1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/snesimpl.h> /*I "petscsnes.h" I*/ 3 #include <petscds.h> 4 #include <petsc/private/petscimpl.h> 5 #include <petsc/private/petscfeimpl.h> 6 7 /************************** Interpolation *******************************/ 8 9 #undef __FUNCT__ 10 #define __FUNCT__ "DMSNESConvertPlex" 11 static PetscErrorCode DMSNESConvertPlex(DM dm, DM *plex, PetscBool copy) 12 { 13 PetscBool isPlex; 14 PetscErrorCode ierr; 15 16 PetscFunctionBegin; 17 ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); 18 if (isPlex) { 19 *plex = dm; 20 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 21 } else { 22 ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); 23 if (!*plex) { 24 ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr); 25 ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); 26 if (copy) { 27 PetscInt i; 28 PetscObject obj; 29 const char *comps[3] = {"A","dmAux","dmCh"}; 30 31 ierr = DMCopyDMSNES(dm, *plex);CHKERRQ(ierr); 32 for (i = 0; i < 3; i++) { 33 ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr); 34 ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr); 35 } 36 } 37 } else { 38 ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); 39 } 40 } 41 PetscFunctionReturn(0); 42 } 43 44 #undef __FUNCT__ 45 #define __FUNCT__ "DMInterpolationCreate" 46 PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx) 47 { 48 PetscErrorCode ierr; 49 50 PetscFunctionBegin; 51 PetscValidPointer(ctx, 2); 52 ierr = PetscMalloc(sizeof(struct _DMInterpolationInfo), ctx);CHKERRQ(ierr); 53 54 (*ctx)->comm = comm; 55 (*ctx)->dim = -1; 56 (*ctx)->nInput = 0; 57 (*ctx)->points = NULL; 58 (*ctx)->cells = NULL; 59 (*ctx)->n = -1; 60 (*ctx)->coords = NULL; 61 PetscFunctionReturn(0); 62 } 63 64 #undef __FUNCT__ 65 #define __FUNCT__ "DMInterpolationSetDim" 66 PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim) 67 { 68 PetscFunctionBegin; 69 if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %d", dim); 70 ctx->dim = dim; 71 PetscFunctionReturn(0); 72 } 73 74 #undef __FUNCT__ 75 #define __FUNCT__ "DMInterpolationGetDim" 76 PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim) 77 { 78 PetscFunctionBegin; 79 PetscValidIntPointer(dim, 2); 80 *dim = ctx->dim; 81 PetscFunctionReturn(0); 82 } 83 84 #undef __FUNCT__ 85 #define __FUNCT__ "DMInterpolationSetDof" 86 PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof) 87 { 88 PetscFunctionBegin; 89 if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %d", dof); 90 ctx->dof = dof; 91 PetscFunctionReturn(0); 92 } 93 94 #undef __FUNCT__ 95 #define __FUNCT__ "DMInterpolationGetDof" 96 PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof) 97 { 98 PetscFunctionBegin; 99 PetscValidIntPointer(dof, 2); 100 *dof = ctx->dof; 101 PetscFunctionReturn(0); 102 } 103 104 #undef __FUNCT__ 105 #define __FUNCT__ "DMInterpolationAddPoints" 106 PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[]) 107 { 108 PetscErrorCode ierr; 109 110 PetscFunctionBegin; 111 if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 112 if (ctx->points) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet"); 113 ctx->nInput = n; 114 115 ierr = PetscMalloc1(n*ctx->dim, &ctx->points);CHKERRQ(ierr); 116 ierr = PetscMemcpy(ctx->points, points, n*ctx->dim * sizeof(PetscReal));CHKERRQ(ierr); 117 PetscFunctionReturn(0); 118 } 119 120 #undef __FUNCT__ 121 #define __FUNCT__ "DMInterpolationSetUp" 122 PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints) 123 { 124 MPI_Comm comm = ctx->comm; 125 PetscScalar *a; 126 PetscInt p, q, i; 127 PetscMPIInt rank, size; 128 PetscErrorCode ierr; 129 Vec pointVec; 130 IS cellIS; 131 PetscLayout layout; 132 PetscReal *globalPoints; 133 PetscScalar *globalPointsScalar; 134 const PetscInt *ranges; 135 PetscMPIInt *counts, *displs; 136 const PetscInt *foundCells; 137 PetscMPIInt *foundProcs, *globalProcs; 138 PetscInt n, N; 139 140 PetscFunctionBegin; 141 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 142 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 143 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 144 if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 145 /* Locate points */ 146 n = ctx->nInput; 147 if (!redundantPoints) { 148 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 149 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 150 ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr); 151 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 152 ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr); 153 /* Communicate all points to all processes */ 154 ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr); 155 ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr); 156 for (p = 0; p < size; ++p) { 157 counts[p] = (ranges[p+1] - ranges[p])*ctx->dim; 158 displs[p] = ranges[p]*ctx->dim; 159 } 160 ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr); 161 } else { 162 N = n; 163 globalPoints = ctx->points; 164 counts = displs = NULL; 165 layout = NULL; 166 } 167 #if 0 168 ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 169 /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */ 170 #else 171 #if defined(PETSC_USE_COMPLEX) 172 ierr = PetscMalloc1(N,&globalPointsScalar);CHKERRQ(ierr); 173 for (i=0; i<N; i++) globalPointsScalar[i] = globalPoints[i]; 174 #else 175 globalPointsScalar = globalPoints; 176 #endif 177 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr); 178 ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 179 ierr = DMLocatePoints(dm, pointVec, &cellIS);CHKERRQ(ierr); 180 ierr = ISGetIndices(cellIS, &foundCells);CHKERRQ(ierr); 181 #endif 182 for (p = 0; p < N; ++p) { 183 if (foundCells[p] >= 0) foundProcs[p] = rank; 184 else foundProcs[p] = size; 185 } 186 /* Let the lowest rank process own each point */ 187 ierr = MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr); 188 ctx->n = 0; 189 for (p = 0; p < N; ++p) { 190 if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, globalPoints[p*ctx->dim+0], ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0, ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0); 191 else if (globalProcs[p] == rank) ctx->n++; 192 } 193 /* Create coordinates vector and array of owned cells */ 194 ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr); 195 ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr); 196 ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr); 197 ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr); 198 ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr); 199 ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr); 200 for (p = 0, q = 0, i = 0; p < N; ++p) { 201 if (globalProcs[p] == rank) { 202 PetscInt d; 203 204 for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d]; 205 ctx->cells[q++] = foundCells[p]; 206 } 207 } 208 ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr); 209 #if 0 210 ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr); 211 #else 212 ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr); 213 ierr = ISRestoreIndices(cellIS, &foundCells);CHKERRQ(ierr); 214 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 215 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 216 #endif 217 if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);} 218 if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);} 219 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 220 PetscFunctionReturn(0); 221 } 222 223 #undef __FUNCT__ 224 #define __FUNCT__ "DMInterpolationGetCoordinates" 225 PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates) 226 { 227 PetscFunctionBegin; 228 PetscValidPointer(coordinates, 2); 229 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 230 *coordinates = ctx->coords; 231 PetscFunctionReturn(0); 232 } 233 234 #undef __FUNCT__ 235 #define __FUNCT__ "DMInterpolationGetVector" 236 PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v) 237 { 238 PetscErrorCode ierr; 239 240 PetscFunctionBegin; 241 PetscValidPointer(v, 2); 242 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 243 ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr); 244 ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr); 245 ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr); 246 ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr); 247 PetscFunctionReturn(0); 248 } 249 250 #undef __FUNCT__ 251 #define __FUNCT__ "DMInterpolationRestoreVector" 252 PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v) 253 { 254 PetscErrorCode ierr; 255 256 PetscFunctionBegin; 257 PetscValidPointer(v, 2); 258 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 259 ierr = VecDestroy(v);CHKERRQ(ierr); 260 PetscFunctionReturn(0); 261 } 262 263 #undef __FUNCT__ 264 #define __FUNCT__ "DMInterpolate_Triangle_Private" 265 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 266 { 267 PetscReal *v0, *J, *invJ, detJ; 268 const PetscScalar *coords; 269 PetscScalar *a; 270 PetscInt p; 271 PetscErrorCode ierr; 272 273 PetscFunctionBegin; 274 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 275 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 276 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 277 for (p = 0; p < ctx->n; ++p) { 278 PetscInt c = ctx->cells[p]; 279 PetscScalar *x = NULL; 280 PetscReal xi[4]; 281 PetscInt d, f, comp; 282 283 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 284 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 285 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 286 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 287 288 for (d = 0; d < ctx->dim; ++d) { 289 xi[d] = 0.0; 290 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 291 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[(d+1)*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 292 } 293 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 294 } 295 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 296 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 297 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 298 PetscFunctionReturn(0); 299 } 300 301 #undef __FUNCT__ 302 #define __FUNCT__ "DMInterpolate_Tetrahedron_Private" 303 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 304 { 305 PetscReal *v0, *J, *invJ, detJ; 306 const PetscScalar *coords; 307 PetscScalar *a; 308 PetscInt p; 309 PetscErrorCode ierr; 310 311 PetscFunctionBegin; 312 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 313 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 314 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 315 for (p = 0; p < ctx->n; ++p) { 316 PetscInt c = ctx->cells[p]; 317 const PetscInt order[3] = {2, 1, 3}; 318 PetscScalar *x = NULL; 319 PetscReal xi[4]; 320 PetscInt d, f, comp; 321 322 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 323 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 324 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 325 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 326 327 for (d = 0; d < ctx->dim; ++d) { 328 xi[d] = 0.0; 329 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 330 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] += PetscRealPart(x[order[d]*ctx->dof+comp] - x[0*ctx->dof+comp])*xi[d]; 331 } 332 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 333 } 334 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 335 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 336 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 337 PetscFunctionReturn(0); 338 } 339 340 #undef __FUNCT__ 341 #define __FUNCT__ "QuadMap_Private" 342 PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 343 { 344 const PetscScalar *vertices = (const PetscScalar*) ctx; 345 const PetscScalar x0 = vertices[0]; 346 const PetscScalar y0 = vertices[1]; 347 const PetscScalar x1 = vertices[2]; 348 const PetscScalar y1 = vertices[3]; 349 const PetscScalar x2 = vertices[4]; 350 const PetscScalar y2 = vertices[5]; 351 const PetscScalar x3 = vertices[6]; 352 const PetscScalar y3 = vertices[7]; 353 const PetscScalar f_1 = x1 - x0; 354 const PetscScalar g_1 = y1 - y0; 355 const PetscScalar f_3 = x3 - x0; 356 const PetscScalar g_3 = y3 - y0; 357 const PetscScalar f_01 = x2 - x1 - x3 + x0; 358 const PetscScalar g_01 = y2 - y1 - y3 + y0; 359 const PetscScalar *ref; 360 PetscScalar *real; 361 PetscErrorCode ierr; 362 363 PetscFunctionBegin; 364 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 365 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 366 { 367 const PetscScalar p0 = ref[0]; 368 const PetscScalar p1 = ref[1]; 369 370 real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1; 371 real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1; 372 } 373 ierr = PetscLogFlops(28);CHKERRQ(ierr); 374 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 375 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 376 PetscFunctionReturn(0); 377 } 378 379 #include <petsc/private/dmimpl.h> 380 #undef __FUNCT__ 381 #define __FUNCT__ "QuadJacobian_Private" 382 PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 383 { 384 const PetscScalar *vertices = (const PetscScalar*) ctx; 385 const PetscScalar x0 = vertices[0]; 386 const PetscScalar y0 = vertices[1]; 387 const PetscScalar x1 = vertices[2]; 388 const PetscScalar y1 = vertices[3]; 389 const PetscScalar x2 = vertices[4]; 390 const PetscScalar y2 = vertices[5]; 391 const PetscScalar x3 = vertices[6]; 392 const PetscScalar y3 = vertices[7]; 393 const PetscScalar f_01 = x2 - x1 - x3 + x0; 394 const PetscScalar g_01 = y2 - y1 - y3 + y0; 395 const PetscScalar *ref; 396 PetscErrorCode ierr; 397 398 PetscFunctionBegin; 399 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 400 { 401 const PetscScalar x = ref[0]; 402 const PetscScalar y = ref[1]; 403 const PetscInt rows[2] = {0, 1}; 404 PetscScalar values[4]; 405 406 values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5; 407 values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5; 408 ierr = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr); 409 } 410 ierr = PetscLogFlops(30);CHKERRQ(ierr); 411 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 412 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 413 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 414 PetscFunctionReturn(0); 415 } 416 417 #undef __FUNCT__ 418 #define __FUNCT__ "DMInterpolate_Quad_Private" 419 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 420 { 421 DM dmCoord; 422 SNES snes; 423 KSP ksp; 424 PC pc; 425 Vec coordsLocal, r, ref, real; 426 Mat J; 427 const PetscScalar *coords; 428 PetscScalar *a; 429 PetscInt p; 430 PetscErrorCode ierr; 431 432 PetscFunctionBegin; 433 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 434 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 435 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 436 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 437 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 438 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 439 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 440 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 441 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 442 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 443 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 444 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 445 ierr = MatSetUp(J);CHKERRQ(ierr); 446 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 447 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 448 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 449 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 450 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 451 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 452 453 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 454 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 455 for (p = 0; p < ctx->n; ++p) { 456 PetscScalar *x = NULL, *vertices = NULL; 457 PetscScalar *xi; 458 PetscReal xir[2]; 459 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 460 461 /* Can make this do all points at once */ 462 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 463 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 4*2); 464 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 465 if (4*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 4*ctx->dof); 466 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 467 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 468 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 469 xi[0] = coords[p*ctx->dim+0]; 470 xi[1] = coords[p*ctx->dim+1]; 471 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 472 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 473 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 474 xir[0] = PetscRealPart(xi[0]); 475 xir[1] = PetscRealPart(xi[1]); 476 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]*(1 - xir[0])*(1 - xir[1]) + x[1*ctx->dof+comp]*xir[0]*(1 - xir[1]) + x[2*ctx->dof+comp]*xir[0]*xir[1] + x[3*ctx->dof+comp]*(1 - xir[0])*xir[1]; 477 478 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 479 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 480 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 481 } 482 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 483 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 484 485 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 486 ierr = VecDestroy(&r);CHKERRQ(ierr); 487 ierr = VecDestroy(&ref);CHKERRQ(ierr); 488 ierr = VecDestroy(&real);CHKERRQ(ierr); 489 ierr = MatDestroy(&J);CHKERRQ(ierr); 490 PetscFunctionReturn(0); 491 } 492 493 #undef __FUNCT__ 494 #define __FUNCT__ "HexMap_Private" 495 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 496 { 497 const PetscScalar *vertices = (const PetscScalar*) ctx; 498 const PetscScalar x0 = vertices[0]; 499 const PetscScalar y0 = vertices[1]; 500 const PetscScalar z0 = vertices[2]; 501 const PetscScalar x1 = vertices[9]; 502 const PetscScalar y1 = vertices[10]; 503 const PetscScalar z1 = vertices[11]; 504 const PetscScalar x2 = vertices[6]; 505 const PetscScalar y2 = vertices[7]; 506 const PetscScalar z2 = vertices[8]; 507 const PetscScalar x3 = vertices[3]; 508 const PetscScalar y3 = vertices[4]; 509 const PetscScalar z3 = vertices[5]; 510 const PetscScalar x4 = vertices[12]; 511 const PetscScalar y4 = vertices[13]; 512 const PetscScalar z4 = vertices[14]; 513 const PetscScalar x5 = vertices[15]; 514 const PetscScalar y5 = vertices[16]; 515 const PetscScalar z5 = vertices[17]; 516 const PetscScalar x6 = vertices[18]; 517 const PetscScalar y6 = vertices[19]; 518 const PetscScalar z6 = vertices[20]; 519 const PetscScalar x7 = vertices[21]; 520 const PetscScalar y7 = vertices[22]; 521 const PetscScalar z7 = vertices[23]; 522 const PetscScalar f_1 = x1 - x0; 523 const PetscScalar g_1 = y1 - y0; 524 const PetscScalar h_1 = z1 - z0; 525 const PetscScalar f_3 = x3 - x0; 526 const PetscScalar g_3 = y3 - y0; 527 const PetscScalar h_3 = z3 - z0; 528 const PetscScalar f_4 = x4 - x0; 529 const PetscScalar g_4 = y4 - y0; 530 const PetscScalar h_4 = z4 - z0; 531 const PetscScalar f_01 = x2 - x1 - x3 + x0; 532 const PetscScalar g_01 = y2 - y1 - y3 + y0; 533 const PetscScalar h_01 = z2 - z1 - z3 + z0; 534 const PetscScalar f_12 = x7 - x3 - x4 + x0; 535 const PetscScalar g_12 = y7 - y3 - y4 + y0; 536 const PetscScalar h_12 = z7 - z3 - z4 + z0; 537 const PetscScalar f_02 = x5 - x1 - x4 + x0; 538 const PetscScalar g_02 = y5 - y1 - y4 + y0; 539 const PetscScalar h_02 = z5 - z1 - z4 + z0; 540 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 541 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 542 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 543 const PetscScalar *ref; 544 PetscScalar *real; 545 PetscErrorCode ierr; 546 547 PetscFunctionBegin; 548 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 549 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 550 { 551 const PetscScalar p0 = ref[0]; 552 const PetscScalar p1 = ref[1]; 553 const PetscScalar p2 = ref[2]; 554 555 real[0] = x0 + f_1*p0 + f_3*p1 + f_4*p2 + f_01*p0*p1 + f_12*p1*p2 + f_02*p0*p2 + f_012*p0*p1*p2; 556 real[1] = y0 + g_1*p0 + g_3*p1 + g_4*p2 + g_01*p0*p1 + g_01*p0*p1 + g_12*p1*p2 + g_02*p0*p2 + g_012*p0*p1*p2; 557 real[2] = z0 + h_1*p0 + h_3*p1 + h_4*p2 + h_01*p0*p1 + h_01*p0*p1 + h_12*p1*p2 + h_02*p0*p2 + h_012*p0*p1*p2; 558 } 559 ierr = PetscLogFlops(114);CHKERRQ(ierr); 560 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 561 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 562 PetscFunctionReturn(0); 563 } 564 565 #undef __FUNCT__ 566 #define __FUNCT__ "HexJacobian_Private" 567 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 568 { 569 const PetscScalar *vertices = (const PetscScalar*) ctx; 570 const PetscScalar x0 = vertices[0]; 571 const PetscScalar y0 = vertices[1]; 572 const PetscScalar z0 = vertices[2]; 573 const PetscScalar x1 = vertices[9]; 574 const PetscScalar y1 = vertices[10]; 575 const PetscScalar z1 = vertices[11]; 576 const PetscScalar x2 = vertices[6]; 577 const PetscScalar y2 = vertices[7]; 578 const PetscScalar z2 = vertices[8]; 579 const PetscScalar x3 = vertices[3]; 580 const PetscScalar y3 = vertices[4]; 581 const PetscScalar z3 = vertices[5]; 582 const PetscScalar x4 = vertices[12]; 583 const PetscScalar y4 = vertices[13]; 584 const PetscScalar z4 = vertices[14]; 585 const PetscScalar x5 = vertices[15]; 586 const PetscScalar y5 = vertices[16]; 587 const PetscScalar z5 = vertices[17]; 588 const PetscScalar x6 = vertices[18]; 589 const PetscScalar y6 = vertices[19]; 590 const PetscScalar z6 = vertices[20]; 591 const PetscScalar x7 = vertices[21]; 592 const PetscScalar y7 = vertices[22]; 593 const PetscScalar z7 = vertices[23]; 594 const PetscScalar f_xy = x2 - x1 - x3 + x0; 595 const PetscScalar g_xy = y2 - y1 - y3 + y0; 596 const PetscScalar h_xy = z2 - z1 - z3 + z0; 597 const PetscScalar f_yz = x7 - x3 - x4 + x0; 598 const PetscScalar g_yz = y7 - y3 - y4 + y0; 599 const PetscScalar h_yz = z7 - z3 - z4 + z0; 600 const PetscScalar f_xz = x5 - x1 - x4 + x0; 601 const PetscScalar g_xz = y5 - y1 - y4 + y0; 602 const PetscScalar h_xz = z5 - z1 - z4 + z0; 603 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 604 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 605 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 606 const PetscScalar *ref; 607 PetscErrorCode ierr; 608 609 PetscFunctionBegin; 610 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 611 { 612 const PetscScalar x = ref[0]; 613 const PetscScalar y = ref[1]; 614 const PetscScalar z = ref[2]; 615 const PetscInt rows[3] = {0, 1, 2}; 616 PetscScalar values[9]; 617 618 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 619 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 620 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 621 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 622 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 623 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 624 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 625 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 626 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 627 628 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 629 } 630 ierr = PetscLogFlops(152);CHKERRQ(ierr); 631 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 632 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 633 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 634 PetscFunctionReturn(0); 635 } 636 637 #undef __FUNCT__ 638 #define __FUNCT__ "DMInterpolate_Hex_Private" 639 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 640 { 641 DM dmCoord; 642 SNES snes; 643 KSP ksp; 644 PC pc; 645 Vec coordsLocal, r, ref, real; 646 Mat J; 647 const PetscScalar *coords; 648 PetscScalar *a; 649 PetscInt p; 650 PetscErrorCode ierr; 651 652 PetscFunctionBegin; 653 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 654 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 655 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 656 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 657 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 658 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 659 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 660 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 661 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 662 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 663 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 664 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 665 ierr = MatSetUp(J);CHKERRQ(ierr); 666 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 667 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 668 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 669 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 670 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 671 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 672 673 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 674 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 675 for (p = 0; p < ctx->n; ++p) { 676 PetscScalar *x = NULL, *vertices = NULL; 677 PetscScalar *xi; 678 PetscReal xir[3]; 679 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 680 681 /* Can make this do all points at once */ 682 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 683 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 8*3); 684 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 685 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 8*ctx->dof); 686 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 687 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 688 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 689 xi[0] = coords[p*ctx->dim+0]; 690 xi[1] = coords[p*ctx->dim+1]; 691 xi[2] = coords[p*ctx->dim+2]; 692 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 693 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 694 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 695 xir[0] = PetscRealPart(xi[0]); 696 xir[1] = PetscRealPart(xi[1]); 697 xir[2] = PetscRealPart(xi[2]); 698 for (comp = 0; comp < ctx->dof; ++comp) { 699 a[p*ctx->dof+comp] = 700 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 701 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 702 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 703 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 704 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 705 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 706 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 707 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 708 } 709 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 710 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 711 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 712 } 713 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 714 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 715 716 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 717 ierr = VecDestroy(&r);CHKERRQ(ierr); 718 ierr = VecDestroy(&ref);CHKERRQ(ierr); 719 ierr = VecDestroy(&real);CHKERRQ(ierr); 720 ierr = MatDestroy(&J);CHKERRQ(ierr); 721 PetscFunctionReturn(0); 722 } 723 724 #undef __FUNCT__ 725 #define __FUNCT__ "DMInterpolationEvaluate" 726 /* 727 Input Parameters: 728 + ctx - The DMInterpolationInfo context 729 . dm - The DM 730 - x - The local vector containing the field to be interpolated 731 732 Output Parameters: 733 . v - The vector containing the interpolated values 734 */ 735 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 736 { 737 PetscInt dim, coneSize, n; 738 PetscErrorCode ierr; 739 740 PetscFunctionBegin; 741 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 742 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 743 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 744 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 745 if (n != ctx->n*ctx->dof) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid input vector size %d should be %d", n, ctx->n*ctx->dof); 746 if (n) { 747 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 748 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 749 if (dim == 2) { 750 if (coneSize == 3) { 751 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 752 } else if (coneSize == 4) { 753 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 754 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 755 } else if (dim == 3) { 756 if (coneSize == 4) { 757 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 758 } else { 759 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 760 } 761 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 762 } 763 PetscFunctionReturn(0); 764 } 765 766 #undef __FUNCT__ 767 #define __FUNCT__ "DMInterpolationDestroy" 768 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 769 { 770 PetscErrorCode ierr; 771 772 PetscFunctionBegin; 773 PetscValidPointer(ctx, 2); 774 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 775 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 776 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 777 ierr = PetscFree(*ctx);CHKERRQ(ierr); 778 *ctx = NULL; 779 PetscFunctionReturn(0); 780 } 781 782 #undef __FUNCT__ 783 #define __FUNCT__ "SNESMonitorFields" 784 /*@C 785 SNESMonitorFields - Monitors the residual for each field separately 786 787 Collective on SNES 788 789 Input Parameters: 790 + snes - the SNES context 791 . its - iteration number 792 . fgnorm - 2-norm of residual 793 - vf - PetscViewerAndFormat of type ASCII 794 795 Notes: 796 This routine prints the residual norm at each iteration. 797 798 Level: intermediate 799 800 .keywords: SNES, nonlinear, default, monitor, norm 801 .seealso: SNESMonitorSet(), SNESMonitorDefault() 802 @*/ 803 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf) 804 { 805 PetscViewer viewer = vf->viewer; 806 Vec res; 807 DM dm; 808 PetscSection s; 809 const PetscScalar *r; 810 PetscReal *lnorms, *norms; 811 PetscInt numFields, f, pStart, pEnd, p; 812 PetscErrorCode ierr; 813 814 PetscFunctionBegin; 815 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4); 816 ierr = SNESGetFunction(snes, &res, 0, 0);CHKERRQ(ierr); 817 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 818 ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr); 819 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 820 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 821 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 822 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 823 for (p = pStart; p < pEnd; ++p) { 824 for (f = 0; f < numFields; ++f) { 825 PetscInt fdof, foff, d; 826 827 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 828 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 829 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 830 } 831 } 832 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 833 ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 834 ierr = PetscViewerPushFormat(viewer,vf->format);CHKERRQ(ierr); 835 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 836 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 837 for (f = 0; f < numFields; ++f) { 838 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 839 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 840 } 841 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 842 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 843 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 844 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 845 PetscFunctionReturn(0); 846 } 847 848 /********************* Residual Computation **************************/ 849 850 #undef __FUNCT__ 851 #define __FUNCT__ "DMPlexSNESGetGeometryFEM" 852 /*@ 853 DMPlexSNESGetGeometryFEM - Return precomputed geometric data 854 855 Input Parameter: 856 . dm - The DM 857 858 Output Parameters: 859 . cellgeom - The values precomputed from cell geometry 860 861 Level: developer 862 863 .seealso: DMPlexSNESSetFunctionLocal() 864 @*/ 865 PetscErrorCode DMPlexSNESGetGeometryFEM(DM dm, Vec *cellgeom) 866 { 867 DMSNES dmsnes; 868 PetscObject obj; 869 PetscErrorCode ierr; 870 871 PetscFunctionBegin; 872 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 873 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 874 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", &obj);CHKERRQ(ierr); 875 if (!obj) { 876 Vec cellgeom; 877 878 ierr = DMPlexComputeGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 879 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", (PetscObject) cellgeom);CHKERRQ(ierr); 880 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 881 } 882 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", (PetscObject *) cellgeom);CHKERRQ(ierr);} 883 PetscFunctionReturn(0); 884 } 885 886 #undef __FUNCT__ 887 #define __FUNCT__ "DMPlexSNESGetGeometryFVM" 888 /*@ 889 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 890 891 Input Parameter: 892 . dm - The DM 893 894 Output Parameters: 895 + facegeom - The values precomputed from face geometry 896 . cellgeom - The values precomputed from cell geometry 897 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 898 899 Level: developer 900 901 .seealso: DMPlexTSSetRHSFunctionLocal() 902 @*/ 903 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 904 { 905 DMSNES dmsnes; 906 PetscObject obj; 907 PetscErrorCode ierr; 908 909 PetscFunctionBegin; 910 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 911 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 912 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", &obj);CHKERRQ(ierr); 913 if (!obj) { 914 Vec cellgeom, facegeom; 915 916 ierr = DMPlexComputeGeometryFVM(dm, &cellgeom, &facegeom);CHKERRQ(ierr); 917 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject) facegeom);CHKERRQ(ierr); 918 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject) cellgeom);CHKERRQ(ierr); 919 ierr = VecDestroy(&facegeom);CHKERRQ(ierr); 920 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 921 } 922 if (facegeom) {PetscValidPointer(facegeom, 2); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject *) facegeom);CHKERRQ(ierr);} 923 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject *) cellgeom);CHKERRQ(ierr);} 924 if (minRadius) {ierr = DMPlexGetMinRadius(dm, minRadius);CHKERRQ(ierr);} 925 PetscFunctionReturn(0); 926 } 927 928 #undef __FUNCT__ 929 #define __FUNCT__ "DMPlexSNESGetGradientDM" 930 /*@ 931 DMPlexSNESGetGradientDM - Return gradient data layout 932 933 Input Parameters: 934 + dm - The DM 935 - fv - The PetscFV 936 937 Output Parameter: 938 . dmGrad - The layout for gradient values 939 940 Level: developer 941 942 .seealso: DMPlexSNESGetGeometryFVM() 943 @*/ 944 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 945 { 946 DMSNES dmsnes; 947 PetscObject obj; 948 PetscBool computeGradients; 949 PetscErrorCode ierr; 950 951 PetscFunctionBegin; 952 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 953 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 954 PetscValidPointer(dmGrad,3); 955 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 956 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 957 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 958 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", &obj);CHKERRQ(ierr); 959 if (!obj) { 960 DM dmGrad; 961 Vec faceGeometry, cellGeometry; 962 963 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometry, &cellGeometry, NULL);CHKERRQ(ierr); 964 ierr = DMPlexComputeGradientFVM(dm, fv, faceGeometry, cellGeometry, &dmGrad);CHKERRQ(ierr); 965 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject) dmGrad);CHKERRQ(ierr); 966 ierr = DMDestroy(&dmGrad);CHKERRQ(ierr); 967 } 968 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject *) dmGrad);CHKERRQ(ierr); 969 PetscFunctionReturn(0); 970 } 971 972 #undef __FUNCT__ 973 #define __FUNCT__ "DMPlexGetCellFields" 974 /*@C 975 DMPlexGetCellFields - Retrieve the field values values for a chunk of cells 976 977 Input Parameters: 978 + dm - The DM 979 . cStart - The first cell to include 980 . cEnd - The first cell to exclude 981 . locX - A local vector with the solution fields 982 . locX_t - A local vector with solution field time derivatives, or NULL 983 - locA - A local vector with auxiliary fields, or NULL 984 985 Output Parameters: 986 + u - The field coefficients 987 . u_t - The fields derivative coefficients 988 - a - The auxiliary field coefficients 989 990 Level: developer 991 992 .seealso: DMPlexGetFaceFields() 993 @*/ 994 PetscErrorCode DMPlexGetCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 995 { 996 DM dmAux; 997 PetscSection section, sectionAux; 998 PetscDS prob; 999 PetscInt numCells = cEnd - cStart, totDim, totDimAux, c; 1000 PetscErrorCode ierr; 1001 1002 PetscFunctionBegin; 1003 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1004 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1005 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1006 if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 6);} 1007 PetscValidPointer(u, 7); 1008 PetscValidPointer(u_t, 8); 1009 PetscValidPointer(a, 9); 1010 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1011 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1012 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1013 if (locA) { 1014 PetscDS probAux; 1015 1016 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1017 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1018 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1019 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1020 } 1021 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u);CHKERRQ(ierr); 1022 if (locX_t) {ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u_t);CHKERRQ(ierr);} else {*u_t = NULL;} 1023 if (locA) {ierr = DMGetWorkArray(dm, numCells*totDimAux, PETSC_SCALAR, a);CHKERRQ(ierr);} else {*a = NULL;} 1024 for (c = cStart; c < cEnd; ++c) { 1025 PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; 1026 PetscInt i; 1027 1028 ierr = DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 1029 for (i = 0; i < totDim; ++i) ul[(c-cStart)*totDim+i] = x[i]; 1030 ierr = DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 1031 if (locX_t) { 1032 ierr = DMPlexVecGetClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 1033 for (i = 0; i < totDim; ++i) ul_t[(c-cStart)*totDim+i] = x_t[i]; 1034 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 1035 } 1036 if (locA) { 1037 DM dmAuxPlex; 1038 1039 ierr = DMSNESConvertPlex(dmAux, &dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 1040 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1041 for (i = 0; i < totDimAux; ++i) al[(c-cStart)*totDimAux+i] = x[i]; 1042 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1043 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 1044 } 1045 } 1046 PetscFunctionReturn(0); 1047 } 1048 1049 #undef __FUNCT__ 1050 #define __FUNCT__ "DMPlexRestoreCellFields" 1051 /*@C 1052 DMPlexRestoreCellFields - Restore the field values values for a chunk of cells 1053 1054 Input Parameters: 1055 + dm - The DM 1056 . cStart - The first cell to include 1057 . cEnd - The first cell to exclude 1058 . locX - A local vector with the solution fields 1059 . locX_t - A local vector with solution field time derivatives, or NULL 1060 - locA - A local vector with auxiliary fields, or NULL 1061 1062 Output Parameters: 1063 + u - The field coefficients 1064 . u_t - The fields derivative coefficients 1065 - a - The auxiliary field coefficients 1066 1067 Level: developer 1068 1069 .seealso: DMPlexGetFaceFields() 1070 @*/ 1071 PetscErrorCode DMPlexRestoreCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 1072 { 1073 PetscErrorCode ierr; 1074 1075 PetscFunctionBegin; 1076 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u);CHKERRQ(ierr); 1077 if (*u_t) {ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u_t);CHKERRQ(ierr);} 1078 if (*a) {ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, a);CHKERRQ(ierr);} 1079 PetscFunctionReturn(0); 1080 } 1081 1082 #undef __FUNCT__ 1083 #define __FUNCT__ "DMPlexGetFaceFields" 1084 /*@C 1085 DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces 1086 1087 Input Parameters: 1088 + dm - The DM 1089 . fStart - The first face to include 1090 . fEnd - The first face to exclude 1091 . locX - A local vector with the solution fields 1092 . locX_t - A local vector with solution field time derivatives, or NULL 1093 . faceGeometry - A local vector with face geometry 1094 . cellGeometry - A local vector with cell geometry 1095 - locaGrad - A local vector with field gradients, or NULL 1096 1097 Output Parameters: 1098 + uL - The field values at the left side of the face 1099 - uR - The field values at the right side of the face 1100 1101 Level: developer 1102 1103 .seealso: DMPlexGetCellFields() 1104 @*/ 1105 PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1106 { 1107 DM dmFace, dmCell, dmGrad = NULL; 1108 PetscSection section; 1109 PetscDS prob; 1110 DMLabel ghostLabel; 1111 const PetscScalar *facegeom, *cellgeom, *x, *lgrad; 1112 PetscBool *isFE; 1113 PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; 1114 PetscErrorCode ierr; 1115 1116 PetscFunctionBegin; 1117 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1118 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1119 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1120 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); 1121 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); 1122 if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} 1123 PetscValidPointer(uL, 9); 1124 PetscValidPointer(uR, 10); 1125 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1126 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1127 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1128 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1129 ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); 1130 ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); 1131 for (f = 0; f < Nf; ++f) { 1132 PetscObject obj; 1133 PetscClassId id; 1134 1135 ierr = DMGetField(dm, f, &obj);CHKERRQ(ierr); 1136 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1137 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 1138 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 1139 else {isFE[f] = PETSC_FALSE;} 1140 } 1141 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1142 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1143 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1144 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1145 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1146 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1147 if (locGrad) { 1148 ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); 1149 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1150 } 1151 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uL);CHKERRQ(ierr); 1152 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uR);CHKERRQ(ierr); 1153 /* Right now just eat the extra work for FE (could make a cell loop) */ 1154 for (face = fStart, iface = 0; face < fEnd; ++face) { 1155 const PetscInt *cells; 1156 PetscFVFaceGeom *fg; 1157 PetscFVCellGeom *cgL, *cgR; 1158 PetscScalar *xL, *xR, *gL, *gR; 1159 PetscScalar *uLl = *uL, *uRl = *uR; 1160 PetscInt ghost, nsupp; 1161 1162 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1163 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1164 if (ghost >= 0) continue; 1165 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1166 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1167 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1168 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1169 for (f = 0; f < Nf; ++f) { 1170 PetscInt off; 1171 1172 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1173 if (isFE[f]) { 1174 const PetscInt *cone; 1175 PetscInt comp, coneSize, faceLocL, faceLocR, ldof, rdof, d; 1176 1177 xL = xR = NULL; 1178 ierr = DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1179 ierr = DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1180 ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); 1181 ierr = DMPlexGetConeSize(dm, cells[0], &coneSize);CHKERRQ(ierr); 1182 for (faceLocL = 0; faceLocL < coneSize; ++faceLocL) if (cone[faceLocL] == face) break; 1183 if (faceLocL == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[0]); 1184 ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); 1185 ierr = DMPlexGetConeSize(dm, cells[1], &coneSize);CHKERRQ(ierr); 1186 for (faceLocR = 0; faceLocR < coneSize; ++faceLocR) if (cone[faceLocR] == face) break; 1187 if (faceLocR == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[1]); 1188 /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */ 1189 ierr = EvaluateFaceFields(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); 1190 if (rdof == ldof) {ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr);} 1191 else {ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); for(d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];} 1192 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1193 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1194 } else { 1195 PetscFV fv; 1196 PetscInt numComp, c; 1197 1198 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); 1199 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1200 if (nsupp > 2) { 1201 for (f = 0; f < Nf; ++f) { 1202 PetscInt off; 1203 1204 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1205 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1206 for (c = 0; c < numComp; ++c) { 1207 uLl[iface*Nc+off+c] = 0.; 1208 uRl[iface*Nc+off+c] = 0.; 1209 } 1210 } 1211 continue; 1212 } 1213 ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); 1214 ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); 1215 if (dmGrad) { 1216 PetscReal dxL[3], dxR[3]; 1217 1218 ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); 1219 ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); 1220 DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); 1221 DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); 1222 for (c = 0; c < numComp; ++c) { 1223 uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); 1224 uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); 1225 } 1226 } else { 1227 for (c = 0; c < numComp; ++c) { 1228 uLl[iface*Nc+off+c] = xL[c]; 1229 uRl[iface*Nc+off+c] = xR[c]; 1230 } 1231 } 1232 } 1233 } 1234 ++iface; 1235 } 1236 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1237 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1238 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1239 if (locGrad) { 1240 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1241 } 1242 ierr = PetscFree(isFE);CHKERRQ(ierr); 1243 PetscFunctionReturn(0); 1244 } 1245 1246 #undef __FUNCT__ 1247 #define __FUNCT__ "DMPlexRestoreFaceFields" 1248 /*@C 1249 DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces 1250 1251 Input Parameters: 1252 + dm - The DM 1253 . fStart - The first face to include 1254 . fEnd - The first face to exclude 1255 . locX - A local vector with the solution fields 1256 . locX_t - A local vector with solution field time derivatives, or NULL 1257 . faceGeometry - A local vector with face geometry 1258 . cellGeometry - A local vector with cell geometry 1259 - locaGrad - A local vector with field gradients, or NULL 1260 1261 Output Parameters: 1262 + uL - The field values at the left side of the face 1263 - uR - The field values at the right side of the face 1264 1265 Level: developer 1266 1267 .seealso: DMPlexGetFaceFields() 1268 @*/ 1269 PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1270 { 1271 PetscErrorCode ierr; 1272 1273 PetscFunctionBegin; 1274 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uL);CHKERRQ(ierr); 1275 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uR);CHKERRQ(ierr); 1276 PetscFunctionReturn(0); 1277 } 1278 1279 #undef __FUNCT__ 1280 #define __FUNCT__ "DMPlexGetFaceGeometry" 1281 /*@C 1282 DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces 1283 1284 Input Parameters: 1285 + dm - The DM 1286 . fStart - The first face to include 1287 . fEnd - The first face to exclude 1288 . faceGeometry - A local vector with face geometry 1289 - cellGeometry - A local vector with cell geometry 1290 1291 Output Parameters: 1292 + fgeom - The extract the face centroid and normal 1293 - vol - The cell volume 1294 1295 Level: developer 1296 1297 .seealso: DMPlexGetCellFields() 1298 @*/ 1299 PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1300 { 1301 DM dmFace, dmCell; 1302 DMLabel ghostLabel; 1303 const PetscScalar *facegeom, *cellgeom; 1304 PetscInt dim, numFaces = fEnd - fStart, iface, face; 1305 PetscErrorCode ierr; 1306 1307 PetscFunctionBegin; 1308 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1309 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); 1310 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); 1311 PetscValidPointer(fgeom, 6); 1312 PetscValidPointer(vol, 7); 1313 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1314 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1315 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1316 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1317 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1318 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1319 ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); 1320 ierr = DMGetWorkArray(dm, numFaces*2, PETSC_SCALAR, vol);CHKERRQ(ierr); 1321 for (face = fStart, iface = 0; face < fEnd; ++face) { 1322 const PetscInt *cells; 1323 PetscFVFaceGeom *fg; 1324 PetscFVCellGeom *cgL, *cgR; 1325 PetscFVFaceGeom *fgeoml = *fgeom; 1326 PetscReal *voll = *vol; 1327 PetscInt ghost, d; 1328 1329 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1330 if (ghost >= 0) continue; 1331 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1332 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1333 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1334 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1335 for (d = 0; d < dim; ++d) { 1336 fgeoml[iface].centroid[d] = fg->centroid[d]; 1337 fgeoml[iface].normal[d] = fg->normal[d]; 1338 } 1339 voll[iface*2+0] = cgL->volume; 1340 voll[iface*2+1] = cgR->volume; 1341 ++iface; 1342 } 1343 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1344 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1345 PetscFunctionReturn(0); 1346 } 1347 1348 #undef __FUNCT__ 1349 #define __FUNCT__ "DMPlexRestoreFaceGeometry" 1350 /*@C 1351 DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces 1352 1353 Input Parameters: 1354 + dm - The DM 1355 . fStart - The first face to include 1356 . fEnd - The first face to exclude 1357 . faceGeometry - A local vector with face geometry 1358 - cellGeometry - A local vector with cell geometry 1359 1360 Output Parameters: 1361 + fgeom - The extract the face centroid and normal 1362 - vol - The cell volume 1363 1364 Level: developer 1365 1366 .seealso: DMPlexGetFaceFields() 1367 @*/ 1368 PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1369 { 1370 PetscErrorCode ierr; 1371 1372 PetscFunctionBegin; 1373 ierr = PetscFree(*fgeom);CHKERRQ(ierr); 1374 ierr = DMRestoreWorkArray(dm, 0, PETSC_REAL, vol);CHKERRQ(ierr); 1375 PetscFunctionReturn(0); 1376 } 1377 1378 #undef __FUNCT__ 1379 #define __FUNCT__ "DMPlexApplyLimiter_Internal" 1380 static PetscErrorCode DMPlexApplyLimiter_Internal (DM dm, DM dmCell, PetscLimiter lim, PetscInt dim, PetscInt totDim, PetscInt cell, PetscInt face, PetscInt fStart, PetscInt fEnd, PetscReal *cellPhi, const PetscScalar *x, 1381 const PetscScalar *cellgeom, const PetscFVCellGeom *cg, const PetscScalar *cx, const PetscScalar *cgrad) 1382 { 1383 const PetscInt *children; 1384 PetscInt numChildren; 1385 PetscErrorCode ierr; 1386 1387 PetscFunctionBegin; 1388 ierr = DMPlexGetTreeChildren(dm,face,&numChildren,&children);CHKERRQ(ierr); 1389 if (numChildren) { 1390 PetscInt c; 1391 1392 for (c = 0; c < numChildren; c++) { 1393 PetscInt childFace = children[c]; 1394 1395 if (childFace >= fStart && childFace < fEnd) { 1396 ierr = DMPlexApplyLimiter_Internal(dm,dmCell,lim,dim,totDim,cell,childFace,fStart,fEnd,cellPhi,x,cellgeom,cg,cx,cgrad);CHKERRQ(ierr); 1397 } 1398 } 1399 } 1400 else { 1401 PetscScalar *ncx; 1402 PetscFVCellGeom *ncg; 1403 const PetscInt *fcells; 1404 PetscInt ncell, d; 1405 PetscReal v[3]; 1406 1407 ierr = DMPlexGetSupport(dm, face, &fcells);CHKERRQ(ierr); 1408 ncell = cell == fcells[0] ? fcells[1] : fcells[0]; 1409 ierr = DMPlexPointLocalRead(dm, ncell, x, &ncx);CHKERRQ(ierr); 1410 ierr = DMPlexPointLocalRead(dmCell, ncell, cellgeom, &ncg);CHKERRQ(ierr); 1411 DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, ncg->centroid, v); 1412 for (d = 0; d < totDim; ++d) { 1413 /* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */ 1414 PetscReal phi, flim = 0.5 * PetscRealPart(ncx[d] - cx[d]) / DMPlex_DotD_Internal(dim, &cgrad[d*dim], v); 1415 1416 ierr = PetscLimiterLimit(lim, flim, &phi);CHKERRQ(ierr); 1417 cellPhi[d] = PetscMin(cellPhi[d], phi); 1418 } 1419 } 1420 PetscFunctionReturn(0); 1421 } 1422 1423 #undef __FUNCT__ 1424 #define __FUNCT__ "DMPlexReconstructGradients_Internal" 1425 PetscErrorCode DMPlexReconstructGradients_Internal(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, Vec locX, Vec grad) 1426 { 1427 DM dmFace, dmCell, dmGrad; 1428 DMLabel ghostLabel; 1429 PetscDS prob; 1430 PetscFV fvm; 1431 PetscLimiter lim; 1432 const PetscScalar *facegeom, *cellgeom, *x; 1433 PetscScalar *gr; 1434 PetscReal *cellPhi; 1435 PetscInt dim, face, cell, totDim, cStart, cEnd, cEndInterior; 1436 PetscErrorCode ierr; 1437 1438 PetscFunctionBegin; 1439 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1440 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1441 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1442 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1443 ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fvm);CHKERRQ(ierr); 1444 ierr = PetscFVGetLimiter(fvm, &lim);CHKERRQ(ierr); 1445 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1446 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1447 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1448 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1449 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1450 ierr = VecGetDM(grad, &dmGrad);CHKERRQ(ierr); 1451 ierr = VecZeroEntries(grad);CHKERRQ(ierr); 1452 ierr = VecGetArray(grad, &gr);CHKERRQ(ierr); 1453 /* Reconstruct gradients */ 1454 for (face = fStart; face < fEnd; ++face) { 1455 const PetscInt *cells; 1456 PetscFVFaceGeom *fg; 1457 PetscScalar *cx[2]; 1458 PetscScalar *cgrad[2]; 1459 PetscBool boundary; 1460 PetscInt ghost, c, pd, d, numChildren, numCells; 1461 1462 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1463 ierr = DMIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr); 1464 ierr = DMPlexGetTreeChildren(dm, face, &numChildren, NULL);CHKERRQ(ierr); 1465 if (ghost >= 0 || boundary || numChildren) continue; 1466 ierr = DMPlexGetSupportSize(dm, face, &numCells);CHKERRQ(ierr); 1467 if (numCells != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "facet %d has %d support points: expected 2",face,numCells); 1468 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1469 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1470 for (c = 0; c < 2; ++c) { 1471 ierr = DMPlexPointLocalRead(dm, cells[c], x, &cx[c]);CHKERRQ(ierr); 1472 ierr = DMPlexPointGlobalRef(dmGrad, cells[c], gr, &cgrad[c]);CHKERRQ(ierr); 1473 } 1474 for (pd = 0; pd < totDim; ++pd) { 1475 PetscScalar delta = cx[1][pd] - cx[0][pd]; 1476 1477 for (d = 0; d < dim; ++d) { 1478 if (cgrad[0]) cgrad[0][pd*dim+d] += fg->grad[0][d] * delta; 1479 if (cgrad[1]) cgrad[1][pd*dim+d] -= fg->grad[1][d] * delta; 1480 } 1481 } 1482 } 1483 /* Limit interior gradients (using cell-based loop because it generalizes better to vector limiters) */ 1484 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1485 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1486 cEndInterior = cEndInterior < 0 ? cEnd : cEndInterior; 1487 ierr = DMGetWorkArray(dm, totDim, PETSC_REAL, &cellPhi);CHKERRQ(ierr); 1488 for (cell = dmGrad && lim ? cStart : cEnd; cell < cEndInterior; ++cell) { 1489 const PetscInt *faces; 1490 PetscScalar *cx; 1491 PetscFVCellGeom *cg; 1492 PetscScalar *cgrad; 1493 PetscInt coneSize, f, pd, d; 1494 1495 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1496 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 1497 ierr = DMPlexPointLocalRead(dm, cell, x, &cx);CHKERRQ(ierr); 1498 ierr = DMPlexPointLocalRead(dmCell, cell, cellgeom, &cg);CHKERRQ(ierr); 1499 ierr = DMPlexPointGlobalRef(dmGrad, cell, gr, &cgrad);CHKERRQ(ierr); 1500 if (!cgrad) continue; /* Unowned overlap cell, we do not compute */ 1501 /* Limiter will be minimum value over all neighbors */ 1502 for (d = 0; d < totDim; ++d) cellPhi[d] = PETSC_MAX_REAL; 1503 for (f = 0; f < coneSize; ++f) { 1504 ierr = DMPlexApplyLimiter_Internal(dm,dmCell,lim,dim,totDim,cell,faces[f],fStart,fEnd,cellPhi,x,cellgeom,cg,cx,cgrad);CHKERRQ(ierr); 1505 } 1506 /* Apply limiter to gradient */ 1507 for (pd = 0; pd < totDim; ++pd) 1508 /* Scalar limiter applied to each component separately */ 1509 for (d = 0; d < dim; ++d) cgrad[pd*dim+d] *= cellPhi[pd]; 1510 } 1511 ierr = DMRestoreWorkArray(dm, totDim, PETSC_REAL, &cellPhi);CHKERRQ(ierr); 1512 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1513 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1514 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1515 ierr = VecRestoreArray(grad, &gr);CHKERRQ(ierr); 1516 PetscFunctionReturn(0); 1517 } 1518 1519 #undef __FUNCT__ 1520 #define __FUNCT__ "DMPlexComputeBdResidual_Internal" 1521 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, Vec locF, void *user) 1522 { 1523 DM_Plex *mesh = (DM_Plex *) dm->data; 1524 PetscSection section; 1525 PetscDS prob; 1526 DMLabel depth; 1527 PetscFECellGeom *cgeom; 1528 PetscScalar *u = NULL, *u_t = NULL, *elemVec = NULL; 1529 PetscInt dim, Nf, f, totDimBd, numBd, bd; 1530 PetscErrorCode ierr; 1531 1532 PetscFunctionBegin; 1533 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1534 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1535 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1536 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1537 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 1538 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1539 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1540 for (bd = 0; bd < numBd; ++bd) { 1541 const char *bdLabel; 1542 DMLabel label; 1543 IS pointIS; 1544 const PetscInt *points; 1545 const PetscInt *values; 1546 PetscInt field, numValues, numPoints, p, dep, numFaces; 1547 PetscBool isEssential; 1548 PetscObject obj; 1549 PetscClassId id; 1550 1551 ierr = DMGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1552 ierr = DMGetField(dm, field, &obj);CHKERRQ(ierr); 1553 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1554 if ((id != PETSCFE_CLASSID) || isEssential) continue; 1555 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 1556 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1557 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 1558 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 1559 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1560 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1561 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1562 if (dep == dim-1) ++numFaces; 1563 } 1564 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd,&elemVec);CHKERRQ(ierr); 1565 if (locX_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 1566 for (p = 0, f = 0; p < numPoints; ++p) { 1567 const PetscInt point = points[p]; 1568 PetscScalar *x = NULL; 1569 PetscInt i; 1570 1571 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1572 if (dep != dim-1) continue; 1573 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 1574 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n);CHKERRQ(ierr); 1575 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 1576 /* TODO: Matt, this is wrong if feBd does not match fe: i.e., if the order differs. */ 1577 ierr = DMPlexVecGetClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1578 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 1579 ierr = DMPlexVecRestoreClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1580 if (locX_t) { 1581 ierr = DMPlexVecGetClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1582 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 1583 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1584 } 1585 ++f; 1586 } 1587 for (f = 0; f < Nf; ++f) { 1588 PetscFE fe; 1589 PetscQuadrature q; 1590 PetscInt numQuadPoints, Nb; 1591 /* Conforming batches */ 1592 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1593 /* Remainder */ 1594 PetscInt Nr, offset; 1595 1596 ierr = PetscDSGetBdDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1597 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1598 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1599 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1600 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1601 blockSize = Nb*numQuadPoints; 1602 batchSize = numBlocks * blockSize; 1603 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1604 numChunks = numFaces / (numBatches*batchSize); 1605 Ne = numChunks*numBatches*batchSize; 1606 Nr = numFaces % (numBatches*batchSize); 1607 offset = numFaces - Nr; 1608 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Ne, cgeom, u, u_t, NULL, NULL, elemVec);CHKERRQ(ierr); 1609 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Nr, &cgeom[offset], &u[offset*totDimBd], u_t ? &u_t[offset*totDimBd] : NULL, NULL, NULL, &elemVec[offset*totDimBd]);CHKERRQ(ierr); 1610 } 1611 for (p = 0, f = 0; p < numPoints; ++p) { 1612 const PetscInt point = points[p]; 1613 1614 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1615 if (dep != dim-1) continue; 1616 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDimBd, &elemVec[f*totDimBd]);CHKERRQ(ierr);} 1617 ierr = DMPlexVecSetClosure(dm, NULL, locF, point, &elemVec[f*totDimBd], ADD_ALL_VALUES);CHKERRQ(ierr); 1618 ++f; 1619 } 1620 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1621 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1622 ierr = PetscFree3(u,cgeom,elemVec);CHKERRQ(ierr); 1623 if (locX_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 1624 } 1625 PetscFunctionReturn(0); 1626 } 1627 1628 #undef __FUNCT__ 1629 #define __FUNCT__ "DMPlexReconstructGradientsFVM" 1630 /*@ 1631 DMPlexReconstructGradientsFVM - reconstruct the gradient of a vector using a finite volume method. 1632 1633 Input Parameters: 1634 + dm - the mesh 1635 - locX - the local representation of the vector 1636 1637 Output Parameter: 1638 . grad - the global representation of the gradient 1639 1640 Level: developer 1641 1642 .seealso: DMPlexSNESGetGradientDM() 1643 @*/ 1644 PetscErrorCode DMPlexReconstructGradientsFVM(DM dm, Vec locX, Vec grad) 1645 { 1646 PetscDS prob; 1647 PetscInt Nf, f, fStart, fEnd; 1648 PetscBool useFVM; 1649 PetscFV fvm = NULL; 1650 Vec faceGeometryFVM, cellGeometryFVM; 1651 PetscFVCellGeom *cgeomFVM = NULL; 1652 PetscFVFaceGeom *fgeomFVM = NULL; 1653 DM dmGrad = NULL; 1654 PetscErrorCode ierr; 1655 1656 PetscFunctionBegin; 1657 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1658 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1659 for (f = 0; f < Nf; ++f) { 1660 PetscObject obj; 1661 PetscClassId id; 1662 1663 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1664 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1665 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1666 } 1667 if (!useFVM) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"This dm does not have a finite volume discretization"); 1668 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1669 if (!dmGrad) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"This dm's finite volume discretization does not reconstruct gradients"); 1670 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1671 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1672 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1673 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1674 ierr = DMPlexReconstructGradients_Internal(dm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1675 PetscFunctionReturn(0); 1676 } 1677 1678 #undef __FUNCT__ 1679 #define __FUNCT__ "DMPlexComputeResidual_Internal" 1680 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, PetscInt cStart, PetscInt cEnd, PetscReal time, Vec locX, Vec locX_t, Vec locF, void *user) 1681 { 1682 DM_Plex *mesh = (DM_Plex *) dm->data; 1683 const char *name = "Residual"; 1684 DM dmAux = NULL; 1685 DM dmGrad = NULL; 1686 DMLabel ghostLabel = NULL; 1687 PetscDS prob = NULL; 1688 PetscDS probAux = NULL; 1689 PetscSection section = NULL; 1690 PetscBool useFEM = PETSC_FALSE; 1691 PetscBool useFVM = PETSC_FALSE; 1692 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1693 PetscFV fvm = NULL; 1694 PetscFECellGeom *cgeomFEM = NULL; 1695 PetscScalar *cgeomScal; 1696 PetscFVCellGeom *cgeomFVM = NULL; 1697 PetscFVFaceGeom *fgeomFVM = NULL; 1698 Vec locA, cellGeometryFEM = NULL, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1699 PetscScalar *u, *u_t, *a, *uL, *uR; 1700 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1701 PetscErrorCode ierr; 1702 1703 PetscFunctionBegin; 1704 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1705 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1706 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1707 /* FEM+FVM */ 1708 /* 1: Get sizes from dm and dmAux */ 1709 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1710 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1711 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1712 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1713 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1714 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1715 if (locA) { 1716 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1717 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1718 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1719 } 1720 /* 2: Get geometric data */ 1721 for (f = 0; f < Nf; ++f) { 1722 PetscObject obj; 1723 PetscClassId id; 1724 PetscBool fimp; 1725 1726 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1727 if (isImplicit != fimp) continue; 1728 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1729 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1730 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1731 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1732 } 1733 if (useFEM) { 1734 ierr = DMPlexSNESGetGeometryFEM(dm, &cellGeometryFEM);CHKERRQ(ierr); 1735 ierr = VecGetArray(cellGeometryFEM, &cgeomScal);CHKERRQ(ierr); 1736 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1737 DM dmCell; 1738 PetscInt c; 1739 1740 ierr = VecGetDM(cellGeometryFEM,&dmCell);CHKERRQ(ierr); 1741 ierr = PetscMalloc1(cEnd-cStart,&cgeomFEM);CHKERRQ(ierr); 1742 for (c = 0; c < cEnd - cStart; c++) { 1743 PetscScalar *thisgeom; 1744 1745 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 1746 cgeomFEM[c] = *((PetscFECellGeom *) thisgeom); 1747 } 1748 } 1749 else { 1750 cgeomFEM = (PetscFECellGeom *) cgeomScal; 1751 } 1752 } 1753 if (useFVM) { 1754 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1755 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1756 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1757 /* Reconstruct and limit cell gradients */ 1758 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1759 if (dmGrad) { 1760 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1761 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1762 ierr = DMPlexReconstructGradients_Internal(dm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1763 /* Communicate gradient values */ 1764 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1765 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1766 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1767 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1768 } 1769 /* Handle non-essential (e.g. outflow) boundary values */ 1770 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1771 } 1772 /* Loop over chunks */ 1773 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1774 numChunks = 1; 1775 cellChunkSize = (cEnd - cStart)/numChunks; 1776 faceChunkSize = (fEnd - fStart)/numChunks; 1777 for (chunk = 0; chunk < numChunks; ++chunk) { 1778 PetscScalar *elemVec, *fluxL, *fluxR; 1779 PetscReal *vol; 1780 PetscFVFaceGeom *fgeom; 1781 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, cell; 1782 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = fE - fS, face; 1783 1784 /* Extract field coefficients */ 1785 if (useFEM) { 1786 ierr = DMPlexGetCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1787 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1788 ierr = PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1789 } 1790 if (useFVM) { 1791 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1792 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1793 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1794 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1795 ierr = PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1796 ierr = PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1797 } 1798 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1799 /* Loop over fields */ 1800 for (f = 0; f < Nf; ++f) { 1801 PetscObject obj; 1802 PetscClassId id; 1803 PetscBool fimp; 1804 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1805 1806 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1807 if (isImplicit != fimp) continue; 1808 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1809 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1810 if (id == PETSCFE_CLASSID) { 1811 PetscFE fe = (PetscFE) obj; 1812 PetscQuadrature q; 1813 PetscInt Nq, Nb; 1814 1815 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1816 1817 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1818 ierr = PetscQuadratureGetData(q, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1819 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1820 blockSize = Nb*Nq; 1821 batchSize = numBlocks * blockSize; 1822 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1823 numChunks = numCells / (numBatches*batchSize); 1824 Ne = numChunks*numBatches*batchSize; 1825 Nr = numCells % (numBatches*batchSize); 1826 offset = numCells - Nr; 1827 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1828 /* For FV, I think we use a P0 basis and the cell coefficients (for subdivided cells, we can tweak the basis tabulation to be the indicator function) */ 1829 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeomFEM, u, u_t, probAux, a, elemVec);CHKERRQ(ierr); 1830 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, &cgeomFEM[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemVec[offset*totDim]);CHKERRQ(ierr); 1831 } else if (id == PETSCFV_CLASSID) { 1832 PetscFV fv = (PetscFV) obj; 1833 1834 Ne = numFaces; 1835 Nr = 0; 1836 /* Riemann solve over faces (need fields at face centroids) */ 1837 /* We need to evaluate FE fields at those coordinates */ 1838 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1839 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f); 1840 } 1841 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1842 ierr = PetscFree(cgeomFEM);CHKERRQ(ierr); 1843 } 1844 else { 1845 cgeomFEM = NULL; 1846 } 1847 if (cellGeometryFEM) {ierr = VecRestoreArray(cellGeometryFEM, &cgeomScal);CHKERRQ(ierr);} 1848 /* Loop over domain */ 1849 if (useFEM) { 1850 /* Add elemVec to locX */ 1851 for (cell = cS; cell < cE; ++cell) { 1852 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cell*totDim]);CHKERRQ(ierr);} 1853 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cell*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1854 } 1855 } 1856 if (useFVM) { 1857 PetscScalar *fa; 1858 PetscInt iface; 1859 1860 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1861 for (f = 0; f < Nf; ++f) { 1862 PetscFV fv; 1863 PetscObject obj; 1864 PetscClassId id; 1865 PetscInt foff, pdim; 1866 1867 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1868 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1869 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1870 if (id != PETSCFV_CLASSID) continue; 1871 fv = (PetscFV) obj; 1872 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1873 /* Accumulate fluxes to cells */ 1874 for (face = fS, iface = 0; face < fE; ++face) { 1875 const PetscInt *cells; 1876 PetscScalar *fL, *fR; 1877 PetscInt ghost, d, nsupp; 1878 1879 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1880 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1881 if (ghost >= 0) continue; 1882 if (nsupp > 2) { /* noop */ 1883 ++iface; 1884 continue; 1885 } 1886 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1887 ierr = DMPlexPointGlobalFieldRef(dm, cells[0], f, fa, &fL);CHKERRQ(ierr); 1888 ierr = DMPlexPointGlobalFieldRef(dm, cells[1], f, fa, &fR);CHKERRQ(ierr); 1889 for (d = 0; d < pdim; ++d) { 1890 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1891 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1892 } 1893 ++iface; 1894 } 1895 } 1896 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1897 } 1898 /* Handle time derivative */ 1899 if (locX_t) { 1900 PetscScalar *x_t, *fa; 1901 1902 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1903 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1904 for (f = 0; f < Nf; ++f) { 1905 PetscFV fv; 1906 PetscObject obj; 1907 PetscClassId id; 1908 PetscInt pdim, d; 1909 1910 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1911 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1912 if (id != PETSCFV_CLASSID) continue; 1913 fv = (PetscFV) obj; 1914 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1915 for (cell = cS; cell < cE; ++cell) { 1916 PetscScalar *u_t, *r; 1917 1918 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1919 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1920 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1921 } 1922 } 1923 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1924 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1925 } 1926 if (useFEM) { 1927 ierr = DMPlexRestoreCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1928 ierr = DMRestoreWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1929 } 1930 if (useFVM) { 1931 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1932 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1933 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1934 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1935 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1936 } 1937 } 1938 1939 if (useFEM) {ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, locF, user);CHKERRQ(ierr);} 1940 1941 /* FEM */ 1942 /* 1: Get sizes from dm and dmAux */ 1943 /* 2: Get geometric data */ 1944 /* 3: Handle boundary values */ 1945 /* 4: Loop over domain */ 1946 /* Extract coefficients */ 1947 /* Loop over fields */ 1948 /* Set tiling for FE*/ 1949 /* Integrate FE residual to get elemVec */ 1950 /* Loop over subdomain */ 1951 /* Loop over quad points */ 1952 /* Transform coords to real space */ 1953 /* Evaluate field and aux fields at point */ 1954 /* Evaluate residual at point */ 1955 /* Transform residual to real space */ 1956 /* Add residual to elemVec */ 1957 /* Loop over domain */ 1958 /* Add elemVec to locX */ 1959 1960 /* FVM */ 1961 /* Get geometric data */ 1962 /* If using gradients */ 1963 /* Compute gradient data */ 1964 /* Loop over domain faces */ 1965 /* Count computational faces */ 1966 /* Reconstruct cell gradient */ 1967 /* Loop over domain cells */ 1968 /* Limit cell gradients */ 1969 /* Handle boundary values */ 1970 /* Loop over domain faces */ 1971 /* Read out field, centroid, normal, volume for each side of face */ 1972 /* Riemann solve over faces */ 1973 /* Loop over domain faces */ 1974 /* Accumulate fluxes to cells */ 1975 /* TODO Change printFEM to printDisc here */ 1976 if (mesh->printFEM) { 1977 Vec locFbc; 1978 PetscInt pStart, pEnd, p, maxDof; 1979 PetscScalar *zeroes; 1980 1981 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1982 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1983 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1984 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1985 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1986 for (p = pStart; p < pEnd; p++) { 1987 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1988 } 1989 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1990 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1991 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1992 } 1993 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1994 PetscFunctionReturn(0); 1995 } 1996 1997 #undef __FUNCT__ 1998 #define __FUNCT__ "DMPlexComputeResidualFEM_Check_Internal" 1999 static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, Vec F, void *user) 2000 { 2001 DM dmCh, dmAux; 2002 Vec A, cellgeom; 2003 PetscDS prob, probCh, probAux = NULL; 2004 PetscQuadrature q; 2005 PetscSection section, sectionAux; 2006 PetscFECellGeom *cgeom = NULL; 2007 PetscScalar *cgeomScal; 2008 PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL; 2009 PetscInt dim, Nf, f, numCells, cStart, cEnd, c; 2010 PetscInt totDim, totDimAux, diffCell = 0; 2011 PetscErrorCode ierr; 2012 2013 PetscFunctionBegin; 2014 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2015 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2016 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2017 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2018 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2019 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2020 numCells = cEnd - cStart; 2021 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);CHKERRQ(ierr); 2022 ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); 2023 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2024 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2025 if (dmAux) { 2026 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 2027 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2028 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2029 } 2030 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 2031 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);CHKERRQ(ierr); 2032 ierr = PetscMalloc1(numCells*totDim,&elemVecCh);CHKERRQ(ierr); 2033 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2034 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 2035 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2036 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2037 DM dmCell; 2038 2039 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 2040 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 2041 for (c = 0; c < cEnd - cStart; c++) { 2042 PetscScalar *thisgeom; 2043 2044 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 2045 cgeom[c] = *((PetscFECellGeom *) thisgeom); 2046 } 2047 } 2048 else { 2049 cgeom = (PetscFECellGeom *) cgeomScal; 2050 } 2051 for (c = cStart; c < cEnd; ++c) { 2052 PetscScalar *x = NULL, *x_t = NULL; 2053 PetscInt i; 2054 2055 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2056 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 2057 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2058 if (X_t) { 2059 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2060 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 2061 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2062 } 2063 if (dmAux) { 2064 DM dmAuxPlex; 2065 2066 ierr = DMSNESConvertPlex(dmAux,&dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 2067 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2068 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 2069 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2070 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 2071 } 2072 } 2073 for (f = 0; f < Nf; ++f) { 2074 PetscFE fe, feCh; 2075 PetscInt numQuadPoints, Nb; 2076 /* Conforming batches */ 2077 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2078 /* Remainder */ 2079 PetscInt Nr, offset; 2080 2081 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 2082 ierr = PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);CHKERRQ(ierr); 2083 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 2084 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2085 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2086 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2087 blockSize = Nb*numQuadPoints; 2088 batchSize = numBlocks * blockSize; 2089 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2090 numChunks = numCells / (numBatches*batchSize); 2091 Ne = numChunks*numBatches*batchSize; 2092 Nr = numCells % (numBatches*batchSize); 2093 offset = numCells - Nr; 2094 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeom, u, u_t, probAux, a, elemVec);CHKERRQ(ierr); 2095 ierr = PetscFEIntegrateResidual(feCh, prob, f, Ne, cgeom, u, u_t, probAux, a, elemVecCh);CHKERRQ(ierr); 2096 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemVec[offset*totDim]);CHKERRQ(ierr); 2097 ierr = PetscFEIntegrateResidual(feCh, prob, f, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemVecCh[offset*totDim]);CHKERRQ(ierr); 2098 } 2099 for (c = cStart; c < cEnd; ++c) { 2100 PetscBool diff = PETSC_FALSE; 2101 PetscInt d; 2102 2103 for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;} 2104 if (diff) { 2105 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);CHKERRQ(ierr); 2106 ierr = DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);CHKERRQ(ierr); 2107 ierr = DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);CHKERRQ(ierr); 2108 ++diffCell; 2109 } 2110 if (diffCell > 9) break; 2111 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 2112 } 2113 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2114 ierr = PetscFree(cgeom);CHKERRQ(ierr); 2115 } 2116 else { 2117 cgeom = NULL; 2118 } 2119 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2120 ierr = PetscFree3(u,u_t,elemVec);CHKERRQ(ierr); 2121 ierr = PetscFree(elemVecCh);CHKERRQ(ierr); 2122 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 2123 PetscFunctionReturn(0); 2124 } 2125 2126 #undef __FUNCT__ 2127 #define __FUNCT__ "DMPlexSNESComputeResidualFEM" 2128 /*@ 2129 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 2130 2131 Input Parameters: 2132 + dm - The mesh 2133 . X - Local solution 2134 - user - The user context 2135 2136 Output Parameter: 2137 . F - Local output vector 2138 2139 Level: developer 2140 2141 .seealso: DMPlexComputeJacobianActionFEM() 2142 @*/ 2143 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 2144 { 2145 PetscObject check; 2146 PetscInt cStart, cEnd, cEndInterior; 2147 DM plex; 2148 PetscErrorCode ierr; 2149 2150 PetscFunctionBegin; 2151 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2152 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 2153 ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2154 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2155 /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */ 2156 ierr = PetscObjectQuery((PetscObject) plex, "dmCh", &check);CHKERRQ(ierr); 2157 if (check) {ierr = DMPlexComputeResidualFEM_Check_Internal(plex, X, NULL, F, user);CHKERRQ(ierr);} 2158 else {ierr = DMPlexComputeResidual_Internal(plex, cStart, cEnd, PETSC_MIN_REAL, X, NULL, F, user);CHKERRQ(ierr);} 2159 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2160 PetscFunctionReturn(0); 2161 } 2162 2163 #undef __FUNCT__ 2164 #define __FUNCT__ "DMPlexSNESComputeBoundaryFEM" 2165 /*@ 2166 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 2167 2168 Input Parameters: 2169 + dm - The mesh 2170 - user - The user context 2171 2172 Output Parameter: 2173 . X - Local solution 2174 2175 Level: developer 2176 2177 .seealso: DMPlexComputeJacobianActionFEM() 2178 @*/ 2179 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 2180 { 2181 DM plex; 2182 PetscErrorCode ierr; 2183 2184 PetscFunctionBegin; 2185 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2186 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 2187 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2188 PetscFunctionReturn(0); 2189 } 2190 2191 #undef __FUNCT__ 2192 #define __FUNCT__ "DMPlexComputeJacobian_Internal" 2193 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, PetscInt cStart, PetscInt cEnd, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 2194 { 2195 DM_Plex *mesh = (DM_Plex *) dm->data; 2196 const char *name = "Jacobian"; 2197 DM dmAux, plex; 2198 DMLabel depth; 2199 Vec A, cellgeom; 2200 PetscDS prob, probAux = NULL; 2201 PetscQuadrature quad; 2202 PetscSection section, globalSection, sectionAux; 2203 PetscFECellGeom *cgeom = NULL; 2204 PetscScalar *cgeomScal; 2205 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 2206 PetscInt dim, Nf, f, fieldI, fieldJ, numCells, c; 2207 PetscInt totDim, totDimBd, totDimAux, numBd, bd; 2208 PetscBool isShell, hasPrec, hasDyn; 2209 PetscErrorCode ierr; 2210 2211 PetscFunctionBegin; 2212 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2213 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2214 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2215 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2216 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2217 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2218 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 2219 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2220 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2221 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2222 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2223 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2224 numCells = cEnd - cStart; 2225 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2226 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2227 if (dmAux) { 2228 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2229 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2230 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2231 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2232 } 2233 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2234 ierr = PetscMalloc5(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim*totDim,&elemMat,hasPrec ? numCells*totDim*totDim : 0, &elemMatP,hasDyn ? numCells*totDim*totDim : 0, &elemMatD);CHKERRQ(ierr); 2235 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2236 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 2237 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2238 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2239 DM dmCell; 2240 2241 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 2242 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 2243 for (c = 0; c < cEnd - cStart; c++) { 2244 PetscScalar *thisgeom; 2245 2246 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 2247 cgeom[c] = *((PetscFECellGeom *) thisgeom); 2248 } 2249 } 2250 else { 2251 cgeom = (PetscFECellGeom *) cgeomScal; 2252 } 2253 for (c = cStart; c < cEnd; ++c) { 2254 PetscScalar *x = NULL, *x_t = NULL; 2255 PetscInt i; 2256 2257 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2258 for (i = 0; i < totDim; ++i) u[(c-cStart)*totDim+i] = x[i]; 2259 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2260 if (X_t) { 2261 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2262 for (i = 0; i < totDim; ++i) u_t[(c-cStart)*totDim+i] = x_t[i]; 2263 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2264 } 2265 if (dmAux) { 2266 ierr = DMPlexVecGetClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2267 for (i = 0; i < totDimAux; ++i) a[(c-cStart)*totDimAux+i] = x[i]; 2268 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2269 } 2270 } 2271 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2272 if (hasPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2273 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2274 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2275 PetscFE fe; 2276 PetscInt numQuadPoints, Nb; 2277 /* Conforming batches */ 2278 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2279 /* Remainder */ 2280 PetscInt Nr, offset; 2281 2282 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2283 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2284 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2285 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2286 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2287 blockSize = Nb*numQuadPoints; 2288 batchSize = numBlocks * blockSize; 2289 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2290 numChunks = numCells / (numBatches*batchSize); 2291 Ne = numChunks*numBatches*batchSize; 2292 Nr = numCells % (numBatches*batchSize); 2293 offset = numCells - Nr; 2294 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2295 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, elemMat);CHKERRQ(ierr); 2296 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 2297 if (hasPrec) { 2298 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, elemMatP);CHKERRQ(ierr); 2299 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 2300 } 2301 if (hasDyn) { 2302 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, elemMatD);CHKERRQ(ierr); 2303 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], &elemMatD[offset*totDim*totDim]);CHKERRQ(ierr); 2304 } 2305 } 2306 } 2307 if (hasDyn) { 2308 for (c = 0; c < (cEnd - cStart)*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2309 } 2310 for (c = cStart; c < cEnd; ++c) { 2311 if (hasPrec) { 2312 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2313 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, c, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2314 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2315 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMatP[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2316 } else { 2317 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2318 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2319 } 2320 } 2321 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2322 ierr = PetscFree(cgeom);CHKERRQ(ierr); 2323 } 2324 else { 2325 cgeom = NULL; 2326 } 2327 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2328 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2329 if (dmAux) { 2330 ierr = PetscFree(a);CHKERRQ(ierr); 2331 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2332 } 2333 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2334 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 2335 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2336 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 2337 for (bd = 0; bd < numBd; ++bd) { 2338 const char *bdLabel; 2339 DMLabel label; 2340 IS pointIS; 2341 const PetscInt *points; 2342 const PetscInt *values; 2343 PetscInt field, numValues, numPoints, p, dep, numFaces; 2344 PetscBool isEssential; 2345 PetscObject obj; 2346 PetscClassId id; 2347 2348 ierr = DMGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 2349 ierr = DMGetField(dm, field, &obj);CHKERRQ(ierr); 2350 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2351 if ((id != PETSCFE_CLASSID) || isEssential) continue; 2352 if (numValues != 1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Bug me and I will fix this"); 2353 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2354 ierr = DMLabelGetStratumSize(label, 1, &numPoints);CHKERRQ(ierr); 2355 ierr = DMLabelGetStratumIS(label, 1, &pointIS);CHKERRQ(ierr); 2356 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2357 for (p = 0, numFaces = 0; p < numPoints; ++p) { 2358 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2359 if (dep == dim-1) ++numFaces; 2360 } 2361 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd*totDimBd,&elemMat);CHKERRQ(ierr); 2362 if (X_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 2363 for (p = 0, f = 0; p < numPoints; ++p) { 2364 const PetscInt point = points[p]; 2365 PetscScalar *x = NULL; 2366 PetscInt i; 2367 2368 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2369 if (dep != dim-1) continue; 2370 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 2371 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n);CHKERRQ(ierr); 2372 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 2373 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2374 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 2375 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2376 if (X_t) { 2377 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2378 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 2379 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2380 } 2381 ++f; 2382 } 2383 ierr = PetscMemzero(elemMat, numFaces*totDimBd*totDimBd * sizeof(PetscScalar));CHKERRQ(ierr); 2384 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2385 PetscFE fe; 2386 PetscInt numQuadPoints, Nb; 2387 /* Conforming batches */ 2388 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2389 /* Remainder */ 2390 PetscInt Nr, offset; 2391 2392 ierr = PetscDSGetBdDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2393 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2394 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2395 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2396 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2397 blockSize = Nb*numQuadPoints; 2398 batchSize = numBlocks * blockSize; 2399 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2400 numChunks = numFaces / (numBatches*batchSize); 2401 Ne = numChunks*numBatches*batchSize; 2402 Nr = numFaces % (numBatches*batchSize); 2403 offset = numFaces - Nr; 2404 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2405 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, cgeom, u, u_t, NULL, NULL, elemMat);CHKERRQ(ierr); 2406 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Nr, &cgeom[offset], &u[offset*totDimBd], u_t ? &u_t[offset*totDimBd] : NULL, NULL, NULL, &elemMat[offset*totDimBd*totDimBd]);CHKERRQ(ierr); 2407 } 2408 } 2409 for (p = 0, f = 0; p < numPoints; ++p) { 2410 const PetscInt point = points[p]; 2411 2412 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 2413 if (dep != dim-1) continue; 2414 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDimBd, totDimBd, &elemMat[f*totDimBd*totDimBd]);CHKERRQ(ierr);} 2415 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, point, &elemMat[f*totDimBd*totDimBd], ADD_VALUES);CHKERRQ(ierr); 2416 ++f; 2417 } 2418 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2419 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2420 ierr = PetscFree3(u,cgeom,elemMat);CHKERRQ(ierr); 2421 if (X_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 2422 } 2423 if (hasPrec) { 2424 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2425 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2426 } 2427 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2428 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2429 if (mesh->printFEM) { 2430 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 2431 ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); 2432 ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2433 } 2434 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2435 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr); 2436 if (isShell) { 2437 JacActionCtx *jctx; 2438 2439 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 2440 ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); 2441 } 2442 PetscFunctionReturn(0); 2443 } 2444 2445 #undef __FUNCT__ 2446 #define __FUNCT__ "DMPlexSNESComputeJacobianFEM" 2447 /*@ 2448 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2449 2450 Input Parameters: 2451 + dm - The mesh 2452 . X - Local input vector 2453 - user - The user context 2454 2455 Output Parameter: 2456 . Jac - Jacobian matrix 2457 2458 Note: 2459 The first member of the user context must be an FEMContext. 2460 2461 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2462 like a GPU, or vectorize on a multicore machine. 2463 2464 Level: developer 2465 2466 .seealso: FormFunctionLocal() 2467 @*/ 2468 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2469 { 2470 PetscInt cStart, cEnd, cEndInterior; 2471 DM plex; 2472 PetscErrorCode ierr; 2473 2474 PetscFunctionBegin; 2475 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2476 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 2477 ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2478 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2479 ierr = DMPlexComputeJacobian_Internal(plex, cStart, cEnd, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2480 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2481 PetscFunctionReturn(0); 2482 } 2483 2484 #undef __FUNCT__ 2485 #define __FUNCT__ "DMPlexSetSNESLocalFEM" 2486 /*@ 2487 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2488 2489 Input Parameters: 2490 + dm - The DM object 2491 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see DMAddBoundary()) 2492 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2493 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2494 @*/ 2495 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2496 { 2497 PetscErrorCode ierr; 2498 2499 PetscFunctionBegin; 2500 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2501 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2502 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2503 PetscFunctionReturn(0); 2504 } 2505 2506 #undef __FUNCT__ 2507 #define __FUNCT__ "DMSNESCheckFromOptions_Internal" 2508 PetscErrorCode DMSNESCheckFromOptions_Internal(SNES snes, DM dm, Vec u, Vec sol, PetscErrorCode (**exactFuncs)(PetscInt, PetscReal, const PetscReal x[], PetscInt, PetscScalar *u, void *ctx), void **ctxs) 2509 { 2510 Mat J, M; 2511 Vec r, b; 2512 MatNullSpace nullSpace; 2513 PetscReal *error, res = 0.0; 2514 PetscInt numFields; 2515 PetscErrorCode ierr; 2516 2517 PetscFunctionBegin; 2518 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2519 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2520 M = J; 2521 /* TODO Null space for J */ 2522 /* Check discretization error */ 2523 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 2524 ierr = PetscMalloc1(PetscMax(1, numFields), &error);CHKERRQ(ierr); 2525 if (numFields > 1) { 2526 PetscInt f; 2527 2528 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs, ctxs, u, error);CHKERRQ(ierr); 2529 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: [");CHKERRQ(ierr); 2530 for (f = 0; f < numFields; ++f) { 2531 if (f) {ierr = PetscPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);} 2532 if (error[f] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "%g", error[f]);CHKERRQ(ierr);} 2533 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "< 1.0e-11");CHKERRQ(ierr);} 2534 } 2535 ierr = PetscPrintf(PETSC_COMM_WORLD, "]\n");CHKERRQ(ierr); 2536 } else { 2537 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs, ctxs, u, &error[0]);CHKERRQ(ierr); 2538 if (error[0] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error[0]);CHKERRQ(ierr);} 2539 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} 2540 } 2541 ierr = PetscFree(error);CHKERRQ(ierr); 2542 /* Check residual */ 2543 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2544 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2545 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); 2546 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2547 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2548 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2549 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2550 /* Check Jacobian */ 2551 ierr = SNESComputeJacobian(snes, u, M, M);CHKERRQ(ierr); 2552 ierr = MatGetNullSpace(J, &nullSpace);CHKERRQ(ierr); 2553 if (nullSpace) { 2554 PetscBool isNull; 2555 ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr); 2556 if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2557 } 2558 ierr = VecDuplicate(u, &b);CHKERRQ(ierr); 2559 ierr = VecSet(r, 0.0);CHKERRQ(ierr); 2560 ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); 2561 ierr = MatMult(M, u, r);CHKERRQ(ierr); 2562 ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); 2563 ierr = VecDestroy(&b);CHKERRQ(ierr); 2564 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2565 ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr); 2566 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2567 ierr = PetscObjectSetName((PetscObject) r, "Au - b = Au + F(0)");CHKERRQ(ierr); 2568 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"linear_res_");CHKERRQ(ierr); 2569 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2570 ierr = VecDestroy(&r);CHKERRQ(ierr); 2571 ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); 2572 ierr = MatDestroy(&J);CHKERRQ(ierr); 2573 PetscFunctionReturn(0); 2574 } 2575 2576 #undef __FUNCT__ 2577 #define __FUNCT__ "DMSNESCheckFromOptions" 2578 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2579 { 2580 DM dm; 2581 Vec sol; 2582 PetscBool check; 2583 PetscErrorCode ierr; 2584 2585 PetscFunctionBegin; 2586 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 2587 if (!check) PetscFunctionReturn(0); 2588 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 2589 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 2590 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 2591 ierr = DMSNESCheckFromOptions_Internal(snes, dm, u, sol, exactFuncs, ctxs);CHKERRQ(ierr); 2592 ierr = VecDestroy(&sol);CHKERRQ(ierr); 2593 PetscFunctionReturn(0); 2594 } 2595