1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 3 #undef __FUNCT__ 4 #define __FUNCT__ "DMPlexGetLineIntersection_2D_Internal" 5 static PetscErrorCode DMPlexGetLineIntersection_2D_Internal(const PetscReal segmentA[], const PetscReal segmentB[], PetscReal intersection[], PetscBool *hasIntersection) 6 { 7 const PetscReal p0_x = segmentA[0*2+0]; 8 const PetscReal p0_y = segmentA[0*2+1]; 9 const PetscReal p1_x = segmentA[1*2+0]; 10 const PetscReal p1_y = segmentA[1*2+1]; 11 const PetscReal p2_x = segmentB[0*2+0]; 12 const PetscReal p2_y = segmentB[0*2+1]; 13 const PetscReal p3_x = segmentB[1*2+0]; 14 const PetscReal p3_y = segmentB[1*2+1]; 15 const PetscReal s1_x = p1_x - p0_x; 16 const PetscReal s1_y = p1_y - p0_y; 17 const PetscReal s2_x = p3_x - p2_x; 18 const PetscReal s2_y = p3_y - p2_y; 19 const PetscReal denom = (-s2_x * s1_y + s1_x * s2_y); 20 21 PetscFunctionBegin; 22 *hasIntersection = PETSC_FALSE; 23 /* Non-parallel lines */ 24 if (denom != 0.0) { 25 const PetscReal s = (-s1_y * (p0_x - p2_x) + s1_x * (p0_y - p2_y)) / denom; 26 const PetscReal t = ( s2_x * (p0_y - p2_y) - s2_y * (p0_x - p2_x)) / denom; 27 28 if (s >= 0 && s <= 1 && t >= 0 && t <= 1) { 29 *hasIntersection = PETSC_TRUE; 30 if (intersection) { 31 intersection[0] = p0_x + (t * s1_x); 32 intersection[1] = p0_y + (t * s1_y); 33 } 34 } 35 } 36 PetscFunctionReturn(0); 37 } 38 39 #undef __FUNCT__ 40 #define __FUNCT__ "DMPlexLocatePoint_Simplex_2D_Internal" 41 static PetscErrorCode DMPlexLocatePoint_Simplex_2D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) 42 { 43 const PetscInt embedDim = 2; 44 const PetscReal eps = PETSC_SQRT_MACHINE_EPSILON; 45 PetscReal x = PetscRealPart(point[0]); 46 PetscReal y = PetscRealPart(point[1]); 47 PetscReal v0[2], J[4], invJ[4], detJ; 48 PetscReal xi, eta; 49 PetscErrorCode ierr; 50 51 PetscFunctionBegin; 52 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 53 xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]); 54 eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]); 55 56 if ((xi >= -eps) && (eta >= -eps) && (xi + eta <= 2.0+eps)) *cell = c; 57 else *cell = -1; 58 PetscFunctionReturn(0); 59 } 60 61 #undef __FUNCT__ 62 #define __FUNCT__ "DMPlexLocatePoint_General_2D_Internal" 63 static PetscErrorCode DMPlexLocatePoint_General_2D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) 64 { 65 PetscSection coordSection; 66 Vec coordsLocal; 67 PetscScalar *coords = NULL; 68 const PetscInt faces[8] = {0, 1, 1, 2, 2, 3, 3, 0}; 69 PetscReal x = PetscRealPart(point[0]); 70 PetscReal y = PetscRealPart(point[1]); 71 PetscInt crossings = 0, f; 72 PetscErrorCode ierr; 73 74 PetscFunctionBegin; 75 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 76 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 77 ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); 78 for (f = 0; f < 4; ++f) { 79 PetscReal x_i = PetscRealPart(coords[faces[2*f+0]*2+0]); 80 PetscReal y_i = PetscRealPart(coords[faces[2*f+0]*2+1]); 81 PetscReal x_j = PetscRealPart(coords[faces[2*f+1]*2+0]); 82 PetscReal y_j = PetscRealPart(coords[faces[2*f+1]*2+1]); 83 PetscReal slope = (y_j - y_i) / (x_j - x_i); 84 PetscBool cond1 = (x_i <= x) && (x < x_j) ? PETSC_TRUE : PETSC_FALSE; 85 PetscBool cond2 = (x_j <= x) && (x < x_i) ? PETSC_TRUE : PETSC_FALSE; 86 PetscBool above = (y < slope * (x - x_i) + y_i) ? PETSC_TRUE : PETSC_FALSE; 87 if ((cond1 || cond2) && above) ++crossings; 88 } 89 if (crossings % 2) *cell = c; 90 else *cell = -1; 91 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); 92 PetscFunctionReturn(0); 93 } 94 95 #undef __FUNCT__ 96 #define __FUNCT__ "DMPlexLocatePoint_Simplex_3D_Internal" 97 static PetscErrorCode DMPlexLocatePoint_Simplex_3D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) 98 { 99 const PetscInt embedDim = 3; 100 PetscReal v0[3], J[9], invJ[9], detJ; 101 PetscReal x = PetscRealPart(point[0]); 102 PetscReal y = PetscRealPart(point[1]); 103 PetscReal z = PetscRealPart(point[2]); 104 PetscReal xi, eta, zeta; 105 PetscErrorCode ierr; 106 107 PetscFunctionBegin; 108 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 109 xi = invJ[0*embedDim+0]*(x - v0[0]) + invJ[0*embedDim+1]*(y - v0[1]) + invJ[0*embedDim+2]*(z - v0[2]); 110 eta = invJ[1*embedDim+0]*(x - v0[0]) + invJ[1*embedDim+1]*(y - v0[1]) + invJ[1*embedDim+2]*(z - v0[2]); 111 zeta = invJ[2*embedDim+0]*(x - v0[0]) + invJ[2*embedDim+1]*(y - v0[1]) + invJ[2*embedDim+2]*(z - v0[2]); 112 113 if ((xi >= 0.0) && (eta >= 0.0) && (zeta >= 0.0) && (xi + eta + zeta <= 2.0)) *cell = c; 114 else *cell = -1; 115 PetscFunctionReturn(0); 116 } 117 118 #undef __FUNCT__ 119 #define __FUNCT__ "DMPlexLocatePoint_General_3D_Internal" 120 static PetscErrorCode DMPlexLocatePoint_General_3D_Internal(DM dm, const PetscScalar point[], PetscInt c, PetscInt *cell) 121 { 122 PetscSection coordSection; 123 Vec coordsLocal; 124 PetscScalar *coords; 125 const PetscInt faces[24] = {0, 3, 2, 1, 5, 4, 7, 6, 3, 0, 4, 5, 126 1, 2, 6, 7, 3, 5, 6, 2, 0, 1, 7, 4}; 127 PetscBool found = PETSC_TRUE; 128 PetscInt f; 129 PetscErrorCode ierr; 130 131 PetscFunctionBegin; 132 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 133 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 134 ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); 135 for (f = 0; f < 6; ++f) { 136 /* Check the point is under plane */ 137 /* Get face normal */ 138 PetscReal v_i[3]; 139 PetscReal v_j[3]; 140 PetscReal normal[3]; 141 PetscReal pp[3]; 142 PetscReal dot; 143 144 v_i[0] = PetscRealPart(coords[faces[f*4+3]*3+0]-coords[faces[f*4+0]*3+0]); 145 v_i[1] = PetscRealPart(coords[faces[f*4+3]*3+1]-coords[faces[f*4+0]*3+1]); 146 v_i[2] = PetscRealPart(coords[faces[f*4+3]*3+2]-coords[faces[f*4+0]*3+2]); 147 v_j[0] = PetscRealPart(coords[faces[f*4+1]*3+0]-coords[faces[f*4+0]*3+0]); 148 v_j[1] = PetscRealPart(coords[faces[f*4+1]*3+1]-coords[faces[f*4+0]*3+1]); 149 v_j[2] = PetscRealPart(coords[faces[f*4+1]*3+2]-coords[faces[f*4+0]*3+2]); 150 normal[0] = v_i[1]*v_j[2] - v_i[2]*v_j[1]; 151 normal[1] = v_i[2]*v_j[0] - v_i[0]*v_j[2]; 152 normal[2] = v_i[0]*v_j[1] - v_i[1]*v_j[0]; 153 pp[0] = PetscRealPart(coords[faces[f*4+0]*3+0] - point[0]); 154 pp[1] = PetscRealPart(coords[faces[f*4+0]*3+1] - point[1]); 155 pp[2] = PetscRealPart(coords[faces[f*4+0]*3+2] - point[2]); 156 dot = normal[0]*pp[0] + normal[1]*pp[1] + normal[2]*pp[2]; 157 158 /* Check that projected point is in face (2D location problem) */ 159 if (dot < 0.0) { 160 found = PETSC_FALSE; 161 break; 162 } 163 } 164 if (found) *cell = c; 165 else *cell = -1; 166 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, NULL, &coords);CHKERRQ(ierr); 167 PetscFunctionReturn(0); 168 } 169 170 #undef __FUNCT__ 171 #define __FUNCT__ "PetscGridHashInitialize_Internal" 172 static PetscErrorCode PetscGridHashInitialize_Internal(PetscGridHash box, PetscInt dim, const PetscScalar point[]) 173 { 174 PetscInt d; 175 176 PetscFunctionBegin; 177 box->dim = dim; 178 for (d = 0; d < dim; ++d) box->lower[d] = box->upper[d] = PetscRealPart(point[d]); 179 PetscFunctionReturn(0); 180 } 181 182 #undef __FUNCT__ 183 #define __FUNCT__ "PetscGridHashCreate" 184 PetscErrorCode PetscGridHashCreate(MPI_Comm comm, PetscInt dim, const PetscScalar point[], PetscGridHash *box) 185 { 186 PetscErrorCode ierr; 187 188 PetscFunctionBegin; 189 ierr = PetscMalloc1(1, box);CHKERRQ(ierr); 190 ierr = PetscGridHashInitialize_Internal(*box, dim, point);CHKERRQ(ierr); 191 PetscFunctionReturn(0); 192 } 193 194 #undef __FUNCT__ 195 #define __FUNCT__ "PetscGridHashEnlarge" 196 PetscErrorCode PetscGridHashEnlarge(PetscGridHash box, const PetscScalar point[]) 197 { 198 PetscInt d; 199 200 PetscFunctionBegin; 201 for (d = 0; d < box->dim; ++d) { 202 box->lower[d] = PetscMin(box->lower[d], PetscRealPart(point[d])); 203 box->upper[d] = PetscMax(box->upper[d], PetscRealPart(point[d])); 204 } 205 PetscFunctionReturn(0); 206 } 207 208 #undef __FUNCT__ 209 #define __FUNCT__ "PetscGridHashSetGrid" 210 PetscErrorCode PetscGridHashSetGrid(PetscGridHash box, const PetscInt n[], const PetscReal h[]) 211 { 212 PetscInt d; 213 214 PetscFunctionBegin; 215 for (d = 0; d < box->dim; ++d) { 216 box->extent[d] = box->upper[d] - box->lower[d]; 217 if (n[d] == PETSC_DETERMINE) { 218 box->h[d] = h[d]; 219 box->n[d] = PetscCeilReal(box->extent[d]/h[d]); 220 } else { 221 box->n[d] = n[d]; 222 box->h[d] = box->extent[d]/n[d]; 223 } 224 } 225 PetscFunctionReturn(0); 226 } 227 228 #undef __FUNCT__ 229 #define __FUNCT__ "PetscGridHashGetEnclosingBox" 230 PetscErrorCode PetscGridHashGetEnclosingBox(PetscGridHash box, PetscInt numPoints, const PetscScalar points[], PetscInt dboxes[], PetscInt boxes[]) 231 { 232 const PetscReal *lower = box->lower; 233 const PetscReal *upper = box->upper; 234 const PetscReal *h = box->h; 235 const PetscInt *n = box->n; 236 const PetscInt dim = box->dim; 237 PetscInt d, p; 238 239 PetscFunctionBegin; 240 for (p = 0; p < numPoints; ++p) { 241 for (d = 0; d < dim; ++d) { 242 PetscInt dbox = PetscFloorReal((PetscRealPart(points[p*dim+d]) - lower[d])/h[d]); 243 244 if (dbox == n[d] && PetscAbsReal(PetscRealPart(points[p*dim+d]) - upper[d]) < 1.0e-9) dbox = n[d]-1; 245 if (dbox < 0 || dbox >= n[d]) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Input point %d (%g, %g, %g) is outside of our bounding box", 246 p, PetscRealPart(points[p*dim+0]), dim > 1 ? PetscRealPart(points[p*dim+1]) : 0.0, dim > 2 ? PetscRealPart(points[p*dim+2]) : 0.0); 247 dboxes[p*dim+d] = dbox; 248 } 249 if (boxes) for (d = 1, boxes[p] = dboxes[p*dim]; d < dim; ++d) boxes[p] += dboxes[p*dim+d]*n[d-1]; 250 } 251 PetscFunctionReturn(0); 252 } 253 254 #undef __FUNCT__ 255 #define __FUNCT__ "PetscGridHashDestroy" 256 PetscErrorCode PetscGridHashDestroy(PetscGridHash *box) 257 { 258 PetscErrorCode ierr; 259 260 PetscFunctionBegin; 261 if (*box) { 262 ierr = PetscSectionDestroy(&(*box)->cellSection);CHKERRQ(ierr); 263 ierr = ISDestroy(&(*box)->cells);CHKERRQ(ierr); 264 ierr = DMLabelDestroy(&(*box)->cellsSparse);CHKERRQ(ierr); 265 } 266 ierr = PetscFree(*box);CHKERRQ(ierr); 267 PetscFunctionReturn(0); 268 } 269 270 #undef __FUNCT__ 271 #define __FUNCT__ "DMPlexLocatePoint_Internal" 272 PetscErrorCode DMPlexLocatePoint_Internal(DM dm, PetscInt dim, const PetscScalar point[], PetscInt cellStart, PetscInt *cell) 273 { 274 PetscInt coneSize; 275 PetscErrorCode ierr; 276 277 PetscFunctionBegin; 278 switch (dim) { 279 case 2: 280 ierr = DMPlexGetConeSize(dm, cellStart, &coneSize);CHKERRQ(ierr); 281 switch (coneSize) { 282 case 3: 283 ierr = DMPlexLocatePoint_Simplex_2D_Internal(dm, point, cellStart, cell);CHKERRQ(ierr); 284 break; 285 case 4: 286 ierr = DMPlexLocatePoint_General_2D_Internal(dm, point, cellStart, cell);CHKERRQ(ierr); 287 break; 288 default: 289 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for cell with cone size %D", coneSize); 290 } 291 break; 292 case 3: 293 ierr = DMPlexGetConeSize(dm, cellStart, &coneSize);CHKERRQ(ierr); 294 switch (coneSize) { 295 case 4: 296 ierr = DMPlexLocatePoint_Simplex_3D_Internal(dm, point, cellStart, cell);CHKERRQ(ierr); 297 break; 298 case 6: 299 ierr = DMPlexLocatePoint_General_3D_Internal(dm, point, cellStart, cell);CHKERRQ(ierr); 300 break; 301 default: 302 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for cell with cone size %D", coneSize); 303 } 304 break; 305 default: 306 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_OUTOFRANGE, "No point location for mesh dimension %D", dim); 307 } 308 PetscFunctionReturn(0); 309 } 310 311 #undef __FUNCT__ 312 #define __FUNCT__ "DMPlexComputeGridHash_Internal" 313 PetscErrorCode DMPlexComputeGridHash_Internal(DM dm, PetscGridHash *localBox) 314 { 315 MPI_Comm comm; 316 PetscGridHash lbox; 317 Vec coordinates; 318 PetscSection coordSection; 319 Vec coordsLocal; 320 const PetscScalar *coords; 321 PetscInt *dboxes, *boxes; 322 PetscInt n[3] = {10, 10, 10}; 323 PetscInt dim, N, cStart, cEnd, cMax, c, i; 324 PetscErrorCode ierr; 325 326 PetscFunctionBegin; 327 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 328 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 329 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 330 if (dim != 2) SETERRQ(comm, PETSC_ERR_SUP, "I have only coded this for 2D"); 331 ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr); 332 ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); 333 ierr = PetscGridHashCreate(comm, dim, coords, &lbox);CHKERRQ(ierr); 334 for (i = 0; i < N; i += dim) {ierr = PetscGridHashEnlarge(lbox, &coords[i]);CHKERRQ(ierr);} 335 ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); 336 ierr = PetscGridHashSetGrid(lbox, n, NULL);CHKERRQ(ierr); 337 #if 0 338 /* Could define a custom reduction to merge these */ 339 ierr = MPIU_Allreduce(lbox->lower, gbox->lower, 3, MPIU_REAL, MPI_MIN, comm);CHKERRQ(ierr); 340 ierr = MPIU_Allreduce(lbox->upper, gbox->upper, 3, MPIU_REAL, MPI_MAX, comm);CHKERRQ(ierr); 341 #endif 342 /* Is there a reason to snap the local bounding box to a division of the global box? */ 343 /* Should we compute all overlaps of local boxes? We could do this with a rendevouz scheme partitioning the global box */ 344 /* Create label */ 345 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 346 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 347 if (cMax >= 0) cEnd = PetscMin(cEnd, cMax); 348 ierr = DMLabelCreate("cells", &lbox->cellsSparse);CHKERRQ(ierr); 349 ierr = DMLabelCreateIndex(lbox->cellsSparse, cStart, cEnd);CHKERRQ(ierr); 350 /* Compute boxes which overlap each cell: http://stackoverflow.com/questions/13790208/triangle-square-intersection-test-in-2d */ 351 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 352 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 353 ierr = PetscCalloc2(16 * dim, &dboxes, 16, &boxes);CHKERRQ(ierr); 354 for (c = cStart; c < cEnd; ++c) { 355 const PetscReal *h = lbox->h; 356 PetscScalar *ccoords = NULL; 357 PetscInt csize = 0; 358 PetscScalar point[3]; 359 PetscInt dlim[6], d, e, i, j, k; 360 361 /* Find boxes enclosing each vertex */ 362 ierr = DMPlexVecGetClosure(dm, coordSection, coordsLocal, c, &csize, &ccoords);CHKERRQ(ierr); 363 ierr = PetscGridHashGetEnclosingBox(lbox, csize/dim, ccoords, dboxes, boxes);CHKERRQ(ierr); 364 /* Mark cells containing the vertices */ 365 for (e = 0; e < csize/dim; ++e) {ierr = DMLabelSetValue(lbox->cellsSparse, c, boxes[e]);CHKERRQ(ierr);} 366 /* Get grid of boxes containing these */ 367 for (d = 0; d < dim; ++d) {dlim[d*2+0] = dlim[d*2+1] = dboxes[d];} 368 for (d = dim; d < 3; ++d) {dlim[d*2+0] = dlim[d*2+1] = 0;} 369 for (e = 1; e < dim+1; ++e) { 370 for (d = 0; d < dim; ++d) { 371 dlim[d*2+0] = PetscMin(dlim[d*2+0], dboxes[e*dim+d]); 372 dlim[d*2+1] = PetscMax(dlim[d*2+1], dboxes[e*dim+d]); 373 } 374 } 375 /* Check for intersection of box with cell */ 376 for (k = dlim[2*2+0], point[2] = lbox->lower[2] + k*h[2]; k <= dlim[2*2+1]; ++k, point[2] += h[2]) { 377 for (j = dlim[1*2+0], point[1] = lbox->lower[1] + j*h[1]; j <= dlim[1*2+1]; ++j, point[1] += h[1]) { 378 for (i = dlim[0*2+0], point[0] = lbox->lower[0] + i*h[0]; i <= dlim[0*2+1]; ++i, point[0] += h[0]) { 379 const PetscInt box = (k*lbox->n[1] + j)*lbox->n[0] + i; 380 PetscScalar cpoint[3]; 381 PetscInt cell, edge, ii, jj, kk; 382 383 /* Check whether cell contains any vertex of these subboxes TODO vectorize this */ 384 for (kk = 0, cpoint[2] = point[2]; kk < (dim > 2 ? 2 : 1); ++kk, cpoint[2] += h[2]) { 385 for (jj = 0, cpoint[1] = point[1]; jj < (dim > 1 ? 2 : 1); ++jj, cpoint[1] += h[1]) { 386 for (ii = 0, cpoint[0] = point[0]; ii < 2; ++ii, cpoint[0] += h[0]) { 387 388 ierr = DMPlexLocatePoint_Internal(dm, dim, cpoint, c, &cell);CHKERRQ(ierr); 389 if (cell >= 0) {DMLabelSetValue(lbox->cellsSparse, c, box);CHKERRQ(ierr); ii = jj = kk = 2;} 390 } 391 } 392 } 393 /* Check whether cell edge intersects any edge of these subboxes TODO vectorize this */ 394 for (edge = 0; edge < dim+1; ++edge) { 395 PetscReal segA[6], segB[6]; 396 397 for (d = 0; d < dim; ++d) {segA[d] = PetscRealPart(ccoords[edge*dim+d]); segA[dim+d] = PetscRealPart(ccoords[((edge+1)%(dim+1))*dim+d]);} 398 for (kk = 0; kk < (dim > 2 ? 2 : 1); ++kk) { 399 if (dim > 2) {segB[2] = PetscRealPart(point[2]); 400 segB[dim+2] = PetscRealPart(point[2]) + kk*h[2];} 401 for (jj = 0; jj < (dim > 1 ? 2 : 1); ++jj) { 402 if (dim > 1) {segB[1] = PetscRealPart(point[1]); 403 segB[dim+1] = PetscRealPart(point[1]) + jj*h[1];} 404 for (ii = 0; ii < 2; ++ii) { 405 PetscBool intersects; 406 407 segB[0] = PetscRealPart(point[0]); 408 segB[dim+0] = PetscRealPart(point[0]) + ii*h[0]; 409 ierr = DMPlexGetLineIntersection_2D_Internal(segA, segB, NULL, &intersects);CHKERRQ(ierr); 410 if (intersects) {DMLabelSetValue(lbox->cellsSparse, c, box);CHKERRQ(ierr); edge = ii = jj = kk = dim+1;} 411 } 412 } 413 } 414 } 415 } 416 } 417 } 418 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordsLocal, c, NULL, &ccoords);CHKERRQ(ierr); 419 } 420 ierr = PetscFree2(dboxes, boxes);CHKERRQ(ierr); 421 ierr = DMLabelConvertToSection(lbox->cellsSparse, &lbox->cellSection, &lbox->cells);CHKERRQ(ierr); 422 ierr = DMLabelDestroy(&lbox->cellsSparse);CHKERRQ(ierr); 423 *localBox = lbox; 424 PetscFunctionReturn(0); 425 } 426 427 #undef __FUNCT__ 428 #define __FUNCT__ "DMLocatePoints_Plex" 429 PetscErrorCode DMLocatePoints_Plex(DM dm, Vec v, PetscSF cellSF) 430 { 431 DM_Plex *mesh = (DM_Plex *) dm->data; 432 PetscBool hash = mesh->useHashLocation; 433 PetscInt bs, numPoints, p, numFound, *found = NULL; 434 PetscInt dim, cStart, cEnd, cMax, numCells, c; 435 const PetscInt *boxCells; 436 PetscSFNode *cells; 437 PetscScalar *a; 438 PetscMPIInt result; 439 PetscErrorCode ierr; 440 441 PetscFunctionBegin; 442 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 443 ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr); 444 ierr = MPI_Comm_compare(PetscObjectComm((PetscObject)cellSF),PETSC_COMM_SELF,&result);CHKERRQ(ierr); 445 if (result != MPI_IDENT && result != MPI_CONGRUENT) SETERRQ(PetscObjectComm((PetscObject)cellSF),PETSC_ERR_SUP, "Trying parallel point location: only local point location supported"); 446 if (bs != dim) SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_ARG_WRONG, "Block size for point vector %D must be the mesh coordinate dimension %D", bs, dim); 447 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 448 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 449 if (cMax >= 0) cEnd = PetscMin(cEnd, cMax); 450 ierr = VecGetLocalSize(v, &numPoints);CHKERRQ(ierr); 451 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 452 numPoints /= bs; 453 ierr = PetscMalloc1(numPoints, &cells);CHKERRQ(ierr); 454 if (hash) { 455 if (!mesh->lbox) {ierr = PetscInfo(dm, "Initializing grid hashing");CHKERRQ(ierr);ierr = DMPlexComputeGridHash_Internal(dm, &mesh->lbox);CHKERRQ(ierr);} 456 /* Designate the local box for each point */ 457 /* Send points to correct process */ 458 /* Search cells that lie in each subbox */ 459 /* Should we bin points before doing search? */ 460 ierr = ISGetIndices(mesh->lbox->cells, &boxCells);CHKERRQ(ierr); 461 } 462 for (p = 0, numFound = 0; p < numPoints; ++p) { 463 const PetscScalar *point = &a[p*bs]; 464 PetscInt dbin[3], bin, cell = -1, cellOffset; 465 466 cells[p].rank = -1; 467 cells[p].index = -1; 468 if (hash) { 469 ierr = PetscGridHashGetEnclosingBox(mesh->lbox, 1, point, dbin, &bin);CHKERRQ(ierr); 470 /* TODO Lay an interface over this so we can switch between Section (dense) and Label (sparse) */ 471 ierr = PetscSectionGetDof(mesh->lbox->cellSection, bin, &numCells);CHKERRQ(ierr); 472 ierr = PetscSectionGetOffset(mesh->lbox->cellSection, bin, &cellOffset);CHKERRQ(ierr); 473 for (c = cellOffset; c < cellOffset + numCells; ++c) { 474 ierr = DMPlexLocatePoint_Internal(dm, dim, point, boxCells[c], &cell);CHKERRQ(ierr); 475 if (cell >= 0) { 476 cells[p].rank = 0; 477 cells[p].index = cell; 478 numFound++; 479 break; 480 } 481 } 482 } else { 483 for (c = cStart; c < cEnd; ++c) { 484 ierr = DMPlexLocatePoint_Internal(dm, dim, point, c, &cell);CHKERRQ(ierr); 485 if (cell >= 0) { 486 cells[p].rank = 0; 487 cells[p].index = cell; 488 numFound++; 489 break; 490 } 491 } 492 } 493 } 494 if (hash) {ierr = ISRestoreIndices(mesh->lbox->cells, &boxCells);CHKERRQ(ierr);} 495 /* Check for highest numbered proc that claims a point (do we care?) */ 496 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 497 if (numFound < numPoints) { 498 ierr = PetscMalloc1(numFound,&found);CHKERRQ(ierr); 499 for (p = 0, numFound = 0; p < numPoints; p++) { 500 if (cells[p].rank >= 0 && cells[p].index >= 0) { 501 if (numFound < p) { 502 cells[numFound] = cells[p]; 503 } 504 found[numFound++] = p; 505 } 506 } 507 } 508 ierr = PetscSFSetGraph(cellSF, cEnd - cStart, numFound, found, PETSC_OWN_POINTER, cells, PETSC_OWN_POINTER);CHKERRQ(ierr); 509 PetscFunctionReturn(0); 510 } 511 512 #undef __FUNCT__ 513 #define __FUNCT__ "DMPlexComputeProjection2Dto1D_Internal" 514 /* 515 DMPlexComputeProjection2Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 2D 516 */ 517 PetscErrorCode DMPlexComputeProjection2Dto1D_Internal(PetscScalar coords[], PetscReal R[]) 518 { 519 const PetscReal x = PetscRealPart(coords[2] - coords[0]); 520 const PetscReal y = PetscRealPart(coords[3] - coords[1]); 521 const PetscReal r = PetscSqrtReal(x*x + y*y), c = x/r, s = y/r; 522 523 PetscFunctionBegin; 524 R[0] = c; R[1] = -s; 525 R[2] = s; R[3] = c; 526 coords[0] = 0.0; 527 coords[1] = r; 528 PetscFunctionReturn(0); 529 } 530 531 #undef __FUNCT__ 532 #define __FUNCT__ "DMPlexComputeProjection3Dto1D_Internal" 533 /* 534 DMPlexComputeProjection3Dto1D_Internal - Rewrite coordinates to be the 1D projection of the 3D 535 536 This uses the basis completion described by Frisvad, 537 538 http://www.imm.dtu.dk/~jerf/papers/abstracts/onb.html 539 DOI:10.1080/2165347X.2012.689606 540 */ 541 PetscErrorCode DMPlexComputeProjection3Dto1D_Internal(PetscScalar coords[], PetscReal R[]) 542 { 543 PetscReal x = PetscRealPart(coords[3] - coords[0]); 544 PetscReal y = PetscRealPart(coords[4] - coords[1]); 545 PetscReal z = PetscRealPart(coords[5] - coords[2]); 546 PetscReal r = PetscSqrtReal(x*x + y*y + z*z); 547 PetscReal rinv = 1. / r; 548 PetscFunctionBegin; 549 550 x *= rinv; y *= rinv; z *= rinv; 551 if (x > 0.) { 552 PetscReal inv1pX = 1./ (1. + x); 553 554 R[0] = x; R[1] = -y; R[2] = -z; 555 R[3] = y; R[4] = 1. - y*y*inv1pX; R[5] = -y*z*inv1pX; 556 R[6] = z; R[7] = -y*z*inv1pX; R[8] = 1. - z*z*inv1pX; 557 } 558 else { 559 PetscReal inv1mX = 1./ (1. - x); 560 561 R[0] = x; R[1] = z; R[2] = y; 562 R[3] = y; R[4] = -y*z*inv1mX; R[5] = 1. - y*y*inv1mX; 563 R[6] = z; R[7] = 1. - z*z*inv1mX; R[8] = -y*z*inv1mX; 564 } 565 coords[0] = 0.0; 566 coords[1] = r; 567 PetscFunctionReturn(0); 568 } 569 570 #undef __FUNCT__ 571 #define __FUNCT__ "DMPlexComputeProjection3Dto2D_Internal" 572 /* 573 DMPlexComputeProjection3Dto2D_Internal - Rewrite coordinates to be the 2D projection of the 3D 574 */ 575 PetscErrorCode DMPlexComputeProjection3Dto2D_Internal(PetscInt coordSize, PetscScalar coords[], PetscReal R[]) 576 { 577 PetscReal x1[3], x2[3], n[3], norm; 578 PetscReal x1p[3], x2p[3], xnp[3]; 579 PetscReal sqrtz, alpha; 580 const PetscInt dim = 3; 581 PetscInt d, e, p; 582 583 PetscFunctionBegin; 584 /* 0) Calculate normal vector */ 585 for (d = 0; d < dim; ++d) { 586 x1[d] = PetscRealPart(coords[1*dim+d] - coords[0*dim+d]); 587 x2[d] = PetscRealPart(coords[2*dim+d] - coords[0*dim+d]); 588 } 589 n[0] = x1[1]*x2[2] - x1[2]*x2[1]; 590 n[1] = x1[2]*x2[0] - x1[0]*x2[2]; 591 n[2] = x1[0]*x2[1] - x1[1]*x2[0]; 592 norm = PetscSqrtReal(n[0]*n[0] + n[1]*n[1] + n[2]*n[2]); 593 n[0] /= norm; 594 n[1] /= norm; 595 n[2] /= norm; 596 /* 1) Take the normal vector and rotate until it is \hat z 597 598 Let the normal vector be <nx, ny, nz> and alpha = 1/sqrt(1 - nz^2), then 599 600 R = / alpha nx nz alpha ny nz -1/alpha \ 601 | -alpha ny alpha nx 0 | 602 \ nx ny nz / 603 604 will rotate the normal vector to \hat z 605 */ 606 sqrtz = PetscSqrtReal(1.0 - n[2]*n[2]); 607 /* Check for n = z */ 608 if (sqrtz < 1.0e-10) { 609 const PetscInt s = PetscSign(n[2]); 610 /* If nz < 0, rotate 180 degrees around x-axis */ 611 for (p = 3; p < coordSize/3; ++p) { 612 coords[p*2+0] = PetscRealPart(coords[p*dim+0] - coords[0*dim+0]); 613 coords[p*2+1] = (PetscRealPart(coords[p*dim+1] - coords[0*dim+1])) * s; 614 } 615 coords[0] = 0.0; 616 coords[1] = 0.0; 617 coords[2] = x1[0]; 618 coords[3] = x1[1] * s; 619 coords[4] = x2[0]; 620 coords[5] = x2[1] * s; 621 R[0] = 1.0; R[1] = 0.0; R[2] = 0.0; 622 R[3] = 0.0; R[4] = 1.0 * s; R[5] = 0.0; 623 R[6] = 0.0; R[7] = 0.0; R[8] = 1.0 * s; 624 PetscFunctionReturn(0); 625 } 626 alpha = 1.0/sqrtz; 627 R[0] = alpha*n[0]*n[2]; R[1] = alpha*n[1]*n[2]; R[2] = -sqrtz; 628 R[3] = -alpha*n[1]; R[4] = alpha*n[0]; R[5] = 0.0; 629 R[6] = n[0]; R[7] = n[1]; R[8] = n[2]; 630 for (d = 0; d < dim; ++d) { 631 x1p[d] = 0.0; 632 x2p[d] = 0.0; 633 for (e = 0; e < dim; ++e) { 634 x1p[d] += R[d*dim+e]*x1[e]; 635 x2p[d] += R[d*dim+e]*x2[e]; 636 } 637 } 638 if (PetscAbsReal(x1p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); 639 if (PetscAbsReal(x2p[2]) > 1.0e-9) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid rotation calculated"); 640 /* 2) Project to (x, y) */ 641 for (p = 3; p < coordSize/3; ++p) { 642 for (d = 0; d < dim; ++d) { 643 xnp[d] = 0.0; 644 for (e = 0; e < dim; ++e) { 645 xnp[d] += R[d*dim+e]*PetscRealPart(coords[p*dim+e] - coords[0*dim+e]); 646 } 647 if (d < dim-1) coords[p*2+d] = xnp[d]; 648 } 649 } 650 coords[0] = 0.0; 651 coords[1] = 0.0; 652 coords[2] = x1p[0]; 653 coords[3] = x1p[1]; 654 coords[4] = x2p[0]; 655 coords[5] = x2p[1]; 656 /* Output R^T which rotates \hat z to the input normal */ 657 for (d = 0; d < dim; ++d) { 658 for (e = d+1; e < dim; ++e) { 659 PetscReal tmp; 660 661 tmp = R[d*dim+e]; 662 R[d*dim+e] = R[e*dim+d]; 663 R[e*dim+d] = tmp; 664 } 665 } 666 PetscFunctionReturn(0); 667 } 668 669 #undef __FUNCT__ 670 #define __FUNCT__ "Volume_Triangle_Internal" 671 PETSC_UNUSED 672 PETSC_STATIC_INLINE void Volume_Triangle_Internal(PetscReal *vol, PetscReal coords[]) 673 { 674 /* Signed volume is 1/2 the determinant 675 676 | 1 1 1 | 677 | x0 x1 x2 | 678 | y0 y1 y2 | 679 680 but if x0,y0 is the origin, we have 681 682 | x1 x2 | 683 | y1 y2 | 684 */ 685 const PetscReal x1 = coords[2] - coords[0], y1 = coords[3] - coords[1]; 686 const PetscReal x2 = coords[4] - coords[0], y2 = coords[5] - coords[1]; 687 PetscReal M[4], detM; 688 M[0] = x1; M[1] = x2; 689 M[2] = y1; M[3] = y2; 690 DMPlex_Det2D_Internal(&detM, M); 691 *vol = 0.5*detM; 692 (void)PetscLogFlops(5.0); 693 } 694 695 #undef __FUNCT__ 696 #define __FUNCT__ "Volume_Triangle_Origin_Internal" 697 PETSC_STATIC_INLINE void Volume_Triangle_Origin_Internal(PetscReal *vol, PetscReal coords[]) 698 { 699 DMPlex_Det2D_Internal(vol, coords); 700 *vol *= 0.5; 701 } 702 703 #undef __FUNCT__ 704 #define __FUNCT__ "Volume_Tetrahedron_Internal" 705 PETSC_UNUSED 706 PETSC_STATIC_INLINE void Volume_Tetrahedron_Internal(PetscReal *vol, PetscReal coords[]) 707 { 708 /* Signed volume is 1/6th of the determinant 709 710 | 1 1 1 1 | 711 | x0 x1 x2 x3 | 712 | y0 y1 y2 y3 | 713 | z0 z1 z2 z3 | 714 715 but if x0,y0,z0 is the origin, we have 716 717 | x1 x2 x3 | 718 | y1 y2 y3 | 719 | z1 z2 z3 | 720 */ 721 const PetscReal x1 = coords[3] - coords[0], y1 = coords[4] - coords[1], z1 = coords[5] - coords[2]; 722 const PetscReal x2 = coords[6] - coords[0], y2 = coords[7] - coords[1], z2 = coords[8] - coords[2]; 723 const PetscReal x3 = coords[9] - coords[0], y3 = coords[10] - coords[1], z3 = coords[11] - coords[2]; 724 PetscReal M[9], detM; 725 M[0] = x1; M[1] = x2; M[2] = x3; 726 M[3] = y1; M[4] = y2; M[5] = y3; 727 M[6] = z1; M[7] = z2; M[8] = z3; 728 DMPlex_Det3D_Internal(&detM, M); 729 *vol = -0.16666666666666666666666*detM; 730 (void)PetscLogFlops(10.0); 731 } 732 733 #undef __FUNCT__ 734 #define __FUNCT__ "Volume_Tetrahedron_Origin_Internal" 735 PETSC_STATIC_INLINE void Volume_Tetrahedron_Origin_Internal(PetscReal *vol, PetscReal coords[]) 736 { 737 DMPlex_Det3D_Internal(vol, coords); 738 *vol *= -0.16666666666666666666666; 739 } 740 741 #undef __FUNCT__ 742 #define __FUNCT__ "DMPlexComputeLineGeometry_Internal" 743 static PetscErrorCode DMPlexComputeLineGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 744 { 745 PetscSection coordSection; 746 Vec coordinates; 747 PetscScalar *coords = NULL; 748 PetscInt numCoords, d; 749 PetscErrorCode ierr; 750 751 PetscFunctionBegin; 752 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 753 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 754 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 755 if (invJ && !J) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "In order to compute invJ, J must not be NULL"); 756 *detJ = 0.0; 757 if (numCoords == 6) { 758 const PetscInt dim = 3; 759 PetscReal R[9], J0; 760 761 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 762 ierr = DMPlexComputeProjection3Dto1D_Internal(coords, R);CHKERRQ(ierr); 763 if (J) { 764 J0 = 0.5*PetscRealPart(coords[1]); 765 J[0] = R[0]*J0; J[1] = R[1]; J[2] = R[2]; 766 J[3] = R[3]*J0; J[4] = R[4]; J[5] = R[5]; 767 J[6] = R[6]*J0; J[7] = R[7]; J[8] = R[8]; 768 DMPlex_Det3D_Internal(detJ, J); 769 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 770 } 771 } else if (numCoords == 4) { 772 const PetscInt dim = 2; 773 PetscReal R[4], J0; 774 775 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 776 ierr = DMPlexComputeProjection2Dto1D_Internal(coords, R);CHKERRQ(ierr); 777 if (J) { 778 J0 = 0.5*PetscRealPart(coords[1]); 779 J[0] = R[0]*J0; J[1] = R[1]; 780 J[2] = R[2]*J0; J[3] = R[3]; 781 DMPlex_Det2D_Internal(detJ, J); 782 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 783 } 784 } else if (numCoords == 2) { 785 const PetscInt dim = 1; 786 787 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 788 if (J) { 789 J[0] = 0.5*(PetscRealPart(coords[1]) - PetscRealPart(coords[0])); 790 *detJ = J[0]; 791 ierr = PetscLogFlops(2.0);CHKERRQ(ierr); 792 if (invJ) {invJ[0] = 1.0/J[0]; ierr = PetscLogFlops(1.0);CHKERRQ(ierr);} 793 } 794 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this segment is %D != 2", numCoords); 795 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 796 PetscFunctionReturn(0); 797 } 798 799 #undef __FUNCT__ 800 #define __FUNCT__ "DMPlexComputeTriangleGeometry_Internal" 801 static PetscErrorCode DMPlexComputeTriangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 802 { 803 PetscSection coordSection; 804 Vec coordinates; 805 PetscScalar *coords = NULL; 806 PetscInt numCoords, d, f, g; 807 PetscErrorCode ierr; 808 809 PetscFunctionBegin; 810 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 811 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 812 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 813 *detJ = 0.0; 814 if (numCoords == 9) { 815 const PetscInt dim = 3; 816 PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; 817 818 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 819 ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); 820 if (J) { 821 const PetscInt pdim = 2; 822 823 for (d = 0; d < pdim; d++) { 824 for (f = 0; f < pdim; f++) { 825 J0[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 826 } 827 } 828 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 829 DMPlex_Det3D_Internal(detJ, J0); 830 for (d = 0; d < dim; d++) { 831 for (f = 0; f < dim; f++) { 832 J[d*dim+f] = 0.0; 833 for (g = 0; g < dim; g++) { 834 J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; 835 } 836 } 837 } 838 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 839 } 840 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 841 } else if (numCoords == 6) { 842 const PetscInt dim = 2; 843 844 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 845 if (J) { 846 for (d = 0; d < dim; d++) { 847 for (f = 0; f < dim; f++) { 848 J[d*dim+f] = 0.5*(PetscRealPart(coords[(f+1)*dim+d]) - PetscRealPart(coords[0*dim+d])); 849 } 850 } 851 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 852 DMPlex_Det2D_Internal(detJ, J); 853 } 854 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 855 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this triangle is %D != 6 or 9", numCoords); 856 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 857 PetscFunctionReturn(0); 858 } 859 860 #undef __FUNCT__ 861 #define __FUNCT__ "DMPlexComputeRectangleGeometry_Internal" 862 static PetscErrorCode DMPlexComputeRectangleGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 863 { 864 PetscSection coordSection; 865 Vec coordinates; 866 PetscScalar *coords = NULL; 867 PetscInt numCoords, d, f, g; 868 PetscErrorCode ierr; 869 870 PetscFunctionBegin; 871 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 872 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 873 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 874 *detJ = 0.0; 875 if (numCoords == 12) { 876 const PetscInt dim = 3; 877 PetscReal R[9], J0[9] = {1.0,0.0,0.0,0.0,1.0,0.0,0.0,0.0,1.0}; 878 879 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 880 ierr = DMPlexComputeProjection3Dto2D_Internal(numCoords, coords, R);CHKERRQ(ierr); 881 if (J) { 882 const PetscInt pdim = 2; 883 884 for (d = 0; d < pdim; d++) { 885 J0[d*dim+0] = 0.5*(PetscRealPart(coords[1*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 886 J0[d*dim+1] = 0.5*(PetscRealPart(coords[3*pdim+d]) - PetscRealPart(coords[0*pdim+d])); 887 } 888 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 889 DMPlex_Det3D_Internal(detJ, J0); 890 for (d = 0; d < dim; d++) { 891 for (f = 0; f < dim; f++) { 892 J[d*dim+f] = 0.0; 893 for (g = 0; g < dim; g++) { 894 J[d*dim+f] += R[d*dim+g]*J0[g*dim+f]; 895 } 896 } 897 } 898 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 899 } 900 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 901 } else if ((numCoords == 8) || (numCoords == 16)) { 902 const PetscInt dim = 2; 903 904 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 905 if (J) { 906 for (d = 0; d < dim; d++) { 907 J[d*dim+0] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 908 J[d*dim+1] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 909 } 910 ierr = PetscLogFlops(8.0);CHKERRQ(ierr); 911 DMPlex_Det2D_Internal(detJ, J); 912 } 913 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 914 } else SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "The number of coordinates for this quadrilateral is %D != 8 or 12", numCoords); 915 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, &numCoords, &coords);CHKERRQ(ierr); 916 PetscFunctionReturn(0); 917 } 918 919 #undef __FUNCT__ 920 #define __FUNCT__ "DMPlexComputeTetrahedronGeometry_Internal" 921 static PetscErrorCode DMPlexComputeTetrahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 922 { 923 PetscSection coordSection; 924 Vec coordinates; 925 PetscScalar *coords = NULL; 926 const PetscInt dim = 3; 927 PetscInt d; 928 PetscErrorCode ierr; 929 930 PetscFunctionBegin; 931 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 932 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 933 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 934 *detJ = 0.0; 935 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 936 if (J) { 937 for (d = 0; d < dim; d++) { 938 /* I orient with outward face normals */ 939 J[d*dim+0] = 0.5*(PetscRealPart(coords[2*dim+d]) - PetscRealPart(coords[0*dim+d])); 940 J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 941 J[d*dim+2] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 942 } 943 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 944 DMPlex_Det3D_Internal(detJ, J); 945 } 946 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 947 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 948 PetscFunctionReturn(0); 949 } 950 951 #undef __FUNCT__ 952 #define __FUNCT__ "DMPlexComputeHexahedronGeometry_Internal" 953 static PetscErrorCode DMPlexComputeHexahedronGeometry_Internal(DM dm, PetscInt e, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 954 { 955 PetscSection coordSection; 956 Vec coordinates; 957 PetscScalar *coords = NULL; 958 const PetscInt dim = 3; 959 PetscInt d; 960 PetscErrorCode ierr; 961 962 PetscFunctionBegin; 963 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 964 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 965 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 966 *detJ = 0.0; 967 if (v0) {for (d = 0; d < dim; d++) v0[d] = PetscRealPart(coords[d]);} 968 if (J) { 969 for (d = 0; d < dim; d++) { 970 J[d*dim+0] = 0.5*(PetscRealPart(coords[3*dim+d]) - PetscRealPart(coords[0*dim+d])); 971 J[d*dim+1] = 0.5*(PetscRealPart(coords[1*dim+d]) - PetscRealPart(coords[0*dim+d])); 972 J[d*dim+2] = 0.5*(PetscRealPart(coords[4*dim+d]) - PetscRealPart(coords[0*dim+d])); 973 } 974 ierr = PetscLogFlops(18.0);CHKERRQ(ierr); 975 DMPlex_Det3D_Internal(detJ, J); 976 } 977 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 978 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, e, NULL, &coords);CHKERRQ(ierr); 979 PetscFunctionReturn(0); 980 } 981 982 #undef __FUNCT__ 983 #define __FUNCT__ "DMPlexComputeCellGeometryAffineFEM" 984 /*@C 985 DMPlexComputeCellGeometryAffineFEM - Assuming an affine map, compute the Jacobian, inverse Jacobian, and Jacobian determinant for a given cell 986 987 Collective on DM 988 989 Input Arguments: 990 + dm - the DM 991 - cell - the cell 992 993 Output Arguments: 994 + v0 - the translation part of this affine transform 995 . J - the Jacobian of the transform from the reference element 996 . invJ - the inverse of the Jacobian 997 - detJ - the Jacobian determinant 998 999 Level: advanced 1000 1001 Fortran Notes: 1002 Since it returns arrays, this routine is only available in Fortran 90, and you must 1003 include petsc.h90 in your code. 1004 1005 .seealso: DMPlexComputeCellGeometryFEM(), DMGetCoordinateSection(), DMGetCoordinateVec() 1006 @*/ 1007 PetscErrorCode DMPlexComputeCellGeometryAffineFEM(DM dm, PetscInt cell, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) 1008 { 1009 PetscInt depth, dim, coneSize; 1010 PetscErrorCode ierr; 1011 1012 PetscFunctionBegin; 1013 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1014 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1015 if (depth == 1) { 1016 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1017 } else { 1018 DMLabel depth; 1019 1020 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1021 ierr = DMLabelGetValue(depth, cell, &dim);CHKERRQ(ierr); 1022 } 1023 switch (dim) { 1024 case 1: 1025 ierr = DMPlexComputeLineGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1026 break; 1027 case 2: 1028 switch (coneSize) { 1029 case 3: 1030 ierr = DMPlexComputeTriangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1031 break; 1032 case 4: 1033 ierr = DMPlexComputeRectangleGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1034 break; 1035 default: 1036 SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of faces %D in cell %D for element geometry computation", coneSize, cell); 1037 } 1038 break; 1039 case 3: 1040 switch (coneSize) { 1041 case 4: 1042 ierr = DMPlexComputeTetrahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1043 break; 1044 case 6: /* Faces */ 1045 case 8: /* Vertices */ 1046 ierr = DMPlexComputeHexahedronGeometry_Internal(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr); 1047 break; 1048 default: 1049 SETERRQ2(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported number of faces %D in cell %D for element geometry computation", coneSize, cell); 1050 } 1051 break; 1052 default: 1053 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); 1054 } 1055 PetscFunctionReturn(0); 1056 } 1057 1058 #undef __FUNCT__ 1059 #define __FUNCT__ "DMPlexComputeIsoparametricGeometry_Internal" 1060 static PetscErrorCode DMPlexComputeIsoparametricGeometry_Internal(DM dm, PetscFE fe, PetscInt point, PetscReal v0[], PetscReal J[], PetscReal invJ[], PetscReal *detJ) 1061 { 1062 PetscQuadrature quad; 1063 PetscSection coordSection; 1064 Vec coordinates; 1065 PetscScalar *coords = NULL; 1066 const PetscReal *quadPoints; 1067 PetscReal *basisDer; 1068 PetscInt dim, cdim, pdim, qdim, Nq, numCoords, d, q; 1069 PetscErrorCode ierr; 1070 1071 PetscFunctionBegin; 1072 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1073 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1074 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, point, &numCoords, &coords);CHKERRQ(ierr); 1075 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1076 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 1077 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 1078 ierr = PetscFEGetDimension(fe, &pdim);CHKERRQ(ierr); 1079 ierr = PetscQuadratureGetData(quad, &qdim, &Nq, &quadPoints, NULL);CHKERRQ(ierr); 1080 ierr = PetscFEGetDefaultTabulation(fe, NULL, &basisDer, NULL);CHKERRQ(ierr); 1081 *detJ = 0.0; 1082 if (qdim != dim) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Point dimension %d != quadrature dimension %d", dim, qdim); 1083 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); 1084 if (v0) {for (d = 0; d < cdim; d++) v0[d] = PetscRealPart(coords[d]);} 1085 if (J) { 1086 ierr = PetscMemzero(J, Nq*cdim*dim*sizeof(PetscReal));CHKERRQ(ierr); 1087 for (q = 0; q < Nq; ++q) { 1088 PetscInt i, j, k, c, r; 1089 1090 /* J = dx_i/d\xi_j = sum[k=0,n-1] dN_k/d\xi_j * x_i(k) */ 1091 for (k = 0; k < pdim; ++k) 1092 for (j = 0; j < dim; ++j) 1093 for (i = 0; i < cdim; ++i) 1094 J[(q*cdim + i)*dim + j] += basisDer[(q*pdim + k)*dim + j] * PetscRealPart(coords[k*cdim + i]); 1095 ierr = PetscLogFlops(2.0*pdim*dim*cdim);CHKERRQ(ierr); 1096 if (cdim > dim) { 1097 for (c = dim; c < cdim; ++c) 1098 for (r = 0; r < cdim; ++r) 1099 J[r*cdim+c] = r == c ? 1.0 : 0.0; 1100 } 1101 switch (cdim) { 1102 case 3: 1103 DMPlex_Det3D_Internal(detJ, J); 1104 if (invJ) {DMPlex_Invert3D_Internal(invJ, J, *detJ);} 1105 break; 1106 case 2: 1107 DMPlex_Det2D_Internal(detJ, J); 1108 if (invJ) {DMPlex_Invert2D_Internal(invJ, J, *detJ);} 1109 break; 1110 case 1: 1111 *detJ = J[0]; 1112 if (invJ) invJ[0] = 1.0/J[0]; 1113 } 1114 } 1115 } 1116 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, point, &numCoords, &coords);CHKERRQ(ierr); 1117 PetscFunctionReturn(0); 1118 } 1119 1120 #undef __FUNCT__ 1121 #define __FUNCT__ "DMPlexComputeCellGeometryFEM" 1122 /*@C 1123 DMPlexComputeCellGeometryFEM - Compute the Jacobian, inverse Jacobian, and Jacobian determinant at each quadrature point in the given cell 1124 1125 Collective on DM 1126 1127 Input Arguments: 1128 + dm - the DM 1129 . cell - the cell 1130 - fe - the finite element containing the quadrature 1131 1132 Output Arguments: 1133 + v0 - the translation part of this transform 1134 . J - the Jacobian of the transform from the reference element at each quadrature point 1135 . invJ - the inverse of the Jacobian at each quadrature point 1136 - detJ - the Jacobian determinant at each quadrature point 1137 1138 Level: advanced 1139 1140 Fortran Notes: 1141 Since it returns arrays, this routine is only available in Fortran 90, and you must 1142 include petsc.h90 in your code. 1143 1144 .seealso: DMGetCoordinateSection(), DMGetCoordinateVec() 1145 @*/ 1146 PetscErrorCode DMPlexComputeCellGeometryFEM(DM dm, PetscInt cell, PetscFE fe, PetscReal *v0, PetscReal *J, PetscReal *invJ, PetscReal *detJ) 1147 { 1148 PetscErrorCode ierr; 1149 1150 PetscFunctionBegin; 1151 if (!fe) {ierr = DMPlexComputeCellGeometryAffineFEM(dm, cell, v0, J, invJ, detJ);CHKERRQ(ierr);} 1152 else {ierr = DMPlexComputeIsoparametricGeometry_Internal(dm, fe, cell, v0, J, invJ, detJ);CHKERRQ(ierr);} 1153 PetscFunctionReturn(0); 1154 } 1155 1156 #undef __FUNCT__ 1157 #define __FUNCT__ "DMPlexComputeGeometryFVM_1D_Internal" 1158 static PetscErrorCode DMPlexComputeGeometryFVM_1D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1159 { 1160 PetscSection coordSection; 1161 Vec coordinates; 1162 PetscScalar *coords = NULL; 1163 PetscScalar tmp[2]; 1164 PetscInt coordSize; 1165 PetscErrorCode ierr; 1166 1167 PetscFunctionBegin; 1168 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1169 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1170 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1171 if (dim != 2) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "We only support 2D edges right now"); 1172 ierr = DMLocalizeCoordinate_Internal(dm, dim, coords, &coords[dim], tmp);CHKERRQ(ierr); 1173 if (centroid) { 1174 centroid[0] = 0.5*PetscRealPart(coords[0] + tmp[0]); 1175 centroid[1] = 0.5*PetscRealPart(coords[1] + tmp[1]); 1176 } 1177 if (normal) { 1178 PetscReal norm; 1179 1180 normal[0] = -PetscRealPart(coords[1] - tmp[1]); 1181 normal[1] = PetscRealPart(coords[0] - tmp[0]); 1182 norm = PetscSqrtReal(normal[0]*normal[0] + normal[1]*normal[1]); 1183 normal[0] /= norm; 1184 normal[1] /= norm; 1185 } 1186 if (vol) { 1187 *vol = PetscSqrtReal(PetscSqr(PetscRealPart(coords[0] - tmp[0])) + PetscSqr(PetscRealPart(coords[1] - tmp[1]))); 1188 } 1189 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1190 PetscFunctionReturn(0); 1191 } 1192 1193 #undef __FUNCT__ 1194 #define __FUNCT__ "DMPlexComputeGeometryFVM_2D_Internal" 1195 /* Centroid_i = (\sum_n A_n Cn_i ) / A */ 1196 static PetscErrorCode DMPlexComputeGeometryFVM_2D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1197 { 1198 PetscSection coordSection; 1199 Vec coordinates; 1200 PetscScalar *coords = NULL; 1201 PetscReal vsum = 0.0, csum[3] = {0.0, 0.0, 0.0}, vtmp, ctmp[4], v0[3], R[9]; 1202 PetscInt tdim = 2, coordSize, numCorners, p, d, e; 1203 PetscErrorCode ierr; 1204 1205 PetscFunctionBegin; 1206 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1207 ierr = DMPlexGetConeSize(dm, cell, &numCorners);CHKERRQ(ierr); 1208 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1209 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1210 ierr = DMGetCoordinateDim(dm, &dim);CHKERRQ(ierr); 1211 if (dim > 2 && centroid) { 1212 v0[0] = PetscRealPart(coords[0]); 1213 v0[1] = PetscRealPart(coords[1]); 1214 v0[2] = PetscRealPart(coords[2]); 1215 } 1216 if (normal) { 1217 if (dim > 2) { 1218 const PetscReal x0 = PetscRealPart(coords[dim+0] - coords[0]), x1 = PetscRealPart(coords[dim*2+0] - coords[0]); 1219 const PetscReal y0 = PetscRealPart(coords[dim+1] - coords[1]), y1 = PetscRealPart(coords[dim*2+1] - coords[1]); 1220 const PetscReal z0 = PetscRealPart(coords[dim+2] - coords[2]), z1 = PetscRealPart(coords[dim*2+2] - coords[2]); 1221 PetscReal norm; 1222 1223 normal[0] = y0*z1 - z0*y1; 1224 normal[1] = z0*x1 - x0*z1; 1225 normal[2] = x0*y1 - y0*x1; 1226 norm = PetscSqrtReal(normal[0]*normal[0] + normal[1]*normal[1] + normal[2]*normal[2]); 1227 normal[0] /= norm; 1228 normal[1] /= norm; 1229 normal[2] /= norm; 1230 } else { 1231 for (d = 0; d < dim; ++d) normal[d] = 0.0; 1232 } 1233 } 1234 if (dim == 3) {ierr = DMPlexComputeProjection3Dto2D_Internal(coordSize, coords, R);CHKERRQ(ierr);} 1235 for (p = 0; p < numCorners; ++p) { 1236 /* Need to do this copy to get types right */ 1237 for (d = 0; d < tdim; ++d) { 1238 ctmp[d] = PetscRealPart(coords[p*tdim+d]); 1239 ctmp[tdim+d] = PetscRealPart(coords[((p+1)%numCorners)*tdim+d]); 1240 } 1241 Volume_Triangle_Origin_Internal(&vtmp, ctmp); 1242 vsum += vtmp; 1243 for (d = 0; d < tdim; ++d) { 1244 csum[d] += (ctmp[d] + ctmp[tdim+d])*vtmp; 1245 } 1246 } 1247 for (d = 0; d < tdim; ++d) { 1248 csum[d] /= (tdim+1)*vsum; 1249 } 1250 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, cell, &coordSize, &coords);CHKERRQ(ierr); 1251 if (vol) *vol = PetscAbsReal(vsum); 1252 if (centroid) { 1253 if (dim > 2) { 1254 for (d = 0; d < dim; ++d) { 1255 centroid[d] = v0[d]; 1256 for (e = 0; e < dim; ++e) { 1257 centroid[d] += R[d*dim+e]*csum[e]; 1258 } 1259 } 1260 } else for (d = 0; d < dim; ++d) centroid[d] = csum[d]; 1261 } 1262 PetscFunctionReturn(0); 1263 } 1264 1265 #undef __FUNCT__ 1266 #define __FUNCT__ "DMPlexComputeGeometryFVM_3D_Internal" 1267 /* Centroid_i = (\sum_n V_n Cn_i ) / V */ 1268 static PetscErrorCode DMPlexComputeGeometryFVM_3D_Internal(DM dm, PetscInt dim, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1269 { 1270 PetscSection coordSection; 1271 Vec coordinates; 1272 PetscScalar *coords = NULL; 1273 PetscReal vsum = 0.0, vtmp, coordsTmp[3*3]; 1274 const PetscInt *faces, *facesO; 1275 PetscInt numFaces, f, coordSize, numCorners, p, d; 1276 PetscErrorCode ierr; 1277 1278 PetscFunctionBegin; 1279 if (PetscUnlikely(dim > 3)) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"No support for dim %D > 3",dim); 1280 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1281 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1282 1283 if (centroid) for (d = 0; d < dim; ++d) centroid[d] = 0.0; 1284 ierr = DMPlexGetConeSize(dm, cell, &numFaces);CHKERRQ(ierr); 1285 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 1286 ierr = DMPlexGetConeOrientation(dm, cell, &facesO);CHKERRQ(ierr); 1287 for (f = 0; f < numFaces; ++f) { 1288 ierr = DMPlexVecGetClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); 1289 numCorners = coordSize/dim; 1290 switch (numCorners) { 1291 case 3: 1292 for (d = 0; d < dim; ++d) { 1293 coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); 1294 coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); 1295 coordsTmp[2*dim+d] = PetscRealPart(coords[2*dim+d]); 1296 } 1297 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1298 if (facesO[f] < 0) vtmp = -vtmp; 1299 vsum += vtmp; 1300 if (centroid) { /* Centroid of OABC = (a+b+c)/4 */ 1301 for (d = 0; d < dim; ++d) { 1302 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1303 } 1304 } 1305 break; 1306 case 4: 1307 /* DO FOR PYRAMID */ 1308 /* First tet */ 1309 for (d = 0; d < dim; ++d) { 1310 coordsTmp[0*dim+d] = PetscRealPart(coords[0*dim+d]); 1311 coordsTmp[1*dim+d] = PetscRealPart(coords[1*dim+d]); 1312 coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); 1313 } 1314 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1315 if (facesO[f] < 0) vtmp = -vtmp; 1316 vsum += vtmp; 1317 if (centroid) { 1318 for (d = 0; d < dim; ++d) { 1319 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1320 } 1321 } 1322 /* Second tet */ 1323 for (d = 0; d < dim; ++d) { 1324 coordsTmp[0*dim+d] = PetscRealPart(coords[1*dim+d]); 1325 coordsTmp[1*dim+d] = PetscRealPart(coords[2*dim+d]); 1326 coordsTmp[2*dim+d] = PetscRealPart(coords[3*dim+d]); 1327 } 1328 Volume_Tetrahedron_Origin_Internal(&vtmp, coordsTmp); 1329 if (facesO[f] < 0) vtmp = -vtmp; 1330 vsum += vtmp; 1331 if (centroid) { 1332 for (d = 0; d < dim; ++d) { 1333 for (p = 0; p < 3; ++p) centroid[d] += coordsTmp[p*dim+d]*vtmp; 1334 } 1335 } 1336 break; 1337 default: 1338 SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Cannot handle faces with %D vertices", numCorners); 1339 } 1340 ierr = DMPlexVecRestoreClosure(dm, coordSection, coordinates, faces[f], &coordSize, &coords);CHKERRQ(ierr); 1341 } 1342 if (vol) *vol = PetscAbsReal(vsum); 1343 if (normal) for (d = 0; d < dim; ++d) normal[d] = 0.0; 1344 if (centroid) for (d = 0; d < dim; ++d) centroid[d] /= (vsum*4); 1345 PetscFunctionReturn(0); 1346 } 1347 1348 #undef __FUNCT__ 1349 #define __FUNCT__ "DMPlexComputeCellGeometryFVM" 1350 /*@C 1351 DMPlexComputeCellGeometryFVM - Compute the volume for a given cell 1352 1353 Collective on DM 1354 1355 Input Arguments: 1356 + dm - the DM 1357 - cell - the cell 1358 1359 Output Arguments: 1360 + volume - the cell volume 1361 . centroid - the cell centroid 1362 - normal - the cell normal, if appropriate 1363 1364 Level: advanced 1365 1366 Fortran Notes: 1367 Since it returns arrays, this routine is only available in Fortran 90, and you must 1368 include petsc.h90 in your code. 1369 1370 .seealso: DMGetCoordinateSection(), DMGetCoordinateVec() 1371 @*/ 1372 PetscErrorCode DMPlexComputeCellGeometryFVM(DM dm, PetscInt cell, PetscReal *vol, PetscReal centroid[], PetscReal normal[]) 1373 { 1374 PetscInt depth, dim; 1375 PetscErrorCode ierr; 1376 1377 PetscFunctionBegin; 1378 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1379 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1380 if (depth != dim) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Mesh must be interpolated"); 1381 /* We need to keep a pointer to the depth label */ 1382 ierr = DMGetLabelValue(dm, "depth", cell, &depth);CHKERRQ(ierr); 1383 /* Cone size is now the number of faces */ 1384 switch (depth) { 1385 case 1: 1386 ierr = DMPlexComputeGeometryFVM_1D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1387 break; 1388 case 2: 1389 ierr = DMPlexComputeGeometryFVM_2D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1390 break; 1391 case 3: 1392 ierr = DMPlexComputeGeometryFVM_3D_Internal(dm, dim, cell, vol, centroid, normal);CHKERRQ(ierr); 1393 break; 1394 default: 1395 SETERRQ1(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Unsupported dimension %D for element geometry computation", dim); 1396 } 1397 PetscFunctionReturn(0); 1398 } 1399 1400 #undef __FUNCT__ 1401 #define __FUNCT__ "DMPlexComputeGeometryFEM" 1402 /* This should also take a PetscFE argument I think */ 1403 PetscErrorCode DMPlexComputeGeometryFEM(DM dm, Vec *cellgeom) 1404 { 1405 DM dmCell; 1406 Vec coordinates; 1407 PetscSection coordSection, sectionCell; 1408 PetscScalar *cgeom; 1409 PetscInt cStart, cEnd, cMax, c; 1410 PetscErrorCode ierr; 1411 1412 PetscFunctionBegin; 1413 ierr = DMClone(dm, &dmCell);CHKERRQ(ierr); 1414 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1415 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1416 ierr = DMSetCoordinateSection(dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1417 ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr); 1418 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr); 1419 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1420 ierr = DMPlexGetHybridBounds(dm, &cMax, NULL, NULL, NULL);CHKERRQ(ierr); 1421 cEnd = cMax < 0 ? cEnd : cMax; 1422 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1423 /* TODO This needs to be multiplied by Nq for non-affine */ 1424 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFECellGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1425 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1426 ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr); 1427 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1428 ierr = DMCreateLocalVector(dmCell, cellgeom);CHKERRQ(ierr); 1429 ierr = VecGetArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1430 for (c = cStart; c < cEnd; ++c) { 1431 PetscFECellGeom *cg; 1432 1433 ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1434 ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr); 1435 ierr = DMPlexComputeCellGeometryFEM(dmCell, c, NULL, cg->v0, cg->J, cg->invJ, &cg->detJ);CHKERRQ(ierr); 1436 if (cg->detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", cg->detJ, c); 1437 } 1438 ierr = VecRestoreArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1439 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1440 PetscFunctionReturn(0); 1441 } 1442 1443 #undef __FUNCT__ 1444 #define __FUNCT__ "DMPlexComputeGeometryFVM" 1445 /*@ 1446 DMPlexComputeGeometryFVM - Computes the cell and face geometry for a finite volume method 1447 1448 Input Parameter: 1449 . dm - The DM 1450 1451 Output Parameters: 1452 + cellgeom - A Vec of PetscFVCellGeom data 1453 . facegeom - A Vec of PetscFVFaceGeom data 1454 1455 Level: developer 1456 1457 .seealso: PetscFVFaceGeom, PetscFVCellGeom, DMPlexComputeGeometryFEM() 1458 @*/ 1459 PetscErrorCode DMPlexComputeGeometryFVM(DM dm, Vec *cellgeom, Vec *facegeom) 1460 { 1461 DM dmFace, dmCell; 1462 DMLabel ghostLabel; 1463 PetscSection sectionFace, sectionCell; 1464 PetscSection coordSection; 1465 Vec coordinates; 1466 PetscScalar *fgeom, *cgeom; 1467 PetscReal minradius, gminradius; 1468 PetscInt dim, cStart, cEnd, cEndInterior, c, fStart, fEnd, f; 1469 PetscErrorCode ierr; 1470 1471 PetscFunctionBegin; 1472 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1473 ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); 1474 ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); 1475 /* Make cell centroids and volumes */ 1476 ierr = DMClone(dm, &dmCell);CHKERRQ(ierr); 1477 ierr = DMSetCoordinateSection(dmCell, PETSC_DETERMINE, coordSection);CHKERRQ(ierr); 1478 ierr = DMSetCoordinatesLocal(dmCell, coordinates);CHKERRQ(ierr); 1479 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionCell);CHKERRQ(ierr); 1480 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1481 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1482 ierr = PetscSectionSetChart(sectionCell, cStart, cEnd);CHKERRQ(ierr); 1483 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionCell, c, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFVCellGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1484 ierr = PetscSectionSetUp(sectionCell);CHKERRQ(ierr); 1485 ierr = DMSetDefaultSection(dmCell, sectionCell);CHKERRQ(ierr); 1486 ierr = PetscSectionDestroy(§ionCell);CHKERRQ(ierr); 1487 ierr = DMCreateLocalVector(dmCell, cellgeom);CHKERRQ(ierr); 1488 if (cEndInterior < 0) { 1489 cEndInterior = cEnd; 1490 } 1491 ierr = VecGetArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1492 for (c = cStart; c < cEndInterior; ++c) { 1493 PetscFVCellGeom *cg; 1494 1495 ierr = DMPlexPointLocalRef(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1496 ierr = PetscMemzero(cg, sizeof(*cg));CHKERRQ(ierr); 1497 ierr = DMPlexComputeCellGeometryFVM(dmCell, c, &cg->volume, cg->centroid, NULL);CHKERRQ(ierr); 1498 } 1499 /* Compute face normals and minimum cell radius */ 1500 ierr = DMClone(dm, &dmFace);CHKERRQ(ierr); 1501 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionFace);CHKERRQ(ierr); 1502 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1503 ierr = PetscSectionSetChart(sectionFace, fStart, fEnd);CHKERRQ(ierr); 1504 for (f = fStart; f < fEnd; ++f) {ierr = PetscSectionSetDof(sectionFace, f, (PetscInt) PetscCeilReal(((PetscReal) sizeof(PetscFVFaceGeom))/sizeof(PetscScalar)));CHKERRQ(ierr);} 1505 ierr = PetscSectionSetUp(sectionFace);CHKERRQ(ierr); 1506 ierr = DMSetDefaultSection(dmFace, sectionFace);CHKERRQ(ierr); 1507 ierr = PetscSectionDestroy(§ionFace);CHKERRQ(ierr); 1508 ierr = DMCreateLocalVector(dmFace, facegeom);CHKERRQ(ierr); 1509 ierr = VecGetArray(*facegeom, &fgeom);CHKERRQ(ierr); 1510 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1511 minradius = PETSC_MAX_REAL; 1512 for (f = fStart; f < fEnd; ++f) { 1513 PetscFVFaceGeom *fg; 1514 PetscReal area; 1515 PetscInt ghost = -1, d, numChildren; 1516 1517 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1518 ierr = DMPlexGetTreeChildren(dm,f,&numChildren,NULL);CHKERRQ(ierr); 1519 if (ghost >= 0 || numChildren) continue; 1520 ierr = DMPlexPointLocalRef(dmFace, f, fgeom, &fg);CHKERRQ(ierr); 1521 ierr = DMPlexComputeCellGeometryFVM(dm, f, &area, fg->centroid, fg->normal);CHKERRQ(ierr); 1522 for (d = 0; d < dim; ++d) fg->normal[d] *= area; 1523 /* Flip face orientation if necessary to match ordering in support, and Update minimum radius */ 1524 { 1525 PetscFVCellGeom *cL, *cR; 1526 PetscInt ncells; 1527 const PetscInt *cells; 1528 PetscReal *lcentroid, *rcentroid; 1529 PetscReal l[3], r[3], v[3]; 1530 1531 ierr = DMPlexGetSupport(dm, f, &cells);CHKERRQ(ierr); 1532 ierr = DMPlexGetSupportSize(dm, f, &ncells);CHKERRQ(ierr); 1533 ierr = DMPlexPointLocalRead(dmCell, cells[0], cgeom, &cL);CHKERRQ(ierr); 1534 lcentroid = cells[0] >= cEndInterior ? fg->centroid : cL->centroid; 1535 if (ncells > 1) { 1536 ierr = DMPlexPointLocalRead(dmCell, cells[1], cgeom, &cR);CHKERRQ(ierr); 1537 rcentroid = cells[1] >= cEndInterior ? fg->centroid : cR->centroid; 1538 } 1539 else { 1540 rcentroid = fg->centroid; 1541 } 1542 ierr = DMLocalizeCoordinateReal_Internal(dm, dim, fg->centroid, lcentroid, l);CHKERRQ(ierr); 1543 ierr = DMLocalizeCoordinateReal_Internal(dm, dim, fg->centroid, rcentroid, r);CHKERRQ(ierr); 1544 DMPlex_WaxpyD_Internal(dim, -1, l, r, v); 1545 if (DMPlex_DotRealD_Internal(dim, fg->normal, v) < 0) { 1546 for (d = 0; d < dim; ++d) fg->normal[d] = -fg->normal[d]; 1547 } 1548 if (DMPlex_DotRealD_Internal(dim, fg->normal, v) <= 0) { 1549 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]); 1550 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]); 1551 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Direction for face %d could not be fixed", f); 1552 } 1553 if (cells[0] < cEndInterior) { 1554 DMPlex_WaxpyD_Internal(dim, -1, fg->centroid, cL->centroid, v); 1555 minradius = PetscMin(minradius, DMPlex_NormD_Internal(dim, v)); 1556 } 1557 if (ncells > 1 && cells[1] < cEndInterior) { 1558 DMPlex_WaxpyD_Internal(dim, -1, fg->centroid, cR->centroid, v); 1559 minradius = PetscMin(minradius, DMPlex_NormD_Internal(dim, v)); 1560 } 1561 } 1562 } 1563 ierr = MPIU_Allreduce(&minradius, &gminradius, 1, MPIU_REAL, MPIU_MIN, PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 1564 ierr = DMPlexSetMinRadius(dm, gminradius);CHKERRQ(ierr); 1565 /* Compute centroids of ghost cells */ 1566 for (c = cEndInterior; c < cEnd; ++c) { 1567 PetscFVFaceGeom *fg; 1568 const PetscInt *cone, *support; 1569 PetscInt coneSize, supportSize, s; 1570 1571 ierr = DMPlexGetConeSize(dmCell, c, &coneSize);CHKERRQ(ierr); 1572 if (coneSize != 1) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Ghost cell %d has cone size %d != 1", c, coneSize); 1573 ierr = DMPlexGetCone(dmCell, c, &cone);CHKERRQ(ierr); 1574 ierr = DMPlexGetSupportSize(dmCell, cone[0], &supportSize);CHKERRQ(ierr); 1575 if (supportSize != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Face %d has support size %d != 2", cone[0], supportSize); 1576 ierr = DMPlexGetSupport(dmCell, cone[0], &support);CHKERRQ(ierr); 1577 ierr = DMPlexPointLocalRef(dmFace, cone[0], fgeom, &fg);CHKERRQ(ierr); 1578 for (s = 0; s < 2; ++s) { 1579 /* Reflect ghost centroid across plane of face */ 1580 if (support[s] == c) { 1581 PetscFVCellGeom *ci; 1582 PetscFVCellGeom *cg; 1583 PetscReal c2f[3], a; 1584 1585 ierr = DMPlexPointLocalRead(dmCell, support[(s+1)%2], cgeom, &ci);CHKERRQ(ierr); 1586 DMPlex_WaxpyD_Internal(dim, -1, ci->centroid, fg->centroid, c2f); /* cell to face centroid */ 1587 a = DMPlex_DotRealD_Internal(dim, c2f, fg->normal)/DMPlex_DotRealD_Internal(dim, fg->normal, fg->normal); 1588 ierr = DMPlexPointLocalRef(dmCell, support[s], cgeom, &cg);CHKERRQ(ierr); 1589 DMPlex_WaxpyD_Internal(dim, 2*a, fg->normal, ci->centroid, cg->centroid); 1590 cg->volume = ci->volume; 1591 } 1592 } 1593 } 1594 ierr = VecRestoreArray(*facegeom, &fgeom);CHKERRQ(ierr); 1595 ierr = VecRestoreArray(*cellgeom, &cgeom);CHKERRQ(ierr); 1596 ierr = DMDestroy(&dmCell);CHKERRQ(ierr); 1597 ierr = DMDestroy(&dmFace);CHKERRQ(ierr); 1598 PetscFunctionReturn(0); 1599 } 1600 1601 #undef __FUNCT__ 1602 #define __FUNCT__ "DMPlexGetMinRadius" 1603 /*@C 1604 DMPlexGetMinRadius - Returns the minimum distance from any cell centroid to a face 1605 1606 Not collective 1607 1608 Input Argument: 1609 . dm - the DM 1610 1611 Output Argument: 1612 . minradius - the minium cell radius 1613 1614 Level: developer 1615 1616 .seealso: DMGetCoordinates() 1617 @*/ 1618 PetscErrorCode DMPlexGetMinRadius(DM dm, PetscReal *minradius) 1619 { 1620 PetscFunctionBegin; 1621 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1622 PetscValidPointer(minradius,2); 1623 *minradius = ((DM_Plex*) dm->data)->minradius; 1624 PetscFunctionReturn(0); 1625 } 1626 1627 #undef __FUNCT__ 1628 #define __FUNCT__ "DMPlexSetMinRadius" 1629 /*@C 1630 DMPlexSetMinRadius - Sets the minimum distance from the cell centroid to a face 1631 1632 Logically collective 1633 1634 Input Arguments: 1635 + dm - the DM 1636 - minradius - the minium cell radius 1637 1638 Level: developer 1639 1640 .seealso: DMSetCoordinates() 1641 @*/ 1642 PetscErrorCode DMPlexSetMinRadius(DM dm, PetscReal minradius) 1643 { 1644 PetscFunctionBegin; 1645 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1646 ((DM_Plex*) dm->data)->minradius = minradius; 1647 PetscFunctionReturn(0); 1648 } 1649 1650 #undef __FUNCT__ 1651 #define __FUNCT__ "BuildGradientReconstruction_Internal" 1652 static PetscErrorCode BuildGradientReconstruction_Internal(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom) 1653 { 1654 DMLabel ghostLabel; 1655 PetscScalar *dx, *grad, **gref; 1656 PetscInt dim, cStart, cEnd, c, cEndInterior, maxNumFaces; 1657 PetscErrorCode ierr; 1658 1659 PetscFunctionBegin; 1660 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1661 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1662 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1663 ierr = DMPlexGetMaxSizes(dm, &maxNumFaces, NULL);CHKERRQ(ierr); 1664 ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr); 1665 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1666 ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr); 1667 for (c = cStart; c < cEndInterior; c++) { 1668 const PetscInt *faces; 1669 PetscInt numFaces, usedFaces, f, d; 1670 PetscFVCellGeom *cg; 1671 PetscBool boundary; 1672 PetscInt ghost; 1673 1674 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1675 ierr = DMPlexGetConeSize(dm, c, &numFaces);CHKERRQ(ierr); 1676 ierr = DMPlexGetCone(dm, c, &faces);CHKERRQ(ierr); 1677 if (numFaces < dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cell %D has only %D faces, not enough for gradient reconstruction", c, numFaces); 1678 for (f = 0, usedFaces = 0; f < numFaces; ++f) { 1679 PetscFVCellGeom *cg1; 1680 PetscFVFaceGeom *fg; 1681 const PetscInt *fcells; 1682 PetscInt ncell, side; 1683 1684 ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr); 1685 ierr = DMIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr); 1686 if ((ghost >= 0) || boundary) continue; 1687 ierr = DMPlexGetSupport(dm, faces[f], &fcells);CHKERRQ(ierr); 1688 side = (c != fcells[0]); /* c is on left=0 or right=1 of face */ 1689 ncell = fcells[!side]; /* the neighbor */ 1690 ierr = DMPlexPointLocalRef(dmFace, faces[f], fgeom, &fg);CHKERRQ(ierr); 1691 ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr); 1692 for (d = 0; d < dim; ++d) dx[usedFaces*dim+d] = cg1->centroid[d] - cg->centroid[d]; 1693 gref[usedFaces++] = fg->grad[side]; /* Gradient reconstruction term will go here */ 1694 } 1695 if (!usedFaces) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_USER, "Mesh contains isolated cell (no neighbors). Is it intentional?"); 1696 ierr = PetscFVComputeGradient(fvm, usedFaces, dx, grad);CHKERRQ(ierr); 1697 for (f = 0, usedFaces = 0; f < numFaces; ++f) { 1698 ierr = DMLabelGetValue(ghostLabel, faces[f], &ghost);CHKERRQ(ierr); 1699 ierr = DMIsBoundaryPoint(dm, faces[f], &boundary);CHKERRQ(ierr); 1700 if ((ghost >= 0) || boundary) continue; 1701 for (d = 0; d < dim; ++d) gref[usedFaces][d] = grad[usedFaces*dim+d]; 1702 ++usedFaces; 1703 } 1704 } 1705 ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr); 1706 PetscFunctionReturn(0); 1707 } 1708 1709 #undef __FUNCT__ 1710 #define __FUNCT__ "BuildGradientReconstruction_Internal_Tree" 1711 static PetscErrorCode BuildGradientReconstruction_Internal_Tree(DM dm, PetscFV fvm, DM dmFace, PetscScalar *fgeom, DM dmCell, PetscScalar *cgeom) 1712 { 1713 DMLabel ghostLabel; 1714 PetscScalar *dx, *grad, **gref; 1715 PetscInt dim, cStart, cEnd, c, cEndInterior, fStart, fEnd, f, nStart, nEnd, maxNumFaces = 0; 1716 PetscSection neighSec; 1717 PetscInt (*neighbors)[2]; 1718 PetscInt *counter; 1719 PetscErrorCode ierr; 1720 1721 PetscFunctionBegin; 1722 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1723 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1724 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1725 if (cEndInterior < 0) { 1726 cEndInterior = cEnd; 1727 } 1728 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dm),&neighSec);CHKERRQ(ierr); 1729 ierr = PetscSectionSetChart(neighSec,cStart,cEndInterior);CHKERRQ(ierr); 1730 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1731 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1732 for (f = fStart; f < fEnd; f++) { 1733 const PetscInt *fcells; 1734 PetscBool boundary; 1735 PetscInt ghost = -1; 1736 PetscInt numChildren, numCells, c; 1737 1738 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1739 ierr = DMIsBoundaryPoint(dm, f, &boundary);CHKERRQ(ierr); 1740 ierr = DMPlexGetTreeChildren(dm, f, &numChildren, NULL);CHKERRQ(ierr); 1741 if ((ghost >= 0) || boundary || numChildren) continue; 1742 ierr = DMPlexGetSupportSize(dm, f, &numCells);CHKERRQ(ierr); 1743 if (numCells == 2) { 1744 ierr = DMPlexGetSupport(dm, f, &fcells);CHKERRQ(ierr); 1745 for (c = 0; c < 2; c++) { 1746 PetscInt cell = fcells[c]; 1747 1748 if (cell >= cStart && cell < cEndInterior) { 1749 ierr = PetscSectionAddDof(neighSec,cell,1);CHKERRQ(ierr); 1750 } 1751 } 1752 } 1753 } 1754 ierr = PetscSectionSetUp(neighSec);CHKERRQ(ierr); 1755 ierr = PetscSectionGetMaxDof(neighSec,&maxNumFaces);CHKERRQ(ierr); 1756 ierr = PetscFVLeastSquaresSetMaxFaces(fvm, maxNumFaces);CHKERRQ(ierr); 1757 nStart = 0; 1758 ierr = PetscSectionGetStorageSize(neighSec,&nEnd);CHKERRQ(ierr); 1759 ierr = PetscMalloc1((nEnd-nStart),&neighbors);CHKERRQ(ierr); 1760 ierr = PetscCalloc1((cEndInterior-cStart),&counter);CHKERRQ(ierr); 1761 for (f = fStart; f < fEnd; f++) { 1762 const PetscInt *fcells; 1763 PetscBool boundary; 1764 PetscInt ghost = -1; 1765 PetscInt numChildren, numCells, c; 1766 1767 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, f, &ghost);CHKERRQ(ierr);} 1768 ierr = DMIsBoundaryPoint(dm, f, &boundary);CHKERRQ(ierr); 1769 ierr = DMPlexGetTreeChildren(dm, f, &numChildren, NULL);CHKERRQ(ierr); 1770 if ((ghost >= 0) || boundary || numChildren) continue; 1771 ierr = DMPlexGetSupportSize(dm, f, &numCells);CHKERRQ(ierr); 1772 if (numCells == 2) { 1773 ierr = DMPlexGetSupport(dm, f, &fcells);CHKERRQ(ierr); 1774 for (c = 0; c < 2; c++) { 1775 PetscInt cell = fcells[c], off; 1776 1777 if (cell >= cStart && cell < cEndInterior) { 1778 ierr = PetscSectionGetOffset(neighSec,cell,&off);CHKERRQ(ierr); 1779 off += counter[cell - cStart]++; 1780 neighbors[off][0] = f; 1781 neighbors[off][1] = fcells[1 - c]; 1782 } 1783 } 1784 } 1785 } 1786 ierr = PetscFree(counter);CHKERRQ(ierr); 1787 ierr = PetscMalloc3(maxNumFaces*dim, &dx, maxNumFaces*dim, &grad, maxNumFaces, &gref);CHKERRQ(ierr); 1788 for (c = cStart; c < cEndInterior; c++) { 1789 PetscInt numFaces, f, d, off, ghost = -1; 1790 PetscFVCellGeom *cg; 1791 1792 ierr = DMPlexPointLocalRead(dmCell, c, cgeom, &cg);CHKERRQ(ierr); 1793 ierr = PetscSectionGetDof(neighSec, c, &numFaces);CHKERRQ(ierr); 1794 ierr = PetscSectionGetOffset(neighSec, c, &off);CHKERRQ(ierr); 1795 if (ghostLabel) {ierr = DMLabelGetValue(ghostLabel, c, &ghost);CHKERRQ(ierr);} 1796 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); 1797 for (f = 0; f < numFaces; ++f) { 1798 PetscFVCellGeom *cg1; 1799 PetscFVFaceGeom *fg; 1800 const PetscInt *fcells; 1801 PetscInt ncell, side, nface; 1802 1803 nface = neighbors[off + f][0]; 1804 ncell = neighbors[off + f][1]; 1805 ierr = DMPlexGetSupport(dm,nface,&fcells);CHKERRQ(ierr); 1806 side = (c != fcells[0]); 1807 ierr = DMPlexPointLocalRef(dmFace, nface, fgeom, &fg);CHKERRQ(ierr); 1808 ierr = DMPlexPointLocalRead(dmCell, ncell, cgeom, &cg1);CHKERRQ(ierr); 1809 for (d = 0; d < dim; ++d) dx[f*dim+d] = cg1->centroid[d] - cg->centroid[d]; 1810 gref[f] = fg->grad[side]; /* Gradient reconstruction term will go here */ 1811 } 1812 ierr = PetscFVComputeGradient(fvm, numFaces, dx, grad);CHKERRQ(ierr); 1813 for (f = 0; f < numFaces; ++f) { 1814 for (d = 0; d < dim; ++d) gref[f][d] = grad[f*dim+d]; 1815 } 1816 } 1817 ierr = PetscFree3(dx, grad, gref);CHKERRQ(ierr); 1818 ierr = PetscSectionDestroy(&neighSec);CHKERRQ(ierr); 1819 ierr = PetscFree(neighbors);CHKERRQ(ierr); 1820 PetscFunctionReturn(0); 1821 } 1822 1823 #undef __FUNCT__ 1824 #define __FUNCT__ "DMPlexComputeGradientFVM" 1825 /*@ 1826 DMPlexComputeGradientFVM - Compute geometric factors for gradient reconstruction, which are stored in the geometry data, and compute layout for gradient data 1827 1828 Collective on DM 1829 1830 Input Arguments: 1831 + dm - The DM 1832 . fvm - The PetscFV 1833 . faceGeometry - The face geometry from DMPlexGetFaceGeometryFVM() 1834 - cellGeometry - The face geometry from DMPlexGetCellGeometryFVM() 1835 1836 Output Parameters: 1837 + faceGeometry - The geometric factors for gradient calculation are inserted 1838 - dmGrad - The DM describing the layout of gradient data 1839 1840 Level: developer 1841 1842 .seealso: DMPlexGetFaceGeometryFVM(), DMPlexGetCellGeometryFVM() 1843 @*/ 1844 PetscErrorCode DMPlexComputeGradientFVM(DM dm, PetscFV fvm, Vec faceGeometry, Vec cellGeometry, DM *dmGrad) 1845 { 1846 DM dmFace, dmCell; 1847 PetscScalar *fgeom, *cgeom; 1848 PetscSection sectionGrad, parentSection; 1849 PetscInt dim, pdim, cStart, cEnd, cEndInterior, c; 1850 PetscErrorCode ierr; 1851 1852 PetscFunctionBegin; 1853 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1854 ierr = PetscFVGetNumComponents(fvm, &pdim);CHKERRQ(ierr); 1855 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1856 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1857 /* Construct the interpolant corresponding to each face from the least-square solution over the cell neighborhood */ 1858 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1859 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1860 ierr = VecGetArray(faceGeometry, &fgeom);CHKERRQ(ierr); 1861 ierr = VecGetArray(cellGeometry, &cgeom);CHKERRQ(ierr); 1862 ierr = DMPlexGetTree(dm,&parentSection,NULL,NULL,NULL,NULL);CHKERRQ(ierr); 1863 if (!parentSection) { 1864 ierr = BuildGradientReconstruction_Internal(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr); 1865 } 1866 else { 1867 ierr = BuildGradientReconstruction_Internal_Tree(dm, fvm, dmFace, fgeom, dmCell, cgeom);CHKERRQ(ierr); 1868 } 1869 ierr = VecRestoreArray(faceGeometry, &fgeom);CHKERRQ(ierr); 1870 ierr = VecRestoreArray(cellGeometry, &cgeom);CHKERRQ(ierr); 1871 /* Create storage for gradients */ 1872 ierr = DMClone(dm, dmGrad);CHKERRQ(ierr); 1873 ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), §ionGrad);CHKERRQ(ierr); 1874 ierr = PetscSectionSetChart(sectionGrad, cStart, cEnd);CHKERRQ(ierr); 1875 for (c = cStart; c < cEnd; ++c) {ierr = PetscSectionSetDof(sectionGrad, c, pdim*dim);CHKERRQ(ierr);} 1876 ierr = PetscSectionSetUp(sectionGrad);CHKERRQ(ierr); 1877 ierr = DMSetDefaultSection(*dmGrad, sectionGrad);CHKERRQ(ierr); 1878 ierr = PetscSectionDestroy(§ionGrad);CHKERRQ(ierr); 1879 PetscFunctionReturn(0); 1880 } 1881