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