PetscFunctionBegin; 1326 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1327 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1328 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1329 if (dim != 2) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "We only support 2D edges right now"); 1330 ierr = DMLocalizeCoordinate_Internal(dm, dim, coords, &coords[dim], tmp);CHKERRQ(ierr); 1331 if (centroid) { 1332 centroid[0] = 0.5*PetscRealPart(coords[0] + tmp[0]); 1333 centroid[1] = 0.5*PetscRealPart(coords[1] + tmp[1]); 1334 } 1335 if (normal) { 1336 PetscReal norm; 1337 1338 normal[0] = -PetscRealPart(coords[1] - tmp[1]); 1339 normal[1] = PetscRealPart(coords[0] - tmp[0]); 1340 norm = PetscSqrtReal(normal[0]*normal[0] + normal[1]*normal[1]); 1341 normal[0] /= norm; 1342 normal[1] /= norm; 1343 } 1344 if (vol) { 1345 *vol = PetscSqrtReal(PetscSqr(PetscRealPart(coords[0] - tmp[0])) + PetscSqr(PetscRealPart(coords[1] - tmp[1]))); 1346 } 1347 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1348 PetscFunctionReturn(0); 1349 } 1350 1351 #undef __FUNCT__ 1352 #define __FUNCT__ "DMPlexComputeGeometryFVM_2D_Internal" 1353 /* Centroid_i = (\sum_n A_n Cn_i ) / A */ 1354 static PetscErrorCode DMPlexComputeGeometryFVM_2D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1355 { 1356 PetscSection coordSection; 1357 Vec coordinates; 1358 PetscScalar *coords = NULL; 1359 PetscReal vsum = 0.0, csum[3] = {0.0, 0.0, 0.0}, vtmp, ctmp[4], v0[3], R[9]; 1360 PetscInt tdim = 2, coordSize, numCorners, p, d, e; 1361 PetscErrorCode ierr; 1362 1363 PetscFunctionBegin; 1364 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1365 ierr = DMPlexGetConeSize(dm, cell, &numCorners);CHKERRQ(ierr); 1366 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1367 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1368 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 1369 if (dim > 2 && centroid) { 1370 v0[0] = PetscRealPart(coords[0]); 1371 v0[1] = PetscRealPart(coords[1]); 1372 v0[2] = PetscRealPart(coords[2]); 1373 } 1374 if (normal) { 1375 if (dim > 2) { 1376 const PetscReal x0 = PetscRealPart(coords[dim+0] - coords[0]), x1 = PetscRealPart(coords[dim*2+0] - coords[0]); 1377 const PetscReal y0 = PetscRealPart(coords[dim+1] - coords[1]), y1 = PetscRealPart(coords[dim*2+1] - coords[1]); 1378 const PetscReal z0 = PetscRealPart(coords[dim+2] - coords[2]), z1 = PetscRealPart(coords[dim*2+2] - coords[2]); 1379 PetscReal norm; 1380 1381 normal[0] = y0*z1 - z0*y1; 1382 normal[1] = z0*x1 - x0*z1; 1383 normal[2] = x0*y1 - y0*x1; 1384 norm = PetscSqrtReal(normal[0]*normal[0] + normal[1]*normal[1] + normal[2]*normal[2]); 1385 normal[0] /= norm; 1386 normal[1] /= norm; 1387 normal[2] /= norm; 1388 } else { 1389 for (d = 0; d < dim; ++d) normal[d] = 0.0; 1390 } 1391 } 1392 if (dim == 3) {ierr = DMPlexComputeProjection3Dto2D_Internal(coordSize, coords, R);CHKERRQ(ierr);} 1393 for (p = 0; p < numCorners; ++p) { 1394 /* Need to do this copy to get types right */ 1395 for (d = 0; d < tdim; ++d) { 1396 ctmp[d] = PetscRealPart(coords[p*tdim+d]); 1397 ctmp[tdim+d] = PetscRealPart(coords[((p+1)%numCorners)*tdim+d]); 1398 } 1399 Volume_Triangle_Origin_Internal(&vtmp, ctmp); 1400 vsum += vtmp; 1401 for (d = 0; d < tdim; ++d) { 1402 csum[d] += (ctmp[d] + ctmp[tdim+d])*vtmp; 1403 } 1404 } 1405 for (d = 0; d < tdim; ++d) { 1406 csum[d] /= (tdim+1)*vsum; 1407 } 1408 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1409 if (vol) *vol = PetscAbsReal(vsum); 1410 if (centroid) { 1411 if (dim > 2) { 1412 for (d = 0; d < dim; ++d) { 1413 centroid[d] = v0[d]; 1414 for (e = 0; e < dim; ++e) { 1415 centroid[d] += R[d*dim+e]*csum[e]; 1416 } 1417 } 1418 } else for (d = 0; d < dim; ++d) centroid[d] = csum[d]; 1419 } 1420 PetscFunctionReturn(0); 1421 } 1422 1423 #undef __FUNCT__ 1424 #define __FUNCT__ "DMPlexComputeGeometryFVM_3D_Internal" 1425 /* Centroid_i = (\sum_n V_n Cn_i ) / V */ 1426 static PetscErrorCode DMPlexComputeGeometryFVM_3D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1427 { 1428 PetscSection coordSection; 1429 Vec coordinates; 1430 PetscScalar *coords = NULL; 1431 PetscReal vsum = 0.0, vtmp, coordsTmp[3*3]; 1432 const PetscInt *faces, *facesO; 1433 PetscInt numFaces, f, coordSize, numCorners, p, d; 1434 PetscErrorCode ierr; 1435 1436 PetscFunctionBegin; 1437 if (PetscUnlikely(dim > 3)) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"No support for dim %D > 3",dim); 1438 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1439 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1440 1441 if (centroid) for (d = 0; d < dim; ++d) centroid[d] = 0.0; 1442 ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr); 1443 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 1444 ierr = DMPlexGetConeOrientation(dm, cell, &facesO);CHKERRQ(ierr); 1445 for (f = 0; f < numFaces; ++f) { 1446 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); 1447 numCorners = coordSize/dim; 1448 switch (numCorners) { 1449 case 3: 1450 for (d = 0; d < dim; ++d) { 1451 coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); 1452 coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); 1453 coordsTmp[2*dim+d] = PetscRealPart(coords[2*dim+d]); 1454 } 1455 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1456 if (facesO[f] < 0) vtmp = -vtmp; 1457 vsum += vtmp; 1458 if (centroid) { /* Centroid of OABC = (a+b+c)/4 */ 1459 for (d = 0; d < dim; ++d) { 1460 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1461 } 1462 } 1463 break; 1464 case 4: 1465 /* DO FOR PYRAMID */ 1466 /* First tet */ 1467 for (d = 0; d < dim; ++d) { 1468 coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); 1469 coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); 1470 coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); 1471 } 1472 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1473 if (facesO[f] < 0) vtmp = -vtmp; 1474 vsum += vtmp; 1475 if (centroid) { 1476 for (d = 0; d < dim; ++d) { 1477 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1478 } 1479 } 1480 /* Second tet */ 1481 for (d = 0; d < dim; ++d) { 1482 coordsTmp[0*dim+d] = PetscRealPart(coords[1*dim+d]); 1483 coordsTmp[1*dim+d] = PetscRealPart(coords[2*dim+d]); 1484 coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); 1485 } 1486 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1487 if (facesO[f] < 0) vtmp = -vtmp; 1488 vsum += vtmp; 1489 if (centroid) { 1490 for (d = 0; d < dim; ++d) { 1491 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1492 } 1493 } 1494 break; 1495 default: 1496 SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle faces with %D vertices", numCorners); 1497 } 1498 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); 1499 } 1500 if (vol) *vol = PetscAbsReal(vsum); 1501 if (normal) for (d = 0; d < dim; ++d) normal[d] = 0.0; 1502 if (centroid) for (d = 0; d < dim; ++d) centroid[d] /= (vsum*4); 1503 PetscFunctionReturn(0); 1504 } 1505 1506 #undef __FUNCT__ 1507 #define __FUNCT__ "DMPlexComputeCellGeometryFVM" 1508 /*@C 1509 DMPlexComputeCellGeometryFVM - Compute the volume for a given cell 1510 1511 Collective on DM 1512 1513 Input Arguments: 1514 + dm - the DM 1515 - cell - the cell 1516 1517 Output Arguments: 1518 + volume - the cell volume 1519 . centroid - the cell centroid 1520 - normal - the cell normal, if appropriate 1521 1522 Level: advanced 1523 1524 Fortran Notes: 1525 Since it returns arrays, this routine is only available in Fortran 90, and you must 1526 include petsc.h90 in your code. 1527 1528 .seealso: DMGetCoordinateSection(), DMGetCoordinateVec() 1529 @*/ 1530 PetscErrorCode DMPlexComputeCellGeometryFVM(DM dm, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1531 { 1532 PetscInt depth, dim; 1533 PetscErrorCode ierr; 1534 1535 PetscFunctionBegin; 1536 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1537 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1538 if (depth != dim) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh must be interpolated"); 1539 /* We need to keep a pointer to the depth label */ 1540 ierr = DMGetLabelValue(dm, "depth", cell, &depth);CHKERRQ(ierr); 1541 /* Cone size is now the number of faces */ 1542 switch (depth) { 1543 case 1: 1544 ierr = DMPlexComputeGeometryFVM_1D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1545 break; 1546 case 2: 1547 ierr = DMPlexComputeGeometryFVM_2D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1548 break; 1549 case 3: 1550 ierr = DMPlexComputeGeometryFVM_3D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1551 break; 1552 default: 1553 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); 1554 } 1555 PetscFunctionReturn(0); 1556 } 1557 1558 #undef __FUNCT__ 1559 #define __FUNCT__ "DMPlexComputeGeometryFEM" 1560 /* This should also take a PetscFE argument I think */ 1561 PetscErrorCode DMPlexComputeGeometryFEM(DM dm, Vec *cellgeom) 1562 { 1563 DM dmCell; 1564 Vec coordinates; 1565 PetscSection coordSection, sectionCell; 1566 PetscScalar *cgeom; 1567 PetscInt cStart, cEnd, cMax, c; 1568 PetscErrorCode ierr; 1569 1570 PetscFunctionBegin; 1571 ierr = DMClone(dm, &dmCell);CHKERRQ(ierr); 1572 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1573 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1574 ierr = DMSetCoordinateSection(dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1575 ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr); 1576 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr); 1577 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1578 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1579 cEnd = cMax < 0 ? cEnd : cMax; 1580 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1581 /* TODO This needs to be multiplied by Nq for non-affine */ 1582 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFECellGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1583 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1584 ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr); 1585 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1586 ierr = DMCreateLocalVector(dmCell, cellgeom);CHKERRQ(ierr); 1587 ierr = VecGetArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1588 for (c = cStart; c < cEnd; ++c) { 1589 PetscFECellGeom *cg; 1590 1591 ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1592 ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr); 1593 ierr = DMPlexComputeCellGeometryFEM(dmCell, c, NULL, cg->v0, cg->J, cg->invJ, &cg->detJ);CHKERRQ(ierr); 1594 if (cg->detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", cg->detJ, c); 1595 } 1596 ierr = VecRestoreArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1597 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1598 PetscFunctionReturn(0); 1599 } 1600 1601 #undef __FUNCT__ 1602 #define __FUNCT__ "DMPlexComputeGeometryFVM" 1603 /*@ 1604 DMPlexComputeGeometryFVM - Computes the cell and face geometry for a finite volume method 1605 1606 Input Parameter: 1607 . dm - The DM 1608 1609 Output Parameters: 1610 + cellgeom - A Vec of PetscFVCellGeom data 1611 . facegeom - A Vec of PetscFVFaceGeom data 1612 1613 Level: developer 1614 1615 .seealso: PetscFVFaceGeom, PetscFVCellGeom, DMPlexComputeGeometryFEM() 1616 @*/ 1617 PetscErrorCode DMPlexComputeGeometryFVM(DM dm, Vec *cellgeom, Vec *facegeom) 1618 { 1619 DM dmFace, dmCell; 1620 DMLabel ghostLabel; 1621 PetscSection sectionFace, sectionCell; 1622 PetscSection coordSection; 1623 Vec coordinates; 1624 PetscScalar *fgeom, *cgeom; 1625 PetscReal minradius, gminradius; 1626 PetscInt dim, cStart, cEnd, cEndInterior, c, fStart, fEnd, f; 1627 PetscErrorCode ierr; 1628 1629 PetscFunctionBegin; 1630 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1631 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1632 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1633 /* Make cell centroids and volumes */ 1634 ierr = DMClone(dm, &dmCell);CHKERRQ(ierr); 1635 ierr = DMSetCoordinateSection(dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1636 ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr); 1637 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr); 1638 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1639 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1640 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1641 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFVCellGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1642 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1643 ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr); 1644 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1645 ierr = DMCreateLocalVector(dmCell, cellgeom);CHKERRQ(ierr); 1646 if (cEndInterior < 0) { 1647 cEndInterior = cEnd; 1648 } 1649 ierr = VecGetArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1650 for (c = cStart; c < cEndInterior; ++c) { 1651 PetscFVCellGeom *cg; 1652 1653 ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1654 ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr); 1655 ierr = DMPlexComputeCellGeometryFVM(dmCell, c, &cg->volume, cg->centroid, NULL);CHKERRQ(ierr); 1656 } 1657 /* Compute face normals and minimum cell radius */ 1658 ierr = DMClone(dm, &dmFace);CHKERRQ(ierr); 1659 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionFace);CHKERRQ(ierr); 1660 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1661 ierr = PetscSectionSetChart(sectionFace, fStart, fEnd);CHKERRQ(ierr); 1662 for (f = fStart; f < fEnd; ++f) {ierr = PetscSectionSetDof(sectionFace, f, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFVFaceGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1663 ierr = PetscSectionSetUp(sectionFace);CHKERRQ(ierr); 1664 ierr = DMSetDefaultSection(dmFace, sectionFace);CHKERRQ(ierr); 1665 ierr = PetscSectionDestroy(§ionFace);CHKERRQ(ierr); 1666 ierr = DMCreateLocalVector(dmFace, facegeom);CHKERRQ(ierr); 1667 ierr = VecGetArray(*facegeom, &fgeom);CHKERRQ(ierr); 1668 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1669 minradius = PETSC_MAX_REAL; 1670 for (f = fStart; f < fEnd; ++f) { 1671 PetscFVFaceGeom *fg; 1672 PetscReal area; 1673 PetscInt ghost = -1, d, numChildren; 1674 1675 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1676 ierr = DMPlexGetTreeChildren(dm,f,&numChildren,NULL);CHKERRQ(ierr); 1677 if (ghost >= 0 || numChildren) continue; 1678 ierr = DMPlexPointLocalRef(dmFace, f, fgeom, &fg);CHKERRQ(ierr); 1679 ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, fg->centroid, fg->normal);CHKERRQ(ierr); 1680 for (d = 0; d < dim; ++d) fg->normal[d] *= area; 1681 /* Flip face orientation if necessary to match ordering in support, and Update minimum radius */ 1682 { 1683 PetscFVCellGeom *cL, *cR; 1684 PetscInt ncells; 1685 const PetscInt *cells; 1686 PetscReal *lcentroid, *rcentroid; 1687 PetscReal l[3], r[3], v[3]; 1688 1689 ierr = DMPlexGetSupport(dm, f, &cells);CHKERRQ(ierr); 1690 ierr = DMPlexGetSupportSize(dm, f, &ncells);CHKERRQ(ierr); 1691 ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cL);CHKERRQ(ierr); 1692 lcentroid = cells[0] >= cEndInterior ? fg->centroid : cL->centroid; 1693 if (ncells > 1) { 1694 ierr = DMPlexPointLocalRead(dmCell, cells[1], cgeom, &cR);CHKERRQ(ierr); 1695 rcentroid = cells[1] >= cEndInterior ? fg->centroid : cR->centroid; 1696 } 1697 else { 1698 rcentroid = fg->centroid; 1699 } 1700 ierr = DMLocalizeCoordinateReal_Internal(dm, dim, fg->centroid, lcentroid, l);CHKERRQ(ierr); 1701 ierr = DMLocalizeCoordinateReal_Internal(dm, dim, fg->centroid, rcentroid, r);CHKERRQ(ierr); 1702 DMPlex_WaxpyD_Internal(dim, -1, l, r, v); 1703 if (DMPlex_DotRealD_Internal(dim, fg->normal, v) < 0) { 1704 for (d = 0; d < dim; ++d) fg->normal[d] = -fg->normal[d]; 1705 } 1706 if (DMPlex_DotRealD_Internal(dim, fg->normal, v) <= 0) { 1707 if (dim == 2) SETERRQ5(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g) v (%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) v[0], (double) v[1]); 1708 if (dim == 3) SETERRQ7(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed, normal (%g,%g,%g) v (%g,%g,%g)", f, (double) fg->normal[0], (double) fg->normal[1], (double) fg->normal[2], (double) v[0], (double) v[1], (double) v[2]); 1709 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed", f); 1710 } 1711 if (cells[0] < cEndInterior) { 1712 DMPlex_WaxpyD_Internal(dim, -1, fg->centroid, cL->centroid, v); 1713 minradius = PetscMin(minradius, DMPlex_NormD_Internal(dim, v)); 1714 } 1715 if (ncells > 1 && cells[1] < cEndInterior) { 1716 DMPlex_WaxpyD_Internal(dim, -1, fg->centroid, cR->centroid, v); 1717 minradius = PetscMin(minradius, DMPlex_NormD_Internal(dim, v)); 1718 } 1719 } 1720 } 1721 ierr = MPIU_Allreduce(&minradius, &gminradius, 1, MPIU_REAL, MPIU_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1722 ierr = DMPlexSetMinRadius(dm, gminradius);CHKERRQ(ierr); 1723 /* Compute centroids of ghost cells */ 1724 for (c = cEndInterior; c < cEnd; ++c) { 1725 PetscFVFaceGeom *fg; 1726 const PetscInt *cone, *support; 1727 PetscInt coneSize, supportSize, s; 1728 1729 ierr = DMPlexGetConeSize(dmCell, c, &coneSize);CHKERRQ(ierr); 1730 if (coneSize != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Ghost cell %d has cone size %d != 1", c, coneSize); 1731 ierr = DMPlexGetCone(dmCell, c, &cone);CHKERRQ(ierr); 1732 ierr = DMPlexGetSupportSize(dmCell, cone[0], &supportSize);CHKERRQ(ierr); 1733 if (supportSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %d has support size %d != 2", cone[0], supportSize); 1734 ierr = DMPlexGetSupport(dmCell, cone[0], &support);CHKERRQ(ierr); 1735 ierr = DMPlexPointLocalRef(dmFace, cone[0], fgeom, &fg);CHKERRQ(ierr); 1736 for (s = 0; s < 2; ++s) { 1737 /* Reflect ghost centroid across plane of face */ 1738 if (support[s] == c) { 1739 PetscFVCellGeom *ci; 1740 PetscFVCellGeom *cg; 1741 PetscReal c2f[3], a; 1742 1743 ierr = DMPlexPointLocalRead(dmCell, support[(s+1)%2], cgeom, &ci);CHKERRQ(ierr); 1744 DMPlex_WaxpyD_Internal(dim, -1, ci->centroid, fg->centroid, c2f); /* cell to face centroid */ 1745 a = DMPlex_DotRealD_Internal(dim, c2f, fg->normal)/DMPlex_DotRealD_Internal(dim, fg->normal, fg->normal); 1746 ierr = DMPlexPointLocalRef(dmCell, support[s], cgeom, &cg);CHKERRQ(ierr); 1747 DMPlex_WaxpyD_Internal(dim, 2*a, fg->normal, ci->centroid, cg->centroid); 1748 cg->volume = ci->volume; 1749 } 1750 } 1751 } 1752 ierr = VecRestoreArray(*facegeom, &fgeom);CHKERRQ(ierr); 1753 ierr = VecRestoreArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1754 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1755 ierr = DMDestroy(&dmFace);CHKERRQ(ierr); 1756 PetscFunctionReturn(0); 1757 } 1758 1759 #undef __FUNCT__ 1760 #define __FUNCT__ "DMPlexGetMinRadius" 1761 /*@C 1762 DMPlexGetMinRadius - Returns the minimum distance from any cell centroid to a face 1763 1764 Not collective 1765 1766 Input Argument: 1767 . dm - the DM 1768 1769 Output Argument: 1770 . minradius - the minium cell radius 1771 1772 Level: developer 1773 1774 .seealso: DMGetCoordinates() 1775 @*/ 1776 PetscErrorCode DMPlexGetMinRadius(DM dm, PetscReal *minradius) 1777 { 1778 PetscFunctionBegin; 1779 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1780 PetscValidPointer(minradius,2); 1781 *minradius = ((DM_Plex*) dm->data)->minradius; 1782 PetscFunctionReturn(0); 1783 } 1784 1785 #undef __FUNCT__ 1786 #define __FUNCT__ "DMPlexSetMinRadius" 1787 /*@C 1788 DMPlexSetMinRadius - Sets the minimum distance from the cell centroid to a face 1789 1790 Logically collective 1791 1792 Input Arguments: 1793 + dm - the DM 1794 - minradius - the minium cell radius 1795 1796 Level: developer 1797 1798 .seealso: DMSetCoordinates() 1799 @*/ 1800 PetscErrorCode DMPlexSetMinRadius(DM dm, PetscReal minradius) 1801 { 1802 PetscFunctionBegin; 1803 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1804 ((DM_Plex*) dm->data)->minradius = minradius; 1805 PetscFunctionReturn(0); 1806 } 1807 1808 #undef __FUNCT__ 1809 #define __FUNCT__ "BuildGradientReconstruction_Internal" 1810 static PetscErrorCode BuildGradientReconstruction_Internal(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom) 1811 { 1812 DMLabel ghostLabel; 1813 PetscScalar *dx, *grad, **gref; 1814 PetscInt dim, cStart, cEnd, c, cEndInterior, maxNumFaces; 1815 PetscErrorCode ierr; 1816 1817 PetscFunctionBegin; 1818 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1819 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1820 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1821 ierr = DMPlexGetMaxSizes(dm, &maxNumFaces, NULL);CHKERRQ(ierr); 1822 ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr); 1823 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1824 ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr); 1825 for (c = cStart; c < cEndInterior; c++) { 1826 const PetscInt *faces; 1827 PetscInt numFaces, usedFaces, f, d; 1828 PetscFVCellGeom *cg; 1829 PetscBool boundary; 1830 PetscInt ghost; 1831 1832 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1833 ierr = DMPlexGetConeSize(dm, c, &numFaces);CHKERRQ(ierr); 1834 ierr = DMPlexGetCone(dm, c, &faces);CHKERRQ(ierr); 1835 if (numFaces < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cell %D has only %D faces, not enough for gradient reconstruction", c, numFaces); 1836 for (f = 0, usedFaces = 0; f < numFaces; ++f) { 1837 PetscFVCellGeom *cg1; 1838 PetscFVFaceGeom *fg; 1839 const PetscInt *fcells; 1840 PetscInt ncell, side; 1841 1842 ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr); 1843 ierr = DMIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr); 1844 if ((ghost >= 0) || boundary) continue; 1845 ierr = DMPlexGetSupport(dm, faces[f], &fcells);CHKERRQ(ierr); 1846 side = (c != fcells[0]); /* c is on left=0 or right=1 of face */ 1847 ncell = fcells[!side]; /* the neighbor */ 1848 ierr = DMPlexPointLocalRef(dmFace, faces[f], fgeom, &fg);CHKERRQ(ierr); 1849 ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr); 1850 for (d = 0; d < dim; ++d) dx[usedFaces*dim+d] = cg1->centroid[d] - cg->centroid[d]; 1851 gref[usedFaces++] = fg->grad[side]; /* Gradient reconstruction term will go here */ 1852 } 1853 if (!usedFaces) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_USER, "Mesh contains isolated cell (no neighbors). Is it intentional?"); 1854 ierr = PetscFVComputeGradient(fvm, usedFaces, dx, grad);CHKERRQ(ierr); 1855 for (f = 0, usedFaces = 0; f < numFaces; ++f) { 1856 ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr); 1857 ierr = DMIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr); 1858 if ((ghost >= 0) || boundary) continue; 1859 for (d = 0; d < dim; ++d) gref[usedFaces][d] = grad[usedFaces*dim+d]; 1860 ++usedFaces; 1861 } 1862 } 1863 ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr); 1864 PetscFunctionReturn(0); 1865 } 1866 1867 #undef __FUNCT__ 1868 #define __FUNCT__ "BuildGradientReconstruction_Internal_Tree" 1869 static PetscErrorCode BuildGradientReconstruction_Internal_Tree(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom) 1870 { 1871 DMLabel ghostLabel; 1872 PetscScalar *dx, *grad, **gref; 1873 PetscInt dim, cStart, cEnd, c, cEndInterior, fStart, fEnd, f, nStart, nEnd, maxNumFaces = 0; 1874 PetscSection neighSec; 1875 PetscInt (*neighbors)[2]; 1876 PetscInt *counter; 1877 PetscErrorCode ierr; 1878 1879 PetscFunctionBegin; 1880 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1881 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1882 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1883 if (cEndInterior < 0) { 1884 cEndInterior = cEnd; 1885 } 1886 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&neighSec);CHKERRQ(ierr); 1887 ierr = PetscSectionSetChart(neighSec,cStart,cEndInterior);CHKERRQ(ierr); 1888 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1889 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1890 for (f = fStart; f < fEnd; f++) { 1891 const PetscInt *fcells; 1892 PetscBool boundary; 1893 PetscInt ghost = -1; 1894 PetscInt numChildren, numCells, c; 1895 1896 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1897 ierr = DMIsBoundaryPoint(dm, f, &boundary);CHKERRQ(ierr); 1898 ierr = DMPlexGetTreeChildren(dm, f, &numChildren, NULL);CHKERRQ(ierr); 1899 if ((ghost >= 0) || boundary || numChildren) continue; 1900 ierr = DMPlexGetSupportSize(dm, f, &numCells);CHKERRQ(ierr); 1901 if (numCells == 2) { 1902 ierr = DMPlexGetSupport(dm, f, &fcells);CHKERRQ(ierr); 1903 for (c = 0; c < 2; c++) { 1904 PetscInt cell = fcells[c]; 1905 1906 if (cell >= cStart && cell < cEndInterior) { 1907 ierr = PetscSectionAddDof(neighSec,cell,1);CHKERRQ(ierr); 1908 } 1909 } 1910 } 1911 } 1912 ierr = PetscSectionSetUp(neighSec);CHKERRQ(ierr); 1913 ierr = PetscSectionGetMaxDof(neighSec,&maxNumFaces);CHKERRQ(ierr); 1914 ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr); 1915 nStart = 0; 1916 ierr = PetscSectionGetStorageSize(neighSec,&nEnd);CHKERRQ(ierr); 1917 ierr = PetscMalloc1((nEnd-nStart),&neighbors);CHKERRQ(ierr); 1918 ierr = PetscCalloc1((cEndInterior-cStart),&counter);CHKERRQ(ierr); 1919 for (f = fStart; f < fEnd; f++) { 1920 const PetscInt *fcells; 1921 PetscBool boundary; 1922 PetscInt ghost = -1; 1923 PetscInt numChildren, numCells, c; 1924 1925 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1926 ierr = DMIsBoundaryPoint(dm, f, &boundary);CHKERRQ(ierr); 1927 ierr = DMPlexGetTreeChildren(dm, f, &numChildren, NULL);CHKERRQ(ierr); 1928 if ((ghost >= 0) || boundary || numChildren) continue; 1929 ierr = DMPlexGetSupportSize(dm, f, &numCells);CHKERRQ(ierr); 1930 if (numCells == 2) { 1931 ierr = DMPlexGetSupport(dm, f, &fcells);CHKERRQ(ierr); 1932 for (c = 0; c < 2; c++) { 1933 PetscInt cell = fcells[c], off; 1934 1935 if (cell >= cStart && cell < cEndInterior) { 1936 ierr = PetscSectionGetOffset(neighSec,cell,&off);CHKERRQ(ierr); 1937 off += counter[cell - cStart]++; 1938 neighbors[off][0] = f; 1939 neighbors[off][1] = fcells[1 - c]; 1940 } 1941 } 1942 } 1943 } 1944 ierr = PetscFree(counter);CHKERRQ(ierr); 1945 ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr); 1946 for (c = cStart; c < cEndInterior; c++) { 1947 PetscInt numFaces, f, d, off, ghost = -1; 1948 PetscFVCellGeom *cg; 1949 1950 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1951 ierr = PetscSectionGetDof(neighSec, c, &numFaces);CHKERRQ(ierr); 1952 ierr = PetscSectionGetOffset(neighSec, c, &off);CHKERRQ(ierr); 1953 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, c, &ghost);CHKERRQ(ierr);} 1954 if (ghost < 0 && numFaces < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cell %D has only %D faces, not enough for gradient reconstruction", c, numFaces); 1955 for (f = 0; f < numFaces; ++f) { 1956 PetscFVCellGeom *cg1; 1957 PetscFVFaceGeom *fg; 1958 const PetscInt *fcells; 1959 PetscInt ncell, side, nface; 1960 1961 nface = neighbors[off + f][0]; 1962 ncell = neighbors[off + f][1]; 1963 ierr = DMPlexGetSupport(dm,nface,&fcells);CHKERRQ(ierr); 1964 side = (c != fcells[0]); 1965 ierr = DMPlexPointLocalRef(dmFace, nface, fgeom, &fg);CHKERRQ(ierr); 1966 ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr); 1967 for (d = 0; d < dim; ++d) dx[f*dim+d] = cg1->centroid[d] - cg->centroid[d]; 1968 gref[f] = fg->grad[side]; /* Gradient reconstruction term will go here */ 1969 } 1970 ierr = PetscFVComputeGradient(fvm, numFaces, dx, grad);CHKERRQ(ierr); 1971 for (f = 0; f < numFaces; ++f) { 1972 for (d = 0; d < dim; ++d) gref[f][d] = grad[f*dim+d]; 1973 } 1974 } 1975 ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr); 1976 ierr = PetscSectionDestroy(&neighSec);CHKERRQ(ierr); 1977 ierr = PetscFree(neighbors);CHKERRQ(ierr); 1978 PetscFunctionReturn(0); 1979 } 1980 1981 #undef __FUNCT__ 1982 #define __FUNCT__ "DMPlexComputeGradientFVM" 1983 /*@ 1984 DMPlexComputeGradientFVM - Compute geometric factors for gradient reconstruction, which are stored in the geometry data, and compute layout for gradient data 1985 1986 Collective on DM 1987 1988 Input Arguments: 1989 + dm - The DM 1990 . fvm - The PetscFV 1991 . faceGeometry - The face geometry from DMPlexComputeFaceGeometryFVM() 1992 - cellGeometry - The face geometry from DMPlexComputeCellGeometryFVM() 1993 1994 Output Parameters: 1995 + faceGeometry - The geometric factors for gradient calculation are inserted 1996 - dmGrad - The DM describing the layout of gradient data 1997 1998 Level: developer 1999 2000 .seealso: DMPlexGetFaceGeometryFVM(), DMPlexGetCellGeometryFVM() 2001 @*/ 2002 PetscErrorCode DMPlexComputeGradientFVM(DM dm, PetscFV fvm, Vec faceGeometry, Vec cellGeometry, DM *dmGrad) 2003 { 2004 DM dmFace, dmCell; 2005 PetscScalar *fgeom, *cgeom; 2006 PetscSection sectionGrad, parentSection; 2007 PetscInt dim, pdim, cStart, cEnd, cEndInterior, c; 2008 PetscErrorCode ierr; 2009 2010 PetscFunctionBegin; 2011 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2012 ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr); 2013 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2014 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2015 /* Construct the interpolant corresponding to each face from the least-square solution over the cell neighborhood */ 2016 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 2017 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 2018 ierr = VecGetArray(faceGeometry, &fgeom);CHKERRQ(ierr); 2019 ierr = VecGetArray(cellGeometry, &cgeom);CHKERRQ(ierr); 2020 ierr = DMPlexGetTree(dm,&parentSection,NULL,NULL,NULL,NULL);CHKERRQ(ierr); 2021 if (!parentSection) { 2022 ierr = BuildGradientReconstruction_Internal(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr); 2023 } else { 2024 ierr = BuildGradientReconstruction_Internal_Tree(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr); 2025 } 2026 ierr = VecRestoreArray(faceGeometry, &fgeom);CHKERRQ(ierr); 2027 ierr = VecRestoreArray(cellGeometry, &cgeom);CHKERRQ(ierr); 2028 /* Create storage for gradients */ 2029 ierr = DMClone(dm, dmGrad);CHKERRQ(ierr); 2030 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionGrad);CHKERRQ(ierr); 2031 ierr = PetscSectionSetChart(sectionGrad, cStart, cEnd);CHKERRQ(ierr); 2032 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionGrad, c, pdim*dim);CHKERRQ(ierr);} 2033 ierr = PetscSectionSetUp(sectionGrad);CHKERRQ(ierr); 2034 ierr = DMSetDefaultSection(*dmGrad, sectionGrad);CHKERRQ(ierr); 2035 ierr = PetscSectionDestroy(§ionGrad);CHKERRQ(ierr); 2036 PetscFunctionReturn(0); 2037 } 2038