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 = -1; 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 = -1; 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 = -1; 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 = -1; 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 = -1; 592 cells[p].index = -1; 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].rank < 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 (numFound < numPoints) { 649 if (ltype == DM_POINTLOCATION_NEAREST) SETERRQ(PetscObjectComm((PetscObject) dm), PETSC_ERR_SUP, "Nearest point location does not support parallel point location."); 650 ierr = PetscMalloc1(numFound,&found);CHKERRQ(ierr); 651 for (p = 0, numFound = 0; p < numPoints; p++) { 652 if (cells[p].rank >= 0 && cells[p].index >= 0) { 653 if (numFound < p) { 654 cells[numFound] = cells[p]; 655 } 656 found[numFound++] = p; 657 } 658 } 659 } 660 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 661 ierr = PetscSFSetGraph(cellSF, cEnd - cStart, numFound, found, PETSC_OWN_POINTER, cells, PETSC_OWN_POINTER);CHKERRQ(ierr); 662 PetscFunctionReturn(0); 663 } 664 665 #undef __FUNCT__ 666 #define __FUNCT__ "DMPlexComputeProjection2Dto1D_Internal" 667 /* 668 DMPlexComputeProjection2Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 2D 669 */ 670 PetscErrorCode DMPlexComputeProjection2Dto1D_Internal(PetscScalar coords[], PetscReal R[]) 671 { 672 const PetscReal x = PetscRealPart(coords[2] - coords[0]); 673 const PetscReal y = PetscRealPart(coords[3] - coords[1]); 674 const PetscReal r = PetscSqrtReal(x*x + y*y), c = x/r, s = y/r; 675 676 PetscFunctionBegin; 677 R[0] = c; R[1] = -s; 678 R[2] = s; R[3] = c; 679 coords[0] = 0.0; 680 coords[1] = r; 681 PetscFunctionReturn(0); 682 } 683 684 #undef __FUNCT__ 685 #define __FUNCT__ "DMPlexComputeProjection3Dto1D_Internal" 686 /* 687 DMPlexComputeProjection3Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 3D 688 689 This uses the basis completion described by Frisvad, 690 691 http://www.imm.dtu.dk/~jerf/papers/abstracts/onb.html 692 DOI:10.1080/2165347X.2012.689606 693 */ 694 PetscErrorCode DMPlexComputeProjection3Dto1D_Internal(PetscScalar coords[], PetscReal R[]) 695 { 696 PetscReal x = PetscRealPart(coords[3] - coords[0]); 697 PetscReal y = PetscRealPart(coords[4] - coords[1]); 698 PetscReal z = PetscRealPart(coords[5] - coords[2]); 699 PetscReal r = PetscSqrtReal(x*x + y*y + z*z); 700 PetscReal rinv = 1. / r; 701 PetscFunctionBegin; 702 703 x *= rinv; y *= rinv; z *= rinv; 704 if (x > 0.) { 705 PetscReal inv1pX = 1./ (1. + x); 706 707 R[0] = x; R[1] = -y; R[2] = -z; 708 R[3] = y; R[4] = 1. - y*y*inv1pX; R[5] = -y*z*inv1pX; 709 R[6] = z; R[7] = -y*z*inv1pX; R[8] = 1. - z*z*inv1pX; 710 } 711 else { 712 PetscReal inv1mX = 1./ (1. - x); 713 714 R[0] = x; R[1] = z; R[2] = y; 715 R[3] = y; R[4] = -y*z*inv1mX; R[5] = 1. - y*y*inv1mX; 716 R[6] = z; R[7] = 1. - z*z*inv1mX; R[8] = -y*z*inv1mX; 717 } 718 coords[0] = 0.0; 719 coords[1] = r; 720 PetscFunctionReturn(0); 721 } 722 723 #undef __FUNCT__ 724 #define __FUNCT__ "DMPlexComputeProjection3Dto2D_Internal" 725 /* 726 DMPlexComputeProjection3Dto2D_Internal - Rewrite coordinates to be the 2D projection of the 3D 727 */ 728 PetscErrorCode DMPlexComputeProjection3Dto2D_Internal(PetscInt coordSize, PetscScalar coords[], PetscReal R[]) 729 { 730 PetscReal x1[3], x2[3], n[3], norm; 731 PetscReal x1p[3], x2p[3], xnp[3]; 732 PetscReal sqrtz, alpha; 733 const PetscInt dim = 3; 734 PetscInt d, e, p; 735 736 PetscFunctionBegin; 737 /* 0) Calculate normal vector */ 738 for (d = 0; d < dim; ++d) { 739 x1[d] = PetscRealPart(coords[1*dim+d] - coords[0*dim+d]); 740 x2[d] = PetscRealPart(coords[2*dim+d] - coords[0*dim+d]); 741 } 742 n[0] = x1[1]*x2[2] - x1[2]*x2[1]; 743 n[1] = x1[2]*x2[0] - x1[0]*x2[2]; 744 n[2] = x1[0]*x2[1] - x1[1]*x2[0]; 745 norm = PetscSqrtReal(n[0]*n[0] + n[1]*n[1] + n[2]*n[2]); 746 n[0] /= norm; 747 n[1] /= norm; 748 n[2] /= norm; 749 /* 1) Take the normal vector and rotate until it is \hat z 750 751 Let the normal vector be <nx, ny, nz> and alpha = 1/sqrt(1 - nz^2), then 752 753 R = / alpha nx nz alpha ny nz -1/alpha \ 754 | -alpha ny alpha nx 0 | 755 \ nx ny nz / 756 757 will rotate the normal vector to \hat z 758 */ 759 sqrtz = PetscSqrtReal(1.0 - n[2]*n[2]); 760 /* Check for n = z */ 761 if (sqrtz < 1.0e-10) { 762 const PetscInt s = PetscSign(n[2]); 763 /* If nz < 0, rotate 180 degrees around x-axis */ 764 for (p = 3; p < coordSize/3; ++p) { 765 coords[p*2+0] = PetscRealPart(coords[p*dim+0] - coords[0*dim+0]); 766 coords[p*2+1] = (PetscRealPart(coords[p*dim+1] - coords[0*dim+1])) * s; 767 } 768 coords[0] = 0.0; 769 coords[1] = 0.0; 770 coords[2] = x1[0]; 771 coords[3] = x1[1] * s; 772 coords[4] = x2[0]; 773 coords[5] = x2[1] * s; 774 R[0] = 1.0; R[1] = 0.0; R[2] = 0.0; 775 R[3] = 0.0; R[4] = 1.0 * s; R[5] = 0.0; 776 R[6] = 0.0; R[7] = 0.0; R[8] = 1.0 * s; 777 PetscFunctionReturn(0); 778 } 779 alpha = 1.0/sqrtz; 780 R[0] = alpha*n[0]*n[2]; R[1] = alpha*n[1]*n[2]; R[2] = -sqrtz; 781 R[3] = -alpha*n[1]; R[4] = alpha*n[0]; R[5] = 0.0; 782 R[6] = n[0]; R[7] = n[1]; R[8] = n[2]; 783 for (d = 0; d < dim; ++d) { 784 x1p[d] = 0.0; 785 x2p[d] = 0.0; 786 for (e = 0; e < dim; ++e) { 787 x1p[d] += R[d*dim+e]*x1[e]; 788 x2p[d] += R[d*dim+e]*x2[e]; 789 } 790 } 791 if (PetscAbsReal(x1p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); 792 if (PetscAbsReal(x2p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); 793 /* 2) Project to (x, y) */ 794 for (p = 3; p < coordSize/3; ++p) { 795 for (d = 0; d < dim; ++d) { 796 xnp[d] = 0.0; 797 for (e = 0; e < dim; ++e) { 798 xnp[d] += R[d*dim+e]*PetscRealPart(coords[p*dim+e] - coords[0*dim+e]); 799 } 800 if (d < dim-1) coords[p*2+d] = xnp[d]; 801 } 802 } 803 coords[0] = 0.0; 804 coords[1] = 0.0; 805 coords[2] = x1p[0]; 806 coords[3] = x1p[1]; 807 coords[4] = x2p[0]; 808 coords[5] = x2p[1]; 809 /* Output R^T which rotates \hat z to the input normal */ 810 for (d = 0; d < dim; ++d) { 811 for (e = d+1; e < dim; ++e) { 812 PetscReal tmp; 813 814 tmp = R[d*dim+e]; 815 R[d*dim+e] = R[e*dim+d]; 816 R[e*dim+d] = tmp; 817 } 818 } 819 PetscFunctionReturn(0); 820 } 821 822 #undef __FUNCT__ 823 #define __FUNCT__ "Volume_Triangle_Internal" 824 PETSC_UNUSED 825 PETSC_STATIC_INLINE void Volume_Triangle_Internal(PetscReal *vol, PetscReal coords[]) 826 { 827 /* Signed volume is 1/2 the determinant 828 829 | 1 1 1 | 830 | x0 x1 x2 | 831 | y0 y1 y2 | 832 833 but if x0,y0 is the origin, we have 834 835 | x1 x2 | 836 | y1 y2 | 837 */ 838 const PetscReal x1 = coords[2] - coords[0], y1 = coords[3] - coords[1]; 839 const PetscReal x2 = coords[4] - coords[0], y2 = coords[5] - coords[1]; 840 PetscReal M[4], detM; 841 M[0] = x1; M[1] = x2; 842 M[2] = y1; M[3] = y2; 843 DMPlex_Det2D_Internal(&detM, M); 844 *vol = 0.5*detM; 845 (void)PetscLogFlops(5.0); 846 } 847 848 #undef __FUNCT__ 849 #define __FUNCT__ "Volume_Triangle_Origin_Internal" 850 PETSC_STATIC_INLINE void Volume_Triangle_Origin_Internal(PetscReal *vol, PetscReal coords[]) 851 { 852 DMPlex_Det2D_Internal(vol, coords); 853 *vol *= 0.5; 854 } 855 856 #undef __FUNCT__ 857 #define __FUNCT__ "Volume_Tetrahedron_Internal" 858 PETSC_UNUSED 859 PETSC_STATIC_INLINE void Volume_Tetrahedron_Internal(PetscReal *vol, PetscReal coords[]) 860 { 861 /* Signed volume is 1/6th of the determinant 862 863 | 1 1 1 1 | 864 | x0 x1 x2 x3 | 865 | y0 y1 y2 y3 | 866 | z0 z1 z2 z3 | 867 868 but if x0,y0,z0 is the origin, we have 869 870 | x1 x2 x3 | 871 | y1 y2 y3 | 872 | z1 z2 z3 | 873 */ 874 const PetscReal x1 = coords[3] - coords[0], y1 = coords[4] - coords[1], z1 = coords[5] - coords[2]; 875 const PetscReal x2 = coords[6] - coords[0], y2 = coords[7] - coords[1], z2 = coords[8] - coords[2]; 876 const PetscReal x3 = coords[9] - coords[0], y3 = coords[10] - coords[1], z3 = coords[11] - coords[2]; 877 PetscReal M[9], detM; 878 M[0] = x1; M[1] = x2; M[2] = x3; 879 M[3] = y1; M[4] = y2; M[5] = y3; 880 M[6] = z1; M[7] = z2; M[8] = z3; 881 DMPlex_Det3D_Internal(&detM, M); 882 *vol = -0.16666666666666666666666*detM; 883 (void)PetscLogFlops(10.0); 884 } 885 886 #undef __FUNCT__ 887 #define __FUNCT__ "Volume_Tetrahedron_Origin_Internal" 888 PETSC_STATIC_INLINE void Volume_Tetrahedron_Origin_Internal(PetscReal *vol, PetscReal coords[]) 889 { 890 DMPlex_Det3D_Internal(vol, coords); 891 *vol *= -0.16666666666666666666666; 892 } 893 894 #undef __FUNCT__ 895 #define __FUNCT__ "DMPlexComputeLineGeometry_Internal" 896 static PetscErrorCode DMPlexComputeLineGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 897 { 898 PetscSection coordSection; 899 Vec coordinates; 900 PetscScalar *coords = NULL; 901 PetscInt numCoords, d, pStart, pEnd, numSelfCoords = 0; 902 PetscErrorCode ierr; 903 904 PetscFunctionBegin; 905 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 906 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 907 ierr = PetscSectionGetChart(coordSection,&pStart,&pEnd);CHKERRQ(ierr); 908 if (e >= pStart && e < pEnd) {ierr = PetscSectionGetDof(coordSection,e,&numSelfCoords);CHKERRQ(ierr);} 909 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 910 numCoords = numSelfCoords ? numSelfCoords : numCoords; 911 if (invJ && !J) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "In order to compute invJ, J must not be NULL"); 912 *detJ = 0.0; 913 if (numCoords == 6) { 914 const PetscInt dim = 3; 915 PetscReal R[9], J0; 916 917 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 918 ierr = DMPlexComputeProjection3Dto1D_Internal(coords, R);CHKERRQ(ierr); 919 if (J) { 920 J0 = 0.5*PetscRealPart(coords[1]); 921 J[0] = R[0]*J0; J[1] = R[1]; J[2] = R[2]; 922 J[3] = R[3]*J0; J[4] = R[4]; J[5] = R[5]; 923 J[6] = R[6]*J0; J[7] = R[7]; J[8] = R[8]; 924 DMPlex_Det3D_Internal(detJ, J); 925 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 926 } 927 } else if (numCoords == 4) { 928 const PetscInt dim = 2; 929 PetscReal R[4], J0; 930 931 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 932 ierr = DMPlexComputeProjection2Dto1D_Internal(coords, R);CHKERRQ(ierr); 933 if (J) { 934 J0 = 0.5*PetscRealPart(coords[1]); 935 J[0] = R[0]*J0; J[1] = R[1]; 936 J[2] = R[2]*J0; J[3] = R[3]; 937 DMPlex_Det2D_Internal(detJ, J); 938 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 939 } 940 } else if (numCoords == 2) { 941 const PetscInt dim = 1; 942 943 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 944 if (J) { 945 J[0] = 0.5*(PetscRealPart(coords[1]) - PetscRealPart(coords[0])); 946 *detJ = J[0]; 947 ierr = PetscLogFlops(2.0);CHKERRQ(ierr); 948 if (invJ) {invJ[0] = 1.0/J[0]; ierr = PetscLogFlops(1.0);CHKERRQ(ierr);} 949 } 950 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this segment is %D != 2", numCoords); 951 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 952 PetscFunctionReturn(0); 953 } 954 955 #undef __FUNCT__ 956 #define __FUNCT__ "DMPlexComputeTriangleGeometry_Internal" 957 static PetscErrorCode DMPlexComputeTriangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 958 { 959 PetscSection coordSection; 960 Vec coordinates; 961 PetscScalar *coords = NULL; 962 PetscInt numCoords, d, f, g; 963 PetscErrorCode ierr; 964 965 PetscFunctionBegin; 966 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 967 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 968 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 969 *detJ = 0.0; 970 if (numCoords == 9) { 971 const PetscInt dim = 3; 972 PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; 973 974 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 975 ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); 976 if (J) { 977 const PetscInt pdim = 2; 978 979 for (d = 0; d < pdim; d++) { 980 for (f = 0; f < pdim; f++) { 981 J0[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 982 } 983 } 984 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 985 DMPlex_Det3D_Internal(detJ, J0); 986 for (d = 0; d < dim; d++) { 987 for (f = 0; f < dim; f++) { 988 J[d*dim+f] = 0.0; 989 for (g = 0; g < dim; g++) { 990 J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; 991 } 992 } 993 } 994 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 995 } 996 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 997 } else if (numCoords == 6) { 998 const PetscInt dim = 2; 999 1000 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1001 if (J) { 1002 for (d = 0; d < dim; d++) { 1003 for (f = 0; f < dim; f++) { 1004 J[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); 1005 } 1006 } 1007 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 1008 DMPlex_Det2D_Internal(detJ, J); 1009 } 1010 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 1011 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this triangle is %D != 6 or 9", numCoords); 1012 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 1013 PetscFunctionReturn(0); 1014 } 1015 1016 #undef __FUNCT__ 1017 #define __FUNCT__ "DMPlexComputeRectangleGeometry_Internal" 1018 static PetscErrorCode DMPlexComputeRectangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1019 { 1020 PetscSection coordSection; 1021 Vec coordinates; 1022 PetscScalar *coords = NULL; 1023 PetscInt numCoords, numSelfCoords = 0, d, f, g, pStart, pEnd; 1024 PetscErrorCode ierr; 1025 1026 PetscFunctionBegin; 1027 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1028 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1029 ierr = PetscSectionGetChart(coordSection,&pStart,&pEnd);CHKERRQ(ierr); 1030 if (e >= pStart && e < pEnd) {ierr = PetscSectionGetDof(coordSection,e,&numSelfCoords);CHKERRQ(ierr);} 1031 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 1032 numCoords = numSelfCoords ? numSelfCoords : numCoords; 1033 *detJ = 0.0; 1034 if (numCoords == 12) { 1035 const PetscInt dim = 3; 1036 PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; 1037 1038 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1039 ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); 1040 if (J) { 1041 const PetscInt pdim = 2; 1042 1043 for (d = 0; d < pdim; d++) { 1044 J0[d*dim+0] = 0.5*(PetscRealPart(coords[1*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 1045 J0[d*dim+1] = 0.5*(PetscRealPart(coords[3*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 1046 } 1047 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 1048 DMPlex_Det3D_Internal(detJ, J0); 1049 for (d = 0; d < dim; d++) { 1050 for (f = 0; f < dim; f++) { 1051 J[d*dim+f] = 0.0; 1052 for (g = 0; g < dim; g++) { 1053 J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; 1054 } 1055 } 1056 } 1057 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 1058 } 1059 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1060 } else if (numCoords == 8) { 1061 const PetscInt dim = 2; 1062 1063 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1064 if (J) { 1065 for (d = 0; d < dim; d++) { 1066 J[d*dim+0] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 1067 J[d*dim+1] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 1068 } 1069 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 1070 DMPlex_Det2D_Internal(detJ, J); 1071 } 1072 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 1073 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this quadrilateral is %D != 8 or 12", numCoords); 1074 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 1075 PetscFunctionReturn(0); 1076 } 1077 1078 #undef __FUNCT__ 1079 #define __FUNCT__ "DMPlexComputeTetrahedronGeometry_Internal" 1080 static PetscErrorCode DMPlexComputeTetrahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1081 { 1082 PetscSection coordSection; 1083 Vec coordinates; 1084 PetscScalar *coords = NULL; 1085 const PetscInt dim = 3; 1086 PetscInt d; 1087 PetscErrorCode ierr; 1088 1089 PetscFunctionBegin; 1090 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1091 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1092 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 1093 *detJ = 0.0; 1094 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1095 if (J) { 1096 for (d = 0; d < dim; d++) { 1097 /* I orient with outward face normals */ 1098 J[d*dim+0] = 0.5*(PetscRealPart(coords[2*dim+d]) - PetscRealPart(coords[0*dim+d])); 1099 J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 1100 J[d*dim+2] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 1101 } 1102 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 1103 DMPlex_Det3D_Internal(detJ, J); 1104 } 1105 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1106 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 1107 PetscFunctionReturn(0); 1108 } 1109 1110 #undef __FUNCT__ 1111 #define __FUNCT__ "DMPlexComputeHexahedronGeometry_Internal" 1112 static PetscErrorCode DMPlexComputeHexahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1113 { 1114 PetscSection coordSection; 1115 Vec coordinates; 1116 PetscScalar *coords = NULL; 1117 const PetscInt dim = 3; 1118 PetscInt d; 1119 PetscErrorCode ierr; 1120 1121 PetscFunctionBegin; 1122 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1123 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1124 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 1125 *detJ = 0.0; 1126 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 1127 if (J) { 1128 for (d = 0; d < dim; d++) { 1129 J[d*dim+0] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 1130 J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 1131 J[d*dim+2] = 0.5*(PetscRealPart(coords[4*dim+d]) - PetscRealPart(coords[0*dim+d])); 1132 } 1133 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 1134 DMPlex_Det3D_Internal(detJ, J); 1135 } 1136 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1137 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 1138 PetscFunctionReturn(0); 1139 } 1140 1141 #undef __FUNCT__ 1142 #define __FUNCT__ "DMPlexComputeCellGeometryAffineFEM" 1143 /*@C 1144 DMPlexComputeCellGeometryAffineFEM - Assuming an affine map, compute the Jacobian, inverse Jacobian, and Jacobian determinant for a given cell 1145 1146 Collective on DM 1147 1148 Input Arguments: 1149 + dm - the DM 1150 - cell - the cell 1151 1152 Output Arguments: 1153 + v0 - the translation part of this affine transform 1154 . J - the Jacobian of the transform from the reference element 1155 . invJ - the inverse of the Jacobian 1156 - detJ - the Jacobian determinant 1157 1158 Level: advanced 1159 1160 Fortran Notes: 1161 Since it returns arrays, this routine is only available in Fortran 90, and you must 1162 include petsc.h90 in your code. 1163 1164 .seealso: DMPlexComputeCellGeometryFEM(), DMGetCoordinateSection(), DMGetCoordinateVec() 1165 @*/ 1166 PetscErrorCode DMPlexComputeCellGeometryAffineFEM(DM dm, PetscInt cell, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) 1167 { 1168 PetscInt depth, dim, coneSize; 1169 PetscErrorCode ierr; 1170 1171 PetscFunctionBegin; 1172 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1173 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1174 if (depth == 1) { 1175 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1176 } else { 1177 DMLabel depth; 1178 1179 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1180 ierr = DMLabelGetValue(depth, cell, &dim);CHKERRQ(ierr); 1181 } 1182 switch (dim) { 1183 case 1: 1184 ierr = DMPlexComputeLineGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1185 break; 1186 case 2: 1187 switch (coneSize) { 1188 case 3: 1189 ierr = DMPlexComputeTriangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1190 break; 1191 case 4: 1192 ierr = DMPlexComputeRectangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1193 break; 1194 default: 1195 SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of faces %D in cell %D for element geometry computation", coneSize, cell); 1196 } 1197 break; 1198 case 3: 1199 switch (coneSize) { 1200 case 4: 1201 ierr = DMPlexComputeTetrahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1202 break; 1203 case 6: /* Faces */ 1204 case 8: /* Vertices */ 1205 ierr = DMPlexComputeHexahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1206 break; 1207 default: 1208 SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of faces %D in cell %D for element geometry computation", coneSize, cell); 1209 } 1210 break; 1211 default: 1212 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); 1213 } 1214 PetscFunctionReturn(0); 1215 } 1216 1217 #undef __FUNCT__ 1218 #define __FUNCT__ "DMPlexComputeIsoparametricGeometry_Internal" 1219 static PetscErrorCode DMPlexComputeIsoparametricGeometry_Internal(DM dm, PetscFE fe, PetscInt point, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1220 { 1221 PetscQuadrature quad; 1222 PetscSection coordSection; 1223 Vec coordinates; 1224 PetscScalar *coords = NULL; 1225 const PetscReal *quadPoints; 1226 PetscReal *basisDer; 1227 PetscInt dim, cdim, pdim, qdim, Nq, numCoords, d, q; 1228 PetscErrorCode ierr; 1229 1230 PetscFunctionBegin; 1231 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1232 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1233 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, point, &numCoords, &coords);CHKERRQ(ierr); 1234 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1235 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 1236 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1237 ierr = PetscFEGetDimension(fe, &pdim);CHKERRQ(ierr); 1238 ierr = PetscQuadratureGetData(quad, &qdim, &Nq, &quadPoints, NULL);CHKERRQ(ierr); 1239 ierr = PetscFEGetDefaultTabulation(fe, NULL, &basisDer, NULL);CHKERRQ(ierr); 1240 *detJ = 0.0; 1241 if (qdim != dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Point dimension %d != quadrature dimension %d", dim, qdim); 1242 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); 1243 if (v0) {for (d = 0; d < cdim; d++) v0[d] = PetscRealPart(coords[d]);} 1244 if (J) { 1245 ierr = PetscMemzero(J, Nq*cdim*dim*sizeof(PetscReal));CHKERRQ(ierr); 1246 for (q = 0; q < Nq; ++q) { 1247 PetscInt i, j, k, c, r; 1248 1249 /* J = dx_i/d\xi_j = sum[k=0,n-1] dN_k/d\xi_j * x_i(k) */ 1250 for (k = 0; k < pdim; ++k) 1251 for (j = 0; j < dim; ++j) 1252 for (i = 0; i < cdim; ++i) 1253 J[(q*cdim + i)*dim + j] += basisDer[(q*pdim + k)*dim + j] * PetscRealPart(coords[k*cdim + i]); 1254 ierr = PetscLogFlops(2.0*pdim*dim*cdim);CHKERRQ(ierr); 1255 if (cdim > dim) { 1256 for (c = dim; c < cdim; ++c) 1257 for (r = 0; r < cdim; ++r) 1258 J[r*cdim+c] = r == c ? 1.0 : 0.0; 1259 } 1260 switch (cdim) { 1261 case 3: 1262 DMPlex_Det3D_Internal(detJ, J); 1263 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1264 break; 1265 case 2: 1266 DMPlex_Det2D_Internal(detJ, J); 1267 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 1268 break; 1269 case 1: 1270 *detJ = J[0]; 1271 if (invJ) invJ[0] = 1.0/J[0]; 1272 } 1273 } 1274 } 1275 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, point, &numCoords, &coords);CHKERRQ(ierr); 1276 PetscFunctionReturn(0); 1277 } 1278 1279 #undef __FUNCT__ 1280 #define __FUNCT__ "DMPlexComputeCellGeometryFEM" 1281 /*@C 1282 DMPlexComputeCellGeometryFEM - Compute the Jacobian, inverse Jacobian, and Jacobian determinant at each quadrature point in the given cell 1283 1284 Collective on DM 1285 1286 Input Arguments: 1287 + dm - the DM 1288 . cell - the cell 1289 - fe - the finite element containing the quadrature 1290 1291 Output Arguments: 1292 + v0 - the translation part of this transform 1293 . J - the Jacobian of the transform from the reference element at each quadrature point 1294 . invJ - the inverse of the Jacobian at each quadrature point 1295 - detJ - the Jacobian determinant at each quadrature point 1296 1297 Level: advanced 1298 1299 Fortran Notes: 1300 Since it returns arrays, this routine is only available in Fortran 90, and you must 1301 include petsc.h90 in your code. 1302 1303 .seealso: DMGetCoordinateSection(), DMGetCoordinateVec() 1304 @*/ 1305 PetscErrorCode DMPlexComputeCellGeometryFEM(DM dm, PetscInt cell, PetscFE fe, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) 1306 { 1307 PetscErrorCode ierr; 1308 1309 PetscFunctionBegin; 1310 if (!fe) {ierr = DMPlexComputeCellGeometryAffineFEM(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr);} 1311 else {ierr = DMPlexComputeIsoparametricGeometry_Internal(dm, fe, cell, v0, J, invJ, detJ);CHKERRQ(ierr);} 1312 PetscFunctionReturn(0); 1313 } 1314 1315 #undef __FUNCT__ 1316 #define __FUNCT__ "DMPlexComputeGeometryFVM_1D_Internal" 1317 static PetscErrorCode DMPlexComputeGeometryFVM_1D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1318 { 1319 PetscSection coordSection; 1320 Vec coordinates; 1321 PetscScalar *coords = NULL; 1322 PetscScalar tmp[2]; 1323 PetscInt coordSize; 1324 PetscErrorCode ierr; 1325 1326 PetscFunctionBegin; 1327 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1328 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1329 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1330 if (dim != 2) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "We only support 2D edges right now"); 1331 ierr = DMLocalizeCoordinate_Internal(dm, dim, coords, &coords[dim], tmp);CHKERRQ(ierr); 1332 if (centroid) { 1333 centroid[0] = 0.5*PetscRealPart(coords[0] + tmp[0]); 1334 centroid[1] = 0.5*PetscRealPart(coords[1] + tmp[1]); 1335 } 1336 if (normal) { 1337 PetscReal norm; 1338 1339 normal[0] = -PetscRealPart(coords[1] - tmp[1]); 1340 normal[1] = PetscRealPart(coords[0] - tmp[0]); 1341 norm = PetscSqrtReal(normal[0]*normal[0] + normal[1]*normal[1]); 1342 normal[0] /= norm; 1343 normal[1] /= norm; 1344 } 1345 if (vol) { 1346 *vol = PetscSqrtReal(PetscSqr(PetscRealPart(coords[0] - tmp[0])) + PetscSqr(PetscRealPart(coords[1] - tmp[1]))); 1347 } 1348 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1349 PetscFunctionReturn(0); 1350 } 1351 1352 #undef __FUNCT__ 1353 #define __FUNCT__ "DMPlexComputeGeometryFVM_2D_Internal" 1354 /* Centroid_i = (\sum_n A_n Cn_i ) / A */ 1355 static PetscErrorCode DMPlexComputeGeometryFVM_2D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1356 { 1357 PetscSection coordSection; 1358 Vec coordinates; 1359 PetscScalar *coords = NULL; 1360 PetscReal vsum = 0.0, csum[3] = {0.0, 0.0, 0.0}, vtmp, ctmp[4], v0[3], R[9]; 1361 PetscInt tdim = 2, coordSize, numCorners, p, d, e; 1362 PetscErrorCode ierr; 1363 1364 PetscFunctionBegin; 1365 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1366 ierr = DMPlexGetConeSize(dm, cell, &numCorners);CHKERRQ(ierr); 1367 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1368 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1369 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 1370 if (dim > 2 && centroid) { 1371 v0[0] = PetscRealPart(coords[0]); 1372 v0[1] = PetscRealPart(coords[1]); 1373 v0[2] = PetscRealPart(coords[2]); 1374 } 1375 if (normal) { 1376 if (dim > 2) { 1377 const PetscReal x0 = PetscRealPart(coords[dim+0] - coords[0]), x1 = PetscRealPart(coords[dim*2+0] - coords[0]); 1378 const PetscReal y0 = PetscRealPart(coords[dim+1] - coords[1]), y1 = PetscRealPart(coords[dim*2+1] - coords[1]); 1379 const PetscReal z0 = PetscRealPart(coords[dim+2] - coords[2]), z1 = PetscRealPart(coords[dim*2+2] - coords[2]); 1380 PetscReal norm; 1381 1382 normal[0] = y0*z1 - z0*y1; 1383 normal[1] = z0*x1 - x0*z1; 1384 normal[2] = x0*y1 - y0*x1; 1385 norm = PetscSqrtReal(normal[0]*normal[0] + normal[1]*normal[1] + normal[2]*normal[2]); 1386 normal[0] /= norm; 1387 normal[1] /= norm; 1388 normal[2] /= norm; 1389 } else { 1390 for (d = 0; d < dim; ++d) normal[d] = 0.0; 1391 } 1392 } 1393 if (dim == 3) {ierr = DMPlexComputeProjection3Dto2D_Internal(coordSize, coords, R);CHKERRQ(ierr);} 1394 for (p = 0; p < numCorners; ++p) { 1395 /* Need to do this copy to get types right */ 1396 for (d = 0; d < tdim; ++d) { 1397 ctmp[d] = PetscRealPart(coords[p*tdim+d]); 1398 ctmp[tdim+d] = PetscRealPart(coords[((p+1)%numCorners)*tdim+d]); 1399 } 1400 Volume_Triangle_Origin_Internal(&vtmp, ctmp); 1401 vsum += vtmp; 1402 for (d = 0; d < tdim; ++d) { 1403 csum[d] += (ctmp[d] + ctmp[tdim+d])*vtmp; 1404 } 1405 } 1406 for (d = 0; d < tdim; ++d) { 1407 csum[d] /= (tdim+1)*vsum; 1408 } 1409 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1410 if (vol) *vol = PetscAbsReal(vsum); 1411 if (centroid) { 1412 if (dim > 2) { 1413 for (d = 0; d < dim; ++d) { 1414 centroid[d] = v0[d]; 1415 for (e = 0; e < dim; ++e) { 1416 centroid[d] += R[d*dim+e]*csum[e]; 1417 } 1418 } 1419 } else for (d = 0; d < dim; ++d) centroid[d] = csum[d]; 1420 } 1421 PetscFunctionReturn(0); 1422 } 1423 1424 #undef __FUNCT__ 1425 #define __FUNCT__ "DMPlexComputeGeometryFVM_3D_Internal" 1426 /* Centroid_i = (\sum_n V_n Cn_i ) / V */ 1427 static PetscErrorCode DMPlexComputeGeometryFVM_3D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1428 { 1429 PetscSection coordSection; 1430 Vec coordinates; 1431 PetscScalar *coords = NULL; 1432 PetscReal vsum = 0.0, vtmp, coordsTmp[3*3]; 1433 const PetscInt *faces, *facesO; 1434 PetscInt numFaces, f, coordSize, numCorners, p, d; 1435 PetscErrorCode ierr; 1436 1437 PetscFunctionBegin; 1438 if (PetscUnlikely(dim > 3)) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"No support for dim %D > 3",dim); 1439 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1440 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1441 1442 if (centroid) for (d = 0; d < dim; ++d) centroid[d] = 0.0; 1443 ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr); 1444 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 1445 ierr = DMPlexGetConeOrientation(dm, cell, &facesO);CHKERRQ(ierr); 1446 for (f = 0; f < numFaces; ++f) { 1447 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); 1448 numCorners = coordSize/dim; 1449 switch (numCorners) { 1450 case 3: 1451 for (d = 0; d < dim; ++d) { 1452 coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); 1453 coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); 1454 coordsTmp[2*dim+d] = PetscRealPart(coords[2*dim+d]); 1455 } 1456 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1457 if (facesO[f] < 0) vtmp = -vtmp; 1458 vsum += vtmp; 1459 if (centroid) { /* Centroid of OABC = (a+b+c)/4 */ 1460 for (d = 0; d < dim; ++d) { 1461 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1462 } 1463 } 1464 break; 1465 case 4: 1466 /* DO FOR PYRAMID */ 1467 /* First tet */ 1468 for (d = 0; d < dim; ++d) { 1469 coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); 1470 coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); 1471 coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); 1472 } 1473 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1474 if (facesO[f] < 0) vtmp = -vtmp; 1475 vsum += vtmp; 1476 if (centroid) { 1477 for (d = 0; d < dim; ++d) { 1478 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1479 } 1480 } 1481 /* Second tet */ 1482 for (d = 0; d < dim; ++d) { 1483 coordsTmp[0*dim+d] = PetscRealPart(coords[1*dim+d]); 1484 coordsTmp[1*dim+d] = PetscRealPart(coords[2*dim+d]); 1485 coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); 1486 } 1487 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1488 if (facesO[f] < 0) vtmp = -vtmp; 1489 vsum += vtmp; 1490 if (centroid) { 1491 for (d = 0; d < dim; ++d) { 1492 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1493 } 1494 } 1495 break; 1496 default: 1497 SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle faces with %D vertices", numCorners); 1498 } 1499 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); 1500 } 1501 if (vol) *vol = PetscAbsReal(vsum); 1502 if (normal) for (d = 0; d < dim; ++d) normal[d] = 0.0; 1503 if (centroid) for (d = 0; d < dim; ++d) centroid[d] /= (vsum*4); 1504 PetscFunctionReturn(0); 1505 } 1506 1507 #undef __FUNCT__ 1508 #define __FUNCT__ "DMPlexComputeCellGeometryFVM" 1509 /*@C 1510 DMPlexComputeCellGeometryFVM - Compute the volume for a given cell 1511 1512 Collective on DM 1513 1514 Input Arguments: 1515 + dm - the DM 1516 - cell - the cell 1517 1518 Output Arguments: 1519 + volume - the cell volume 1520 . centroid - the cell centroid 1521 - normal - the cell normal, if appropriate 1522 1523 Level: advanced 1524 1525 Fortran Notes: 1526 Since it returns arrays, this routine is only available in Fortran 90, and you must 1527 include petsc.h90 in your code. 1528 1529 .seealso: DMGetCoordinateSection(), DMGetCoordinateVec() 1530 @*/ 1531 PetscErrorCode DMPlexComputeCellGeometryFVM(DM dm, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1532 { 1533 PetscInt depth, dim; 1534 PetscErrorCode ierr; 1535 1536 PetscFunctionBegin; 1537 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1538 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1539 if (depth != dim) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh must be interpolated"); 1540 /* We need to keep a pointer to the depth label */ 1541 ierr = DMGetLabelValue(dm, "depth", cell, &depth);CHKERRQ(ierr); 1542 /* Cone size is now the number of faces */ 1543 switch (depth) { 1544 case 1: 1545 ierr = DMPlexComputeGeometryFVM_1D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1546 break; 1547 case 2: 1548 ierr = DMPlexComputeGeometryFVM_2D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1549 break; 1550 case 3: 1551 ierr = DMPlexComputeGeometryFVM_3D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1552 break; 1553 default: 1554 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); 1555 } 1556 PetscFunctionReturn(0); 1557 } 1558 1559 #undef __FUNCT__ 1560 #define __FUNCT__ "DMPlexComputeGeometryFEM" 1561 /* This should also take a PetscFE argument I think */ 1562 PetscErrorCode DMPlexComputeGeometryFEM(DM dm, Vec *cellgeom) 1563 { 1564 DM dmCell; 1565 Vec coordinates; 1566 PetscSection coordSection, sectionCell; 1567 PetscScalar *cgeom; 1568 PetscInt cStart, cEnd, cMax, c; 1569 PetscErrorCode ierr; 1570 1571 PetscFunctionBegin; 1572 ierr = DMClone(dm, &dmCell);CHKERRQ(ierr); 1573 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1574 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1575 ierr = DMSetCoordinateSection(dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1576 ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr); 1577 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr); 1578 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1579 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1580 cEnd = cMax < 0 ? cEnd : cMax; 1581 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1582 /* TODO This needs to be multiplied by Nq for non-affine */ 1583 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFECellGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1584 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1585 ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr); 1586 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1587 ierr = DMCreateLocalVector(dmCell, cellgeom);CHKERRQ(ierr); 1588 ierr = VecGetArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1589 for (c = cStart; c < cEnd; ++c) { 1590 PetscFECellGeom *cg; 1591 1592 ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1593 ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr); 1594 ierr = DMPlexComputeCellGeometryFEM(dmCell, c, NULL, cg->v0, cg->J, cg->invJ, &cg->detJ);CHKERRQ(ierr); 1595 if (cg->detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", cg->detJ, c); 1596 } 1597 ierr = VecRestoreArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1598 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1599 PetscFunctionReturn(0); 1600 } 1601 1602 #undef __FUNCT__ 1603 #define __FUNCT__ "DMPlexComputeGeometryFVM" 1604 /*@ 1605 DMPlexComputeGeometryFVM - Computes the cell and face geometry for a finite volume method 1606 1607 Input Parameter: 1608 . dm - The DM 1609 1610 Output Parameters: 1611 + cellgeom - A Vec of PetscFVCellGeom data 1612 . facegeom - A Vec of PetscFVFaceGeom data 1613 1614 Level: developer 1615 1616 .seealso: PetscFVFaceGeom, PetscFVCellGeom, DMPlexComputeGeometryFEM() 1617 @*/ 1618 PetscErrorCode DMPlexComputeGeometryFVM(DM dm, Vec *cellgeom, Vec *facegeom) 1619 { 1620 DM dmFace, dmCell; 1621 DMLabel ghostLabel; 1622 PetscSection sectionFace, sectionCell; 1623 PetscSection coordSection; 1624 Vec coordinates; 1625 PetscScalar *fgeom, *cgeom; 1626 PetscReal minradius, gminradius; 1627 PetscInt dim, cStart, cEnd, cEndInterior, c, fStart, fEnd, f; 1628 PetscErrorCode ierr; 1629 1630 PetscFunctionBegin; 1631 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1632 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1633 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1634 /* Make cell centroids and volumes */ 1635 ierr = DMClone(dm, &dmCell);CHKERRQ(ierr); 1636 ierr = DMSetCoordinateSection(dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1637 ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr); 1638 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr); 1639 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1640 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1641 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1642 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFVCellGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1643 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1644 ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr); 1645 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1646 ierr = DMCreateLocalVector(dmCell, cellgeom);CHKERRQ(ierr); 1647 if (cEndInterior < 0) { 1648 cEndInterior = cEnd; 1649 } 1650 ierr = VecGetArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1651 for (c = cStart; c < cEndInterior; ++c) { 1652 PetscFVCellGeom *cg; 1653 1654 ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1655 ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr); 1656 ierr = DMPlexComputeCellGeometryFVM(dmCell, c, &cg->volume, cg->centroid, NULL);CHKERRQ(ierr); 1657 } 1658 /* Compute face normals and minimum cell radius */ 1659 ierr = DMClone(dm, &dmFace);CHKERRQ(ierr); 1660 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionFace);CHKERRQ(ierr); 1661 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1662 ierr = PetscSectionSetChart(sectionFace, fStart, fEnd);CHKERRQ(ierr); 1663 for (f = fStart; f < fEnd; ++f) {ierr = PetscSectionSetDof(sectionFace, f, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFVFaceGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1664 ierr = PetscSectionSetUp(sectionFace);CHKERRQ(ierr); 1665 ierr = DMSetDefaultSection(dmFace, sectionFace);CHKERRQ(ierr); 1666 ierr = PetscSectionDestroy(§ionFace);CHKERRQ(ierr); 1667 ierr = DMCreateLocalVector(dmFace, facegeom);CHKERRQ(ierr); 1668 ierr = VecGetArray(*facegeom, &fgeom);CHKERRQ(ierr); 1669 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1670 minradius = PETSC_MAX_REAL; 1671 for (f = fStart; f < fEnd; ++f) { 1672 PetscFVFaceGeom *fg; 1673 PetscReal area; 1674 PetscInt ghost = -1, d, numChildren; 1675 1676 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1677 ierr = DMPlexGetTreeChildren(dm,f,&numChildren,NULL);CHKERRQ(ierr); 1678 if (ghost >= 0 || numChildren) continue; 1679 ierr = DMPlexPointLocalRef(dmFace, f, fgeom, &fg);CHKERRQ(ierr); 1680 ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, fg->centroid, fg->normal);CHKERRQ(ierr); 1681 for (d = 0; d < dim; ++d) fg->normal[d] *= area; 1682 /* Flip face orientation if necessary to match ordering in support, and Update minimum radius */ 1683 { 1684 PetscFVCellGeom *cL, *cR; 1685 PetscInt ncells; 1686 const PetscInt *cells; 1687 PetscReal *lcentroid, *rcentroid; 1688 PetscReal l[3], r[3], v[3]; 1689 1690 ierr = DMPlexGetSupport(dm, f, &cells);CHKERRQ(ierr); 1691 ierr = DMPlexGetSupportSize(dm, f, &ncells);CHKERRQ(ierr); 1692 ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cL);CHKERRQ(ierr); 1693 lcentroid = cells[0] >= cEndInterior ? fg->centroid : cL->centroid; 1694 if (ncells > 1) { 1695 ierr = DMPlexPointLocalRead(dmCell, cells[1], cgeom, &cR);CHKERRQ(ierr); 1696 rcentroid = cells[1] >= cEndInterior ? fg->centroid : cR->centroid; 1697 } 1698 else { 1699 rcentroid = fg->centroid; 1700 } 1701 ierr = DMLocalizeCoordinateReal_Internal(dm, dim, fg->centroid, lcentroid, l);CHKERRQ(ierr); 1702 ierr = DMLocalizeCoordinateReal_Internal(dm, dim, fg->centroid, rcentroid, r);CHKERRQ(ierr); 1703 DMPlex_WaxpyD_Internal(dim, -1, l, r, v); 1704 if (DMPlex_DotRealD_Internal(dim, fg->normal, v) < 0) { 1705 for (d = 0; d < dim; ++d) fg->normal[d] = -fg->normal[d]; 1706 } 1707 if (DMPlex_DotRealD_Internal(dim, fg->normal, v) <= 0) { 1708 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]); 1709 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]); 1710 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed", f); 1711 } 1712 if (cells[0] < cEndInterior) { 1713 DMPlex_WaxpyD_Internal(dim, -1, fg->centroid, cL->centroid, v); 1714 minradius = PetscMin(minradius, DMPlex_NormD_Internal(dim, v)); 1715 } 1716 if (ncells > 1 && cells[1] < cEndInterior) { 1717 DMPlex_WaxpyD_Internal(dim, -1, fg->centroid, cR->centroid, v); 1718 minradius = PetscMin(minradius, DMPlex_NormD_Internal(dim, v)); 1719 } 1720 } 1721 } 1722 ierr = MPIU_Allreduce(&minradius, &gminradius, 1, MPIU_REAL, MPIU_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1723 ierr = DMPlexSetMinRadius(dm, gminradius);CHKERRQ(ierr); 1724 /* Compute centroids of ghost cells */ 1725 for (c = cEndInterior; c < cEnd; ++c) { 1726 PetscFVFaceGeom *fg; 1727 const PetscInt *cone, *support; 1728 PetscInt coneSize, supportSize, s; 1729 1730 ierr = DMPlexGetConeSize(dmCell, c, &coneSize);CHKERRQ(ierr); 1731 if (coneSize != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Ghost cell %d has cone size %d != 1", c, coneSize); 1732 ierr = DMPlexGetCone(dmCell, c, &cone);CHKERRQ(ierr); 1733 ierr = DMPlexGetSupportSize(dmCell, cone[0], &supportSize);CHKERRQ(ierr); 1734 if (supportSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %d has support size %d != 2", cone[0], supportSize); 1735 ierr = DMPlexGetSupport(dmCell, cone[0], &support);CHKERRQ(ierr); 1736 ierr = DMPlexPointLocalRef(dmFace, cone[0], fgeom, &fg);CHKERRQ(ierr); 1737 for (s = 0; s < 2; ++s) { 1738 /* Reflect ghost centroid across plane of face */ 1739 if (support[s] == c) { 1740 PetscFVCellGeom *ci; 1741 PetscFVCellGeom *cg; 1742 PetscReal c2f[3], a; 1743 1744 ierr = DMPlexPointLocalRead(dmCell, support[(s+1)%2], cgeom, &ci);CHKERRQ(ierr); 1745 DMPlex_WaxpyD_Internal(dim, -1, ci->centroid, fg->centroid, c2f); /* cell to face centroid */ 1746 a = DMPlex_DotRealD_Internal(dim, c2f, fg->normal)/DMPlex_DotRealD_Internal(dim, fg->normal, fg->normal); 1747 ierr = DMPlexPointLocalRef(dmCell, support[s], cgeom, &cg);CHKERRQ(ierr); 1748 DMPlex_WaxpyD_Internal(dim, 2*a, fg->normal, ci->centroid, cg->centroid); 1749 cg->volume = ci->volume; 1750 } 1751 } 1752 } 1753 ierr = VecRestoreArray(*facegeom, &fgeom);CHKERRQ(ierr); 1754 ierr = VecRestoreArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1755 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1756 ierr = DMDestroy(&dmFace);CHKERRQ(ierr); 1757 PetscFunctionReturn(0); 1758 } 1759 1760 #undef __FUNCT__ 1761 #define __FUNCT__ "DMPlexGetMinRadius" 1762 /*@C 1763 DMPlexGetMinRadius - Returns the minimum distance from any cell centroid to a face 1764 1765 Not collective 1766 1767 Input Argument: 1768 . dm - the DM 1769 1770 Output Argument: 1771 . minradius - the minium cell radius 1772 1773 Level: developer 1774 1775 .seealso: DMGetCoordinates() 1776 @*/ 1777 PetscErrorCode DMPlexGetMinRadius(DM dm, PetscReal *minradius) 1778 { 1779 PetscFunctionBegin; 1780 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1781 PetscValidPointer(minradius,2); 1782 *minradius = ((DM_Plex*) dm->data)->minradius; 1783 PetscFunctionReturn(0); 1784 } 1785 1786 #undef __FUNCT__ 1787 #define __FUNCT__ "DMPlexSetMinRadius" 1788 /*@C 1789 DMPlexSetMinRadius - Sets the minimum distance from the cell centroid to a face 1790 1791 Logically collective 1792 1793 Input Arguments: 1794 + dm - the DM 1795 - minradius - the minium cell radius 1796 1797 Level: developer 1798 1799 .seealso: DMSetCoordinates() 1800 @*/ 1801 PetscErrorCode DMPlexSetMinRadius(DM dm, PetscReal minradius) 1802 { 1803 PetscFunctionBegin; 1804 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1805 ((DM_Plex*) dm->data)->minradius = minradius; 1806 PetscFunctionReturn(0); 1807 } 1808 1809 #undef __FUNCT__ 1810 #define __FUNCT__ "BuildGradientReconstruction_Internal" 1811 static PetscErrorCode BuildGradientReconstruction_Internal(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom) 1812 { 1813 DMLabel ghostLabel; 1814 PetscScalar *dx, *grad, **gref; 1815 PetscInt dim, cStart, cEnd, c, cEndInterior, maxNumFaces; 1816 PetscErrorCode ierr; 1817 1818 PetscFunctionBegin; 1819 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1820 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1821 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1822 ierr = DMPlexGetMaxSizes(dm, &maxNumFaces, NULL);CHKERRQ(ierr); 1823 ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr); 1824 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1825 ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr); 1826 for (c = cStart; c < cEndInterior; c++) { 1827 const PetscInt *faces; 1828 PetscInt numFaces, usedFaces, f, d; 1829 PetscFVCellGeom *cg; 1830 PetscBool boundary; 1831 PetscInt ghost; 1832 1833 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1834 ierr = DMPlexGetConeSize(dm, c, &numFaces);CHKERRQ(ierr); 1835 ierr = DMPlexGetCone(dm, c, &faces);CHKERRQ(ierr); 1836 if (numFaces < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cell %D has only %D faces, not enough for gradient reconstruction", c, numFaces); 1837 for (f = 0, usedFaces = 0; f < numFaces; ++f) { 1838 PetscFVCellGeom *cg1; 1839 PetscFVFaceGeom *fg; 1840 const PetscInt *fcells; 1841 PetscInt ncell, side; 1842 1843 ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr); 1844 ierr = DMIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr); 1845 if ((ghost >= 0) || boundary) continue; 1846 ierr = DMPlexGetSupport(dm, faces[f], &fcells);CHKERRQ(ierr); 1847 side = (c != fcells[0]); /* c is on left=0 or right=1 of face */ 1848 ncell = fcells[!side]; /* the neighbor */ 1849 ierr = DMPlexPointLocalRef(dmFace, faces[f], fgeom, &fg);CHKERRQ(ierr); 1850 ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr); 1851 for (d = 0; d < dim; ++d) dx[usedFaces*dim+d] = cg1->centroid[d] - cg->centroid[d]; 1852 gref[usedFaces++] = fg->grad[side]; /* Gradient reconstruction term will go here */ 1853 } 1854 if (!usedFaces) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_USER, "Mesh contains isolated cell (no neighbors). Is it intentional?"); 1855 ierr = PetscFVComputeGradient(fvm, usedFaces, dx, grad);CHKERRQ(ierr); 1856 for (f = 0, usedFaces = 0; f < numFaces; ++f) { 1857 ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr); 1858 ierr = DMIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr); 1859 if ((ghost >= 0) || boundary) continue; 1860 for (d = 0; d < dim; ++d) gref[usedFaces][d] = grad[usedFaces*dim+d]; 1861 ++usedFaces; 1862 } 1863 } 1864 ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr); 1865 PetscFunctionReturn(0); 1866 } 1867 1868 #undef __FUNCT__ 1869 #define __FUNCT__ "BuildGradientReconstruction_Internal_Tree" 1870 static PetscErrorCode BuildGradientReconstruction_Internal_Tree(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom) 1871 { 1872 DMLabel ghostLabel; 1873 PetscScalar *dx, *grad, **gref; 1874 PetscInt dim, cStart, cEnd, c, cEndInterior, fStart, fEnd, f, nStart, nEnd, maxNumFaces = 0; 1875 PetscSection neighSec; 1876 PetscInt (*neighbors)[2]; 1877 PetscInt *counter; 1878 PetscErrorCode ierr; 1879 1880 PetscFunctionBegin; 1881 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1882 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1883 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1884 if (cEndInterior < 0) { 1885 cEndInterior = cEnd; 1886 } 1887 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&neighSec);CHKERRQ(ierr); 1888 ierr = PetscSectionSetChart(neighSec,cStart,cEndInterior);CHKERRQ(ierr); 1889 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1890 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1891 for (f = fStart; f < fEnd; f++) { 1892 const PetscInt *fcells; 1893 PetscBool boundary; 1894 PetscInt ghost = -1; 1895 PetscInt numChildren, numCells, c; 1896 1897 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1898 ierr = DMIsBoundaryPoint(dm, f, &boundary);CHKERRQ(ierr); 1899 ierr = DMPlexGetTreeChildren(dm, f, &numChildren, NULL);CHKERRQ(ierr); 1900 if ((ghost >= 0) || boundary || numChildren) continue; 1901 ierr = DMPlexGetSupportSize(dm, f, &numCells);CHKERRQ(ierr); 1902 if (numCells == 2) { 1903 ierr = DMPlexGetSupport(dm, f, &fcells);CHKERRQ(ierr); 1904 for (c = 0; c < 2; c++) { 1905 PetscInt cell = fcells[c]; 1906 1907 if (cell >= cStart && cell < cEndInterior) { 1908 ierr = PetscSectionAddDof(neighSec,cell,1);CHKERRQ(ierr); 1909 } 1910 } 1911 } 1912 } 1913 ierr = PetscSectionSetUp(neighSec);CHKERRQ(ierr); 1914 ierr = PetscSectionGetMaxDof(neighSec,&maxNumFaces);CHKERRQ(ierr); 1915 ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr); 1916 nStart = 0; 1917 ierr = PetscSectionGetStorageSize(neighSec,&nEnd);CHKERRQ(ierr); 1918 ierr = PetscMalloc1((nEnd-nStart),&neighbors);CHKERRQ(ierr); 1919 ierr = PetscCalloc1((cEndInterior-cStart),&counter);CHKERRQ(ierr); 1920 for (f = fStart; f < fEnd; f++) { 1921 const PetscInt *fcells; 1922 PetscBool boundary; 1923 PetscInt ghost = -1; 1924 PetscInt numChildren, numCells, c; 1925 1926 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1927 ierr = DMIsBoundaryPoint(dm, f, &boundary);CHKERRQ(ierr); 1928 ierr = DMPlexGetTreeChildren(dm, f, &numChildren, NULL);CHKERRQ(ierr); 1929 if ((ghost >= 0) || boundary || numChildren) continue; 1930 ierr = DMPlexGetSupportSize(dm, f, &numCells);CHKERRQ(ierr); 1931 if (numCells == 2) { 1932 ierr = DMPlexGetSupport(dm, f, &fcells);CHKERRQ(ierr); 1933 for (c = 0; c < 2; c++) { 1934 PetscInt cell = fcells[c], off; 1935 1936 if (cell >= cStart && cell < cEndInterior) { 1937 ierr = PetscSectionGetOffset(neighSec,cell,&off);CHKERRQ(ierr); 1938 off += counter[cell - cStart]++; 1939 neighbors[off][0] = f; 1940 neighbors[off][1] = fcells[1 - c]; 1941 } 1942 } 1943 } 1944 } 1945 ierr = PetscFree(counter);CHKERRQ(ierr); 1946 ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr); 1947 for (c = cStart; c < cEndInterior; c++) { 1948 PetscInt numFaces, f, d, off, ghost = -1; 1949 PetscFVCellGeom *cg; 1950 1951 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1952 ierr = PetscSectionGetDof(neighSec, c, &numFaces);CHKERRQ(ierr); 1953 ierr = PetscSectionGetOffset(neighSec, c, &off);CHKERRQ(ierr); 1954 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, c, &ghost);CHKERRQ(ierr);} 1955 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); 1956 for (f = 0; f < numFaces; ++f) { 1957 PetscFVCellGeom *cg1; 1958 PetscFVFaceGeom *fg; 1959 const PetscInt *fcells; 1960 PetscInt ncell, side, nface; 1961 1962 nface = neighbors[off + f][0]; 1963 ncell = neighbors[off + f][1]; 1964 ierr = DMPlexGetSupport(dm,nface,&fcells);CHKERRQ(ierr); 1965 side = (c != fcells[0]); 1966 ierr = DMPlexPointLocalRef(dmFace, nface, fgeom, &fg);CHKERRQ(ierr); 1967 ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr); 1968 for (d = 0; d < dim; ++d) dx[f*dim+d] = cg1->centroid[d] - cg->centroid[d]; 1969 gref[f] = fg->grad[side]; /* Gradient reconstruction term will go here */ 1970 } 1971 ierr = PetscFVComputeGradient(fvm, numFaces, dx, grad);CHKERRQ(ierr); 1972 for (f = 0; f < numFaces; ++f) { 1973 for (d = 0; d < dim; ++d) gref[f][d] = grad[f*dim+d]; 1974 } 1975 } 1976 ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr); 1977 ierr = PetscSectionDestroy(&neighSec);CHKERRQ(ierr); 1978 ierr = PetscFree(neighbors);CHKERRQ(ierr); 1979 PetscFunctionReturn(0); 1980 } 1981 1982 #undef __FUNCT__ 1983 #define __FUNCT__ "DMPlexComputeGradientFVM" 1984 /*@ 1985 DMPlexComputeGradientFVM - Compute geometric factors for gradient reconstruction, which are stored in the geometry data, and compute layout for gradient data 1986 1987 Collective on DM 1988 1989 Input Arguments: 1990 + dm - The DM 1991 . fvm - The PetscFV 1992 . faceGeometry - The face geometry from DMPlexGetFaceGeometryFVM() 1993 - cellGeometry - The face geometry from DMPlexGetCellGeometryFVM() 1994 1995 Output Parameters: 1996 + faceGeometry - The geometric factors for gradient calculation are inserted 1997 - dmGrad - The DM describing the layout of gradient data 1998 1999 Level: developer 2000 2001 .seealso: DMPlexGetFaceGeometryFVM(), DMPlexGetCellGeometryFVM() 2002 @*/ 2003 PetscErrorCode DMPlexComputeGradientFVM(DM dm, PetscFV fvm, Vec faceGeometry, Vec cellGeometry, DM *dmGrad) 2004 { 2005 DM dmFace, dmCell; 2006 PetscScalar *fgeom, *cgeom; 2007 PetscSection sectionGrad, parentSection; 2008 PetscInt dim, pdim, cStart, cEnd, cEndInterior, c; 2009 PetscErrorCode ierr; 2010 2011 PetscFunctionBegin; 2012 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2013 ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr); 2014 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2015 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2016 /* Construct the interpolant corresponding to each face from the least-square solution over the cell neighborhood */ 2017 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 2018 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 2019 ierr = VecGetArray(faceGeometry, &fgeom);CHKERRQ(ierr); 2020 ierr = VecGetArray(cellGeometry, &cgeom);CHKERRQ(ierr); 2021 ierr = DMPlexGetTree(dm,&parentSection,NULL,NULL,NULL,NULL);CHKERRQ(ierr); 2022 if (!parentSection) { 2023 ierr = BuildGradientReconstruction_Internal(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr); 2024 } else { 2025 ierr = BuildGradientReconstruction_Internal_Tree(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr); 2026 } 2027 ierr = VecRestoreArray(faceGeometry, &fgeom);CHKERRQ(ierr); 2028 ierr = VecRestoreArray(cellGeometry, &cgeom);CHKERRQ(ierr); 2029 /* Create storage for gradients */ 2030 ierr = DMClone(dm, dmGrad);CHKERRQ(ierr); 2031 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionGrad);CHKERRQ(ierr); 2032 ierr = PetscSectionSetChart(sectionGrad, cStart, cEnd);CHKERRQ(ierr); 2033 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionGrad, c, pdim*dim);CHKERRQ(ierr);} 2034 ierr = PetscSectionSetUp(sectionGrad);CHKERRQ(ierr); 2035 ierr = DMSetDefaultSection(*dmGrad, sectionGrad);CHKERRQ(ierr); 2036 ierr = PetscSectionDestroy(§ionGrad);CHKERRQ(ierr); 2037 PetscFunctionReturn(0); 2038 } 2039