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