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 <petscblaslapack.h> 5 #include <petsc/private/petscimpl.h> 6 #include <petsc/private/petscfeimpl.h> 7 8 /************************** Interpolation *******************************/ 9 10 #undef __FUNCT__ 11 #define __FUNCT__ "DMSNESConvertPlex" 12 static PetscErrorCode DMSNESConvertPlex(DM dm, DM *plex, PetscBool copy) 13 { 14 PetscBool isPlex; 15 PetscErrorCode ierr; 16 17 PetscFunctionBegin; 18 ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); 19 if (isPlex) { 20 *plex = dm; 21 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 22 } else { 23 ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); 24 if (!*plex) { 25 ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr); 26 ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); 27 if (copy) { 28 PetscInt i; 29 PetscObject obj; 30 const char *comps[3] = {"A","dmAux","dmCh"}; 31 32 ierr = DMCopyDMSNES(dm, *plex);CHKERRQ(ierr); 33 for (i = 0; i < 3; i++) { 34 ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr); 35 ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr); 36 } 37 } 38 } else { 39 ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); 40 } 41 } 42 PetscFunctionReturn(0); 43 } 44 45 #undef __FUNCT__ 46 #define __FUNCT__ "DMInterpolationCreate" 47 PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx) 48 { 49 PetscErrorCode ierr; 50 51 PetscFunctionBegin; 52 PetscValidPointer(ctx, 2); 53 ierr = PetscMalloc(sizeof(struct _DMInterpolationInfo), ctx);CHKERRQ(ierr); 54 55 (*ctx)->comm = comm; 56 (*ctx)->dim = -1; 57 (*ctx)->nInput = 0; 58 (*ctx)->points = NULL; 59 (*ctx)->cells = NULL; 60 (*ctx)->n = -1; 61 (*ctx)->coords = NULL; 62 PetscFunctionReturn(0); 63 } 64 65 #undef __FUNCT__ 66 #define __FUNCT__ "DMInterpolationSetDim" 67 PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim) 68 { 69 PetscFunctionBegin; 70 if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %d", dim); 71 ctx->dim = dim; 72 PetscFunctionReturn(0); 73 } 74 75 #undef __FUNCT__ 76 #define __FUNCT__ "DMInterpolationGetDim" 77 PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim) 78 { 79 PetscFunctionBegin; 80 PetscValidIntPointer(dim, 2); 81 *dim = ctx->dim; 82 PetscFunctionReturn(0); 83 } 84 85 #undef __FUNCT__ 86 #define __FUNCT__ "DMInterpolationSetDof" 87 PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof) 88 { 89 PetscFunctionBegin; 90 if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %d", dof); 91 ctx->dof = dof; 92 PetscFunctionReturn(0); 93 } 94 95 #undef __FUNCT__ 96 #define __FUNCT__ "DMInterpolationGetDof" 97 PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof) 98 { 99 PetscFunctionBegin; 100 PetscValidIntPointer(dof, 2); 101 *dof = ctx->dof; 102 PetscFunctionReturn(0); 103 } 104 105 #undef __FUNCT__ 106 #define __FUNCT__ "DMInterpolationAddPoints" 107 PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[]) 108 { 109 PetscErrorCode ierr; 110 111 PetscFunctionBegin; 112 if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 113 if (ctx->points) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet"); 114 ctx->nInput = n; 115 116 ierr = PetscMalloc1(n*ctx->dim, &ctx->points);CHKERRQ(ierr); 117 ierr = PetscMemcpy(ctx->points, points, n*ctx->dim * sizeof(PetscReal));CHKERRQ(ierr); 118 PetscFunctionReturn(0); 119 } 120 121 #undef __FUNCT__ 122 #define __FUNCT__ "DMInterpolationSetUp" 123 PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints) 124 { 125 MPI_Comm comm = ctx->comm; 126 PetscScalar *a; 127 PetscInt p, q, i; 128 PetscMPIInt rank, size; 129 PetscErrorCode ierr; 130 Vec pointVec; 131 PetscSF cellSF; 132 PetscLayout layout; 133 PetscReal *globalPoints; 134 PetscScalar *globalPointsScalar; 135 const PetscInt *ranges; 136 PetscMPIInt *counts, *displs; 137 const PetscSFNode *foundCells; 138 const PetscInt *foundPoints; 139 PetscMPIInt *foundProcs, *globalProcs; 140 PetscInt n, N, numFound; 141 142 PetscFunctionBegin; 143 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 144 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 145 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 146 if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 147 /* Locate points */ 148 n = ctx->nInput; 149 if (!redundantPoints) { 150 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 151 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 152 ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr); 153 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 154 ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr); 155 /* Communicate all points to all processes */ 156 ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr); 157 ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr); 158 for (p = 0; p < size; ++p) { 159 counts[p] = (ranges[p+1] - ranges[p])*ctx->dim; 160 displs[p] = ranges[p]*ctx->dim; 161 } 162 ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr); 163 } else { 164 N = n; 165 globalPoints = ctx->points; 166 counts = displs = NULL; 167 layout = NULL; 168 } 169 #if 0 170 ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 171 /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */ 172 #else 173 #if defined(PETSC_USE_COMPLEX) 174 ierr = PetscMalloc1(N,&globalPointsScalar);CHKERRQ(ierr); 175 for (i=0; i<N; i++) globalPointsScalar[i] = globalPoints[i]; 176 #else 177 globalPointsScalar = globalPoints; 178 #endif 179 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr); 180 ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 181 cellSF = NULL; 182 ierr = DMLocatePoints(dm, pointVec, &cellSF);CHKERRQ(ierr); 183 ierr = PetscSFGetGraph(cellSF,NULL,&numFound,&foundPoints,&foundCells);CHKERRQ(ierr); 184 #endif 185 for (p = 0; p < numFound; ++p) { 186 if (foundCells[p].index >= 0) foundProcs[foundPoints ? foundPoints[p] : p] = rank; 187 else foundProcs[foundPoints ? foundPoints[p] : p] = size; 188 } 189 /* Let the lowest rank process own each point */ 190 ierr = MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr); 191 ctx->n = 0; 192 for (p = 0; p < N; ++p) { 193 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); 194 else if (globalProcs[p] == rank) ctx->n++; 195 } 196 /* Create coordinates vector and array of owned cells */ 197 ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr); 198 ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr); 199 ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr); 200 ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr); 201 ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr); 202 ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr); 203 for (p = 0, q = 0, i = 0; p < N; ++p) { 204 if (globalProcs[p] == rank) { 205 PetscInt d; 206 207 for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d]; 208 ctx->cells[q++] = foundCells[p].index; 209 } 210 } 211 ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr); 212 #if 0 213 ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr); 214 #else 215 ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr); 216 ierr = PetscSFDestroy(&cellSF);CHKERRQ(ierr); 217 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 218 #endif 219 if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);} 220 if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);} 221 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 222 PetscFunctionReturn(0); 223 } 224 225 #undef __FUNCT__ 226 #define __FUNCT__ "DMInterpolationGetCoordinates" 227 PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates) 228 { 229 PetscFunctionBegin; 230 PetscValidPointer(coordinates, 2); 231 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 232 *coordinates = ctx->coords; 233 PetscFunctionReturn(0); 234 } 235 236 #undef __FUNCT__ 237 #define __FUNCT__ "DMInterpolationGetVector" 238 PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v) 239 { 240 PetscErrorCode ierr; 241 242 PetscFunctionBegin; 243 PetscValidPointer(v, 2); 244 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 245 ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr); 246 ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr); 247 ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr); 248 ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr); 249 PetscFunctionReturn(0); 250 } 251 252 #undef __FUNCT__ 253 #define __FUNCT__ "DMInterpolationRestoreVector" 254 PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v) 255 { 256 PetscErrorCode ierr; 257 258 PetscFunctionBegin; 259 PetscValidPointer(v, 2); 260 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 261 ierr = VecDestroy(v);CHKERRQ(ierr); 262 PetscFunctionReturn(0); 263 } 264 265 #undef __FUNCT__ 266 #define __FUNCT__ "DMInterpolate_Triangle_Private" 267 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 268 { 269 PetscReal *v0, *J, *invJ, detJ; 270 const PetscScalar *coords; 271 PetscScalar *a; 272 PetscInt p; 273 PetscErrorCode ierr; 274 275 PetscFunctionBegin; 276 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 277 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 278 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 279 for (p = 0; p < ctx->n; ++p) { 280 PetscInt c = ctx->cells[p]; 281 PetscScalar *x = NULL; 282 PetscReal xi[4]; 283 PetscInt d, f, comp; 284 285 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 286 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 287 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 288 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 289 290 for (d = 0; d < ctx->dim; ++d) { 291 xi[d] = 0.0; 292 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 293 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]; 294 } 295 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 296 } 297 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 298 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 299 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 300 PetscFunctionReturn(0); 301 } 302 303 #undef __FUNCT__ 304 #define __FUNCT__ "DMInterpolate_Tetrahedron_Private" 305 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 306 { 307 PetscReal *v0, *J, *invJ, detJ; 308 const PetscScalar *coords; 309 PetscScalar *a; 310 PetscInt p; 311 PetscErrorCode ierr; 312 313 PetscFunctionBegin; 314 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 315 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 316 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 317 for (p = 0; p < ctx->n; ++p) { 318 PetscInt c = ctx->cells[p]; 319 const PetscInt order[3] = {2, 1, 3}; 320 PetscScalar *x = NULL; 321 PetscReal xi[4]; 322 PetscInt d, f, comp; 323 324 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 325 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", detJ, c); 326 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 327 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 328 329 for (d = 0; d < ctx->dim; ++d) { 330 xi[d] = 0.0; 331 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 332 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]; 333 } 334 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 335 } 336 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 337 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 338 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 339 PetscFunctionReturn(0); 340 } 341 342 #undef __FUNCT__ 343 #define __FUNCT__ "QuadMap_Private" 344 PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 345 { 346 const PetscScalar *vertices = (const PetscScalar*) ctx; 347 const PetscScalar x0 = vertices[0]; 348 const PetscScalar y0 = vertices[1]; 349 const PetscScalar x1 = vertices[2]; 350 const PetscScalar y1 = vertices[3]; 351 const PetscScalar x2 = vertices[4]; 352 const PetscScalar y2 = vertices[5]; 353 const PetscScalar x3 = vertices[6]; 354 const PetscScalar y3 = vertices[7]; 355 const PetscScalar f_1 = x1 - x0; 356 const PetscScalar g_1 = y1 - y0; 357 const PetscScalar f_3 = x3 - x0; 358 const PetscScalar g_3 = y3 - y0; 359 const PetscScalar f_01 = x2 - x1 - x3 + x0; 360 const PetscScalar g_01 = y2 - y1 - y3 + y0; 361 const PetscScalar *ref; 362 PetscScalar *real; 363 PetscErrorCode ierr; 364 365 PetscFunctionBegin; 366 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 367 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 368 { 369 const PetscScalar p0 = ref[0]; 370 const PetscScalar p1 = ref[1]; 371 372 real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1; 373 real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1; 374 } 375 ierr = PetscLogFlops(28);CHKERRQ(ierr); 376 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 377 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 378 PetscFunctionReturn(0); 379 } 380 381 #include <petsc/private/dmimpl.h> 382 #undef __FUNCT__ 383 #define __FUNCT__ "QuadJacobian_Private" 384 PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 385 { 386 const PetscScalar *vertices = (const PetscScalar*) ctx; 387 const PetscScalar x0 = vertices[0]; 388 const PetscScalar y0 = vertices[1]; 389 const PetscScalar x1 = vertices[2]; 390 const PetscScalar y1 = vertices[3]; 391 const PetscScalar x2 = vertices[4]; 392 const PetscScalar y2 = vertices[5]; 393 const PetscScalar x3 = vertices[6]; 394 const PetscScalar y3 = vertices[7]; 395 const PetscScalar f_01 = x2 - x1 - x3 + x0; 396 const PetscScalar g_01 = y2 - y1 - y3 + y0; 397 const PetscScalar *ref; 398 PetscErrorCode ierr; 399 400 PetscFunctionBegin; 401 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 402 { 403 const PetscScalar x = ref[0]; 404 const PetscScalar y = ref[1]; 405 const PetscInt rows[2] = {0, 1}; 406 PetscScalar values[4]; 407 408 values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5; 409 values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5; 410 ierr = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr); 411 } 412 ierr = PetscLogFlops(30);CHKERRQ(ierr); 413 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 414 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 415 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 416 PetscFunctionReturn(0); 417 } 418 419 #undef __FUNCT__ 420 #define __FUNCT__ "DMInterpolate_Quad_Private" 421 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 422 { 423 DM dmCoord; 424 SNES snes; 425 KSP ksp; 426 PC pc; 427 Vec coordsLocal, r, ref, real; 428 Mat J; 429 const PetscScalar *coords; 430 PetscScalar *a; 431 PetscInt p; 432 PetscErrorCode ierr; 433 434 PetscFunctionBegin; 435 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 436 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 437 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 438 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 439 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 440 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 441 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 442 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 443 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 444 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 445 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 446 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 447 ierr = MatSetUp(J);CHKERRQ(ierr); 448 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 449 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 450 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 451 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 452 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 453 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 454 455 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 456 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 457 for (p = 0; p < ctx->n; ++p) { 458 PetscScalar *x = NULL, *vertices = NULL; 459 PetscScalar *xi; 460 PetscReal xir[2]; 461 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 462 463 /* Can make this do all points at once */ 464 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 465 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 4*2); 466 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 467 if (4*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 4*ctx->dof); 468 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 469 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 470 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 471 xi[0] = coords[p*ctx->dim+0]; 472 xi[1] = coords[p*ctx->dim+1]; 473 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 474 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 475 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 476 xir[0] = PetscRealPart(xi[0]); 477 xir[1] = PetscRealPart(xi[1]); 478 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]; 479 480 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 481 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 482 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 483 } 484 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 485 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 486 487 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 488 ierr = VecDestroy(&r);CHKERRQ(ierr); 489 ierr = VecDestroy(&ref);CHKERRQ(ierr); 490 ierr = VecDestroy(&real);CHKERRQ(ierr); 491 ierr = MatDestroy(&J);CHKERRQ(ierr); 492 PetscFunctionReturn(0); 493 } 494 495 #undef __FUNCT__ 496 #define __FUNCT__ "HexMap_Private" 497 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 498 { 499 const PetscScalar *vertices = (const PetscScalar*) ctx; 500 const PetscScalar x0 = vertices[0]; 501 const PetscScalar y0 = vertices[1]; 502 const PetscScalar z0 = vertices[2]; 503 const PetscScalar x1 = vertices[9]; 504 const PetscScalar y1 = vertices[10]; 505 const PetscScalar z1 = vertices[11]; 506 const PetscScalar x2 = vertices[6]; 507 const PetscScalar y2 = vertices[7]; 508 const PetscScalar z2 = vertices[8]; 509 const PetscScalar x3 = vertices[3]; 510 const PetscScalar y3 = vertices[4]; 511 const PetscScalar z3 = vertices[5]; 512 const PetscScalar x4 = vertices[12]; 513 const PetscScalar y4 = vertices[13]; 514 const PetscScalar z4 = vertices[14]; 515 const PetscScalar x5 = vertices[15]; 516 const PetscScalar y5 = vertices[16]; 517 const PetscScalar z5 = vertices[17]; 518 const PetscScalar x6 = vertices[18]; 519 const PetscScalar y6 = vertices[19]; 520 const PetscScalar z6 = vertices[20]; 521 const PetscScalar x7 = vertices[21]; 522 const PetscScalar y7 = vertices[22]; 523 const PetscScalar z7 = vertices[23]; 524 const PetscScalar f_1 = x1 - x0; 525 const PetscScalar g_1 = y1 - y0; 526 const PetscScalar h_1 = z1 - z0; 527 const PetscScalar f_3 = x3 - x0; 528 const PetscScalar g_3 = y3 - y0; 529 const PetscScalar h_3 = z3 - z0; 530 const PetscScalar f_4 = x4 - x0; 531 const PetscScalar g_4 = y4 - y0; 532 const PetscScalar h_4 = z4 - z0; 533 const PetscScalar f_01 = x2 - x1 - x3 + x0; 534 const PetscScalar g_01 = y2 - y1 - y3 + y0; 535 const PetscScalar h_01 = z2 - z1 - z3 + z0; 536 const PetscScalar f_12 = x7 - x3 - x4 + x0; 537 const PetscScalar g_12 = y7 - y3 - y4 + y0; 538 const PetscScalar h_12 = z7 - z3 - z4 + z0; 539 const PetscScalar f_02 = x5 - x1 - x4 + x0; 540 const PetscScalar g_02 = y5 - y1 - y4 + y0; 541 const PetscScalar h_02 = z5 - z1 - z4 + z0; 542 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 543 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 544 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 545 const PetscScalar *ref; 546 PetscScalar *real; 547 PetscErrorCode ierr; 548 549 PetscFunctionBegin; 550 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 551 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 552 { 553 const PetscScalar p0 = ref[0]; 554 const PetscScalar p1 = ref[1]; 555 const PetscScalar p2 = ref[2]; 556 557 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; 558 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; 559 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; 560 } 561 ierr = PetscLogFlops(114);CHKERRQ(ierr); 562 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 563 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 564 PetscFunctionReturn(0); 565 } 566 567 #undef __FUNCT__ 568 #define __FUNCT__ "HexJacobian_Private" 569 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 570 { 571 const PetscScalar *vertices = (const PetscScalar*) ctx; 572 const PetscScalar x0 = vertices[0]; 573 const PetscScalar y0 = vertices[1]; 574 const PetscScalar z0 = vertices[2]; 575 const PetscScalar x1 = vertices[9]; 576 const PetscScalar y1 = vertices[10]; 577 const PetscScalar z1 = vertices[11]; 578 const PetscScalar x2 = vertices[6]; 579 const PetscScalar y2 = vertices[7]; 580 const PetscScalar z2 = vertices[8]; 581 const PetscScalar x3 = vertices[3]; 582 const PetscScalar y3 = vertices[4]; 583 const PetscScalar z3 = vertices[5]; 584 const PetscScalar x4 = vertices[12]; 585 const PetscScalar y4 = vertices[13]; 586 const PetscScalar z4 = vertices[14]; 587 const PetscScalar x5 = vertices[15]; 588 const PetscScalar y5 = vertices[16]; 589 const PetscScalar z5 = vertices[17]; 590 const PetscScalar x6 = vertices[18]; 591 const PetscScalar y6 = vertices[19]; 592 const PetscScalar z6 = vertices[20]; 593 const PetscScalar x7 = vertices[21]; 594 const PetscScalar y7 = vertices[22]; 595 const PetscScalar z7 = vertices[23]; 596 const PetscScalar f_xy = x2 - x1 - x3 + x0; 597 const PetscScalar g_xy = y2 - y1 - y3 + y0; 598 const PetscScalar h_xy = z2 - z1 - z3 + z0; 599 const PetscScalar f_yz = x7 - x3 - x4 + x0; 600 const PetscScalar g_yz = y7 - y3 - y4 + y0; 601 const PetscScalar h_yz = z7 - z3 - z4 + z0; 602 const PetscScalar f_xz = x5 - x1 - x4 + x0; 603 const PetscScalar g_xz = y5 - y1 - y4 + y0; 604 const PetscScalar h_xz = z5 - z1 - z4 + z0; 605 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 606 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 607 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 608 const PetscScalar *ref; 609 PetscErrorCode ierr; 610 611 PetscFunctionBegin; 612 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 613 { 614 const PetscScalar x = ref[0]; 615 const PetscScalar y = ref[1]; 616 const PetscScalar z = ref[2]; 617 const PetscInt rows[3] = {0, 1, 2}; 618 PetscScalar values[9]; 619 620 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 621 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 622 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 623 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 624 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 625 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 626 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 627 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 628 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 629 630 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 631 } 632 ierr = PetscLogFlops(152);CHKERRQ(ierr); 633 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 634 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 635 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 636 PetscFunctionReturn(0); 637 } 638 639 #undef __FUNCT__ 640 #define __FUNCT__ "DMInterpolate_Hex_Private" 641 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 642 { 643 DM dmCoord; 644 SNES snes; 645 KSP ksp; 646 PC pc; 647 Vec coordsLocal, r, ref, real; 648 Mat J; 649 const PetscScalar *coords; 650 PetscScalar *a; 651 PetscInt p; 652 PetscErrorCode ierr; 653 654 PetscFunctionBegin; 655 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 656 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 657 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 658 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 659 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 660 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 661 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 662 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 663 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 664 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 665 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 666 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 667 ierr = MatSetUp(J);CHKERRQ(ierr); 668 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 669 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 670 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 671 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 672 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 673 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 674 675 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 676 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 677 for (p = 0; p < ctx->n; ++p) { 678 PetscScalar *x = NULL, *vertices = NULL; 679 PetscScalar *xi; 680 PetscReal xir[3]; 681 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 682 683 /* Can make this do all points at once */ 684 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 685 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 8*3); 686 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 687 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 8*ctx->dof); 688 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 689 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 690 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 691 xi[0] = coords[p*ctx->dim+0]; 692 xi[1] = coords[p*ctx->dim+1]; 693 xi[2] = coords[p*ctx->dim+2]; 694 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 695 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 696 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 697 xir[0] = PetscRealPart(xi[0]); 698 xir[1] = PetscRealPart(xi[1]); 699 xir[2] = PetscRealPart(xi[2]); 700 for (comp = 0; comp < ctx->dof; ++comp) { 701 a[p*ctx->dof+comp] = 702 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 703 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 704 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 705 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 706 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 707 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 708 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 709 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 710 } 711 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 712 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 713 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 714 } 715 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 716 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 717 718 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 719 ierr = VecDestroy(&r);CHKERRQ(ierr); 720 ierr = VecDestroy(&ref);CHKERRQ(ierr); 721 ierr = VecDestroy(&real);CHKERRQ(ierr); 722 ierr = MatDestroy(&J);CHKERRQ(ierr); 723 PetscFunctionReturn(0); 724 } 725 726 #undef __FUNCT__ 727 #define __FUNCT__ "DMInterpolationEvaluate" 728 /* 729 Input Parameters: 730 + ctx - The DMInterpolationInfo context 731 . dm - The DM 732 - x - The local vector containing the field to be interpolated 733 734 Output Parameters: 735 . v - The vector containing the interpolated values 736 */ 737 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 738 { 739 PetscInt dim, coneSize, n; 740 PetscErrorCode ierr; 741 742 PetscFunctionBegin; 743 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 744 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 745 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 746 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 747 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); 748 if (n) { 749 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 750 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 751 if (dim == 2) { 752 if (coneSize == 3) { 753 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 754 } else if (coneSize == 4) { 755 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 756 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 757 } else if (dim == 3) { 758 if (coneSize == 4) { 759 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 760 } else { 761 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 762 } 763 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 764 } 765 PetscFunctionReturn(0); 766 } 767 768 #undef __FUNCT__ 769 #define __FUNCT__ "DMInterpolationDestroy" 770 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 771 { 772 PetscErrorCode ierr; 773 774 PetscFunctionBegin; 775 PetscValidPointer(ctx, 2); 776 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 777 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 778 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 779 ierr = PetscFree(*ctx);CHKERRQ(ierr); 780 *ctx = NULL; 781 PetscFunctionReturn(0); 782 } 783 784 #undef __FUNCT__ 785 #define __FUNCT__ "SNESMonitorFields" 786 /*@C 787 SNESMonitorFields - Monitors the residual for each field separately 788 789 Collective on SNES 790 791 Input Parameters: 792 + snes - the SNES context 793 . its - iteration number 794 . fgnorm - 2-norm of residual 795 - vf - PetscViewerAndFormat of type ASCII 796 797 Notes: 798 This routine prints the residual norm at each iteration. 799 800 Level: intermediate 801 802 .keywords: SNES, nonlinear, default, monitor, norm 803 .seealso: SNESMonitorSet(), SNESMonitorDefault() 804 @*/ 805 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf) 806 { 807 PetscViewer viewer = vf->viewer; 808 Vec res; 809 DM dm; 810 PetscSection s; 811 const PetscScalar *r; 812 PetscReal *lnorms, *norms; 813 PetscInt numFields, f, pStart, pEnd, p; 814 PetscErrorCode ierr; 815 816 PetscFunctionBegin; 817 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4); 818 ierr = SNESGetFunction(snes, &res, 0, 0);CHKERRQ(ierr); 819 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 820 ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr); 821 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 822 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 823 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 824 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 825 for (p = pStart; p < pEnd; ++p) { 826 for (f = 0; f < numFields; ++f) { 827 PetscInt fdof, foff, d; 828 829 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 830 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 831 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 832 } 833 } 834 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 835 ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 836 ierr = PetscViewerPushFormat(viewer,vf->format);CHKERRQ(ierr); 837 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 838 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 839 for (f = 0; f < numFields; ++f) { 840 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 841 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 842 } 843 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 844 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 845 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 846 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 847 PetscFunctionReturn(0); 848 } 849 850 /********************* Residual Computation **************************/ 851 852 #undef __FUNCT__ 853 #define __FUNCT__ "DMPlexSNESGetGeometryFEM" 854 /*@ 855 DMPlexSNESGetGeometryFEM - Return precomputed geometric data 856 857 Input Parameter: 858 . dm - The DM 859 860 Output Parameters: 861 . cellgeom - The values precomputed from cell geometry 862 863 Level: developer 864 865 .seealso: DMPlexSNESSetFunctionLocal() 866 @*/ 867 PetscErrorCode DMPlexSNESGetGeometryFEM(DM dm, Vec *cellgeom) 868 { 869 DMSNES dmsnes; 870 PetscObject obj; 871 PetscErrorCode ierr; 872 873 PetscFunctionBegin; 874 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 875 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 876 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", &obj);CHKERRQ(ierr); 877 if (!obj) { 878 Vec cellgeom; 879 880 ierr = DMPlexComputeGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 881 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", (PetscObject) cellgeom);CHKERRQ(ierr); 882 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 883 } 884 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fem", (PetscObject *) cellgeom);CHKERRQ(ierr);} 885 PetscFunctionReturn(0); 886 } 887 888 #undef __FUNCT__ 889 #define __FUNCT__ "DMPlexSNESGetGeometryFVM" 890 /*@ 891 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 892 893 Input Parameter: 894 . dm - The DM 895 896 Output Parameters: 897 + facegeom - The values precomputed from face geometry 898 . cellgeom - The values precomputed from cell geometry 899 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 900 901 Level: developer 902 903 .seealso: DMPlexTSSetRHSFunctionLocal() 904 @*/ 905 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 906 { 907 DMSNES dmsnes; 908 PetscObject obj; 909 PetscErrorCode ierr; 910 911 PetscFunctionBegin; 912 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 913 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 914 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", &obj);CHKERRQ(ierr); 915 if (!obj) { 916 Vec cellgeom, facegeom; 917 918 ierr = DMPlexComputeGeometryFVM(dm, &cellgeom, &facegeom);CHKERRQ(ierr); 919 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject) facegeom);CHKERRQ(ierr); 920 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject) cellgeom);CHKERRQ(ierr); 921 ierr = VecDestroy(&facegeom);CHKERRQ(ierr); 922 ierr = VecDestroy(&cellgeom);CHKERRQ(ierr); 923 } 924 if (facegeom) {PetscValidPointer(facegeom, 2); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_facegeom_fvm", (PetscObject *) facegeom);CHKERRQ(ierr);} 925 if (cellgeom) {PetscValidPointer(cellgeom, 3); ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_cellgeom_fvm", (PetscObject *) cellgeom);CHKERRQ(ierr);} 926 if (minRadius) {ierr = DMPlexGetMinRadius(dm, minRadius);CHKERRQ(ierr);} 927 PetscFunctionReturn(0); 928 } 929 930 #undef __FUNCT__ 931 #define __FUNCT__ "DMPlexSNESGetGradientDM" 932 /*@ 933 DMPlexSNESGetGradientDM - Return gradient data layout 934 935 Input Parameters: 936 + dm - The DM 937 - fv - The PetscFV 938 939 Output Parameter: 940 . dmGrad - The layout for gradient values 941 942 Level: developer 943 944 .seealso: DMPlexSNESGetGeometryFVM() 945 @*/ 946 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 947 { 948 DMSNES dmsnes; 949 PetscObject obj; 950 PetscBool computeGradients; 951 PetscErrorCode ierr; 952 953 PetscFunctionBegin; 954 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 955 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 956 PetscValidPointer(dmGrad,3); 957 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 958 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 959 ierr = DMGetDMSNES(dm, &dmsnes);CHKERRQ(ierr); 960 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", &obj);CHKERRQ(ierr); 961 if (!obj) { 962 DM dmGrad; 963 Vec faceGeometry, cellGeometry; 964 965 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometry, &cellGeometry, NULL);CHKERRQ(ierr); 966 ierr = DMPlexComputeGradientFVM(dm, fv, faceGeometry, cellGeometry, &dmGrad);CHKERRQ(ierr); 967 ierr = PetscObjectCompose((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject) dmGrad);CHKERRQ(ierr); 968 ierr = DMDestroy(&dmGrad);CHKERRQ(ierr); 969 } 970 ierr = PetscObjectQuery((PetscObject) dmsnes, "DMPlexSNES_dmgrad_fvm", (PetscObject *) dmGrad);CHKERRQ(ierr); 971 PetscFunctionReturn(0); 972 } 973 974 #undef __FUNCT__ 975 #define __FUNCT__ "DMPlexGetCellFields" 976 /*@C 977 DMPlexGetCellFields - Retrieve the field values values for a chunk of cells 978 979 Input Parameters: 980 + dm - The DM 981 . cStart - The first cell to include 982 . cEnd - The first cell to exclude 983 . locX - A local vector with the solution fields 984 . locX_t - A local vector with solution field time derivatives, or NULL 985 - locA - A local vector with auxiliary fields, or NULL 986 987 Output Parameters: 988 + u - The field coefficients 989 . u_t - The fields derivative coefficients 990 - a - The auxiliary field coefficients 991 992 Level: developer 993 994 .seealso: DMPlexGetFaceFields() 995 @*/ 996 PetscErrorCode DMPlexGetCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 997 { 998 DM dmAux; 999 PetscSection section, sectionAux; 1000 PetscDS prob; 1001 PetscInt numCells = cEnd - cStart, totDim, totDimAux, c; 1002 PetscErrorCode ierr; 1003 1004 PetscFunctionBegin; 1005 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1006 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1007 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1008 if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 6);} 1009 PetscValidPointer(u, 7); 1010 PetscValidPointer(u_t, 8); 1011 PetscValidPointer(a, 9); 1012 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1013 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1014 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1015 if (locA) { 1016 PetscDS probAux; 1017 1018 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1019 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1020 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1021 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1022 } 1023 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u);CHKERRQ(ierr); 1024 if (locX_t) {ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, u_t);CHKERRQ(ierr);} else {*u_t = NULL;} 1025 if (locA) {ierr = DMGetWorkArray(dm, numCells*totDimAux, PETSC_SCALAR, a);CHKERRQ(ierr);} else {*a = NULL;} 1026 for (c = cStart; c < cEnd; ++c) { 1027 PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; 1028 PetscInt i; 1029 1030 ierr = DMPlexVecGetClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 1031 for (i = 0; i < totDim; ++i) ul[(c-cStart)*totDim+i] = x[i]; 1032 ierr = DMPlexVecRestoreClosure(dm, section, locX, c, NULL, &x);CHKERRQ(ierr); 1033 if (locX_t) { 1034 ierr = DMPlexVecGetClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 1035 for (i = 0; i < totDim; ++i) ul_t[(c-cStart)*totDim+i] = x_t[i]; 1036 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, c, NULL, &x_t);CHKERRQ(ierr); 1037 } 1038 if (locA) { 1039 DM dmAuxPlex; 1040 1041 ierr = DMSNESConvertPlex(dmAux, &dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 1042 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1043 for (i = 0; i < totDimAux; ++i) al[(c-cStart)*totDimAux+i] = x[i]; 1044 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, locA, c, NULL, &x);CHKERRQ(ierr); 1045 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 1046 } 1047 } 1048 PetscFunctionReturn(0); 1049 } 1050 1051 #undef __FUNCT__ 1052 #define __FUNCT__ "DMPlexRestoreCellFields" 1053 /*@C 1054 DMPlexRestoreCellFields - Restore the field values values for a chunk of cells 1055 1056 Input Parameters: 1057 + dm - The DM 1058 . cStart - The first cell to include 1059 . cEnd - The first cell to exclude 1060 . locX - A local vector with the solution fields 1061 . locX_t - A local vector with solution field time derivatives, or NULL 1062 - locA - A local vector with auxiliary fields, or NULL 1063 1064 Output Parameters: 1065 + u - The field coefficients 1066 . u_t - The fields derivative coefficients 1067 - a - The auxiliary field coefficients 1068 1069 Level: developer 1070 1071 .seealso: DMPlexGetFaceFields() 1072 @*/ 1073 PetscErrorCode DMPlexRestoreCellFields(DM dm, PetscInt cStart, PetscInt cEnd, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 1074 { 1075 PetscErrorCode ierr; 1076 1077 PetscFunctionBegin; 1078 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u);CHKERRQ(ierr); 1079 if (*u_t) {ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, u_t);CHKERRQ(ierr);} 1080 if (*a) {ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, a);CHKERRQ(ierr);} 1081 PetscFunctionReturn(0); 1082 } 1083 1084 #undef __FUNCT__ 1085 #define __FUNCT__ "DMPlexGetFaceFields" 1086 /*@C 1087 DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces 1088 1089 Input Parameters: 1090 + dm - The DM 1091 . fStart - The first face to include 1092 . fEnd - The first face to exclude 1093 . locX - A local vector with the solution fields 1094 . locX_t - A local vector with solution field time derivatives, or NULL 1095 . faceGeometry - A local vector with face geometry 1096 . cellGeometry - A local vector with cell geometry 1097 - locaGrad - A local vector with field gradients, or NULL 1098 1099 Output Parameters: 1100 + uL - The field values at the left side of the face 1101 - uR - The field values at the right side of the face 1102 1103 Level: developer 1104 1105 .seealso: DMPlexGetCellFields() 1106 @*/ 1107 PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1108 { 1109 DM dmFace, dmCell, dmGrad = NULL; 1110 PetscSection section; 1111 PetscDS prob; 1112 DMLabel ghostLabel; 1113 const PetscScalar *facegeom, *cellgeom, *x, *lgrad; 1114 PetscBool *isFE; 1115 PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; 1116 PetscErrorCode ierr; 1117 1118 PetscFunctionBegin; 1119 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1120 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1121 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1122 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); 1123 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); 1124 if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} 1125 PetscValidPointer(uL, 9); 1126 PetscValidPointer(uR, 10); 1127 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1128 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1129 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1130 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1131 ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); 1132 ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); 1133 for (f = 0; f < Nf; ++f) { 1134 PetscObject obj; 1135 PetscClassId id; 1136 1137 ierr = DMGetField(dm, f, &obj);CHKERRQ(ierr); 1138 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1139 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 1140 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 1141 else {isFE[f] = PETSC_FALSE;} 1142 } 1143 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1144 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1145 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1146 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1147 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1148 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1149 if (locGrad) { 1150 ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); 1151 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1152 } 1153 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uL);CHKERRQ(ierr); 1154 ierr = DMGetWorkArray(dm, numFaces*Nc, PETSC_SCALAR, uR);CHKERRQ(ierr); 1155 /* Right now just eat the extra work for FE (could make a cell loop) */ 1156 for (face = fStart, iface = 0; face < fEnd; ++face) { 1157 const PetscInt *cells; 1158 PetscFVFaceGeom *fg; 1159 PetscFVCellGeom *cgL, *cgR; 1160 PetscScalar *xL, *xR, *gL, *gR; 1161 PetscScalar *uLl = *uL, *uRl = *uR; 1162 PetscInt ghost, nsupp; 1163 1164 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1165 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1166 if (ghost >= 0) continue; 1167 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1168 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1169 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1170 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1171 for (f = 0; f < Nf; ++f) { 1172 PetscInt off; 1173 1174 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1175 if (isFE[f]) { 1176 const PetscInt *cone; 1177 PetscInt comp, coneSize, faceLocL, faceLocR, ldof, rdof, d; 1178 1179 xL = xR = NULL; 1180 ierr = DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1181 ierr = DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1182 ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); 1183 ierr = DMPlexGetConeSize(dm, cells[0], &coneSize);CHKERRQ(ierr); 1184 for (faceLocL = 0; faceLocL < coneSize; ++faceLocL) if (cone[faceLocL] == face) break; 1185 if (faceLocL == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[0]); 1186 ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); 1187 ierr = DMPlexGetConeSize(dm, cells[1], &coneSize);CHKERRQ(ierr); 1188 for (faceLocR = 0; faceLocR < coneSize; ++faceLocR) if (cone[faceLocR] == face) break; 1189 if (faceLocR == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d", face, cells[1]); 1190 /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */ 1191 ierr = EvaluateFaceFields(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); 1192 if (rdof == ldof) {ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr);} 1193 else {ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); for(d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];} 1194 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1195 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1196 } else { 1197 PetscFV fv; 1198 PetscInt numComp, c; 1199 1200 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); 1201 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1202 if (nsupp > 2) { 1203 for (f = 0; f < Nf; ++f) { 1204 PetscInt off; 1205 1206 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1207 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1208 for (c = 0; c < numComp; ++c) { 1209 uLl[iface*Nc+off+c] = 0.; 1210 uRl[iface*Nc+off+c] = 0.; 1211 } 1212 } 1213 continue; 1214 } 1215 ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); 1216 ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); 1217 if (dmGrad) { 1218 PetscReal dxL[3], dxR[3]; 1219 1220 ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); 1221 ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); 1222 DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); 1223 DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); 1224 for (c = 0; c < numComp; ++c) { 1225 uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); 1226 uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); 1227 } 1228 } else { 1229 for (c = 0; c < numComp; ++c) { 1230 uLl[iface*Nc+off+c] = xL[c]; 1231 uRl[iface*Nc+off+c] = xR[c]; 1232 } 1233 } 1234 } 1235 } 1236 ++iface; 1237 } 1238 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1239 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1240 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1241 if (locGrad) { 1242 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1243 } 1244 ierr = PetscFree(isFE);CHKERRQ(ierr); 1245 PetscFunctionReturn(0); 1246 } 1247 1248 #undef __FUNCT__ 1249 #define __FUNCT__ "DMPlexRestoreFaceFields" 1250 /*@C 1251 DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces 1252 1253 Input Parameters: 1254 + dm - The DM 1255 . fStart - The first face to include 1256 . fEnd - The first face to exclude 1257 . locX - A local vector with the solution fields 1258 . locX_t - A local vector with solution field time derivatives, or NULL 1259 . faceGeometry - A local vector with face geometry 1260 . cellGeometry - A local vector with cell geometry 1261 - locaGrad - A local vector with field gradients, or NULL 1262 1263 Output Parameters: 1264 + uL - The field values at the left side of the face 1265 - uR - The field values at the right side of the face 1266 1267 Level: developer 1268 1269 .seealso: DMPlexGetFaceFields() 1270 @*/ 1271 PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscScalar **uL, PetscScalar **uR) 1272 { 1273 PetscErrorCode ierr; 1274 1275 PetscFunctionBegin; 1276 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uL);CHKERRQ(ierr); 1277 ierr = DMRestoreWorkArray(dm, 0, PETSC_SCALAR, uR);CHKERRQ(ierr); 1278 PetscFunctionReturn(0); 1279 } 1280 1281 #undef __FUNCT__ 1282 #define __FUNCT__ "DMPlexGetFaceGeometry" 1283 /*@C 1284 DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces 1285 1286 Input Parameters: 1287 + dm - The DM 1288 . fStart - The first face to include 1289 . fEnd - The first face to exclude 1290 . faceGeometry - A local vector with face geometry 1291 - cellGeometry - A local vector with cell geometry 1292 1293 Output Parameters: 1294 + fgeom - The extract the face centroid and normal 1295 - vol - The cell volume 1296 1297 Level: developer 1298 1299 .seealso: DMPlexGetCellFields() 1300 @*/ 1301 PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1302 { 1303 DM dmFace, dmCell; 1304 DMLabel ghostLabel; 1305 const PetscScalar *facegeom, *cellgeom; 1306 PetscInt dim, numFaces = fEnd - fStart, iface, face; 1307 PetscErrorCode ierr; 1308 1309 PetscFunctionBegin; 1310 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1311 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); 1312 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); 1313 PetscValidPointer(fgeom, 6); 1314 PetscValidPointer(vol, 7); 1315 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1316 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1317 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1318 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1319 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1320 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1321 ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); 1322 ierr = DMGetWorkArray(dm, numFaces*2, PETSC_SCALAR, vol);CHKERRQ(ierr); 1323 for (face = fStart, iface = 0; face < fEnd; ++face) { 1324 const PetscInt *cells; 1325 PetscFVFaceGeom *fg; 1326 PetscFVCellGeom *cgL, *cgR; 1327 PetscFVFaceGeom *fgeoml = *fgeom; 1328 PetscReal *voll = *vol; 1329 PetscInt ghost, d; 1330 1331 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1332 if (ghost >= 0) continue; 1333 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1334 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1335 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1336 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1337 for (d = 0; d < dim; ++d) { 1338 fgeoml[iface].centroid[d] = fg->centroid[d]; 1339 fgeoml[iface].normal[d] = fg->normal[d]; 1340 } 1341 voll[iface*2+0] = cgL->volume; 1342 voll[iface*2+1] = cgR->volume; 1343 ++iface; 1344 } 1345 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1346 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1347 PetscFunctionReturn(0); 1348 } 1349 1350 #undef __FUNCT__ 1351 #define __FUNCT__ "DMPlexRestoreFaceGeometry" 1352 /*@C 1353 DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces 1354 1355 Input Parameters: 1356 + dm - The DM 1357 . fStart - The first face to include 1358 . fEnd - The first face to exclude 1359 . faceGeometry - A local vector with face geometry 1360 - cellGeometry - A local vector with cell geometry 1361 1362 Output Parameters: 1363 + fgeom - The extract the face centroid and normal 1364 - vol - The cell volume 1365 1366 Level: developer 1367 1368 .seealso: DMPlexGetFaceFields() 1369 @*/ 1370 PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscFVFaceGeom **fgeom, PetscReal **vol) 1371 { 1372 PetscErrorCode ierr; 1373 1374 PetscFunctionBegin; 1375 ierr = PetscFree(*fgeom);CHKERRQ(ierr); 1376 ierr = DMRestoreWorkArray(dm, 0, PETSC_REAL, vol);CHKERRQ(ierr); 1377 PetscFunctionReturn(0); 1378 } 1379 1380 #undef __FUNCT__ 1381 #define __FUNCT__ "DMPlexApplyLimiter_Internal" 1382 static PetscErrorCode DMPlexApplyLimiter_Internal(DM dm, DM dmCell, PetscLimiter lim, PetscInt dim, PetscInt dof, PetscInt off, PetscInt cell, PetscInt face, PetscInt fStart, PetscInt fEnd, 1383 PetscReal *cellPhi, const PetscScalar *x, const PetscScalar *cellgeom, const PetscFVCellGeom *cg, const PetscScalar *cx, const PetscScalar *cgrad) 1384 { 1385 const PetscInt *children; 1386 PetscInt numChildren; 1387 PetscErrorCode ierr; 1388 1389 PetscFunctionBegin; 1390 ierr = DMPlexGetTreeChildren(dm,face,&numChildren,&children);CHKERRQ(ierr); 1391 if (numChildren) { 1392 PetscInt c; 1393 1394 for (c = 0; c < numChildren; c++) { 1395 PetscInt childFace = children[c]; 1396 1397 if (childFace >= fStart && childFace < fEnd) { 1398 ierr = DMPlexApplyLimiter_Internal(dm,dmCell,lim,dim,dof,off,cell,childFace,fStart,fEnd,cellPhi,x,cellgeom,cg,cx,cgrad);CHKERRQ(ierr); 1399 } 1400 } 1401 } else { 1402 PetscScalar *ncx; 1403 PetscFVCellGeom *ncg; 1404 const PetscInt *fcells; 1405 PetscInt ncell, d; 1406 PetscReal v[3]; 1407 1408 ierr = DMPlexGetSupport(dm, face, &fcells);CHKERRQ(ierr); 1409 ncell = cell == fcells[0] ? fcells[1] : fcells[0]; 1410 ierr = DMPlexPointLocalRead(dm, ncell, x, &ncx);CHKERRQ(ierr); 1411 ierr = DMPlexPointLocalRead(dmCell, ncell, cellgeom, &ncg);CHKERRQ(ierr); 1412 DMPlex_WaxpyD_Internal(dim, -1, cg->centroid, ncg->centroid, v); 1413 for (d = 0; d < dof; ++d) { 1414 /* We use the symmetric slope limited form of Berger, Aftosmis, and Murman 2005 */ 1415 PetscReal phi, flim = 0.5 * PetscRealPart(ncx[off+d] - cx[off+d]) / DMPlex_DotD_Internal(dim, &cgrad[d*dim], v); 1416 1417 ierr = PetscLimiterLimit(lim, flim, &phi);CHKERRQ(ierr); 1418 cellPhi[d] = PetscMin(cellPhi[d], phi); 1419 } 1420 } 1421 PetscFunctionReturn(0); 1422 } 1423 1424 #undef __FUNCT__ 1425 #define __FUNCT__ "DMPlexReconstructGradients_Internal" 1426 PetscErrorCode DMPlexReconstructGradients_Internal(DM dm, PetscFV fvm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, Vec locX, Vec grad) 1427 { 1428 DM dmFace, dmCell, dmGrad; 1429 DMLabel ghostLabel; 1430 PetscDS prob; 1431 PetscLimiter lim; 1432 const PetscScalar *facegeom, *cellgeom, *x; 1433 PetscScalar *gr; 1434 PetscReal *cellPhi; 1435 PetscInt dim, face, cell, field, dof, off, 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 = PetscDSGetFieldIndex(prob, (PetscObject) fvm, &field);CHKERRQ(ierr); 1442 ierr = PetscDSGetFieldOffset(prob, field, &off);CHKERRQ(ierr); 1443 ierr = PetscDSGetFieldSize(prob, field, &dof);CHKERRQ(ierr); 1444 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1445 ierr = PetscFVGetLimiter(fvm, &lim);CHKERRQ(ierr); 1446 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1447 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1448 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1449 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1450 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1451 ierr = VecGetDM(grad, &dmGrad);CHKERRQ(ierr); 1452 ierr = VecZeroEntries(grad);CHKERRQ(ierr); 1453 ierr = VecGetArray(grad, &gr);CHKERRQ(ierr); 1454 /* Reconstruct gradients */ 1455 for (face = fStart; face < fEnd; ++face) { 1456 const PetscInt *cells; 1457 PetscFVFaceGeom *fg; 1458 PetscScalar *cx[2]; 1459 PetscScalar *cgrad[2]; 1460 PetscBool boundary; 1461 PetscInt ghost, c, pd, d, numChildren, numCells; 1462 1463 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1464 ierr = DMIsBoundaryPoint(dm, face, &boundary);CHKERRQ(ierr); 1465 ierr = DMPlexGetTreeChildren(dm, face, &numChildren, NULL);CHKERRQ(ierr); 1466 if (ghost >= 0 || boundary || numChildren) continue; 1467 ierr = DMPlexGetSupportSize(dm, face, &numCells);CHKERRQ(ierr); 1468 if (numCells != 2) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "facet %d has %d support points: expected 2",face,numCells); 1469 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1470 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1471 for (c = 0; c < 2; ++c) { 1472 ierr = DMPlexPointLocalRead(dm, cells[c], x, &cx[c]);CHKERRQ(ierr); 1473 ierr = DMPlexPointGlobalRef(dmGrad, cells[c], gr, &cgrad[c]);CHKERRQ(ierr); 1474 } 1475 for (pd = 0; pd < dof; ++pd) { 1476 PetscScalar delta = cx[1][off+pd] - cx[0][off+pd]; 1477 1478 for (d = 0; d < dim; ++d) { 1479 if (cgrad[0]) cgrad[0][pd*dim+d] += fg->grad[0][d] * delta; 1480 if (cgrad[1]) cgrad[1][pd*dim+d] -= fg->grad[1][d] * delta; 1481 } 1482 } 1483 } 1484 /* Limit interior gradients (using cell-based loop because it generalizes better to vector limiters) */ 1485 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1486 ierr = DMPlexGetHybridBounds(dm, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 1487 cEndInterior = cEndInterior < 0 ? cEnd : cEndInterior; 1488 ierr = DMGetWorkArray(dm, dof, PETSC_REAL, &cellPhi);CHKERRQ(ierr); 1489 for (cell = dmGrad && lim ? cStart : cEnd; cell < cEndInterior; ++cell) { 1490 const PetscInt *faces; 1491 PetscScalar *cx; 1492 PetscFVCellGeom *cg; 1493 PetscScalar *cgrad; 1494 PetscInt coneSize, f, pd, d; 1495 1496 ierr = DMPlexGetConeSize(dm, cell, &coneSize);CHKERRQ(ierr); 1497 ierr = DMPlexGetCone(dm, cell, &faces);CHKERRQ(ierr); 1498 ierr = DMPlexPointLocalRead(dm, cell, x, &cx);CHKERRQ(ierr); 1499 ierr = DMPlexPointLocalRead(dmCell, cell, cellgeom, &cg);CHKERRQ(ierr); 1500 ierr = DMPlexPointGlobalRef(dmGrad, cell, gr, &cgrad);CHKERRQ(ierr); 1501 if (!cgrad) continue; /* Unowned overlap cell, we do not compute */ 1502 /* Limiter will be minimum value over all neighbors */ 1503 for (d = 0; d < dof; ++d) cellPhi[d] = PETSC_MAX_REAL; 1504 for (f = 0; f < coneSize; ++f) { 1505 ierr = DMPlexApplyLimiter_Internal(dm,dmCell,lim,dim,dof,off,cell,faces[f],fStart,fEnd,cellPhi,x,cellgeom,cg,cx,cgrad);CHKERRQ(ierr); 1506 } 1507 /* Apply limiter to gradient */ 1508 for (pd = 0; pd < dof; ++pd) 1509 /* Scalar limiter applied to each component separately */ 1510 for (d = 0; d < dim; ++d) cgrad[pd*dim+d] *= cellPhi[pd]; 1511 } 1512 ierr = DMRestoreWorkArray(dm, dof, PETSC_REAL, &cellPhi);CHKERRQ(ierr); 1513 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1514 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1515 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1516 ierr = VecRestoreArray(grad, &gr);CHKERRQ(ierr); 1517 PetscFunctionReturn(0); 1518 } 1519 1520 #undef __FUNCT__ 1521 #define __FUNCT__ "DMPlexComputeBdResidual_Internal" 1522 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1523 { 1524 DM_Plex *mesh = (DM_Plex *) dm->data; 1525 PetscSection section; 1526 PetscDS prob; 1527 DMLabel depth; 1528 PetscFECellGeom *cgeom; 1529 PetscScalar *u = NULL, *u_t = NULL, *elemVec = NULL; 1530 PetscInt dim, Nf, f, totDimBd, numBd, bd; 1531 PetscErrorCode ierr; 1532 1533 PetscFunctionBegin; 1534 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1535 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1536 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1537 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1538 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 1539 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1540 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 1541 for (bd = 0; bd < numBd; ++bd) { 1542 const char *bdLabel; 1543 DMLabel label; 1544 IS pointIS; 1545 const PetscInt *points; 1546 const PetscInt *values; 1547 PetscInt field, numValues, v, numPoints, p, dep, numFaces; 1548 PetscBool isEssential; 1549 PetscObject obj; 1550 PetscClassId id; 1551 1552 ierr = DMGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1553 ierr = DMGetField(dm, field, &obj);CHKERRQ(ierr); 1554 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1555 if ((id != PETSCFE_CLASSID) || isEssential) continue; 1556 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1557 for (v = 0; v < numValues; ++v) { 1558 ierr = DMLabelGetStratumSize(label, values[v], &numPoints);CHKERRQ(ierr); 1559 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1560 if (!pointIS) continue; /* No points with that id on this process */ 1561 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 1562 for (p = 0, numFaces = 0; p < numPoints; ++p) { 1563 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1564 if (dep == dim-1) ++numFaces; 1565 } 1566 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd,&elemVec);CHKERRQ(ierr); 1567 if (locX_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 1568 for (p = 0, f = 0; p < numPoints; ++p) { 1569 const PetscInt point = points[p]; 1570 PetscScalar *x = NULL; 1571 PetscInt i; 1572 1573 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 1574 if (dep != dim-1) continue; 1575 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 1576 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n);CHKERRQ(ierr); 1577 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 1578 /* TODO: Matt, this is wrong if feBd does not match fe: i.e., if the order differs. */ 1579 ierr = DMPlexVecGetClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1580 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 1581 ierr = DMPlexVecRestoreClosure(dm, section, locX, point, NULL, &x);CHKERRQ(ierr); 1582 if (locX_t) { 1583 ierr = DMPlexVecGetClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1584 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 1585 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, point, NULL, &x);CHKERRQ(ierr); 1586 } 1587 ++f; 1588 } 1589 for (f = 0; f < Nf; ++f) { 1590 PetscFE fe; 1591 PetscQuadrature q; 1592 PetscInt numQuadPoints, Nb; 1593 /* Conforming batches */ 1594 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1595 /* Remainder */ 1596 PetscInt Nr, offset; 1597 1598 ierr = PetscDSGetBdDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1599 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1600 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1601 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1602 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 1603 blockSize = Nb*numQuadPoints; 1604 batchSize = numBlocks * blockSize; 1605 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1606 numChunks = numFaces / (numBatches*batchSize); 1607 Ne = numChunks*numBatches*batchSize; 1608 Nr = numFaces % (numBatches*batchSize); 1609 offset = numFaces - Nr; 1610 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Ne, cgeom, u, u_t, NULL, NULL, t, elemVec);CHKERRQ(ierr); 1611 ierr = PetscFEIntegrateBdResidual(fe, prob, f, Nr, &cgeom[offset], &u[offset*totDimBd], u_t ? &u_t[offset*totDimBd] : NULL, NULL, NULL, t, &elemVec[offset*totDimBd]);CHKERRQ(ierr); 1612 } 1613 for (p = 0, f = 0; p < numPoints; ++p) { 1614 const PetscInt point = points[p]; 1615 1616 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 1617 if (dep != dim-1) continue; 1618 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDimBd, &elemVec[f*totDimBd]);CHKERRQ(ierr);} 1619 ierr = DMPlexVecSetClosure(dm, NULL, locF, point, &elemVec[f*totDimBd], ADD_ALL_VALUES);CHKERRQ(ierr); 1620 ++f; 1621 } 1622 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1623 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1624 ierr = PetscFree3(u,cgeom,elemVec);CHKERRQ(ierr); 1625 if (locX_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 1626 } 1627 } 1628 PetscFunctionReturn(0); 1629 } 1630 1631 #undef __FUNCT__ 1632 #define __FUNCT__ "DMPlexReconstructGradientsFVM" 1633 /*@ 1634 DMPlexReconstructGradientsFVM - reconstruct the gradient of a vector using a finite volume method. 1635 1636 Input Parameters: 1637 + dm - the mesh 1638 - locX - the local representation of the vector 1639 1640 Output Parameter: 1641 . grad - the global representation of the gradient 1642 1643 Level: developer 1644 1645 .seealso: DMPlexSNESGetGradientDM() 1646 @*/ 1647 PetscErrorCode DMPlexReconstructGradientsFVM(DM dm, Vec locX, Vec grad) 1648 { 1649 PetscDS prob; 1650 PetscInt Nf, f, fStart, fEnd; 1651 PetscBool useFVM = PETSC_FALSE; 1652 PetscFV fvm = NULL; 1653 Vec faceGeometryFVM, cellGeometryFVM; 1654 PetscFVCellGeom *cgeomFVM = NULL; 1655 PetscFVFaceGeom *fgeomFVM = NULL; 1656 DM dmGrad = NULL; 1657 PetscErrorCode ierr; 1658 1659 PetscFunctionBegin; 1660 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1661 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1662 for (f = 0; f < Nf; ++f) { 1663 PetscObject obj; 1664 PetscClassId id; 1665 1666 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1667 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1668 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1669 } 1670 if (!useFVM) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"This dm does not have a finite volume discretization"); 1671 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1672 if (!dmGrad) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"This dm's finite volume discretization does not reconstruct gradients"); 1673 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1674 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1675 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1676 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1677 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1678 PetscFunctionReturn(0); 1679 } 1680 1681 #undef __FUNCT__ 1682 #define __FUNCT__ "DMPlexComputeResidual_Internal" 1683 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, PetscInt cStart, PetscInt cEnd, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1684 { 1685 DM_Plex *mesh = (DM_Plex *) dm->data; 1686 const char *name = "Residual"; 1687 DM dmAux = NULL; 1688 DM dmGrad = NULL; 1689 DMLabel ghostLabel = NULL; 1690 PetscDS prob = NULL; 1691 PetscDS probAux = NULL; 1692 PetscSection section = NULL; 1693 PetscBool useFEM = PETSC_FALSE; 1694 PetscBool useFVM = PETSC_FALSE; 1695 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1696 PetscFV fvm = NULL; 1697 PetscFECellGeom *cgeomFEM = NULL; 1698 PetscScalar *cgeomScal; 1699 PetscFVCellGeom *cgeomFVM = NULL; 1700 PetscFVFaceGeom *fgeomFVM = NULL; 1701 Vec locA, cellGeometryFEM = NULL, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1702 PetscScalar *u, *u_t, *a, *uL, *uR; 1703 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1704 PetscErrorCode ierr; 1705 1706 PetscFunctionBegin; 1707 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1708 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1709 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1710 /* FEM+FVM */ 1711 /* 1: Get sizes from dm and dmAux */ 1712 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1713 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1714 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1715 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1716 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1717 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1718 if (locA) { 1719 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1720 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1721 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1722 } 1723 /* 2: Get geometric data */ 1724 for (f = 0; f < Nf; ++f) { 1725 PetscObject obj; 1726 PetscClassId id; 1727 PetscBool fimp; 1728 1729 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1730 if (isImplicit != fimp) continue; 1731 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1732 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1733 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1734 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1735 } 1736 if (useFEM) { 1737 ierr = DMPlexSNESGetGeometryFEM(dm, &cellGeometryFEM);CHKERRQ(ierr); 1738 ierr = VecGetArray(cellGeometryFEM, &cgeomScal);CHKERRQ(ierr); 1739 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1740 DM dmCell; 1741 PetscInt c; 1742 1743 ierr = VecGetDM(cellGeometryFEM,&dmCell);CHKERRQ(ierr); 1744 ierr = PetscMalloc1(cEnd-cStart,&cgeomFEM);CHKERRQ(ierr); 1745 for (c = 0; c < cEnd - cStart; c++) { 1746 PetscScalar *thisgeom; 1747 1748 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 1749 cgeomFEM[c] = *((PetscFECellGeom *) thisgeom); 1750 } 1751 } 1752 else { 1753 cgeomFEM = (PetscFECellGeom *) cgeomScal; 1754 } 1755 } 1756 if (useFVM) { 1757 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1758 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1759 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1760 /* Reconstruct and limit cell gradients */ 1761 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1762 if (dmGrad) { 1763 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1764 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1765 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1766 /* Communicate gradient values */ 1767 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1768 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1769 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1770 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1771 } 1772 /* Handle non-essential (e.g. outflow) boundary values */ 1773 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1774 } 1775 /* Loop over chunks */ 1776 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1777 numChunks = 1; 1778 cellChunkSize = (cEnd - cStart)/numChunks; 1779 faceChunkSize = (fEnd - fStart)/numChunks; 1780 for (chunk = 0; chunk < numChunks; ++chunk) { 1781 PetscScalar *elemVec, *fluxL, *fluxR; 1782 PetscReal *vol; 1783 PetscFVFaceGeom *fgeom; 1784 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, cell; 1785 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = fE - fS, face; 1786 1787 /* Extract field coefficients */ 1788 if (useFEM) { 1789 ierr = DMPlexGetCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1790 ierr = DMGetWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1791 ierr = PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1792 } 1793 if (useFVM) { 1794 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1795 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1796 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1797 ierr = DMGetWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1798 ierr = PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1799 ierr = PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1800 } 1801 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1802 /* Loop over fields */ 1803 for (f = 0; f < Nf; ++f) { 1804 PetscObject obj; 1805 PetscClassId id; 1806 PetscBool fimp; 1807 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1808 1809 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1810 if (isImplicit != fimp) continue; 1811 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1812 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1813 if (id == PETSCFE_CLASSID) { 1814 PetscFE fe = (PetscFE) obj; 1815 PetscQuadrature q; 1816 PetscInt Nq, Nb; 1817 1818 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1819 1820 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 1821 ierr = PetscQuadratureGetData(q, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1822 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1823 blockSize = Nb*Nq; 1824 batchSize = numBlocks * blockSize; 1825 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1826 numChunks = numCells / (numBatches*batchSize); 1827 Ne = numChunks*numBatches*batchSize; 1828 Nr = numCells % (numBatches*batchSize); 1829 offset = numCells - Nr; 1830 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1831 /* 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) */ 1832 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeomFEM, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1833 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, &cgeomFEM[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1834 } else if (id == PETSCFV_CLASSID) { 1835 PetscFV fv = (PetscFV) obj; 1836 1837 Ne = numFaces; 1838 /* Riemann solve over faces (need fields at face centroids) */ 1839 /* We need to evaluate FE fields at those coordinates */ 1840 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1841 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f); 1842 } 1843 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 1844 ierr = PetscFree(cgeomFEM);CHKERRQ(ierr); 1845 } 1846 else { 1847 cgeomFEM = NULL; 1848 } 1849 if (cellGeometryFEM) {ierr = VecRestoreArray(cellGeometryFEM, &cgeomScal);CHKERRQ(ierr);} 1850 /* Loop over domain */ 1851 if (useFEM) { 1852 /* Add elemVec to locX */ 1853 for (cell = cS; cell < cE; ++cell) { 1854 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cell*totDim]);CHKERRQ(ierr);} 1855 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cell*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1856 } 1857 } 1858 if (useFVM) { 1859 PetscScalar *fa; 1860 PetscInt iface; 1861 1862 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1863 for (f = 0; f < Nf; ++f) { 1864 PetscFV fv; 1865 PetscObject obj; 1866 PetscClassId id; 1867 PetscInt foff, pdim; 1868 1869 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1870 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1871 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1872 if (id != PETSCFV_CLASSID) continue; 1873 fv = (PetscFV) obj; 1874 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1875 /* Accumulate fluxes to cells */ 1876 for (face = fS, iface = 0; face < fE; ++face) { 1877 const PetscInt *cells; 1878 PetscScalar *fL, *fR; 1879 PetscInt ghost, d, nsupp; 1880 1881 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1882 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1883 if (ghost >= 0) continue; 1884 if (nsupp > 2) { /* noop */ 1885 ++iface; 1886 continue; 1887 } 1888 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1889 ierr = DMPlexPointGlobalFieldRef(dm, cells[0], f, fa, &fL);CHKERRQ(ierr); 1890 ierr = DMPlexPointGlobalFieldRef(dm, cells[1], f, fa, &fR);CHKERRQ(ierr); 1891 for (d = 0; d < pdim; ++d) { 1892 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1893 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1894 } 1895 ++iface; 1896 } 1897 } 1898 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1899 } 1900 /* Handle time derivative */ 1901 if (locX_t) { 1902 PetscScalar *x_t, *fa; 1903 1904 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1905 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1906 for (f = 0; f < Nf; ++f) { 1907 PetscFV fv; 1908 PetscObject obj; 1909 PetscClassId id; 1910 PetscInt pdim, d; 1911 1912 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1913 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1914 if (id != PETSCFV_CLASSID) continue; 1915 fv = (PetscFV) obj; 1916 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1917 for (cell = cS; cell < cE; ++cell) { 1918 PetscScalar *u_t, *r; 1919 1920 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1921 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1922 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1923 } 1924 } 1925 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1926 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1927 } 1928 if (useFEM) { 1929 ierr = DMPlexRestoreCellFields(dm, cS, cE, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1930 ierr = DMRestoreWorkArray(dm, numCells*totDim, PETSC_SCALAR, &elemVec);CHKERRQ(ierr); 1931 } 1932 if (useFVM) { 1933 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &uL, &uR);CHKERRQ(ierr); 1934 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &fgeom, &vol);CHKERRQ(ierr); 1935 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxL);CHKERRQ(ierr); 1936 ierr = DMRestoreWorkArray(dm, numFaces*totDim, PETSC_SCALAR, &fluxR);CHKERRQ(ierr); 1937 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1938 } 1939 } 1940 1941 if (useFEM) {ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr);} 1942 1943 /* FEM */ 1944 /* 1: Get sizes from dm and dmAux */ 1945 /* 2: Get geometric data */ 1946 /* 3: Handle boundary values */ 1947 /* 4: Loop over domain */ 1948 /* Extract coefficients */ 1949 /* Loop over fields */ 1950 /* Set tiling for FE*/ 1951 /* Integrate FE residual to get elemVec */ 1952 /* Loop over subdomain */ 1953 /* Loop over quad points */ 1954 /* Transform coords to real space */ 1955 /* Evaluate field and aux fields at point */ 1956 /* Evaluate residual at point */ 1957 /* Transform residual to real space */ 1958 /* Add residual to elemVec */ 1959 /* Loop over domain */ 1960 /* Add elemVec to locX */ 1961 1962 /* FVM */ 1963 /* Get geometric data */ 1964 /* If using gradients */ 1965 /* Compute gradient data */ 1966 /* Loop over domain faces */ 1967 /* Count computational faces */ 1968 /* Reconstruct cell gradient */ 1969 /* Loop over domain cells */ 1970 /* Limit cell gradients */ 1971 /* Handle boundary values */ 1972 /* Loop over domain faces */ 1973 /* Read out field, centroid, normal, volume for each side of face */ 1974 /* Riemann solve over faces */ 1975 /* Loop over domain faces */ 1976 /* Accumulate fluxes to cells */ 1977 /* TODO Change printFEM to printDisc here */ 1978 if (mesh->printFEM) { 1979 Vec locFbc; 1980 PetscInt pStart, pEnd, p, maxDof; 1981 PetscScalar *zeroes; 1982 1983 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1984 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1985 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1986 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1987 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1988 for (p = pStart; p < pEnd; p++) { 1989 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1990 } 1991 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1992 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1993 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1994 } 1995 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1996 PetscFunctionReturn(0); 1997 } 1998 1999 #undef __FUNCT__ 2000 #define __FUNCT__ "DMPlexComputeResidualFEM_Check_Internal" 2001 static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, PetscReal t, Vec F, void *user) 2002 { 2003 DM dmCh, dmAux; 2004 Vec A, cellgeom; 2005 PetscDS prob, probCh, probAux = NULL; 2006 PetscQuadrature q; 2007 PetscSection section, sectionAux; 2008 PetscFECellGeom *cgeom = NULL; 2009 PetscScalar *cgeomScal; 2010 PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL; 2011 PetscInt dim, Nf, f, numCells, cStart, cEnd, c; 2012 PetscInt totDim, totDimAux, diffCell = 0; 2013 PetscErrorCode ierr; 2014 2015 PetscFunctionBegin; 2016 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2017 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2018 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2019 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2020 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2021 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2022 numCells = cEnd - cStart; 2023 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);CHKERRQ(ierr); 2024 ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); 2025 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2026 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2027 if (dmAux) { 2028 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 2029 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2030 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2031 } 2032 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 2033 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);CHKERRQ(ierr); 2034 ierr = PetscMalloc1(numCells*totDim,&elemVecCh);CHKERRQ(ierr); 2035 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2036 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 2037 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2038 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2039 DM dmCell; 2040 2041 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 2042 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 2043 for (c = 0; c < cEnd - cStart; c++) { 2044 PetscScalar *thisgeom; 2045 2046 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 2047 cgeom[c] = *((PetscFECellGeom *) thisgeom); 2048 } 2049 } 2050 else { 2051 cgeom = (PetscFECellGeom *) cgeomScal; 2052 } 2053 for (c = cStart; c < cEnd; ++c) { 2054 PetscScalar *x = NULL, *x_t = NULL; 2055 PetscInt i; 2056 2057 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2058 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 2059 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2060 if (X_t) { 2061 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2062 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 2063 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2064 } 2065 if (dmAux) { 2066 DM dmAuxPlex; 2067 2068 ierr = DMSNESConvertPlex(dmAux,&dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 2069 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2070 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 2071 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2072 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 2073 } 2074 } 2075 for (f = 0; f < Nf; ++f) { 2076 PetscFE fe, feCh; 2077 PetscInt numQuadPoints, Nb; 2078 /* Conforming batches */ 2079 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2080 /* Remainder */ 2081 PetscInt Nr, offset; 2082 2083 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 2084 ierr = PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);CHKERRQ(ierr); 2085 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 2086 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2087 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2088 ierr = PetscQuadratureGetData(q, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2089 blockSize = Nb*numQuadPoints; 2090 batchSize = numBlocks * blockSize; 2091 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2092 numChunks = numCells / (numBatches*batchSize); 2093 Ne = numChunks*numBatches*batchSize; 2094 Nr = numCells % (numBatches*batchSize); 2095 offset = numCells - Nr; 2096 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, cgeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 2097 ierr = PetscFEIntegrateResidual(feCh, prob, f, Ne, cgeom, u, u_t, probAux, a, t, elemVecCh);CHKERRQ(ierr); 2098 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 2099 ierr = PetscFEIntegrateResidual(feCh, prob, f, Nr, &cgeom[offset], &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVecCh[offset*totDim]);CHKERRQ(ierr); 2100 } 2101 for (c = cStart; c < cEnd; ++c) { 2102 PetscBool diff = PETSC_FALSE; 2103 PetscInt d; 2104 2105 for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;} 2106 if (diff) { 2107 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);CHKERRQ(ierr); 2108 ierr = DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);CHKERRQ(ierr); 2109 ierr = DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);CHKERRQ(ierr); 2110 ++diffCell; 2111 } 2112 if (diffCell > 9) break; 2113 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 2114 } 2115 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2116 ierr = PetscFree(cgeom);CHKERRQ(ierr); 2117 } 2118 else { 2119 cgeom = NULL; 2120 } 2121 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2122 ierr = PetscFree3(u,u_t,elemVec);CHKERRQ(ierr); 2123 ierr = PetscFree(elemVecCh);CHKERRQ(ierr); 2124 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 2125 PetscFunctionReturn(0); 2126 } 2127 2128 #undef __FUNCT__ 2129 #define __FUNCT__ "DMPlexSNESComputeResidualFEM" 2130 /*@ 2131 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 2132 2133 Input Parameters: 2134 + dm - The mesh 2135 . X - Local solution 2136 - user - The user context 2137 2138 Output Parameter: 2139 . F - Local output vector 2140 2141 Level: developer 2142 2143 .seealso: DMPlexComputeJacobianActionFEM() 2144 @*/ 2145 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 2146 { 2147 PetscObject check; 2148 PetscInt cStart, cEnd, cEndInterior; 2149 DM plex; 2150 PetscErrorCode ierr; 2151 2152 PetscFunctionBegin; 2153 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2154 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 2155 ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2156 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2157 /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */ 2158 ierr = PetscObjectQuery((PetscObject) plex, "dmCh", &check);CHKERRQ(ierr); 2159 if (check) {ierr = DMPlexComputeResidualFEM_Check_Internal(plex, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 2160 else {ierr = DMPlexComputeResidual_Internal(plex, cStart, cEnd, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 2161 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2162 PetscFunctionReturn(0); 2163 } 2164 2165 #undef __FUNCT__ 2166 #define __FUNCT__ "DMPlexSNESComputeBoundaryFEM" 2167 /*@ 2168 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 2169 2170 Input Parameters: 2171 + dm - The mesh 2172 - user - The user context 2173 2174 Output Parameter: 2175 . X - Local solution 2176 2177 Level: developer 2178 2179 .seealso: DMPlexComputeJacobianActionFEM() 2180 @*/ 2181 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 2182 { 2183 DM plex; 2184 PetscErrorCode ierr; 2185 2186 PetscFunctionBegin; 2187 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2188 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 2189 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2190 PetscFunctionReturn(0); 2191 } 2192 2193 #undef __FUNCT__ 2194 #define __FUNCT__ "DMPlexComputeJacobian_Internal" 2195 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) 2196 { 2197 DM_Plex *mesh = (DM_Plex *) dm->data; 2198 const char *name = "Jacobian"; 2199 DM dmAux, plex; 2200 DMLabel depth; 2201 Vec A, cellgeom; 2202 PetscDS prob, probAux = NULL; 2203 PetscQuadrature quad; 2204 PetscSection section, globalSection, sectionAux; 2205 PetscFECellGeom *cgeom = NULL; 2206 PetscScalar *cgeomScal; 2207 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 2208 PetscInt dim, Nf, f, fieldI, fieldJ, numCells, c; 2209 PetscInt totDim, totDimBd, totDimAux, numBd, bd; 2210 PetscBool isShell, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE; 2211 PetscErrorCode ierr; 2212 2213 PetscFunctionBegin; 2214 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2215 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2216 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2217 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2218 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2219 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2220 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 2221 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2222 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2223 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2224 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2225 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2226 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2227 numCells = cEnd - cStart; 2228 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2229 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2230 if (dmAux) { 2231 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2232 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2233 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2234 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2235 } 2236 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2237 ierr = PetscMalloc5(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,hasJac ? numCells*totDim*totDim : 0,&elemMat,hasPrec ? numCells*totDim*totDim : 0, &elemMatP,hasDyn ? numCells*totDim*totDim : 0, &elemMatD);CHKERRQ(ierr); 2238 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2239 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 2240 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2241 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2242 DM dmCell; 2243 2244 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 2245 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 2246 for (c = 0; c < cEnd - cStart; c++) { 2247 PetscScalar *thisgeom; 2248 2249 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 2250 cgeom[c] = *((PetscFECellGeom *) thisgeom); 2251 } 2252 } else { 2253 cgeom = (PetscFECellGeom *) cgeomScal; 2254 } 2255 for (c = cStart; c < cEnd; ++c) { 2256 PetscScalar *x = NULL, *x_t = NULL; 2257 PetscInt i; 2258 2259 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2260 for (i = 0; i < totDim; ++i) u[(c-cStart)*totDim+i] = x[i]; 2261 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2262 if (X_t) { 2263 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2264 for (i = 0; i < totDim; ++i) u_t[(c-cStart)*totDim+i] = x_t[i]; 2265 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2266 } 2267 if (dmAux) { 2268 ierr = DMPlexVecGetClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2269 for (i = 0; i < totDimAux; ++i) a[(c-cStart)*totDimAux+i] = x[i]; 2270 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2271 } 2272 } 2273 if (hasJac) {ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2274 if (hasPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2275 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2276 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2277 PetscClassId id; 2278 PetscFE fe; 2279 PetscInt numQuadPoints, Nb; 2280 /* Conforming batches */ 2281 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2282 /* Remainder */ 2283 PetscInt Nr, offset; 2284 2285 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2286 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 2287 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 2288 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2289 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2290 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2291 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2292 blockSize = Nb*numQuadPoints; 2293 batchSize = numBlocks * blockSize; 2294 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2295 numChunks = numCells / (numBatches*batchSize); 2296 Ne = numChunks*numBatches*batchSize; 2297 Nr = numCells % (numBatches*batchSize); 2298 offset = numCells - Nr; 2299 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2300 if (hasJac) { 2301 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2302 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], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 2303 } 2304 if (hasPrec) { 2305 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2306 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], t, X_tShift, &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 2307 } 2308 if (hasDyn) { 2309 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2310 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], t, X_tShift, &elemMatD[offset*totDim*totDim]);CHKERRQ(ierr); 2311 } 2312 } 2313 } 2314 if (hasDyn) { 2315 for (c = 0; c < (cEnd - cStart)*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2316 } 2317 if (hasFV) { 2318 PetscClassId id; 2319 PetscFV fv; 2320 PetscInt offsetI, NcI, NbI = 1, fc, f; 2321 2322 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2323 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2324 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 2325 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 2326 if (id != PETSCFV_CLASSID) continue; 2327 /* Put in the identity */ 2328 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 2329 for (c = cStart; c < cEnd; ++c) { 2330 const PetscInt eOffset = (c-cStart)*totDim*totDim; 2331 for (fc = 0; fc < NcI; ++fc) { 2332 for (f = 0; f < NbI; ++f) { 2333 const PetscInt i = offsetI + f*NcI+fc; 2334 if (hasPrec) { 2335 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 2336 elemMatP[eOffset+i*totDim+i] = 1.0; 2337 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 2338 } 2339 } 2340 } 2341 } 2342 /* No allocated space for FV stuff, so ignore the zero entries */ 2343 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 2344 } 2345 for (c = cStart; c < cEnd; ++c) { 2346 if (hasPrec) { 2347 if (hasJac) { 2348 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2349 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, c, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2350 } 2351 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2352 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMatP[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2353 } else { 2354 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2355 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, c, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2356 } 2357 } 2358 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2359 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2360 ierr = PetscFree(cgeom);CHKERRQ(ierr); 2361 } else { 2362 cgeom = NULL; 2363 } 2364 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2365 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2366 if (dmAux) { 2367 ierr = PetscFree(a);CHKERRQ(ierr); 2368 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2369 } 2370 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2371 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 2372 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2373 ierr = DMGetNumBoundary(dm, &numBd);CHKERRQ(ierr); 2374 for (bd = 0; bd < numBd; ++bd) { 2375 const char *bdLabel; 2376 DMLabel label; 2377 IS pointIS; 2378 const PetscInt *points; 2379 const PetscInt *values; 2380 PetscInt field, numValues, v, numPoints, p, dep, numFaces; 2381 PetscBool isEssential; 2382 PetscObject obj; 2383 PetscClassId id; 2384 2385 ierr = DMGetBoundary(dm, bd, &isEssential, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 2386 ierr = DMGetField(dm, field, &obj);CHKERRQ(ierr); 2387 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2388 if ((id != PETSCFE_CLASSID) || isEssential) continue; 2389 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2390 for (v = 0; v < numValues; ++v) { 2391 ierr = DMLabelGetStratumSize(label, values[v], &numPoints);CHKERRQ(ierr); 2392 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 2393 if (!pointIS) continue; /* No points with that id on this process */ 2394 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2395 for (p = 0, numFaces = 0; p < numPoints; ++p) { 2396 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2397 if (dep == dim-1) ++numFaces; 2398 } 2399 ierr = PetscMalloc3(numFaces*totDimBd,&u,numFaces,&cgeom,numFaces*totDimBd*totDimBd,&elemMat);CHKERRQ(ierr); 2400 if (X_t) {ierr = PetscMalloc1(numFaces*totDimBd,&u_t);CHKERRQ(ierr);} 2401 for (p = 0, f = 0; p < numPoints; ++p) { 2402 const PetscInt point = points[p]; 2403 PetscScalar *x = NULL; 2404 PetscInt i; 2405 2406 ierr = DMLabelGetValue(depth, points[p], &dep);CHKERRQ(ierr); 2407 if (dep != dim-1) continue; 2408 ierr = DMPlexComputeCellGeometryFEM(dm, point, NULL, cgeom[f].v0, cgeom[f].J, cgeom[f].invJ, &cgeom[f].detJ);CHKERRQ(ierr); 2409 ierr = DMPlexComputeCellGeometryFVM(dm, point, NULL, NULL, cgeom[f].n);CHKERRQ(ierr); 2410 if (cgeom[f].detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for face %d", cgeom[f].detJ, point); 2411 ierr = DMPlexVecGetClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2412 for (i = 0; i < totDimBd; ++i) u[f*totDimBd+i] = x[i]; 2413 ierr = DMPlexVecRestoreClosure(dm, section, X, point, NULL, &x);CHKERRQ(ierr); 2414 if (X_t) { 2415 ierr = DMPlexVecGetClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2416 for (i = 0; i < totDimBd; ++i) u_t[f*totDimBd+i] = x[i]; 2417 ierr = DMPlexVecRestoreClosure(dm, section, X_t, point, NULL, &x);CHKERRQ(ierr); 2418 } 2419 ++f; 2420 } 2421 ierr = PetscMemzero(elemMat, numFaces*totDimBd*totDimBd * sizeof(PetscScalar));CHKERRQ(ierr); 2422 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2423 PetscFE fe; 2424 PetscInt numQuadPoints, Nb; 2425 /* Conforming batches */ 2426 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2427 /* Remainder */ 2428 PetscInt Nr, offset; 2429 2430 ierr = PetscDSGetBdDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2431 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2432 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2433 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2434 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2435 blockSize = Nb*numQuadPoints; 2436 batchSize = numBlocks * blockSize; 2437 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2438 numChunks = numFaces / (numBatches*batchSize); 2439 Ne = numChunks*numBatches*batchSize; 2440 Nr = numFaces % (numBatches*batchSize); 2441 offset = numFaces - Nr; 2442 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2443 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, cgeom, u, u_t, NULL, NULL, t, X_tShift, elemMat);CHKERRQ(ierr); 2444 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Nr, &cgeom[offset], &u[offset*totDimBd], u_t ? &u_t[offset*totDimBd] : NULL, NULL, NULL, t, X_tShift, &elemMat[offset*totDimBd*totDimBd]);CHKERRQ(ierr); 2445 } 2446 } 2447 for (p = 0, f = 0; p < numPoints; ++p) { 2448 const PetscInt point = points[p]; 2449 2450 ierr = DMLabelGetValue(depth, point, &dep);CHKERRQ(ierr); 2451 if (dep != dim-1) continue; 2452 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDimBd, totDimBd, &elemMat[f*totDimBd*totDimBd]);CHKERRQ(ierr);} 2453 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, point, &elemMat[f*totDimBd*totDimBd], ADD_VALUES);CHKERRQ(ierr); 2454 ++f; 2455 } 2456 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2457 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2458 ierr = PetscFree3(u,cgeom,elemMat);CHKERRQ(ierr); 2459 if (X_t) {ierr = PetscFree(u_t);CHKERRQ(ierr);} 2460 } 2461 } 2462 if (hasJac && hasPrec) { 2463 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2464 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2465 } 2466 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2467 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2468 if (mesh->printFEM) { 2469 ierr = PetscPrintf(PETSC_COMM_WORLD, "%s:\n", name);CHKERRQ(ierr); 2470 ierr = MatChop(JacP, 1.0e-10);CHKERRQ(ierr); 2471 ierr = MatView(JacP, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2472 } 2473 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2474 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATSHELL, &isShell);CHKERRQ(ierr); 2475 if (isShell) { 2476 JacActionCtx *jctx; 2477 2478 ierr = MatShellGetContext(Jac, &jctx);CHKERRQ(ierr); 2479 ierr = VecCopy(X, jctx->u);CHKERRQ(ierr); 2480 } 2481 PetscFunctionReturn(0); 2482 } 2483 2484 2485 #undef __FUNCT__ 2486 #define __FUNCT__ "DMPlexComputeJacobianAction_Internal" 2487 PetscErrorCode DMPlexComputeJacobianAction_Internal(DM dm, PetscInt cStart, PetscInt cEnd, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 2488 { 2489 DM_Plex *mesh = (DM_Plex *) dm->data; 2490 const char *name = "Jacobian"; 2491 DM dmAux, plex; 2492 Vec A, cellgeom; 2493 PetscDS prob, probAux = NULL; 2494 PetscQuadrature quad; 2495 PetscSection section, globalSection, sectionAux; 2496 PetscFECellGeom *cgeom = NULL; 2497 PetscScalar *cgeomScal; 2498 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2499 PetscInt dim, Nf, fieldI, fieldJ, numCells, c; 2500 PetscInt totDim, totDimBd, totDimAux; 2501 PetscBool hasDyn; 2502 PetscErrorCode ierr; 2503 2504 PetscFunctionBegin; 2505 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2506 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2507 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2508 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2509 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2510 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2511 ierr = PetscDSGetTotalBdDimension(prob, &totDimBd);CHKERRQ(ierr); 2512 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2513 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2514 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2515 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 2516 numCells = cEnd - cStart; 2517 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2518 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2519 if (dmAux) { 2520 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2521 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2522 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2523 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2524 } 2525 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2526 ierr = PetscMalloc6(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim*totDim,&elemMat,hasDyn ? numCells*totDim*totDim : 0, &elemMatD,numCells*totDim,&y,totDim,&z);CHKERRQ(ierr); 2527 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2528 ierr = DMPlexSNESGetGeometryFEM(dm, &cellgeom);CHKERRQ(ierr); 2529 ierr = VecGetArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2530 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) { 2531 DM dmCell; 2532 2533 ierr = VecGetDM(cellgeom,&dmCell);CHKERRQ(ierr); 2534 ierr = PetscMalloc1(cEnd-cStart,&cgeom);CHKERRQ(ierr); 2535 for (c = 0; c < cEnd - cStart; c++) { 2536 PetscScalar *thisgeom; 2537 2538 ierr = DMPlexPointLocalRef(dmCell, c + cStart, cgeomScal, &thisgeom);CHKERRQ(ierr); 2539 cgeom[c] = *((PetscFECellGeom *) thisgeom); 2540 } 2541 } else { 2542 cgeom = (PetscFECellGeom *) cgeomScal; 2543 } 2544 for (c = cStart; c < cEnd; ++c) { 2545 PetscScalar *x = NULL, *x_t = NULL; 2546 PetscInt i; 2547 2548 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2549 for (i = 0; i < totDim; ++i) u[(c-cStart)*totDim+i] = x[i]; 2550 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 2551 if (X_t) { 2552 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2553 for (i = 0; i < totDim; ++i) u_t[(c-cStart)*totDim+i] = x_t[i]; 2554 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 2555 } 2556 if (dmAux) { 2557 ierr = DMPlexVecGetClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2558 for (i = 0; i < totDimAux; ++i) a[(c-cStart)*totDimAux+i] = x[i]; 2559 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 2560 } 2561 ierr = DMPlexVecGetClosure(dm, section, Y, c, NULL, &x);CHKERRQ(ierr); 2562 for (i = 0; i < totDim; ++i) y[(c-cStart)*totDim+i] = x[i]; 2563 ierr = DMPlexVecRestoreClosure(dm, section, Y, c, NULL, &x);CHKERRQ(ierr); 2564 } 2565 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2566 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2567 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2568 PetscFE fe; 2569 PetscInt numQuadPoints, Nb; 2570 /* Conforming batches */ 2571 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2572 /* Remainder */ 2573 PetscInt Nr, offset; 2574 2575 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2576 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2577 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2578 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2579 ierr = PetscQuadratureGetData(quad, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2580 blockSize = Nb*numQuadPoints; 2581 batchSize = numBlocks * blockSize; 2582 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2583 numChunks = numCells / (numBatches*batchSize); 2584 Ne = numChunks*numBatches*batchSize; 2585 Nr = numCells % (numBatches*batchSize); 2586 offset = numCells - Nr; 2587 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2588 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2589 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], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 2590 if (hasDyn) { 2591 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, cgeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2592 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], t, X_tShift, &elemMatD[offset*totDim*totDim]);CHKERRQ(ierr); 2593 } 2594 } 2595 } 2596 if (hasDyn) { 2597 for (c = 0; c < (cEnd - cStart)*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2598 } 2599 for (c = cStart; c < cEnd; ++c) { 2600 const PetscBLASInt M = totDim, one = 1; 2601 const PetscScalar a = 1.0, b = 0.0; 2602 2603 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[(c-cStart)*totDim*totDim], &M, &y[(c-cStart)*totDim], &one, &b, z, &one)); 2604 if (mesh->printFEM > 1) { 2605 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr); 2606 ierr = DMPrintCellVector(c, "Y", totDim, &y[(c-cStart)*totDim]);CHKERRQ(ierr); 2607 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2608 } 2609 ierr = DMPlexVecSetClosure(dm, section, Z, c, z, ADD_VALUES);CHKERRQ(ierr); 2610 } 2611 if (sizeof(PetscFECellGeom) % sizeof(PetscScalar)) {ierr = PetscFree(cgeom);CHKERRQ(ierr);} 2612 else {cgeom = NULL;} 2613 ierr = VecRestoreArray(cellgeom, &cgeomScal);CHKERRQ(ierr); 2614 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2615 if (dmAux) { 2616 ierr = PetscFree(a);CHKERRQ(ierr); 2617 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2618 } 2619 if (mesh->printFEM) { 2620 ierr = PetscPrintf(PETSC_COMM_WORLD, "Z:\n");CHKERRQ(ierr); 2621 ierr = VecView(Z, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2622 } 2623 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2624 PetscFunctionReturn(0); 2625 } 2626 2627 #undef __FUNCT__ 2628 #define __FUNCT__ "DMPlexSNESComputeJacobianFEM" 2629 /*@ 2630 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2631 2632 Input Parameters: 2633 + dm - The mesh 2634 . X - Local input vector 2635 - user - The user context 2636 2637 Output Parameter: 2638 . Jac - Jacobian matrix 2639 2640 Note: 2641 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2642 like a GPU, or vectorize on a multicore machine. 2643 2644 Level: developer 2645 2646 .seealso: FormFunctionLocal() 2647 @*/ 2648 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2649 { 2650 PetscInt cStart, cEnd, cEndInterior; 2651 DM plex; 2652 PetscErrorCode ierr; 2653 2654 PetscFunctionBegin; 2655 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2656 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 2657 ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2658 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2659 ierr = DMPlexComputeJacobian_Internal(plex, cStart, cEnd, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2660 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2661 PetscFunctionReturn(0); 2662 } 2663 2664 #undef __FUNCT__ 2665 #define __FUNCT__ "DMPlexSNESComputeJacobianActionFEM" 2666 /*@ 2667 DMPlexSNESComputeJacobianActionFEM - Form the local portion of the Jacobian action Z = J(X) Y at the local solution X using pointwise functions specified by the user. 2668 2669 Input Parameters: 2670 + dm - The mesh 2671 . X - Local solution vector 2672 . Y - Local input vector 2673 - user - The user context 2674 2675 Output Parameter: 2676 . Z - Local output vector 2677 2678 Note: 2679 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2680 like a GPU, or vectorize on a multicore machine. 2681 2682 Level: developer 2683 2684 .seealso: FormFunctionLocal() 2685 @*/ 2686 PetscErrorCode DMPlexSNESComputeJacobianActionFEM(DM dm, Vec X, Vec Y, Vec Z, void *user) 2687 { 2688 PetscInt cStart, cEnd, cEndInterior; 2689 DM plex; 2690 PetscErrorCode ierr; 2691 2692 PetscFunctionBegin; 2693 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2694 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 2695 ierr = DMPlexGetHybridBounds(plex, &cEndInterior, NULL, NULL, NULL);CHKERRQ(ierr); 2696 cEnd = cEndInterior < 0 ? cEnd : cEndInterior; 2697 ierr = DMPlexComputeJacobianAction_Internal(plex, cStart, cEnd, 0.0, 0.0, X, NULL, Y, Z, user);CHKERRQ(ierr); 2698 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2699 PetscFunctionReturn(0); 2700 } 2701 2702 #undef __FUNCT__ 2703 #define __FUNCT__ "DMPlexSetSNESLocalFEM" 2704 /*@ 2705 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2706 2707 Input Parameters: 2708 + dm - The DM object 2709 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see DMAddBoundary()) 2710 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2711 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2712 2713 Level: developer 2714 @*/ 2715 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2716 { 2717 PetscErrorCode ierr; 2718 2719 PetscFunctionBegin; 2720 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2721 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2722 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2723 PetscFunctionReturn(0); 2724 } 2725 2726 #undef __FUNCT__ 2727 #define __FUNCT__ "DMSNESCheckFromOptions_Internal" 2728 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) 2729 { 2730 Mat J, M; 2731 Vec r, b; 2732 MatNullSpace nullSpace; 2733 PetscReal *error, res = 0.0; 2734 PetscInt numFields; 2735 PetscErrorCode ierr; 2736 2737 PetscFunctionBegin; 2738 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2739 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2740 M = J; 2741 /* TODO Null space for J */ 2742 /* Check discretization error */ 2743 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 2744 ierr = PetscMalloc1(PetscMax(1, numFields), &error);CHKERRQ(ierr); 2745 if (numFields > 1) { 2746 PetscInt f; 2747 2748 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs, ctxs, u, error);CHKERRQ(ierr); 2749 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: [");CHKERRQ(ierr); 2750 for (f = 0; f < numFields; ++f) { 2751 if (f) {ierr = PetscPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);} 2752 if (error[f] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "%g", error[f]);CHKERRQ(ierr);} 2753 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "< 1.0e-11");CHKERRQ(ierr);} 2754 } 2755 ierr = PetscPrintf(PETSC_COMM_WORLD, "]\n");CHKERRQ(ierr); 2756 } else { 2757 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs, ctxs, u, &error[0]);CHKERRQ(ierr); 2758 if (error[0] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error[0]);CHKERRQ(ierr);} 2759 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} 2760 } 2761 ierr = PetscFree(error);CHKERRQ(ierr); 2762 /* Check residual */ 2763 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2764 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2765 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); 2766 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2767 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2768 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2769 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2770 /* Check Jacobian */ 2771 ierr = SNESComputeJacobian(snes, u, M, M);CHKERRQ(ierr); 2772 ierr = MatGetNullSpace(J, &nullSpace);CHKERRQ(ierr); 2773 if (nullSpace) { 2774 PetscBool isNull; 2775 ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr); 2776 if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2777 } 2778 ierr = VecDuplicate(u, &b);CHKERRQ(ierr); 2779 ierr = VecSet(r, 0.0);CHKERRQ(ierr); 2780 ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); 2781 ierr = MatMult(M, u, r);CHKERRQ(ierr); 2782 ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); 2783 ierr = VecDestroy(&b);CHKERRQ(ierr); 2784 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2785 ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr); 2786 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2787 ierr = PetscObjectSetName((PetscObject) r, "Au - b = Au + F(0)");CHKERRQ(ierr); 2788 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"linear_res_");CHKERRQ(ierr); 2789 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2790 ierr = VecDestroy(&r);CHKERRQ(ierr); 2791 ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); 2792 ierr = MatDestroy(&J);CHKERRQ(ierr); 2793 PetscFunctionReturn(0); 2794 } 2795 2796 #undef __FUNCT__ 2797 #define __FUNCT__ "DMSNESCheckFromOptions" 2798 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2799 { 2800 DM dm; 2801 Vec sol; 2802 PetscBool check; 2803 PetscErrorCode ierr; 2804 2805 PetscFunctionBegin; 2806 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 2807 if (!check) PetscFunctionReturn(0); 2808 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 2809 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 2810 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 2811 ierr = DMSNESCheckFromOptions_Internal(snes, dm, u, sol, exactFuncs, ctxs);CHKERRQ(ierr); 2812 ierr = VecDestroy(&sol);CHKERRQ(ierr); 2813 PetscFunctionReturn(0); 2814 } 2815