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