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