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 = MPIU_Allreduce(lbox->lower, gbox->lower, 3, MPIU_REAL, MPI_MIN, comm);CHKERRQ(ierr); 339 ierr = MPIU_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, PetscSF cellSF) 429 { 430 DM_Plex *mesh = (DM_Plex *) dm->data; 431 PetscBool hash = mesh->useHashLocation; 432 PetscInt bs, numPoints, p, numFound, *found = NULL; 433 PetscInt dim, cStart, cEnd, cMax, numCells, c; 434 const PetscInt *boxCells; 435 PetscSFNode *cells; 436 PetscScalar *a; 437 PetscMPIInt result; 438 PetscErrorCode ierr; 439 440 PetscFunctionBegin; 441 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 442 ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr); 443 ierr = MPI_Comm_compare(PetscObjectComm((PetscObject)cellSF),PETSC_COMM_SELF,&result);CHKERRQ(ierr); 444 if (result != MPI_IDENT && result != MPI_CONGRUENT) SETERRQ(PetscObjectComm((PetscObject)cellSF),PETSC_ERR_SUP, "Trying parallel point location: only local point location supported"); 445 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); 446 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 447 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 448 if (cMax >= 0) cEnd = PetscMin(cEnd, cMax); 449 ierr = VecGetLocalSize(v, &numPoints);CHKERRQ(ierr); 450 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 451 numPoints /= bs; 452 ierr = PetscMalloc1(numPoints, &cells);CHKERRQ(ierr); 453 if (hash) { 454 if (!mesh->lbox) {ierr = PetscInfo(dm, "Initializing grid hashing");CHKERRQ(ierr);ierr = DMPlexComputeGridHash_Internal(dm, &mesh->lbox);CHKERRQ(ierr);} 455 /* Designate the local box for each point */ 456 /* Send points to correct process */ 457 /* Search cells that lie in each subbox */ 458 /* Should we bin points before doing search? */ 459 ierr = ISGetIndices(mesh->lbox->cells, &boxCells);CHKERRQ(ierr); 460 } 461 for (p = 0, numFound = 0; p < numPoints; ++p) { 462 const PetscScalar *point = &a[p*bs]; 463 PetscInt dbin[3], bin, cell = -1, cellOffset; 464 465 cells[p].rank = -1; 466 cells[p].index = -1; 467 if (hash) { 468 ierr = PetscGridHashGetEnclosingBox(mesh->lbox, 1, point, dbin, &bin);CHKERRQ(ierr); 469 /* TODO Lay an interface over this so we can switch between Section (dense) and Label (sparse) */ 470 ierr = PetscSectionGetDof(mesh->lbox->cellSection, bin, &numCells);CHKERRQ(ierr); 471 ierr = PetscSectionGetOffset(mesh->lbox->cellSection, bin, &cellOffset);CHKERRQ(ierr); 472 for (c = cellOffset; c < cellOffset + numCells; ++c) { 473 ierr = DMPlexLocatePoint_Internal(dm, dim, point, boxCells[c], &cell);CHKERRQ(ierr); 474 if (cell >= 0) { 475 cells[p].rank = 0; 476 cells[p].index = cell; 477 numFound++; 478 break; 479 } 480 } 481 } else { 482 for (c = cStart; c < cEnd; ++c) { 483 ierr = DMPlexLocatePoint_Internal(dm, dim, point, c, &cell);CHKERRQ(ierr); 484 if (cell >= 0) { 485 cells[p].rank = 0; 486 cells[p].index = cell; 487 numFound++; 488 break; 489 } 490 } 491 } 492 } 493 if (hash) {ierr = ISRestoreIndices(mesh->lbox->cells, &boxCells);CHKERRQ(ierr);} 494 /* Check for highest numbered proc that claims a point (do we care?) */ 495 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 496 if (numFound < numPoints) { 497 ierr = PetscMalloc1(numFound,&found);CHKERRQ(ierr); 498 for (p = 0, numFound = 0; p < numPoints; p++) { 499 if (cells[p].rank >= 0 && cells[p].index >= 0) { 500 if (numFound < p) { 501 cells[numFound] = cells[p]; 502 } 503 found[numFound++] = p; 504 } 505 } 506 } 507 ierr = PetscSFSetGraph(cellSF, cEnd - cStart, numFound, found, PETSC_OWN_POINTER, cells, PETSC_OWN_POINTER);CHKERRQ(ierr); 508 PetscFunctionReturn(0); 509 } 510 511 #undef __FUNCT__ 512 #define __FUNCT__ "DMPlexComputeProjection2Dto1D_Internal" 513 /* 514 DMPlexComputeProjection2Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 2D 515 */ 516 PetscErrorCode DMPlexComputeProjection2Dto1D_Internal(PetscScalar coords[], PetscReal R[]) 517 { 518 const PetscReal x = PetscRealPart(coords[2] - coords[0]); 519 const PetscReal y = PetscRealPart(coords[3] - coords[1]); 520 const PetscReal r = PetscSqrtReal(x*x + y*y), c = x/r, s = y/r; 521 522 PetscFunctionBegin; 523 R[0] = c; R[1] = -s; 524 R[2] = s; R[3] = c; 525 coords[0] = 0.0; 526 coords[1] = r; 527 PetscFunctionReturn(0); 528 } 529 530 #undef __FUNCT__ 531 #define __FUNCT__ "DMPlexComputeProjection3Dto1D_Internal" 532 /* 533 DMPlexComputeProjection3Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 3D 534 535 This uses the basis completion described by Frisvad, 536 537 http://www.imm.dtu.dk/~jerf/papers/abstracts/onb.html 538 DOI:10.1080/2165347X.2012.689606 539 */ 540 PetscErrorCode DMPlexComputeProjection3Dto1D_Internal(PetscScalar coords[], PetscReal R[]) 541 { 542 PetscReal x = PetscRealPart(coords[3] - coords[0]); 543 PetscReal y = PetscRealPart(coords[4] - coords[1]); 544 PetscReal z = PetscRealPart(coords[5] - coords[2]); 545 PetscReal r = PetscSqrtReal(x*x + y*y + z*z); 546 PetscReal rinv = 1. / r; 547 PetscFunctionBegin; 548 549 x *= rinv; y *= rinv; z *= rinv; 550 if (x > 0.) { 551 PetscReal inv1pX = 1./ (1. + x); 552 553 R[0] = x; R[1] = -y; R[2] = -z; 554 R[3] = y; R[4] = 1. - y*y*inv1pX; R[5] = -y*z*inv1pX; 555 R[6] = z; R[7] = -y*z*inv1pX; R[8] = 1. - z*z*inv1pX; 556 } 557 else { 558 PetscReal inv1mX = 1./ (1. - x); 559 560 R[0] = x; R[1] = z; R[2] = y; 561 R[3] = y; R[4] = -y*z*inv1mX; R[5] = 1. - y*y*inv1mX; 562 R[6] = z; R[7] = 1. - z*z*inv1mX; R[8] = -y*z*inv1mX; 563 } 564 coords[0] = 0.0; 565 coords[1] = r; 566 PetscFunctionReturn(0); 567 } 568 569 #undef __FUNCT__ 570 #define __FUNCT__ "DMPlexComputeProjection3Dto2D_Internal" 571 /* 572 DMPlexComputeProjection3Dto2D_Internal - Rewrite coordinates to be the 2D projection of the 3D 573 */ 574 PetscErrorCode DMPlexComputeProjection3Dto2D_Internal(PetscInt coordSize, PetscScalar coords[], PetscReal R[]) 575 { 576 PetscReal x1[3], x2[3], n[3], norm; 577 PetscReal x1p[3], x2p[3], xnp[3]; 578 PetscReal sqrtz, alpha; 579 const PetscInt dim = 3; 580 PetscInt d, e, p; 581 582 PetscFunctionBegin; 583 /* 0) Calculate normal vector */ 584 for (d = 0; d < dim; ++d) { 585 x1[d] = PetscRealPart(coords[1*dim+d] - coords[0*dim+d]); 586 x2[d] = PetscRealPart(coords[2*dim+d] - coords[0*dim+d]); 587 } 588 n[0] = x1[1]*x2[2] - x1[2]*x2[1]; 589 n[1] = x1[2]*x2[0] - x1[0]*x2[2]; 590 n[2] = x1[0]*x2[1] - x1[1]*x2[0]; 591 norm = PetscSqrtReal(n[0]*n[0] + n[1]*n[1] + n[2]*n[2]); 592 n[0] /= norm; 593 n[1] /= norm; 594 n[2] /= norm; 595 /* 1) Take the normal vector and rotate until it is \hat z 596 597 Let the normal vector be <nx, ny, nz> and alpha = 1/sqrt(1 - nz^2), then 598 599 R = / alpha nx nz alpha ny nz -1/alpha \ 600 | -alpha ny alpha nx 0 | 601 \ nx ny nz / 602 603 will rotate the normal vector to \hat z 604 */ 605 sqrtz = PetscSqrtReal(1.0 - n[2]*n[2]); 606 /* Check for n = z */ 607 if (sqrtz < 1.0e-10) { 608 if (n[2] < 0.0) { 609 if (coordSize > 9) { 610 coords[2] = PetscRealPart(coords[3*dim+0] - coords[0*dim+0]); 611 coords[3] = PetscRealPart(coords[3*dim+1] - coords[0*dim+1]); 612 coords[4] = x2[0]; 613 coords[5] = x2[1]; 614 coords[6] = x1[0]; 615 coords[7] = x1[1]; 616 } else { 617 coords[2] = x2[0]; 618 coords[3] = x2[1]; 619 coords[4] = x1[0]; 620 coords[5] = x1[1]; 621 } 622 R[0] = 1.0; R[1] = 0.0; R[2] = 0.0; 623 R[3] = 0.0; R[4] = 1.0; R[5] = 0.0; 624 R[6] = 0.0; R[7] = 0.0; R[8] = -1.0; 625 } else { 626 for (p = 3; p < coordSize/3; ++p) { 627 coords[p*2+0] = PetscRealPart(coords[p*dim+0] - coords[0*dim+0]); 628 coords[p*2+1] = PetscRealPart(coords[p*dim+1] - coords[0*dim+1]); 629 } 630 coords[2] = x1[0]; 631 coords[3] = x1[1]; 632 coords[4] = x2[0]; 633 coords[5] = x2[1]; 634 R[0] = 1.0; R[1] = 0.0; R[2] = 0.0; 635 R[3] = 0.0; R[4] = 1.0; R[5] = 0.0; 636 R[6] = 0.0; R[7] = 0.0; R[8] = 1.0; 637 } 638 coords[0] = 0.0; 639 coords[1] = 0.0; 640 PetscFunctionReturn(0); 641 } 642 alpha = 1.0/sqrtz; 643 R[0] = alpha*n[0]*n[2]; R[1] = alpha*n[1]*n[2]; R[2] = -sqrtz; 644 R[3] = -alpha*n[1]; R[4] = alpha*n[0]; R[5] = 0.0; 645 R[6] = n[0]; R[7] = n[1]; R[8] = n[2]; 646 for (d = 0; d < dim; ++d) { 647 x1p[d] = 0.0; 648 x2p[d] = 0.0; 649 for (e = 0; e < dim; ++e) { 650 x1p[d] += R[d*dim+e]*x1[e]; 651 x2p[d] += R[d*dim+e]*x2[e]; 652 } 653 } 654 if (PetscAbsReal(x1p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); 655 if (PetscAbsReal(x2p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); 656 /* 2) Project to (x, y) */ 657 for (p = 3; p < coordSize/3; ++p) { 658 for (d = 0; d < dim; ++d) { 659 xnp[d] = 0.0; 660 for (e = 0; e < dim; ++e) { 661 xnp[d] += R[d*dim+e]*PetscRealPart(coords[p*dim+e] - coords[0*dim+e]); 662 } 663 if (d < dim-1) coords[p*2+d] = xnp[d]; 664 } 665 } 666 coords[0] = 0.0; 667 coords[1] = 0.0; 668 coords[2] = x1p[0]; 669 coords[3] = x1p[1]; 670 coords[4] = x2p[0]; 671 coords[5] = x2p[1]; 672 /* Output R^T which rotates \hat z to the input normal */ 673 for (d = 0; d < dim; ++d) { 674 for (e = d+1; e < dim; ++e) { 675 PetscReal tmp; 676 677 tmp = R[d*dim+e]; 678 R[d*dim+e] = R[e*dim+d]; 679 R[e*dim+d] = tmp; 680 } 681 } 682 PetscFunctionReturn(0); 683 } 684 685 #undef __FUNCT__ 686 #define __FUNCT__ "Volume_Triangle_Internal" 687 PETSC_UNUSED 688 PETSC_STATIC_INLINE void Volume_Triangle_Internal(PetscReal *vol, PetscReal coords[]) 689 { 690 /* Signed volume is 1/2 the determinant 691 692 | 1 1 1 | 693 | x0 x1 x2 | 694 | y0 y1 y2 | 695 696 but if x0,y0 is the origin, we have 697 698 | x1 x2 | 699 | y1 y2 | 700 */ 701 const PetscReal x1 = coords[2] - coords[0], y1 = coords[3] - coords[1]; 702 const PetscReal x2 = coords[4] - coords[0], y2 = coords[5] - coords[1]; 703 PetscReal M[4], detM; 704 M[0] = x1; M[1] = x2; 705 M[2] = y1; M[3] = y2; 706 DMPlex_Det2D_Internal(&detM, M); 707 *vol = 0.5*detM; 708 (void)PetscLogFlops(5.0); 709 } 710 711 #undef __FUNCT__ 712 #define __FUNCT__ "Volume_Triangle_Origin_Internal" 713 PETSC_STATIC_INLINE void Volume_Triangle_Origin_Internal(PetscReal *vol, PetscReal coords[]) 714 { 715 DMPlex_Det2D_Internal(vol, coords); 716 *vol *= 0.5; 717 } 718 719 #undef __FUNCT__ 720 #define __FUNCT__ "Volume_Tetrahedron_Internal" 721 PETSC_UNUSED 722 PETSC_STATIC_INLINE void Volume_Tetrahedron_Internal(PetscReal *vol, PetscReal coords[]) 723 { 724 /* Signed volume is 1/6th of the determinant 725 726 | 1 1 1 1 | 727 | x0 x1 x2 x3 | 728 | y0 y1 y2 y3 | 729 | z0 z1 z2 z3 | 730 731 but if x0,y0,z0 is the origin, we have 732 733 | x1 x2 x3 | 734 | y1 y2 y3 | 735 | z1 z2 z3 | 736 */ 737 const PetscReal x1 = coords[3] - coords[0], y1 = coords[4] - coords[1], z1 = coords[5] - coords[2]; 738 const PetscReal x2 = coords[6] - coords[0], y2 = coords[7] - coords[1], z2 = coords[8] - coords[2]; 739 const PetscReal x3 = coords[9] - coords[0], y3 = coords[10] - coords[1], z3 = coords[11] - coords[2]; 740 PetscReal M[9], detM; 741 M[0] = x1; M[1] = x2; M[2] = x3; 742 M[3] = y1; M[4] = y2; M[5] = y3; 743 M[6] = z1; M[7] = z2; M[8] = z3; 744 DMPlex_Det3D_Internal(&detM, M); 745 *vol = -0.16666666666666666666666*detM; 746 (void)PetscLogFlops(10.0); 747 } 748 749 #undef __FUNCT__ 750 #define __FUNCT__ "Volume_Tetrahedron_Origin_Internal" 751 PETSC_STATIC_INLINE void Volume_Tetrahedron_Origin_Internal(PetscReal *vol, PetscReal coords[]) 752 { 753 DMPlex_Det3D_Internal(vol, coords); 754 *vol *= -0.16666666666666666666666; 755 } 756 757 #undef __FUNCT__ 758 #define __FUNCT__ "DMPlexComputeLineGeometry_Internal" 759 static PetscErrorCode DMPlexComputeLineGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 760 { 761 PetscSection coordSection; 762 Vec coordinates; 763 PetscScalar *coords = NULL; 764 PetscInt numCoords, d; 765 PetscErrorCode ierr; 766 767 PetscFunctionBegin; 768 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 769 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 770 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 771 *detJ = 0.0; 772 if (numCoords == 6) { 773 const PetscInt dim = 3; 774 PetscReal R[9], J0; 775 776 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 777 ierr = DMPlexComputeProjection3Dto1D_Internal(coords, R);CHKERRQ(ierr); 778 if (J) { 779 J0 = 0.5*PetscRealPart(coords[1]); 780 J[0] = R[0]*J0; J[1] = R[1]; J[2] = R[2]; 781 J[3] = R[3]*J0; J[4] = R[4]; J[5] = R[5]; 782 J[6] = R[6]*J0; J[7] = R[7]; J[8] = R[8]; 783 DMPlex_Det3D_Internal(detJ, J); 784 } 785 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 786 } else if (numCoords == 4) { 787 const PetscInt dim = 2; 788 PetscReal R[4], J0; 789 790 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 791 ierr = DMPlexComputeProjection2Dto1D_Internal(coords, R);CHKERRQ(ierr); 792 if (J) { 793 J0 = 0.5*PetscRealPart(coords[1]); 794 J[0] = R[0]*J0; J[1] = R[1]; 795 J[2] = R[2]*J0; J[3] = R[3]; 796 DMPlex_Det2D_Internal(detJ, J); 797 } 798 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 799 } else if (numCoords == 2) { 800 const PetscInt dim = 1; 801 802 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 803 if (J) { 804 J[0] = 0.5*(PetscRealPart(coords[1]) - PetscRealPart(coords[0])); 805 *detJ = J[0]; 806 ierr = PetscLogFlops(2.0);CHKERRQ(ierr); 807 } 808 if (invJ) {invJ[0] = 1.0/J[0]; ierr = PetscLogFlops(1.0);CHKERRQ(ierr);} 809 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this segment is %D != 2", numCoords); 810 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 811 PetscFunctionReturn(0); 812 } 813 814 #undef __FUNCT__ 815 #define __FUNCT__ "DMPlexComputeTriangleGeometry_Internal" 816 static PetscErrorCode DMPlexComputeTriangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 817 { 818 PetscSection coordSection; 819 Vec coordinates; 820 PetscScalar *coords = NULL; 821 PetscInt numCoords, d, f, g; 822 PetscErrorCode ierr; 823 824 PetscFunctionBegin; 825 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 826 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 827 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 828 *detJ = 0.0; 829 if (numCoords == 9) { 830 const PetscInt dim = 3; 831 PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; 832 833 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 834 ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); 835 if (J) { 836 const PetscInt pdim = 2; 837 838 for (d = 0; d < pdim; d++) { 839 for (f = 0; f < pdim; f++) { 840 J0[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 841 } 842 } 843 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 844 DMPlex_Det3D_Internal(detJ, J0); 845 for (d = 0; d < dim; d++) { 846 for (f = 0; f < dim; f++) { 847 J[d*dim+f] = 0.0; 848 for (g = 0; g < dim; g++) { 849 J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; 850 } 851 } 852 } 853 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 854 } 855 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 856 } else if (numCoords == 6) { 857 const PetscInt dim = 2; 858 859 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 860 if (J) { 861 for (d = 0; d < dim; d++) { 862 for (f = 0; f < dim; f++) { 863 J[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); 864 } 865 } 866 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 867 DMPlex_Det2D_Internal(detJ, J); 868 } 869 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 870 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this triangle is %D != 6 or 9", numCoords); 871 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 872 PetscFunctionReturn(0); 873 } 874 875 #undef __FUNCT__ 876 #define __FUNCT__ "DMPlexComputeRectangleGeometry_Internal" 877 static PetscErrorCode DMPlexComputeRectangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 878 { 879 PetscSection coordSection; 880 Vec coordinates; 881 PetscScalar *coords = NULL; 882 PetscInt numCoords, d, f, g; 883 PetscErrorCode ierr; 884 885 PetscFunctionBegin; 886 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 887 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 888 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 889 *detJ = 0.0; 890 if (numCoords == 12) { 891 const PetscInt dim = 3; 892 PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; 893 894 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 895 ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); 896 if (J) { 897 const PetscInt pdim = 2; 898 899 for (d = 0; d < pdim; d++) { 900 J0[d*dim+0] = 0.5*(PetscRealPart(coords[1*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 901 J0[d*dim+1] = 0.5*(PetscRealPart(coords[3*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 902 } 903 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 904 DMPlex_Det3D_Internal(detJ, J0); 905 for (d = 0; d < dim; d++) { 906 for (f = 0; f < dim; f++) { 907 J[d*dim+f] = 0.0; 908 for (g = 0; g < dim; g++) { 909 J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; 910 } 911 } 912 } 913 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 914 } 915 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 916 } else if ((numCoords == 8) || (numCoords == 16)) { 917 const PetscInt dim = 2; 918 919 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 920 if (J) { 921 for (d = 0; d < dim; d++) { 922 J[d*dim+0] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 923 J[d*dim+1] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 924 } 925 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 926 DMPlex_Det2D_Internal(detJ, J); 927 } 928 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 929 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this quadrilateral is %D != 8 or 12", numCoords); 930 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 931 PetscFunctionReturn(0); 932 } 933 934 #undef __FUNCT__ 935 #define __FUNCT__ "DMPlexComputeTetrahedronGeometry_Internal" 936 static PetscErrorCode DMPlexComputeTetrahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 937 { 938 PetscSection coordSection; 939 Vec coordinates; 940 PetscScalar *coords = NULL; 941 const PetscInt dim = 3; 942 PetscInt d; 943 PetscErrorCode ierr; 944 945 PetscFunctionBegin; 946 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 947 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 948 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 949 *detJ = 0.0; 950 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 951 if (J) { 952 for (d = 0; d < dim; d++) { 953 /* I orient with outward face normals */ 954 J[d*dim+0] = 0.5*(PetscRealPart(coords[2*dim+d]) - PetscRealPart(coords[0*dim+d])); 955 J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 956 J[d*dim+2] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 957 } 958 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 959 DMPlex_Det3D_Internal(detJ, J); 960 } 961 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 962 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 963 PetscFunctionReturn(0); 964 } 965 966 #undef __FUNCT__ 967 #define __FUNCT__ "DMPlexComputeHexahedronGeometry_Internal" 968 static PetscErrorCode DMPlexComputeHexahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 969 { 970 PetscSection coordSection; 971 Vec coordinates; 972 PetscScalar *coords = NULL; 973 const PetscInt dim = 3; 974 PetscInt d; 975 PetscErrorCode ierr; 976 977 PetscFunctionBegin; 978 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 979 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 980 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 981 *detJ = 0.0; 982 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 983 if (J) { 984 for (d = 0; d < dim; d++) { 985 J[d*dim+0] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 986 J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 987 J[d*dim+2] = 0.5*(PetscRealPart(coords[4*dim+d]) - PetscRealPart(coords[0*dim+d])); 988 } 989 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 990 DMPlex_Det3D_Internal(detJ, J); 991 } 992 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 993 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 994 PetscFunctionReturn(0); 995 } 996 997 #undef __FUNCT__ 998 #define __FUNCT__ "DMPlexComputeCellGeometryAffineFEM" 999 /*@C 1000 DMPlexComputeCellGeometryAffineFEM - Assuming an affine map, compute the Jacobian, inverse Jacobian, and Jacobian determinant for a given cell 1001 1002 Collective on DM 1003 1004 Input Arguments: 1005 + dm - the DM 1006 - cell - the cell 1007 1008 Output Arguments: 1009 + v0 - the translation part of this affine transform 1010 . J - the Jacobian of the transform from the reference element 1011 . invJ - the inverse of the Jacobian 1012 - detJ - the Jacobian determinant 1013 1014 Level: advanced 1015 1016 Fortran Notes: 1017 Since it returns arrays, this routine is only available in Fortran 90, and you must 1018 include petsc.h90 in your code. 1019 1020 .seealso: DMPlexComputeCellGeometryFEM(), DMGetCoordinateSection(), DMGetCoordinateVec() 1021 @*/ 1022 PetscErrorCode DMPlexComputeCellGeometryAffineFEM(DM dm, PetscInt cell, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) 1023 { 1024 PetscInt depth, dim, coneSize; 1025 PetscErrorCode ierr; 1026 1027 PetscFunctionBegin; 1028 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1029 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1030 if (depth == 1) { 1031 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1032 } else { 1033 DMLabel depth; 1034 1035 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1036 ierr = DMLabelGetValue(depth, cell, &dim);CHKERRQ(ierr); 1037 } 1038 switch (dim) { 1039 case 1: 1040 ierr = DMPlexComputeLineGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1041 break; 1042 case 2: 1043 switch (coneSize) { 1044 case 3: 1045 ierr = DMPlexComputeTriangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1046 break; 1047 case 4: 1048 ierr = DMPlexComputeRectangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1049 break; 1050 default: 1051 SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of faces %D in cell %D for element geometry computation", coneSize, cell); 1052 } 1053 break; 1054 case 3: 1055 switch (coneSize) { 1056 case 4: 1057 ierr = DMPlexComputeTetrahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1058 break; 1059 case 6: /* Faces */ 1060 case 8: /* Vertices */ 1061 ierr = DMPlexComputeHexahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1062 break; 1063 default: 1064 SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of faces %D in cell %D for element geometry computation", coneSize, cell); 1065 } 1066 break; 1067 default: 1068 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); 1069 } 1070 PetscFunctionReturn(0); 1071 } 1072 1073 #undef __FUNCT__ 1074 #define __FUNCT__ "DMPlexComputeIsoparametricGeometry_Internal" 1075 static PetscErrorCode DMPlexComputeIsoparametricGeometry_Internal(DM dm, PetscFE fe, PetscInt point, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1076 { 1077 PetscQuadrature quad; 1078 PetscSection coordSection; 1079 Vec coordinates; 1080 PetscScalar *coords = NULL; 1081 const PetscReal *quadPoints; 1082 PetscReal *basisDer; 1083 PetscInt dim, cdim, pdim, qdim, Nq, numCoords, d, q; 1084 PetscErrorCode ierr; 1085 1086 PetscFunctionBegin; 1087 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1088 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1089 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, point, &numCoords, &coords);CHKERRQ(ierr); 1090 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1091 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 1092 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1093 ierr = PetscFEGetDimension(fe, &pdim);CHKERRQ(ierr); 1094 ierr = PetscQuadratureGetData(quad, &qdim, &Nq, &quadPoints, NULL);CHKERRQ(ierr); 1095 ierr = PetscFEGetDefaultTabulation(fe, NULL, &basisDer, NULL);CHKERRQ(ierr); 1096 *detJ = 0.0; 1097 if (qdim != dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Point dimension %d != quadrature dimension %d", dim, qdim); 1098 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); 1099 if (v0) {for (d = 0; d < cdim; d++) v0[d] = PetscRealPart(coords[d]);} 1100 if (J) { 1101 for (q = 0; q < Nq; ++q) { 1102 PetscInt i, j, k, c, r; 1103 1104 /* J = dx_i/d\xi_j = sum[k=0,n-1] dN_k/d\xi_j * x_i(k) */ 1105 for (k = 0; k < pdim; ++k) 1106 for (j = 0; j < dim; ++j) 1107 for (i = 0; i < cdim; ++i) 1108 J[(q*cdim + i)*dim + j] += basisDer[(q*pdim + k)*dim + j] * PetscRealPart(coords[k*cdim + i]); 1109 ierr = PetscLogFlops(2.0*pdim*dim*cdim);CHKERRQ(ierr); 1110 if (cdim > dim) { 1111 for (c = dim; c < cdim; ++c) 1112 for (r = 0; r < cdim; ++r) 1113 J[r*cdim+c] = r == c ? 1.0 : 0.0; 1114 } 1115 switch (cdim) { 1116 case 3: 1117 DMPlex_Det3D_Internal(detJ, J); 1118 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1119 break; 1120 case 2: 1121 DMPlex_Det2D_Internal(detJ, J); 1122 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 1123 break; 1124 case 1: 1125 *detJ = J[0]; 1126 if (invJ) invJ[0] = 1.0/J[0]; 1127 } 1128 } 1129 } 1130 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, point, &numCoords, &coords);CHKERRQ(ierr); 1131 PetscFunctionReturn(0); 1132 } 1133 1134 #undef __FUNCT__ 1135 #define __FUNCT__ "DMPlexComputeCellGeometryFEM" 1136 /*@C 1137 DMPlexComputeCellGeometryFEM - Compute the Jacobian, inverse Jacobian, and Jacobian determinant at each quadrature point in the given cell 1138 1139 Collective on DM 1140 1141 Input Arguments: 1142 + dm - the DM 1143 . cell - the cell 1144 - fe - the finite element containing the quadrature 1145 1146 Output Arguments: 1147 + v0 - the translation part of this transform 1148 . J - the Jacobian of the transform from the reference element at each quadrature point 1149 . invJ - the inverse of the Jacobian at each quadrature point 1150 - detJ - the Jacobian determinant at each quadrature point 1151 1152 Level: advanced 1153 1154 Fortran Notes: 1155 Since it returns arrays, this routine is only available in Fortran 90, and you must 1156 include petsc.h90 in your code. 1157 1158 .seealso: DMGetCoordinateSection(), DMGetCoordinateVec() 1159 @*/ 1160 PetscErrorCode DMPlexComputeCellGeometryFEM(DM dm, PetscInt cell, PetscFE fe, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) 1161 { 1162 PetscErrorCode ierr; 1163 1164 PetscFunctionBegin; 1165 if (!fe) {ierr = DMPlexComputeCellGeometryAffineFEM(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr);} 1166 else {ierr = DMPlexComputeIsoparametricGeometry_Internal(dm, fe, cell, v0, J, invJ, detJ);CHKERRQ(ierr);} 1167 PetscFunctionReturn(0); 1168 } 1169 1170 #undef __FUNCT__ 1171 #define __FUNCT__ "DMPlexComputeGeometryFVM_1D_Internal" 1172 static PetscErrorCode DMPlexComputeGeometryFVM_1D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1173 { 1174 PetscSection coordSection; 1175 Vec coordinates; 1176 PetscScalar *coords = NULL; 1177 PetscScalar tmp[2]; 1178 PetscInt coordSize; 1179 PetscErrorCode ierr; 1180 1181 PetscFunctionBegin; 1182 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1183 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1184 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1185 if (dim != 2) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "We only support 2D edges right now"); 1186 ierr = DMLocalizeCoordinate_Internal(dm, dim, coords, &coords[dim], tmp);CHKERRQ(ierr); 1187 if (centroid) { 1188 centroid[0] = 0.5*PetscRealPart(coords[0] + tmp[0]); 1189 centroid[1] = 0.5*PetscRealPart(coords[1] + tmp[1]); 1190 } 1191 if (normal) { 1192 PetscReal norm; 1193 1194 normal[0] = -PetscRealPart(coords[1] - tmp[1]); 1195 normal[1] = PetscRealPart(coords[0] - tmp[0]); 1196 norm = PetscSqrtReal(normal[0]*normal[0] + normal[1]*normal[1]); 1197 normal[0] /= norm; 1198 normal[1] /= norm; 1199 } 1200 if (vol) { 1201 *vol = PetscSqrtReal(PetscSqr(PetscRealPart(coords[0] - tmp[0])) + PetscSqr(PetscRealPart(coords[1] - tmp[1]))); 1202 } 1203 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1204 PetscFunctionReturn(0); 1205 } 1206 1207 #undef __FUNCT__ 1208 #define __FUNCT__ "DMPlexComputeGeometryFVM_2D_Internal" 1209 /* Centroid_i = (\sum_n A_n Cn_i ) / A */ 1210 static PetscErrorCode DMPlexComputeGeometryFVM_2D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1211 { 1212 PetscSection coordSection; 1213 Vec coordinates; 1214 PetscScalar *coords = NULL; 1215 PetscReal vsum = 0.0, csum[3] = {0.0, 0.0, 0.0}, vtmp, ctmp[4], v0[3], R[9]; 1216 PetscInt tdim = 2, coordSize, numCorners, p, d, e; 1217 PetscErrorCode ierr; 1218 1219 PetscFunctionBegin; 1220 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1221 ierr = DMPlexGetConeSize(dm, cell, &numCorners);CHKERRQ(ierr); 1222 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1223 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1224 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 1225 if (normal) { 1226 if (dim > 2) { 1227 const PetscReal x0 = PetscRealPart(coords[dim+0] - coords[0]), x1 = PetscRealPart(coords[dim*2+0] - coords[0]); 1228 const PetscReal y0 = PetscRealPart(coords[dim+1] - coords[1]), y1 = PetscRealPart(coords[dim*2+1] - coords[1]); 1229 const PetscReal z0 = PetscRealPart(coords[dim+2] - coords[2]), z1 = PetscRealPart(coords[dim*2+2] - coords[2]); 1230 PetscReal norm; 1231 1232 v0[0] = PetscRealPart(coords[0]); 1233 v0[1] = PetscRealPart(coords[1]); 1234 v0[2] = PetscRealPart(coords[2]); 1235 normal[0] = y0*z1 - z0*y1; 1236 normal[1] = z0*x1 - x0*z1; 1237 normal[2] = x0*y1 - y0*x1; 1238 norm = PetscSqrtReal(normal[0]*normal[0] + normal[1]*normal[1] + normal[2]*normal[2]); 1239 normal[0] /= norm; 1240 normal[1] /= norm; 1241 normal[2] /= norm; 1242 } else { 1243 for (d = 0; d < dim; ++d) normal[d] = 0.0; 1244 } 1245 } 1246 if (dim == 3) {ierr = DMPlexComputeProjection3Dto2D_Internal(coordSize, coords, R);CHKERRQ(ierr);} 1247 for (p = 0; p < numCorners; ++p) { 1248 /* Need to do this copy to get types right */ 1249 for (d = 0; d < tdim; ++d) { 1250 ctmp[d] = PetscRealPart(coords[p*tdim+d]); 1251 ctmp[tdim+d] = PetscRealPart(coords[((p+1)%numCorners)*tdim+d]); 1252 } 1253 Volume_Triangle_Origin_Internal(&vtmp, ctmp); 1254 vsum += vtmp; 1255 for (d = 0; d < tdim; ++d) { 1256 csum[d] += (ctmp[d] + ctmp[tdim+d])*vtmp; 1257 } 1258 } 1259 for (d = 0; d < tdim; ++d) { 1260 csum[d] /= (tdim+1)*vsum; 1261 } 1262 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1263 if (vol) *vol = PetscAbsReal(vsum); 1264 if (centroid) { 1265 if (dim > 2) { 1266 for (d = 0; d < dim; ++d) { 1267 centroid[d] = v0[d]; 1268 for (e = 0; e < dim; ++e) { 1269 centroid[d] += R[d*dim+e]*csum[e]; 1270 } 1271 } 1272 } else for (d = 0; d < dim; ++d) centroid[d] = csum[d]; 1273 } 1274 PetscFunctionReturn(0); 1275 } 1276 1277 #undef __FUNCT__ 1278 #define __FUNCT__ "DMPlexComputeGeometryFVM_3D_Internal" 1279 /* Centroid_i = (\sum_n V_n Cn_i ) / V */ 1280 static PetscErrorCode DMPlexComputeGeometryFVM_3D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1281 { 1282 PetscSection coordSection; 1283 Vec coordinates; 1284 PetscScalar *coords = NULL; 1285 PetscReal vsum = 0.0, vtmp, coordsTmp[3*3]; 1286 const PetscInt *faces, *facesO; 1287 PetscInt numFaces, f, coordSize, numCorners, p, d; 1288 PetscErrorCode ierr; 1289 1290 PetscFunctionBegin; 1291 if (PetscUnlikely(dim > 3)) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"No support for dim %D > 3",dim); 1292 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1293 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1294 1295 if (centroid) for (d = 0; d < dim; ++d) centroid[d] = 0.0; 1296 ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr); 1297 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 1298 ierr = DMPlexGetConeOrientation(dm, cell, &facesO);CHKERRQ(ierr); 1299 for (f = 0; f < numFaces; ++f) { 1300 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); 1301 numCorners = coordSize/dim; 1302 switch (numCorners) { 1303 case 3: 1304 for (d = 0; d < dim; ++d) { 1305 coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); 1306 coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); 1307 coordsTmp[2*dim+d] = PetscRealPart(coords[2*dim+d]); 1308 } 1309 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1310 if (facesO[f] < 0) vtmp = -vtmp; 1311 vsum += vtmp; 1312 if (centroid) { /* Centroid of OABC = (a+b+c)/4 */ 1313 for (d = 0; d < dim; ++d) { 1314 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1315 } 1316 } 1317 break; 1318 case 4: 1319 /* DO FOR PYRAMID */ 1320 /* First tet */ 1321 for (d = 0; d < dim; ++d) { 1322 coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); 1323 coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); 1324 coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); 1325 } 1326 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1327 if (facesO[f] < 0) vtmp = -vtmp; 1328 vsum += vtmp; 1329 if (centroid) { 1330 for (d = 0; d < dim; ++d) { 1331 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1332 } 1333 } 1334 /* Second tet */ 1335 for (d = 0; d < dim; ++d) { 1336 coordsTmp[0*dim+d] = PetscRealPart(coords[1*dim+d]); 1337 coordsTmp[1*dim+d] = PetscRealPart(coords[2*dim+d]); 1338 coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); 1339 } 1340 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1341 if (facesO[f] < 0) vtmp = -vtmp; 1342 vsum += vtmp; 1343 if (centroid) { 1344 for (d = 0; d < dim; ++d) { 1345 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1346 } 1347 } 1348 break; 1349 default: 1350 SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle faces with %D vertices", numCorners); 1351 } 1352 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); 1353 } 1354 if (vol) *vol = PetscAbsReal(vsum); 1355 if (normal) for (d = 0; d < dim; ++d) normal[d] = 0.0; 1356 if (centroid) for (d = 0; d < dim; ++d) centroid[d] /= (vsum*4); 1357 PetscFunctionReturn(0); 1358 } 1359 1360 #undef __FUNCT__ 1361 #define __FUNCT__ "DMPlexComputeCellGeometryFVM" 1362 /*@C 1363 DMPlexComputeCellGeometryFVM - Compute the volume for a given cell 1364 1365 Collective on DM 1366 1367 Input Arguments: 1368 + dm - the DM 1369 - cell - the cell 1370 1371 Output Arguments: 1372 + volume - the cell volume 1373 . centroid - the cell centroid 1374 - normal - the cell normal, if appropriate 1375 1376 Level: advanced 1377 1378 Fortran Notes: 1379 Since it returns arrays, this routine is only available in Fortran 90, and you must 1380 include petsc.h90 in your code. 1381 1382 .seealso: DMGetCoordinateSection(), DMGetCoordinateVec() 1383 @*/ 1384 PetscErrorCode DMPlexComputeCellGeometryFVM(DM dm, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1385 { 1386 PetscInt depth, dim; 1387 PetscErrorCode ierr; 1388 1389 PetscFunctionBegin; 1390 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1391 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1392 if (depth != dim) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh must be interpolated"); 1393 /* We need to keep a pointer to the depth label */ 1394 ierr = DMGetLabelValue(dm, "depth", cell, &depth);CHKERRQ(ierr); 1395 /* Cone size is now the number of faces */ 1396 switch (depth) { 1397 case 1: 1398 ierr = DMPlexComputeGeometryFVM_1D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1399 break; 1400 case 2: 1401 ierr = DMPlexComputeGeometryFVM_2D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1402 break; 1403 case 3: 1404 ierr = DMPlexComputeGeometryFVM_3D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1405 break; 1406 default: 1407 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); 1408 } 1409 PetscFunctionReturn(0); 1410 } 1411 1412 #undef __FUNCT__ 1413 #define __FUNCT__ "DMPlexComputeGeometryFEM" 1414 /* This should also take a PetscFE argument I think */ 1415 PetscErrorCode DMPlexComputeGeometryFEM(DM dm, Vec *cellgeom) 1416 { 1417 DM dmCell; 1418 Vec coordinates; 1419 PetscSection coordSection, sectionCell; 1420 PetscScalar *cgeom; 1421 PetscInt cStart, cEnd, cMax, c; 1422 PetscErrorCode ierr; 1423 1424 PetscFunctionBegin; 1425 ierr = DMClone(dm, &dmCell);CHKERRQ(ierr); 1426 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1427 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1428 ierr = DMSetCoordinateSection(dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1429 ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr); 1430 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr); 1431 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1432 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1433 cEnd = cMax < 0 ? cEnd : cMax; 1434 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1435 /* TODO This needs to be multiplied by Nq for non-affine */ 1436 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFECellGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1437 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1438 ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr); 1439 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1440 ierr = DMCreateLocalVector(dmCell, cellgeom);CHKERRQ(ierr); 1441 ierr = VecGetArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1442 for (c = cStart; c < cEnd; ++c) { 1443 PetscFECellGeom *cg; 1444 1445 ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1446 ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr); 1447 ierr = DMPlexComputeCellGeometryFEM(dmCell, c, NULL, cg->v0, cg->J, cg->invJ, &cg->detJ);CHKERRQ(ierr); 1448 if (cg->detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", cg->detJ, c); 1449 } 1450 ierr = VecRestoreArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1451 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1452 PetscFunctionReturn(0); 1453 } 1454 1455 #undef __FUNCT__ 1456 #define __FUNCT__ "DMPlexComputeGeometryFVM" 1457 /*@ 1458 DMPlexComputeGeometryFVM - Computes the cell and face geometry for a finite volume method 1459 1460 Input Parameter: 1461 . dm - The DM 1462 1463 Output Parameters: 1464 + cellgeom - A Vec of PetscFVCellGeom data 1465 . facegeom - A Vec of PetscFVFaceGeom data 1466 1467 Level: developer 1468 1469 .seealso: PetscFVFaceGeom, PetscFVCellGeom, DMPlexComputeGeometryFEM() 1470 @*/ 1471 PetscErrorCode DMPlexComputeGeometryFVM(DM dm, Vec *cellgeom, Vec *facegeom) 1472 { 1473 DM dmFace, dmCell; 1474 DMLabel ghostLabel; 1475 PetscSection sectionFace, sectionCell; 1476 PetscSection coordSection; 1477 Vec coordinates; 1478 PetscScalar *fgeom, *cgeom; 1479 PetscReal minradius, gminradius; 1480 PetscInt dim, cStart, cEnd, cEndInterior, c, fStart, fEnd, f; 1481 PetscErrorCode ierr; 1482 1483 PetscFunctionBegin; 1484 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1485 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1486 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1487 /* Make cell centroids and volumes */ 1488 ierr = DMClone(dm, &dmCell);CHKERRQ(ierr); 1489 ierr = DMSetCoordinateSection(dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1490 ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr); 1491 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr); 1492 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1493 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1494 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1495 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFVCellGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1496 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1497 ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr); 1498 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1499 ierr = DMCreateLocalVector(dmCell, cellgeom);CHKERRQ(ierr); 1500 if (cEndInterior < 0) { 1501 cEndInterior = cEnd; 1502 } 1503 ierr = VecGetArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1504 for (c = cStart; c < cEndInterior; ++c) { 1505 PetscFVCellGeom *cg; 1506 1507 ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1508 ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr); 1509 ierr = DMPlexComputeCellGeometryFVM(dmCell, c, &cg->volume, cg->centroid, NULL);CHKERRQ(ierr); 1510 } 1511 /* Compute face normals and minimum cell radius */ 1512 ierr = DMClone(dm, &dmFace);CHKERRQ(ierr); 1513 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionFace);CHKERRQ(ierr); 1514 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1515 ierr = PetscSectionSetChart(sectionFace, fStart, fEnd);CHKERRQ(ierr); 1516 for (f = fStart; f < fEnd; ++f) {ierr = PetscSectionSetDof(sectionFace, f, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFVFaceGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1517 ierr = PetscSectionSetUp(sectionFace);CHKERRQ(ierr); 1518 ierr = DMSetDefaultSection(dmFace, sectionFace);CHKERRQ(ierr); 1519 ierr = PetscSectionDestroy(§ionFace);CHKERRQ(ierr); 1520 ierr = DMCreateLocalVector(dmFace, facegeom);CHKERRQ(ierr); 1521 ierr = VecGetArray(*facegeom, &fgeom);CHKERRQ(ierr); 1522 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1523 minradius = PETSC_MAX_REAL; 1524 for (f = fStart; f < fEnd; ++f) { 1525 PetscFVFaceGeom *fg; 1526 PetscReal area; 1527 PetscInt ghost = -1, d, numChildren; 1528 1529 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1530 ierr = DMPlexGetTreeChildren(dm,f,&numChildren,NULL);CHKERRQ(ierr); 1531 if (ghost >= 0 || numChildren) continue; 1532 ierr = DMPlexPointLocalRef(dmFace, f, fgeom, &fg);CHKERRQ(ierr); 1533 ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, fg->centroid, fg->normal);CHKERRQ(ierr); 1534 for (d = 0; d < dim; ++d) fg->normal[d] *= area; 1535 /* Flip face orientation if necessary to match ordering in support, and Update minimum radius */ 1536 { 1537 PetscFVCellGeom *cL, *cR; 1538 PetscInt ncells; 1539 const PetscInt *cells; 1540 PetscReal *lcentroid, *rcentroid; 1541 PetscReal l[3], r[3], v[3]; 1542 1543 ierr = DMPlexGetSupport(dm, f, &cells);CHKERRQ(ierr); 1544 ierr = DMPlexGetSupportSize(dm, f, &ncells);CHKERRQ(ierr); 1545 ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cL);CHKERRQ(ierr); 1546 lcentroid = cells[0] >= cEndInterior ? fg->centroid : cL->centroid; 1547 if (ncells > 1) { 1548 ierr = DMPlexPointLocalRead(dmCell, cells[1], cgeom, &cR);CHKERRQ(ierr); 1549 rcentroid = cells[1] >= cEndInterior ? fg->centroid : cR->centroid; 1550 } 1551 else { 1552 rcentroid = fg->centroid; 1553 } 1554 ierr = DMLocalizeCoordinateReal_Internal(dm, dim, fg->centroid, lcentroid, l);CHKERRQ(ierr); 1555 ierr = DMLocalizeCoordinateReal_Internal(dm, dim, fg->centroid, rcentroid, r);CHKERRQ(ierr); 1556 DMPlex_WaxpyD_Internal(dim, -1, l, r, v); 1557 if (DMPlex_DotRealD_Internal(dim, fg->normal, v) < 0) { 1558 for (d = 0; d < dim; ++d) fg->normal[d] = -fg->normal[d]; 1559 } 1560 if (DMPlex_DotRealD_Internal(dim, fg->normal, v) <= 0) { 1561 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]); 1562 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]); 1563 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed", f); 1564 } 1565 if (cells[0] < cEndInterior) { 1566 DMPlex_WaxpyD_Internal(dim, -1, fg->centroid, cL->centroid, v); 1567 minradius = PetscMin(minradius, DMPlex_NormD_Internal(dim, v)); 1568 } 1569 if (ncells > 1 && cells[1] < cEndInterior) { 1570 DMPlex_WaxpyD_Internal(dim, -1, fg->centroid, cR->centroid, v); 1571 minradius = PetscMin(minradius, DMPlex_NormD_Internal(dim, v)); 1572 } 1573 } 1574 } 1575 ierr = MPIU_Allreduce(&minradius, &gminradius, 1, MPIU_REAL, MPIU_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1576 ierr = DMPlexSetMinRadius(dm, gminradius);CHKERRQ(ierr); 1577 /* Compute centroids of ghost cells */ 1578 for (c = cEndInterior; c < cEnd; ++c) { 1579 PetscFVFaceGeom *fg; 1580 const PetscInt *cone, *support; 1581 PetscInt coneSize, supportSize, s; 1582 1583 ierr = DMPlexGetConeSize(dmCell, c, &coneSize);CHKERRQ(ierr); 1584 if (coneSize != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Ghost cell %d has cone size %d != 1", c, coneSize); 1585 ierr = DMPlexGetCone(dmCell, c, &cone);CHKERRQ(ierr); 1586 ierr = DMPlexGetSupportSize(dmCell, cone[0], &supportSize);CHKERRQ(ierr); 1587 if (supportSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %d has support size %d != 2", cone[0], supportSize); 1588 ierr = DMPlexGetSupport(dmCell, cone[0], &support);CHKERRQ(ierr); 1589 ierr = DMPlexPointLocalRef(dmFace, cone[0], fgeom, &fg);CHKERRQ(ierr); 1590 for (s = 0; s < 2; ++s) { 1591 /* Reflect ghost centroid across plane of face */ 1592 if (support[s] == c) { 1593 PetscFVCellGeom *ci; 1594 PetscFVCellGeom *cg; 1595 PetscReal c2f[3], a; 1596 1597 ierr = DMPlexPointLocalRead(dmCell, support[(s+1)%2], cgeom, &ci);CHKERRQ(ierr); 1598 DMPlex_WaxpyD_Internal(dim, -1, ci->centroid, fg->centroid, c2f); /* cell to face centroid */ 1599 a = DMPlex_DotRealD_Internal(dim, c2f, fg->normal)/DMPlex_DotRealD_Internal(dim, fg->normal, fg->normal); 1600 ierr = DMPlexPointLocalRef(dmCell, support[s], cgeom, &cg);CHKERRQ(ierr); 1601 DMPlex_WaxpyD_Internal(dim, 2*a, fg->normal, ci->centroid, cg->centroid); 1602 cg->volume = ci->volume; 1603 } 1604 } 1605 } 1606 ierr = VecRestoreArray(*facegeom, &fgeom);CHKERRQ(ierr); 1607 ierr = VecRestoreArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1608 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1609 ierr = DMDestroy(&dmFace);CHKERRQ(ierr); 1610 PetscFunctionReturn(0); 1611 } 1612 1613 #undef __FUNCT__ 1614 #define __FUNCT__ "DMPlexGetMinRadius" 1615 /*@C 1616 DMPlexGetMinRadius - Returns the minimum distance from any cell centroid to a face 1617 1618 Not collective 1619 1620 Input Argument: 1621 . dm - the DM 1622 1623 Output Argument: 1624 . minradius - the minium cell radius 1625 1626 Level: developer 1627 1628 .seealso: DMGetCoordinates() 1629 @*/ 1630 PetscErrorCode DMPlexGetMinRadius(DM dm, PetscReal *minradius) 1631 { 1632 PetscFunctionBegin; 1633 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1634 PetscValidPointer(minradius,2); 1635 *minradius = ((DM_Plex*) dm->data)->minradius; 1636 PetscFunctionReturn(0); 1637 } 1638 1639 #undef __FUNCT__ 1640 #define __FUNCT__ "DMPlexSetMinRadius" 1641 /*@C 1642 DMPlexSetMinRadius - Sets the minimum distance from the cell centroid to a face 1643 1644 Logically collective 1645 1646 Input Arguments: 1647 + dm - the DM 1648 - minradius - the minium cell radius 1649 1650 Level: developer 1651 1652 .seealso: DMSetCoordinates() 1653 @*/ 1654 PetscErrorCode DMPlexSetMinRadius(DM dm, PetscReal minradius) 1655 { 1656 PetscFunctionBegin; 1657 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1658 ((DM_Plex*) dm->data)->minradius = minradius; 1659 PetscFunctionReturn(0); 1660 } 1661 1662 #undef __FUNCT__ 1663 #define __FUNCT__ "BuildGradientReconstruction_Internal" 1664 static PetscErrorCode BuildGradientReconstruction_Internal(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom) 1665 { 1666 DMLabel ghostLabel; 1667 PetscScalar *dx, *grad, **gref; 1668 PetscInt dim, cStart, cEnd, c, cEndInterior, maxNumFaces; 1669 PetscErrorCode ierr; 1670 1671 PetscFunctionBegin; 1672 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1673 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1674 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1675 ierr = DMPlexGetMaxSizes(dm, &maxNumFaces, NULL);CHKERRQ(ierr); 1676 ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr); 1677 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1678 ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr); 1679 for (c = cStart; c < cEndInterior; c++) { 1680 const PetscInt *faces; 1681 PetscInt numFaces, usedFaces, f, d; 1682 PetscFVCellGeom *cg; 1683 PetscBool boundary; 1684 PetscInt ghost; 1685 1686 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1687 ierr = DMPlexGetConeSize(dm, c, &numFaces);CHKERRQ(ierr); 1688 ierr = DMPlexGetCone(dm, c, &faces);CHKERRQ(ierr); 1689 if (numFaces < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cell %D has only %D faces, not enough for gradient reconstruction", c, numFaces); 1690 for (f = 0, usedFaces = 0; f < numFaces; ++f) { 1691 PetscFVCellGeom *cg1; 1692 PetscFVFaceGeom *fg; 1693 const PetscInt *fcells; 1694 PetscInt ncell, side; 1695 1696 ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr); 1697 ierr = DMIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr); 1698 if ((ghost >= 0) || boundary) continue; 1699 ierr = DMPlexGetSupport(dm, faces[f], &fcells);CHKERRQ(ierr); 1700 side = (c != fcells[0]); /* c is on left=0 or right=1 of face */ 1701 ncell = fcells[!side]; /* the neighbor */ 1702 ierr = DMPlexPointLocalRef(dmFace, faces[f], fgeom, &fg);CHKERRQ(ierr); 1703 ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr); 1704 for (d = 0; d < dim; ++d) dx[usedFaces*dim+d] = cg1->centroid[d] - cg->centroid[d]; 1705 gref[usedFaces++] = fg->grad[side]; /* Gradient reconstruction term will go here */ 1706 } 1707 if (!usedFaces) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_USER, "Mesh contains isolated cell (no neighbors). Is it intentional?"); 1708 ierr = PetscFVComputeGradient(fvm, usedFaces, dx, grad);CHKERRQ(ierr); 1709 for (f = 0, usedFaces = 0; f < numFaces; ++f) { 1710 ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr); 1711 ierr = DMIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr); 1712 if ((ghost >= 0) || boundary) continue; 1713 for (d = 0; d < dim; ++d) gref[usedFaces][d] = grad[usedFaces*dim+d]; 1714 ++usedFaces; 1715 } 1716 } 1717 ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr); 1718 PetscFunctionReturn(0); 1719 } 1720 1721 #undef __FUNCT__ 1722 #define __FUNCT__ "BuildGradientReconstruction_Internal_Tree" 1723 static PetscErrorCode BuildGradientReconstruction_Internal_Tree(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom) 1724 { 1725 DMLabel ghostLabel; 1726 PetscScalar *dx, *grad, **gref; 1727 PetscInt dim, cStart, cEnd, c, cEndInterior, fStart, fEnd, f, nStart, nEnd, maxNumFaces = 0; 1728 PetscSection neighSec; 1729 PetscInt (*neighbors)[2]; 1730 PetscInt *counter; 1731 PetscErrorCode ierr; 1732 1733 PetscFunctionBegin; 1734 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1735 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1736 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1737 if (cEndInterior < 0) { 1738 cEndInterior = cEnd; 1739 } 1740 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&neighSec);CHKERRQ(ierr); 1741 ierr = PetscSectionSetChart(neighSec,cStart,cEndInterior);CHKERRQ(ierr); 1742 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1743 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1744 for (f = fStart; f < fEnd; f++) { 1745 const PetscInt *fcells; 1746 PetscBool boundary; 1747 PetscInt ghost = -1; 1748 PetscInt numChildren, numCells, c; 1749 1750 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1751 ierr = DMIsBoundaryPoint(dm, f, &boundary);CHKERRQ(ierr); 1752 ierr = DMPlexGetTreeChildren(dm, f, &numChildren, NULL);CHKERRQ(ierr); 1753 if ((ghost >= 0) || boundary || numChildren) continue; 1754 ierr = DMPlexGetSupportSize(dm, f, &numCells);CHKERRQ(ierr); 1755 if (numCells == 2) { 1756 ierr = DMPlexGetSupport(dm, f, &fcells);CHKERRQ(ierr); 1757 for (c = 0; c < 2; c++) { 1758 PetscInt cell = fcells[c]; 1759 1760 if (cell >= cStart && cell < cEndInterior) { 1761 ierr = PetscSectionAddDof(neighSec,cell,1);CHKERRQ(ierr); 1762 } 1763 } 1764 } 1765 } 1766 ierr = PetscSectionSetUp(neighSec);CHKERRQ(ierr); 1767 ierr = PetscSectionGetMaxDof(neighSec,&maxNumFaces);CHKERRQ(ierr); 1768 ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr); 1769 nStart = 0; 1770 ierr = PetscSectionGetStorageSize(neighSec,&nEnd);CHKERRQ(ierr); 1771 ierr = PetscMalloc1((nEnd-nStart),&neighbors);CHKERRQ(ierr); 1772 ierr = PetscCalloc1((cEndInterior-cStart),&counter);CHKERRQ(ierr); 1773 for (f = fStart; f < fEnd; f++) { 1774 const PetscInt *fcells; 1775 PetscBool boundary; 1776 PetscInt ghost = -1; 1777 PetscInt numChildren, numCells, c; 1778 1779 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1780 ierr = DMIsBoundaryPoint(dm, f, &boundary);CHKERRQ(ierr); 1781 ierr = DMPlexGetTreeChildren(dm, f, &numChildren, NULL);CHKERRQ(ierr); 1782 if ((ghost >= 0) || boundary || numChildren) continue; 1783 ierr = DMPlexGetSupportSize(dm, f, &numCells);CHKERRQ(ierr); 1784 if (numCells == 2) { 1785 ierr = DMPlexGetSupport(dm, f, &fcells);CHKERRQ(ierr); 1786 for (c = 0; c < 2; c++) { 1787 PetscInt cell = fcells[c], off; 1788 1789 if (cell >= cStart && cell < cEndInterior) { 1790 ierr = PetscSectionGetOffset(neighSec,cell,&off);CHKERRQ(ierr); 1791 off += counter[cell - cStart]++; 1792 neighbors[off][0] = f; 1793 neighbors[off][1] = fcells[1 - c]; 1794 } 1795 } 1796 } 1797 } 1798 ierr = PetscFree(counter);CHKERRQ(ierr); 1799 ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr); 1800 for (c = cStart; c < cEndInterior; c++) { 1801 PetscInt numFaces, f, d, off, ghost = -1; 1802 PetscFVCellGeom *cg; 1803 1804 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1805 ierr = PetscSectionGetDof(neighSec, c, &numFaces);CHKERRQ(ierr); 1806 ierr = PetscSectionGetOffset(neighSec, c, &off);CHKERRQ(ierr); 1807 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, c, &ghost);CHKERRQ(ierr);} 1808 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); 1809 for (f = 0; f < numFaces; ++f) { 1810 PetscFVCellGeom *cg1; 1811 PetscFVFaceGeom *fg; 1812 const PetscInt *fcells; 1813 PetscInt ncell, side, nface; 1814 1815 nface = neighbors[off + f][0]; 1816 ncell = neighbors[off + f][1]; 1817 ierr = DMPlexGetSupport(dm,nface,&fcells);CHKERRQ(ierr); 1818 side = (c != fcells[0]); 1819 ierr = DMPlexPointLocalRef(dmFace, nface, fgeom, &fg);CHKERRQ(ierr); 1820 ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr); 1821 for (d = 0; d < dim; ++d) dx[f*dim+d] = cg1->centroid[d] - cg->centroid[d]; 1822 gref[f] = fg->grad[side]; /* Gradient reconstruction term will go here */ 1823 } 1824 ierr = PetscFVComputeGradient(fvm, numFaces, dx, grad);CHKERRQ(ierr); 1825 for (f = 0; f < numFaces; ++f) { 1826 for (d = 0; d < dim; ++d) gref[f][d] = grad[f*dim+d]; 1827 } 1828 } 1829 ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr); 1830 ierr = PetscSectionDestroy(&neighSec);CHKERRQ(ierr); 1831 ierr = PetscFree(neighbors);CHKERRQ(ierr); 1832 PetscFunctionReturn(0); 1833 } 1834 1835 #undef __FUNCT__ 1836 #define __FUNCT__ "DMPlexComputeGradientFVM" 1837 /*@ 1838 DMPlexComputeGradientFVM - Compute geometric factors for gradient reconstruction, which are stored in the geometry data, and compute layout for gradient data 1839 1840 Collective on DM 1841 1842 Input Arguments: 1843 + dm - The DM 1844 . fvm - The PetscFV 1845 . faceGeometry - The face geometry from DMPlexGetFaceGeometryFVM() 1846 - cellGeometry - The face geometry from DMPlexGetCellGeometryFVM() 1847 1848 Output Parameters: 1849 + faceGeometry - The geometric factors for gradient calculation are inserted 1850 - dmGrad - The DM describing the layout of gradient data 1851 1852 Level: developer 1853 1854 .seealso: DMPlexGetFaceGeometryFVM(), DMPlexGetCellGeometryFVM() 1855 @*/ 1856 PetscErrorCode DMPlexComputeGradientFVM(DM dm, PetscFV fvm, Vec faceGeometry, Vec cellGeometry, DM *dmGrad) 1857 { 1858 DM dmFace, dmCell; 1859 PetscScalar *fgeom, *cgeom; 1860 PetscSection sectionGrad, parentSection; 1861 PetscInt dim, pdim, cStart, cEnd, cEndInterior, c; 1862 PetscErrorCode ierr; 1863 1864 PetscFunctionBegin; 1865 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1866 ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr); 1867 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1868 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1869 /* Construct the interpolant corresponding to each face from the least-square solution over the cell neighborhood */ 1870 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1871 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1872 ierr = VecGetArray(faceGeometry, &fgeom);CHKERRQ(ierr); 1873 ierr = VecGetArray(cellGeometry, &cgeom);CHKERRQ(ierr); 1874 ierr = DMPlexGetTree(dm,&parentSection,NULL,NULL,NULL,NULL);CHKERRQ(ierr); 1875 if (!parentSection) { 1876 ierr = BuildGradientReconstruction_Internal(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr); 1877 } 1878 else { 1879 ierr = BuildGradientReconstruction_Internal_Tree(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr); 1880 } 1881 ierr = VecRestoreArray(faceGeometry, &fgeom);CHKERRQ(ierr); 1882 ierr = VecRestoreArray(cellGeometry, &cgeom);CHKERRQ(ierr); 1883 /* Create storage for gradients */ 1884 ierr = DMClone(dm, dmGrad);CHKERRQ(ierr); 1885 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionGrad);CHKERRQ(ierr); 1886 ierr = PetscSectionSetChart(sectionGrad, cStart, cEnd);CHKERRQ(ierr); 1887 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionGrad, c, pdim*dim);CHKERRQ(ierr);} 1888 ierr = PetscSectionSetUp(sectionGrad);CHKERRQ(ierr); 1889 ierr = DMSetDefaultSection(*dmGrad, sectionGrad);CHKERRQ(ierr); 1890 ierr = PetscSectionDestroy(§ionGrad);CHKERRQ(ierr); 1891 PetscFunctionReturn(0); 1892 } 1893