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