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 static PetscErrorCode DMSNESConvertPlex(DM dm, DM *plex, PetscBool copy) 11 { 12 PetscBool isPlex; 13 PetscErrorCode ierr; 14 15 PetscFunctionBegin; 16 ierr = PetscObjectTypeCompare((PetscObject) dm, DMPLEX, &isPlex);CHKERRQ(ierr); 17 if (isPlex) { 18 *plex = dm; 19 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 20 } else { 21 ierr = PetscObjectQuery((PetscObject) dm, "dm_plex", (PetscObject *) plex);CHKERRQ(ierr); 22 if (!*plex) { 23 ierr = DMConvert(dm,DMPLEX,plex);CHKERRQ(ierr); 24 ierr = PetscObjectCompose((PetscObject) dm, "dm_plex", (PetscObject) *plex);CHKERRQ(ierr); 25 if (copy) { 26 PetscInt i; 27 PetscObject obj; 28 const char *comps[3] = {"A","dmAux","dmCh"}; 29 30 ierr = DMCopyDMSNES(dm, *plex);CHKERRQ(ierr); 31 for (i = 0; i < 3; i++) { 32 ierr = PetscObjectQuery((PetscObject) dm, comps[i], &obj);CHKERRQ(ierr); 33 ierr = PetscObjectCompose((PetscObject) *plex, comps[i], obj);CHKERRQ(ierr); 34 } 35 } 36 } else { 37 ierr = PetscObjectReference((PetscObject) *plex);CHKERRQ(ierr); 38 } 39 } 40 PetscFunctionReturn(0); 41 } 42 43 PetscErrorCode DMInterpolationCreate(MPI_Comm comm, DMInterpolationInfo *ctx) 44 { 45 PetscErrorCode ierr; 46 47 PetscFunctionBegin; 48 PetscValidPointer(ctx, 2); 49 ierr = PetscNew(ctx);CHKERRQ(ierr); 50 51 (*ctx)->comm = comm; 52 (*ctx)->dim = -1; 53 (*ctx)->nInput = 0; 54 (*ctx)->points = NULL; 55 (*ctx)->cells = NULL; 56 (*ctx)->n = -1; 57 (*ctx)->coords = NULL; 58 PetscFunctionReturn(0); 59 } 60 61 PetscErrorCode DMInterpolationSetDim(DMInterpolationInfo ctx, PetscInt dim) 62 { 63 PetscFunctionBegin; 64 if ((dim < 1) || (dim > 3)) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid dimension for points: %d", dim); 65 ctx->dim = dim; 66 PetscFunctionReturn(0); 67 } 68 69 PetscErrorCode DMInterpolationGetDim(DMInterpolationInfo ctx, PetscInt *dim) 70 { 71 PetscFunctionBegin; 72 PetscValidIntPointer(dim, 2); 73 *dim = ctx->dim; 74 PetscFunctionReturn(0); 75 } 76 77 PetscErrorCode DMInterpolationSetDof(DMInterpolationInfo ctx, PetscInt dof) 78 { 79 PetscFunctionBegin; 80 if (dof < 1) SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid number of components: %d", dof); 81 ctx->dof = dof; 82 PetscFunctionReturn(0); 83 } 84 85 PetscErrorCode DMInterpolationGetDof(DMInterpolationInfo ctx, PetscInt *dof) 86 { 87 PetscFunctionBegin; 88 PetscValidIntPointer(dof, 2); 89 *dof = ctx->dof; 90 PetscFunctionReturn(0); 91 } 92 93 PetscErrorCode DMInterpolationAddPoints(DMInterpolationInfo ctx, PetscInt n, PetscReal points[]) 94 { 95 PetscErrorCode ierr; 96 97 PetscFunctionBegin; 98 if (ctx->dim < 0) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 99 if (ctx->points) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "Cannot add points multiple times yet"); 100 ctx->nInput = n; 101 102 ierr = PetscMalloc1(n*ctx->dim, &ctx->points);CHKERRQ(ierr); 103 ierr = PetscMemcpy(ctx->points, points, n*ctx->dim * sizeof(PetscReal));CHKERRQ(ierr); 104 PetscFunctionReturn(0); 105 } 106 107 PetscErrorCode DMInterpolationSetUp(DMInterpolationInfo ctx, DM dm, PetscBool redundantPoints) 108 { 109 MPI_Comm comm = ctx->comm; 110 PetscScalar *a; 111 PetscInt p, q, i; 112 PetscMPIInt rank, size; 113 PetscErrorCode ierr; 114 Vec pointVec; 115 PetscSF cellSF; 116 PetscLayout layout; 117 PetscReal *globalPoints; 118 PetscScalar *globalPointsScalar; 119 const PetscInt *ranges; 120 PetscMPIInt *counts, *displs; 121 const PetscSFNode *foundCells; 122 const PetscInt *foundPoints; 123 PetscMPIInt *foundProcs, *globalProcs; 124 PetscInt n, N, numFound; 125 126 PetscFunctionBegin; 127 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 128 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 129 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 130 if (ctx->dim < 0) SETERRQ(comm, PETSC_ERR_ARG_WRONGSTATE, "The spatial dimension has not been set"); 131 /* Locate points */ 132 n = ctx->nInput; 133 if (!redundantPoints) { 134 ierr = PetscLayoutCreate(comm, &layout);CHKERRQ(ierr); 135 ierr = PetscLayoutSetBlockSize(layout, 1);CHKERRQ(ierr); 136 ierr = PetscLayoutSetLocalSize(layout, n);CHKERRQ(ierr); 137 ierr = PetscLayoutSetUp(layout);CHKERRQ(ierr); 138 ierr = PetscLayoutGetSize(layout, &N);CHKERRQ(ierr); 139 /* Communicate all points to all processes */ 140 ierr = PetscMalloc3(N*ctx->dim,&globalPoints,size,&counts,size,&displs);CHKERRQ(ierr); 141 ierr = PetscLayoutGetRanges(layout, &ranges);CHKERRQ(ierr); 142 for (p = 0; p < size; ++p) { 143 counts[p] = (ranges[p+1] - ranges[p])*ctx->dim; 144 displs[p] = ranges[p]*ctx->dim; 145 } 146 ierr = MPI_Allgatherv(ctx->points, n*ctx->dim, MPIU_REAL, globalPoints, counts, displs, MPIU_REAL, comm);CHKERRQ(ierr); 147 } else { 148 N = n; 149 globalPoints = ctx->points; 150 counts = displs = NULL; 151 layout = NULL; 152 } 153 #if 0 154 ierr = PetscMalloc3(N,&foundCells,N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 155 /* foundCells[p] = m->locatePoint(&globalPoints[p*ctx->dim]); */ 156 #else 157 #if defined(PETSC_USE_COMPLEX) 158 ierr = PetscMalloc1(N*ctx->dim,&globalPointsScalar);CHKERRQ(ierr); 159 for (i=0; i<N*ctx->dim; i++) globalPointsScalar[i] = globalPoints[i]; 160 #else 161 globalPointsScalar = globalPoints; 162 #endif 163 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, ctx->dim, N*ctx->dim, globalPointsScalar, &pointVec);CHKERRQ(ierr); 164 ierr = PetscMalloc2(N,&foundProcs,N,&globalProcs);CHKERRQ(ierr); 165 for (p = 0; p < N; ++p) {foundProcs[p] = size;} 166 cellSF = NULL; 167 ierr = DMLocatePoints(dm, pointVec, DM_POINTLOCATION_REMOVE, &cellSF);CHKERRQ(ierr); 168 ierr = PetscSFGetGraph(cellSF,NULL,&numFound,&foundPoints,&foundCells);CHKERRQ(ierr); 169 #endif 170 for (p = 0; p < numFound; ++p) { 171 if (foundCells[p].index >= 0) foundProcs[foundPoints ? foundPoints[p] : p] = rank; 172 } 173 /* Let the lowest rank process own each point */ 174 ierr = MPIU_Allreduce(foundProcs, globalProcs, N, MPI_INT, MPI_MIN, comm);CHKERRQ(ierr); 175 ctx->n = 0; 176 for (p = 0; p < N; ++p) { 177 if (globalProcs[p] == size) SETERRQ4(comm, PETSC_ERR_PLIB, "Point %d: %g %g %g not located in mesh", p, (double)globalPoints[p*ctx->dim+0], (double)(ctx->dim > 1 ? globalPoints[p*ctx->dim+1] : 0.0), (double)(ctx->dim > 2 ? globalPoints[p*ctx->dim+2] : 0.0)); 178 else if (globalProcs[p] == rank) ctx->n++; 179 } 180 /* Create coordinates vector and array of owned cells */ 181 ierr = PetscMalloc1(ctx->n, &ctx->cells);CHKERRQ(ierr); 182 ierr = VecCreate(comm, &ctx->coords);CHKERRQ(ierr); 183 ierr = VecSetSizes(ctx->coords, ctx->n*ctx->dim, PETSC_DECIDE);CHKERRQ(ierr); 184 ierr = VecSetBlockSize(ctx->coords, ctx->dim);CHKERRQ(ierr); 185 ierr = VecSetType(ctx->coords,VECSTANDARD);CHKERRQ(ierr); 186 ierr = VecGetArray(ctx->coords, &a);CHKERRQ(ierr); 187 for (p = 0, q = 0, i = 0; p < N; ++p) { 188 if (globalProcs[p] == rank) { 189 PetscInt d; 190 191 for (d = 0; d < ctx->dim; ++d, ++i) a[i] = globalPoints[p*ctx->dim+d]; 192 ctx->cells[q] = foundCells[q].index; 193 ++q; 194 } 195 } 196 ierr = VecRestoreArray(ctx->coords, &a);CHKERRQ(ierr); 197 #if 0 198 ierr = PetscFree3(foundCells,foundProcs,globalProcs);CHKERRQ(ierr); 199 #else 200 ierr = PetscFree2(foundProcs,globalProcs);CHKERRQ(ierr); 201 ierr = PetscSFDestroy(&cellSF);CHKERRQ(ierr); 202 ierr = VecDestroy(&pointVec);CHKERRQ(ierr); 203 #endif 204 if ((void*)globalPointsScalar != (void*)globalPoints) {ierr = PetscFree(globalPointsScalar);CHKERRQ(ierr);} 205 if (!redundantPoints) {ierr = PetscFree3(globalPoints,counts,displs);CHKERRQ(ierr);} 206 ierr = PetscLayoutDestroy(&layout);CHKERRQ(ierr); 207 PetscFunctionReturn(0); 208 } 209 210 PetscErrorCode DMInterpolationGetCoordinates(DMInterpolationInfo ctx, Vec *coordinates) 211 { 212 PetscFunctionBegin; 213 PetscValidPointer(coordinates, 2); 214 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 215 *coordinates = ctx->coords; 216 PetscFunctionReturn(0); 217 } 218 219 PetscErrorCode DMInterpolationGetVector(DMInterpolationInfo ctx, Vec *v) 220 { 221 PetscErrorCode ierr; 222 223 PetscFunctionBegin; 224 PetscValidPointer(v, 2); 225 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 226 ierr = VecCreate(ctx->comm, v);CHKERRQ(ierr); 227 ierr = VecSetSizes(*v, ctx->n*ctx->dof, PETSC_DECIDE);CHKERRQ(ierr); 228 ierr = VecSetBlockSize(*v, ctx->dof);CHKERRQ(ierr); 229 ierr = VecSetType(*v,VECSTANDARD);CHKERRQ(ierr); 230 PetscFunctionReturn(0); 231 } 232 233 PetscErrorCode DMInterpolationRestoreVector(DMInterpolationInfo ctx, Vec *v) 234 { 235 PetscErrorCode ierr; 236 237 PetscFunctionBegin; 238 PetscValidPointer(v, 2); 239 if (!ctx->coords) SETERRQ(ctx->comm, PETSC_ERR_ARG_WRONGSTATE, "The interpolation context has not been setup."); 240 ierr = VecDestroy(v);CHKERRQ(ierr); 241 PetscFunctionReturn(0); 242 } 243 244 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Triangle_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 245 { 246 PetscReal *v0, *J, *invJ, detJ; 247 const PetscScalar *coords; 248 PetscScalar *a; 249 PetscInt p; 250 PetscErrorCode ierr; 251 252 PetscFunctionBegin; 253 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 254 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 255 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 256 for (p = 0; p < ctx->n; ++p) { 257 PetscInt c = ctx->cells[p]; 258 PetscScalar *x = NULL; 259 PetscReal xi[4]; 260 PetscInt d, f, comp; 261 262 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 263 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", (double)detJ, c); 264 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 265 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 266 267 for (d = 0; d < ctx->dim; ++d) { 268 xi[d] = 0.0; 269 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 270 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]; 271 } 272 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 273 } 274 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 275 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 276 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 277 PetscFunctionReturn(0); 278 } 279 280 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Tetrahedron_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 281 { 282 PetscReal *v0, *J, *invJ, detJ; 283 const PetscScalar *coords; 284 PetscScalar *a; 285 PetscInt p; 286 PetscErrorCode ierr; 287 288 PetscFunctionBegin; 289 ierr = PetscMalloc3(ctx->dim,&v0,ctx->dim*ctx->dim,&J,ctx->dim*ctx->dim,&invJ);CHKERRQ(ierr); 290 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 291 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 292 for (p = 0; p < ctx->n; ++p) { 293 PetscInt c = ctx->cells[p]; 294 const PetscInt order[3] = {2, 1, 3}; 295 PetscScalar *x = NULL; 296 PetscReal xi[4]; 297 PetscInt d, f, comp; 298 299 ierr = DMPlexComputeCellGeometryFEM(dm, c, NULL, v0, J, invJ, &detJ);CHKERRQ(ierr); 300 if (detJ <= 0.0) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid determinant %g for element %d", (double)detJ, c); 301 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 302 for (comp = 0; comp < ctx->dof; ++comp) a[p*ctx->dof+comp] = x[0*ctx->dof+comp]; 303 304 for (d = 0; d < ctx->dim; ++d) { 305 xi[d] = 0.0; 306 for (f = 0; f < ctx->dim; ++f) xi[d] += invJ[d*ctx->dim+f]*0.5*PetscRealPart(coords[p*ctx->dim+f] - v0[f]); 307 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]; 308 } 309 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, NULL, &x);CHKERRQ(ierr); 310 } 311 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 312 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 313 ierr = PetscFree3(v0, J, invJ);CHKERRQ(ierr); 314 PetscFunctionReturn(0); 315 } 316 317 PETSC_STATIC_INLINE PetscErrorCode QuadMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 318 { 319 const PetscScalar *vertices = (const PetscScalar*) ctx; 320 const PetscScalar x0 = vertices[0]; 321 const PetscScalar y0 = vertices[1]; 322 const PetscScalar x1 = vertices[2]; 323 const PetscScalar y1 = vertices[3]; 324 const PetscScalar x2 = vertices[4]; 325 const PetscScalar y2 = vertices[5]; 326 const PetscScalar x3 = vertices[6]; 327 const PetscScalar y3 = vertices[7]; 328 const PetscScalar f_1 = x1 - x0; 329 const PetscScalar g_1 = y1 - y0; 330 const PetscScalar f_3 = x3 - x0; 331 const PetscScalar g_3 = y3 - y0; 332 const PetscScalar f_01 = x2 - x1 - x3 + x0; 333 const PetscScalar g_01 = y2 - y1 - y3 + y0; 334 const PetscScalar *ref; 335 PetscScalar *real; 336 PetscErrorCode ierr; 337 338 PetscFunctionBegin; 339 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 340 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 341 { 342 const PetscScalar p0 = ref[0]; 343 const PetscScalar p1 = ref[1]; 344 345 real[0] = x0 + f_1 * p0 + f_3 * p1 + f_01 * p0 * p1; 346 real[1] = y0 + g_1 * p0 + g_3 * p1 + g_01 * p0 * p1; 347 } 348 ierr = PetscLogFlops(28);CHKERRQ(ierr); 349 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 350 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 351 PetscFunctionReturn(0); 352 } 353 354 #include <petsc/private/dmimpl.h> 355 PETSC_STATIC_INLINE PetscErrorCode QuadJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 356 { 357 const PetscScalar *vertices = (const PetscScalar*) ctx; 358 const PetscScalar x0 = vertices[0]; 359 const PetscScalar y0 = vertices[1]; 360 const PetscScalar x1 = vertices[2]; 361 const PetscScalar y1 = vertices[3]; 362 const PetscScalar x2 = vertices[4]; 363 const PetscScalar y2 = vertices[5]; 364 const PetscScalar x3 = vertices[6]; 365 const PetscScalar y3 = vertices[7]; 366 const PetscScalar f_01 = x2 - x1 - x3 + x0; 367 const PetscScalar g_01 = y2 - y1 - y3 + y0; 368 const PetscScalar *ref; 369 PetscErrorCode ierr; 370 371 PetscFunctionBegin; 372 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 373 { 374 const PetscScalar x = ref[0]; 375 const PetscScalar y = ref[1]; 376 const PetscInt rows[2] = {0, 1}; 377 PetscScalar values[4]; 378 379 values[0] = (x1 - x0 + f_01*y) * 0.5; values[1] = (x3 - x0 + f_01*x) * 0.5; 380 values[2] = (y1 - y0 + g_01*y) * 0.5; values[3] = (y3 - y0 + g_01*x) * 0.5; 381 ierr = MatSetValues(J, 2, rows, 2, rows, values, INSERT_VALUES);CHKERRQ(ierr); 382 } 383 ierr = PetscLogFlops(30);CHKERRQ(ierr); 384 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 385 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 386 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 387 PetscFunctionReturn(0); 388 } 389 390 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Quad_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 391 { 392 DM dmCoord; 393 PetscFE fem = NULL; 394 SNES snes; 395 KSP ksp; 396 PC pc; 397 Vec coordsLocal, r, ref, real; 398 Mat J; 399 const PetscScalar *coords; 400 PetscScalar *a; 401 PetscInt Nf, p; 402 const PetscInt dof = ctx->dof; 403 PetscErrorCode ierr; 404 405 PetscFunctionBegin; 406 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 407 if (Nf) {ierr = DMGetField(dm, 0, (PetscObject *) &fem);CHKERRQ(ierr);} 408 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 409 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 410 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 411 ierr = SNESSetOptionsPrefix(snes, "quad_interp_");CHKERRQ(ierr); 412 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 413 ierr = VecSetSizes(r, 2, 2);CHKERRQ(ierr); 414 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 415 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 416 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 417 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 418 ierr = MatSetSizes(J, 2, 2, 2, 2);CHKERRQ(ierr); 419 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 420 ierr = MatSetUp(J);CHKERRQ(ierr); 421 ierr = SNESSetFunction(snes, r, QuadMap_Private, NULL);CHKERRQ(ierr); 422 ierr = SNESSetJacobian(snes, J, J, QuadJacobian_Private, NULL);CHKERRQ(ierr); 423 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 424 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 425 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 426 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 427 428 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 429 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 430 for (p = 0; p < ctx->n; ++p) { 431 PetscScalar *x = NULL, *vertices = NULL; 432 PetscScalar *xi; 433 PetscReal xir[2]; 434 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 435 436 /* Can make this do all points at once */ 437 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 438 if (4*2 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 4*2); 439 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 440 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 441 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 442 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 443 xi[0] = coords[p*ctx->dim+0]; 444 xi[1] = coords[p*ctx->dim+1]; 445 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 446 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 447 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 448 xir[0] = PetscRealPart(xi[0]); 449 xir[1] = PetscRealPart(xi[1]); 450 if (4*dof != xSize) { 451 PetscReal *B; 452 PetscInt d; 453 454 xir[0] = 2.0*xir[0] - 1.0; xir[1] = 2.0*xir[1] - 1.0; 455 ierr = PetscFEGetTabulation(fem, 1, xir, &B, NULL, NULL);CHKERRQ(ierr); 456 for (comp = 0; comp < dof; ++comp) { 457 a[p*dof+comp] = 0.0; 458 for (d = 0; d < xSize/dof; ++d) { 459 a[p*dof+comp] += x[d*dof+comp]*B[d*dof+comp]; 460 } 461 } 462 ierr = PetscFERestoreTabulation(fem, 1, xir, &B, NULL, NULL);CHKERRQ(ierr); 463 } else { 464 for (comp = 0; comp < dof; ++comp) 465 a[p*dof+comp] = x[0*dof+comp]*(1 - xir[0])*(1 - xir[1]) + x[1*dof+comp]*xir[0]*(1 - xir[1]) + x[2*dof+comp]*xir[0]*xir[1] + x[3*dof+comp]*(1 - xir[0])*xir[1]; 466 } 467 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 468 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 469 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 470 } 471 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 472 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 473 474 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 475 ierr = VecDestroy(&r);CHKERRQ(ierr); 476 ierr = VecDestroy(&ref);CHKERRQ(ierr); 477 ierr = VecDestroy(&real);CHKERRQ(ierr); 478 ierr = MatDestroy(&J);CHKERRQ(ierr); 479 PetscFunctionReturn(0); 480 } 481 482 PETSC_STATIC_INLINE PetscErrorCode HexMap_Private(SNES snes, Vec Xref, Vec Xreal, void *ctx) 483 { 484 const PetscScalar *vertices = (const PetscScalar*) ctx; 485 const PetscScalar x0 = vertices[0]; 486 const PetscScalar y0 = vertices[1]; 487 const PetscScalar z0 = vertices[2]; 488 const PetscScalar x1 = vertices[9]; 489 const PetscScalar y1 = vertices[10]; 490 const PetscScalar z1 = vertices[11]; 491 const PetscScalar x2 = vertices[6]; 492 const PetscScalar y2 = vertices[7]; 493 const PetscScalar z2 = vertices[8]; 494 const PetscScalar x3 = vertices[3]; 495 const PetscScalar y3 = vertices[4]; 496 const PetscScalar z3 = vertices[5]; 497 const PetscScalar x4 = vertices[12]; 498 const PetscScalar y4 = vertices[13]; 499 const PetscScalar z4 = vertices[14]; 500 const PetscScalar x5 = vertices[15]; 501 const PetscScalar y5 = vertices[16]; 502 const PetscScalar z5 = vertices[17]; 503 const PetscScalar x6 = vertices[18]; 504 const PetscScalar y6 = vertices[19]; 505 const PetscScalar z6 = vertices[20]; 506 const PetscScalar x7 = vertices[21]; 507 const PetscScalar y7 = vertices[22]; 508 const PetscScalar z7 = vertices[23]; 509 const PetscScalar f_1 = x1 - x0; 510 const PetscScalar g_1 = y1 - y0; 511 const PetscScalar h_1 = z1 - z0; 512 const PetscScalar f_3 = x3 - x0; 513 const PetscScalar g_3 = y3 - y0; 514 const PetscScalar h_3 = z3 - z0; 515 const PetscScalar f_4 = x4 - x0; 516 const PetscScalar g_4 = y4 - y0; 517 const PetscScalar h_4 = z4 - z0; 518 const PetscScalar f_01 = x2 - x1 - x3 + x0; 519 const PetscScalar g_01 = y2 - y1 - y3 + y0; 520 const PetscScalar h_01 = z2 - z1 - z3 + z0; 521 const PetscScalar f_12 = x7 - x3 - x4 + x0; 522 const PetscScalar g_12 = y7 - y3 - y4 + y0; 523 const PetscScalar h_12 = z7 - z3 - z4 + z0; 524 const PetscScalar f_02 = x5 - x1 - x4 + x0; 525 const PetscScalar g_02 = y5 - y1 - y4 + y0; 526 const PetscScalar h_02 = z5 - z1 - z4 + z0; 527 const PetscScalar f_012 = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 528 const PetscScalar g_012 = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 529 const PetscScalar h_012 = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 530 const PetscScalar *ref; 531 PetscScalar *real; 532 PetscErrorCode ierr; 533 534 PetscFunctionBegin; 535 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 536 ierr = VecGetArray(Xreal, &real);CHKERRQ(ierr); 537 { 538 const PetscScalar p0 = ref[0]; 539 const PetscScalar p1 = ref[1]; 540 const PetscScalar p2 = ref[2]; 541 542 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; 543 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; 544 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; 545 } 546 ierr = PetscLogFlops(114);CHKERRQ(ierr); 547 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 548 ierr = VecRestoreArray(Xreal, &real);CHKERRQ(ierr); 549 PetscFunctionReturn(0); 550 } 551 552 PETSC_STATIC_INLINE PetscErrorCode HexJacobian_Private(SNES snes, Vec Xref, Mat J, Mat M, void *ctx) 553 { 554 const PetscScalar *vertices = (const PetscScalar*) ctx; 555 const PetscScalar x0 = vertices[0]; 556 const PetscScalar y0 = vertices[1]; 557 const PetscScalar z0 = vertices[2]; 558 const PetscScalar x1 = vertices[9]; 559 const PetscScalar y1 = vertices[10]; 560 const PetscScalar z1 = vertices[11]; 561 const PetscScalar x2 = vertices[6]; 562 const PetscScalar y2 = vertices[7]; 563 const PetscScalar z2 = vertices[8]; 564 const PetscScalar x3 = vertices[3]; 565 const PetscScalar y3 = vertices[4]; 566 const PetscScalar z3 = vertices[5]; 567 const PetscScalar x4 = vertices[12]; 568 const PetscScalar y4 = vertices[13]; 569 const PetscScalar z4 = vertices[14]; 570 const PetscScalar x5 = vertices[15]; 571 const PetscScalar y5 = vertices[16]; 572 const PetscScalar z5 = vertices[17]; 573 const PetscScalar x6 = vertices[18]; 574 const PetscScalar y6 = vertices[19]; 575 const PetscScalar z6 = vertices[20]; 576 const PetscScalar x7 = vertices[21]; 577 const PetscScalar y7 = vertices[22]; 578 const PetscScalar z7 = vertices[23]; 579 const PetscScalar f_xy = x2 - x1 - x3 + x0; 580 const PetscScalar g_xy = y2 - y1 - y3 + y0; 581 const PetscScalar h_xy = z2 - z1 - z3 + z0; 582 const PetscScalar f_yz = x7 - x3 - x4 + x0; 583 const PetscScalar g_yz = y7 - y3 - y4 + y0; 584 const PetscScalar h_yz = z7 - z3 - z4 + z0; 585 const PetscScalar f_xz = x5 - x1 - x4 + x0; 586 const PetscScalar g_xz = y5 - y1 - y4 + y0; 587 const PetscScalar h_xz = z5 - z1 - z4 + z0; 588 const PetscScalar f_xyz = x6 - x0 + x1 - x2 + x3 + x4 - x5 - x7; 589 const PetscScalar g_xyz = y6 - y0 + y1 - y2 + y3 + y4 - y5 - y7; 590 const PetscScalar h_xyz = z6 - z0 + z1 - z2 + z3 + z4 - z5 - z7; 591 const PetscScalar *ref; 592 PetscErrorCode ierr; 593 594 PetscFunctionBegin; 595 ierr = VecGetArrayRead(Xref, &ref);CHKERRQ(ierr); 596 { 597 const PetscScalar x = ref[0]; 598 const PetscScalar y = ref[1]; 599 const PetscScalar z = ref[2]; 600 const PetscInt rows[3] = {0, 1, 2}; 601 PetscScalar values[9]; 602 603 values[0] = (x1 - x0 + f_xy*y + f_xz*z + f_xyz*y*z) / 2.0; 604 values[1] = (x3 - x0 + f_xy*x + f_yz*z + f_xyz*x*z) / 2.0; 605 values[2] = (x4 - x0 + f_yz*y + f_xz*x + f_xyz*x*y) / 2.0; 606 values[3] = (y1 - y0 + g_xy*y + g_xz*z + g_xyz*y*z) / 2.0; 607 values[4] = (y3 - y0 + g_xy*x + g_yz*z + g_xyz*x*z) / 2.0; 608 values[5] = (y4 - y0 + g_yz*y + g_xz*x + g_xyz*x*y) / 2.0; 609 values[6] = (z1 - z0 + h_xy*y + h_xz*z + h_xyz*y*z) / 2.0; 610 values[7] = (z3 - z0 + h_xy*x + h_yz*z + h_xyz*x*z) / 2.0; 611 values[8] = (z4 - z0 + h_yz*y + h_xz*x + h_xyz*x*y) / 2.0; 612 613 ierr = MatSetValues(J, 3, rows, 3, rows, values, INSERT_VALUES);CHKERRQ(ierr); 614 } 615 ierr = PetscLogFlops(152);CHKERRQ(ierr); 616 ierr = VecRestoreArrayRead(Xref, &ref);CHKERRQ(ierr); 617 ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 618 ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 619 PetscFunctionReturn(0); 620 } 621 622 PETSC_STATIC_INLINE PetscErrorCode DMInterpolate_Hex_Private(DMInterpolationInfo ctx, DM dm, Vec xLocal, Vec v) 623 { 624 DM dmCoord; 625 SNES snes; 626 KSP ksp; 627 PC pc; 628 Vec coordsLocal, r, ref, real; 629 Mat J; 630 const PetscScalar *coords; 631 PetscScalar *a; 632 PetscInt p; 633 PetscErrorCode ierr; 634 635 PetscFunctionBegin; 636 ierr = DMGetCoordinatesLocal(dm, &coordsLocal);CHKERRQ(ierr); 637 ierr = DMGetCoordinateDM(dm, &dmCoord);CHKERRQ(ierr); 638 ierr = SNESCreate(PETSC_COMM_SELF, &snes);CHKERRQ(ierr); 639 ierr = SNESSetOptionsPrefix(snes, "hex_interp_");CHKERRQ(ierr); 640 ierr = VecCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 641 ierr = VecSetSizes(r, 3, 3);CHKERRQ(ierr); 642 ierr = VecSetType(r,dm->vectype);CHKERRQ(ierr); 643 ierr = VecDuplicate(r, &ref);CHKERRQ(ierr); 644 ierr = VecDuplicate(r, &real);CHKERRQ(ierr); 645 ierr = MatCreate(PETSC_COMM_SELF, &J);CHKERRQ(ierr); 646 ierr = MatSetSizes(J, 3, 3, 3, 3);CHKERRQ(ierr); 647 ierr = MatSetType(J, MATSEQDENSE);CHKERRQ(ierr); 648 ierr = MatSetUp(J);CHKERRQ(ierr); 649 ierr = SNESSetFunction(snes, r, HexMap_Private, NULL);CHKERRQ(ierr); 650 ierr = SNESSetJacobian(snes, J, J, HexJacobian_Private, NULL);CHKERRQ(ierr); 651 ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); 652 ierr = KSPGetPC(ksp, &pc);CHKERRQ(ierr); 653 ierr = PCSetType(pc, PCLU);CHKERRQ(ierr); 654 ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); 655 656 ierr = VecGetArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 657 ierr = VecGetArray(v, &a);CHKERRQ(ierr); 658 for (p = 0; p < ctx->n; ++p) { 659 PetscScalar *x = NULL, *vertices = NULL; 660 PetscScalar *xi; 661 PetscReal xir[3]; 662 PetscInt c = ctx->cells[p], comp, coordSize, xSize; 663 664 /* Can make this do all points at once */ 665 ierr = DMPlexVecGetClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 666 if (8*3 != coordSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", coordSize, 8*3); 667 ierr = DMPlexVecGetClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 668 if (8*ctx->dof != xSize) SETERRQ2(ctx->comm, PETSC_ERR_ARG_SIZ, "Invalid closure size %d should be %d", xSize, 8*ctx->dof); 669 ierr = SNESSetFunction(snes, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 670 ierr = SNESSetJacobian(snes, NULL, NULL, NULL, (void*) vertices);CHKERRQ(ierr); 671 ierr = VecGetArray(real, &xi);CHKERRQ(ierr); 672 xi[0] = coords[p*ctx->dim+0]; 673 xi[1] = coords[p*ctx->dim+1]; 674 xi[2] = coords[p*ctx->dim+2]; 675 ierr = VecRestoreArray(real, &xi);CHKERRQ(ierr); 676 ierr = SNESSolve(snes, real, ref);CHKERRQ(ierr); 677 ierr = VecGetArray(ref, &xi);CHKERRQ(ierr); 678 xir[0] = PetscRealPart(xi[0]); 679 xir[1] = PetscRealPart(xi[1]); 680 xir[2] = PetscRealPart(xi[2]); 681 for (comp = 0; comp < ctx->dof; ++comp) { 682 a[p*ctx->dof+comp] = 683 x[0*ctx->dof+comp]*(1-xir[0])*(1-xir[1])*(1-xir[2]) + 684 x[3*ctx->dof+comp]* xir[0]*(1-xir[1])*(1-xir[2]) + 685 x[2*ctx->dof+comp]* xir[0]* xir[1]*(1-xir[2]) + 686 x[1*ctx->dof+comp]*(1-xir[0])* xir[1]*(1-xir[2]) + 687 x[4*ctx->dof+comp]*(1-xir[0])*(1-xir[1])* xir[2] + 688 x[5*ctx->dof+comp]* xir[0]*(1-xir[1])* xir[2] + 689 x[6*ctx->dof+comp]* xir[0]* xir[1]* xir[2] + 690 x[7*ctx->dof+comp]*(1-xir[0])* xir[1]* xir[2]; 691 } 692 ierr = VecRestoreArray(ref, &xi);CHKERRQ(ierr); 693 ierr = DMPlexVecRestoreClosure(dmCoord, NULL, coordsLocal, c, &coordSize, &vertices);CHKERRQ(ierr); 694 ierr = DMPlexVecRestoreClosure(dm, NULL, xLocal, c, &xSize, &x);CHKERRQ(ierr); 695 } 696 ierr = VecRestoreArray(v, &a);CHKERRQ(ierr); 697 ierr = VecRestoreArrayRead(ctx->coords, &coords);CHKERRQ(ierr); 698 699 ierr = SNESDestroy(&snes);CHKERRQ(ierr); 700 ierr = VecDestroy(&r);CHKERRQ(ierr); 701 ierr = VecDestroy(&ref);CHKERRQ(ierr); 702 ierr = VecDestroy(&real);CHKERRQ(ierr); 703 ierr = MatDestroy(&J);CHKERRQ(ierr); 704 PetscFunctionReturn(0); 705 } 706 707 /* 708 Input Parameters: 709 + ctx - The DMInterpolationInfo context 710 . dm - The DM 711 - x - The local vector containing the field to be interpolated 712 713 Output Parameters: 714 . v - The vector containing the interpolated values 715 */ 716 PetscErrorCode DMInterpolationEvaluate(DMInterpolationInfo ctx, DM dm, Vec x, Vec v) 717 { 718 PetscInt dim, coneSize, n; 719 PetscErrorCode ierr; 720 721 PetscFunctionBegin; 722 PetscValidHeaderSpecific(dm, DM_CLASSID, 2); 723 PetscValidHeaderSpecific(x, VEC_CLASSID, 3); 724 PetscValidHeaderSpecific(v, VEC_CLASSID, 4); 725 ierr = VecGetLocalSize(v, &n);CHKERRQ(ierr); 726 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); 727 if (n) { 728 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 729 ierr = DMPlexGetConeSize(dm, ctx->cells[0], &coneSize);CHKERRQ(ierr); 730 if (dim == 2) { 731 if (coneSize == 3) { 732 ierr = DMInterpolate_Triangle_Private(ctx, dm, x, v);CHKERRQ(ierr); 733 } else if (coneSize == 4) { 734 ierr = DMInterpolate_Quad_Private(ctx, dm, x, v);CHKERRQ(ierr); 735 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 736 } else if (dim == 3) { 737 if (coneSize == 4) { 738 ierr = DMInterpolate_Tetrahedron_Private(ctx, dm, x, v);CHKERRQ(ierr); 739 } else { 740 ierr = DMInterpolate_Hex_Private(ctx, dm, x, v);CHKERRQ(ierr); 741 } 742 } else SETERRQ1(ctx->comm, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported dimension %d for point interpolation", dim); 743 } 744 PetscFunctionReturn(0); 745 } 746 747 PetscErrorCode DMInterpolationDestroy(DMInterpolationInfo *ctx) 748 { 749 PetscErrorCode ierr; 750 751 PetscFunctionBegin; 752 PetscValidPointer(ctx, 2); 753 ierr = VecDestroy(&(*ctx)->coords);CHKERRQ(ierr); 754 ierr = PetscFree((*ctx)->points);CHKERRQ(ierr); 755 ierr = PetscFree((*ctx)->cells);CHKERRQ(ierr); 756 ierr = PetscFree(*ctx);CHKERRQ(ierr); 757 *ctx = NULL; 758 PetscFunctionReturn(0); 759 } 760 761 /*@C 762 SNESMonitorFields - Monitors the residual for each field separately 763 764 Collective on SNES 765 766 Input Parameters: 767 + snes - the SNES context 768 . its - iteration number 769 . fgnorm - 2-norm of residual 770 - vf - PetscViewerAndFormat of type ASCII 771 772 Notes: 773 This routine prints the residual norm at each iteration. 774 775 Level: intermediate 776 777 .keywords: SNES, nonlinear, default, monitor, norm 778 .seealso: SNESMonitorSet(), SNESMonitorDefault() 779 @*/ 780 PetscErrorCode SNESMonitorFields(SNES snes, PetscInt its, PetscReal fgnorm, PetscViewerAndFormat *vf) 781 { 782 PetscViewer viewer = vf->viewer; 783 Vec res; 784 DM dm; 785 PetscSection s; 786 const PetscScalar *r; 787 PetscReal *lnorms, *norms; 788 PetscInt numFields, f, pStart, pEnd, p; 789 PetscErrorCode ierr; 790 791 PetscFunctionBegin; 792 PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,4); 793 ierr = SNESGetFunction(snes, &res, 0, 0);CHKERRQ(ierr); 794 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 795 ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr); 796 ierr = PetscSectionGetNumFields(s, &numFields);CHKERRQ(ierr); 797 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 798 ierr = PetscCalloc2(numFields, &lnorms, numFields, &norms);CHKERRQ(ierr); 799 ierr = VecGetArrayRead(res, &r);CHKERRQ(ierr); 800 for (p = pStart; p < pEnd; ++p) { 801 for (f = 0; f < numFields; ++f) { 802 PetscInt fdof, foff, d; 803 804 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 805 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 806 for (d = 0; d < fdof; ++d) lnorms[f] += PetscRealPart(PetscSqr(r[foff+d])); 807 } 808 } 809 ierr = VecRestoreArrayRead(res, &r);CHKERRQ(ierr); 810 ierr = MPIU_Allreduce(lnorms, norms, numFields, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject) dm));CHKERRQ(ierr); 811 ierr = PetscViewerPushFormat(viewer,vf->format);CHKERRQ(ierr); 812 ierr = PetscViewerASCIIAddTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 813 ierr = PetscViewerASCIIPrintf(viewer, "%3D SNES Function norm %14.12e [", its, (double) fgnorm);CHKERRQ(ierr); 814 for (f = 0; f < numFields; ++f) { 815 if (f > 0) {ierr = PetscViewerASCIIPrintf(viewer, ", ");CHKERRQ(ierr);} 816 ierr = PetscViewerASCIIPrintf(viewer, "%14.12e", (double) PetscSqrtReal(norms[f]));CHKERRQ(ierr); 817 } 818 ierr = PetscViewerASCIIPrintf(viewer, "]\n");CHKERRQ(ierr); 819 ierr = PetscViewerASCIISubtractTab(viewer, ((PetscObject) snes)->tablevel);CHKERRQ(ierr); 820 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 821 ierr = PetscFree2(lnorms, norms);CHKERRQ(ierr); 822 PetscFunctionReturn(0); 823 } 824 825 /********************* Residual Computation **************************/ 826 827 static PetscErrorCode PetscContainerUserDestroy_PetscFEGeom (void *ctx) 828 { 829 PetscFEGeom *geom = (PetscFEGeom *) ctx; 830 PetscErrorCode ierr; 831 832 PetscFunctionBegin; 833 ierr = PetscFEGeomDestroy(&geom);CHKERRQ(ierr); 834 PetscFunctionReturn(0); 835 } 836 837 static PetscErrorCode DMSNESGetFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) 838 { 839 char composeStr[33] = {0}; 840 PetscObjectId id; 841 PetscContainer container; 842 PetscErrorCode ierr; 843 844 PetscFunctionBegin; 845 ierr = PetscObjectGetId((PetscObject)quad,&id);CHKERRQ(ierr); 846 ierr = PetscSNPrintf(composeStr, 32, "DMSNESGetFEGeom_%x\n", id);CHKERRQ(ierr); 847 ierr = PetscObjectQuery((PetscObject) pointIS, composeStr, (PetscObject *) &container);CHKERRQ(ierr); 848 if (container) { 849 ierr = PetscContainerGetPointer(container, (void **) geom);CHKERRQ(ierr); 850 } else { 851 ierr = DMFieldCreateFEGeom(coordField, pointIS, quad, faceData, geom);CHKERRQ(ierr); 852 ierr = PetscContainerCreate(PETSC_COMM_SELF,&container);CHKERRQ(ierr); 853 ierr = PetscContainerSetPointer(container, (void *) *geom);CHKERRQ(ierr); 854 ierr = PetscContainerSetUserDestroy(container, PetscContainerUserDestroy_PetscFEGeom);CHKERRQ(ierr); 855 ierr = PetscObjectCompose((PetscObject) pointIS, composeStr, (PetscObject) container);CHKERRQ(ierr); 856 ierr = PetscContainerDestroy(&container);CHKERRQ(ierr); 857 } 858 PetscFunctionReturn(0); 859 } 860 861 static PetscErrorCode DMSNESRestoreFEGeom(DMField coordField, IS pointIS, PetscQuadrature quad, PetscBool faceData, PetscFEGeom **geom) 862 { 863 PetscFunctionBegin; 864 *geom = NULL; 865 PetscFunctionReturn(0); 866 } 867 868 /*@ 869 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 870 871 Input Parameter: 872 . dm - The DM 873 874 Output Parameters: 875 + facegeom - The values precomputed from face geometry 876 . cellgeom - The values precomputed from cell geometry 877 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 878 879 Level: developer 880 881 .seealso: DMPlexTSSetRHSFunctionLocal() 882 @*/ 883 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 884 { 885 DM plex; 886 PetscErrorCode ierr; 887 888 PetscFunctionBegin; 889 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 890 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 891 ierr = DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);CHKERRQ(ierr); 892 if (minRadius) {ierr = DMPlexGetMinRadius(plex, minRadius);CHKERRQ(ierr);} 893 ierr = DMDestroy(&plex);CHKERRQ(ierr); 894 PetscFunctionReturn(0); 895 } 896 897 /*@ 898 DMPlexSNESGetGradientDM - Return gradient data layout 899 900 Input Parameters: 901 + dm - The DM 902 - fv - The PetscFV 903 904 Output Parameter: 905 . dmGrad - The layout for gradient values 906 907 Level: developer 908 909 .seealso: DMPlexSNESGetGeometryFVM() 910 @*/ 911 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 912 { 913 DM plex; 914 PetscBool computeGradients; 915 PetscErrorCode ierr; 916 917 PetscFunctionBegin; 918 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 919 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 920 PetscValidPointer(dmGrad,3); 921 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 922 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 923 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 924 ierr = DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);CHKERRQ(ierr); 925 ierr = DMDestroy(&plex);CHKERRQ(ierr); 926 PetscFunctionReturn(0); 927 } 928 929 /*@C 930 DMPlexGetCellFields - Retrieve the field values values for a chunk of cells 931 932 Input Parameters: 933 + dm - The DM 934 . cellIS - The cells to include 935 . locX - A local vector with the solution fields 936 . locX_t - A local vector with solution field time derivatives, or NULL 937 - locA - A local vector with auxiliary fields, or NULL 938 939 Output Parameters: 940 + u - The field coefficients 941 . u_t - The fields derivative coefficients 942 - a - The auxiliary field coefficients 943 944 Level: developer 945 946 .seealso: DMPlexGetFaceFields() 947 @*/ 948 PetscErrorCode DMPlexGetCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 949 { 950 DM plex, plexA = NULL; 951 PetscSection section, sectionAux; 952 PetscDS prob; 953 const PetscInt *cells; 954 PetscInt cStart, cEnd, numCells, totDim, totDimAux, c; 955 PetscErrorCode ierr; 956 957 PetscFunctionBegin; 958 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 959 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 960 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 961 if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 6);} 962 PetscValidPointer(u, 7); 963 PetscValidPointer(u_t, 8); 964 PetscValidPointer(a, 9); 965 ierr = DMSNESConvertPlex(dm, &plex, PETSC_FALSE);CHKERRQ(ierr); 966 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 967 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 968 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 969 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 970 if (locA) { 971 DM dmAux; 972 PetscDS probAux; 973 974 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 975 ierr = DMSNESConvertPlex(dmAux, &plexA, PETSC_FALSE);CHKERRQ(ierr); 976 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 977 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 978 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 979 } 980 numCells = cEnd - cStart; 981 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u);CHKERRQ(ierr); 982 if (locX_t) {ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u_t);CHKERRQ(ierr);} else {*u_t = NULL;} 983 if (locA) {ierr = DMGetWorkArray(dm, numCells*totDimAux, MPIU_SCALAR, a);CHKERRQ(ierr);} else {*a = NULL;} 984 for (c = cStart; c < cEnd; ++c) { 985 const PetscInt cell = cells ? cells[c] : c; 986 const PetscInt cind = c - cStart; 987 PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; 988 PetscInt i; 989 990 ierr = DMPlexVecGetClosure(plex, section, locX, cell, NULL, &x);CHKERRQ(ierr); 991 for (i = 0; i < totDim; ++i) ul[cind*totDim+i] = x[i]; 992 ierr = DMPlexVecRestoreClosure(plex, section, locX, cell, NULL, &x);CHKERRQ(ierr); 993 if (locX_t) { 994 ierr = DMPlexVecGetClosure(plex, section, locX_t, cell, NULL, &x_t);CHKERRQ(ierr); 995 for (i = 0; i < totDim; ++i) ul_t[cind*totDim+i] = x_t[i]; 996 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, cell, NULL, &x_t);CHKERRQ(ierr); 997 } 998 if (locA) { 999 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, cell, NULL, &x);CHKERRQ(ierr); 1000 for (i = 0; i < totDimAux; ++i) al[cind*totDimAux+i] = x[i]; 1001 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, cell, NULL, &x);CHKERRQ(ierr); 1002 } 1003 } 1004 ierr = DMDestroy(&plex);CHKERRQ(ierr); 1005 if (locA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1006 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1007 PetscFunctionReturn(0); 1008 } 1009 1010 /*@C 1011 DMPlexRestoreCellFields - Restore the field values values for a chunk of cells 1012 1013 Input Parameters: 1014 + dm - The DM 1015 . cellIS - The cells to include 1016 . locX - A local vector with the solution fields 1017 . locX_t - A local vector with solution field time derivatives, or NULL 1018 - locA - A local vector with auxiliary fields, or NULL 1019 1020 Output Parameters: 1021 + u - The field coefficients 1022 . u_t - The fields derivative coefficients 1023 - a - The auxiliary field coefficients 1024 1025 Level: developer 1026 1027 .seealso: DMPlexGetFaceFields() 1028 @*/ 1029 PetscErrorCode DMPlexRestoreCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 1030 { 1031 PetscErrorCode ierr; 1032 1033 PetscFunctionBegin; 1034 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u);CHKERRQ(ierr); 1035 if (locX_t) {ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u_t);CHKERRQ(ierr);} 1036 if (locA) {ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, a);CHKERRQ(ierr);} 1037 PetscFunctionReturn(0); 1038 } 1039 1040 /*@C 1041 DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces 1042 1043 Input Parameters: 1044 + dm - The DM 1045 . fStart - The first face to include 1046 . fEnd - The first face to exclude 1047 . locX - A local vector with the solution fields 1048 . locX_t - A local vector with solution field time derivatives, or NULL 1049 . faceGeometry - A local vector with face geometry 1050 . cellGeometry - A local vector with cell geometry 1051 - locaGrad - A local vector with field gradients, or NULL 1052 1053 Output Parameters: 1054 + Nface - The number of faces with field values 1055 . uL - The field values at the left side of the face 1056 - uR - The field values at the right side of the face 1057 1058 Level: developer 1059 1060 .seealso: DMPlexGetCellFields() 1061 @*/ 1062 PetscErrorCode DMPlexGetFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscInt *Nface, PetscScalar **uL, PetscScalar **uR) 1063 { 1064 DM dmFace, dmCell, dmGrad = NULL; 1065 PetscSection section; 1066 PetscDS prob; 1067 DMLabel ghostLabel; 1068 const PetscScalar *facegeom, *cellgeom, *x, *lgrad; 1069 PetscBool *isFE; 1070 PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; 1071 PetscErrorCode ierr; 1072 1073 PetscFunctionBegin; 1074 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1075 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1076 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1077 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); 1078 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); 1079 if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} 1080 PetscValidPointer(uL, 9); 1081 PetscValidPointer(uR, 10); 1082 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1083 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1084 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1085 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1086 ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); 1087 ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); 1088 for (f = 0; f < Nf; ++f) { 1089 PetscObject obj; 1090 PetscClassId id; 1091 1092 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1093 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1094 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 1095 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 1096 else {isFE[f] = PETSC_FALSE;} 1097 } 1098 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1099 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1100 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1101 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1102 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1103 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1104 if (locGrad) { 1105 ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); 1106 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1107 } 1108 ierr = DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uL);CHKERRQ(ierr); 1109 ierr = DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uR);CHKERRQ(ierr); 1110 /* Right now just eat the extra work for FE (could make a cell loop) */ 1111 for (face = fStart, iface = 0; face < fEnd; ++face) { 1112 const PetscInt *cells; 1113 PetscFVFaceGeom *fg; 1114 PetscFVCellGeom *cgL, *cgR; 1115 PetscScalar *xL, *xR, *gL, *gR; 1116 PetscScalar *uLl = *uL, *uRl = *uR; 1117 PetscInt ghost, nsupp, nchild; 1118 1119 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1120 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1121 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1122 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1123 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1124 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1125 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1126 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1127 for (f = 0; f < Nf; ++f) { 1128 PetscInt off; 1129 1130 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1131 if (isFE[f]) { 1132 const PetscInt *cone; 1133 PetscInt comp, coneSizeL, coneSizeR, faceLocL, faceLocR, ldof, rdof, d; 1134 1135 xL = xR = NULL; 1136 ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); 1137 ierr = DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1138 ierr = DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1139 ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); 1140 ierr = DMPlexGetConeSize(dm, cells[0], &coneSizeL);CHKERRQ(ierr); 1141 for (faceLocL = 0; faceLocL < coneSizeL; ++faceLocL) if (cone[faceLocL] == face) break; 1142 ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); 1143 ierr = DMPlexGetConeSize(dm, cells[1], &coneSizeR);CHKERRQ(ierr); 1144 for (faceLocR = 0; faceLocR < coneSizeR; ++faceLocR) if (cone[faceLocR] == face) break; 1145 if (faceLocL == coneSizeL && faceLocR == coneSizeR) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of cell %d or cell %d", face, cells[0], cells[1]); 1146 /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */ 1147 /* TODO: this is a hack that might not be right for nonconforming */ 1148 if (faceLocL < coneSizeL) { 1149 ierr = EvaluateFaceFields(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); 1150 if (rdof == ldof && faceLocR < coneSizeR) {ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr);} 1151 else {for(d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];} 1152 } 1153 else { 1154 ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr); 1155 ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); 1156 for(d = 0; d < comp; ++d) uLl[iface*Nc+off+d] = uRl[iface*Nc+off+d]; 1157 } 1158 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1159 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1160 } else { 1161 PetscFV fv; 1162 PetscInt numComp, c; 1163 1164 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); 1165 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1166 ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); 1167 ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); 1168 if (dmGrad) { 1169 PetscReal dxL[3], dxR[3]; 1170 1171 ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); 1172 ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); 1173 DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); 1174 DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); 1175 for (c = 0; c < numComp; ++c) { 1176 uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); 1177 uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); 1178 } 1179 } else { 1180 for (c = 0; c < numComp; ++c) { 1181 uLl[iface*Nc+off+c] = xL[c]; 1182 uRl[iface*Nc+off+c] = xR[c]; 1183 } 1184 } 1185 } 1186 } 1187 ++iface; 1188 } 1189 *Nface = iface; 1190 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1191 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1192 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1193 if (locGrad) { 1194 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1195 } 1196 ierr = PetscFree(isFE);CHKERRQ(ierr); 1197 PetscFunctionReturn(0); 1198 } 1199 1200 /*@C 1201 DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces 1202 1203 Input Parameters: 1204 + dm - The DM 1205 . fStart - The first face to include 1206 . fEnd - The first face to exclude 1207 . locX - A local vector with the solution fields 1208 . locX_t - A local vector with solution field time derivatives, or NULL 1209 . faceGeometry - A local vector with face geometry 1210 . cellGeometry - A local vector with cell geometry 1211 - locaGrad - A local vector with field gradients, or NULL 1212 1213 Output Parameters: 1214 + Nface - The number of faces with field values 1215 . uL - The field values at the left side of the face 1216 - uR - The field values at the right side of the face 1217 1218 Level: developer 1219 1220 .seealso: DMPlexGetFaceFields() 1221 @*/ 1222 PetscErrorCode DMPlexRestoreFaceFields(DM dm, PetscInt fStart, PetscInt fEnd, Vec locX, Vec locX_t, Vec faceGeometry, Vec cellGeometry, Vec locGrad, PetscInt *Nface, PetscScalar **uL, PetscScalar **uR) 1223 { 1224 PetscErrorCode ierr; 1225 1226 PetscFunctionBegin; 1227 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uL);CHKERRQ(ierr); 1228 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uR);CHKERRQ(ierr); 1229 PetscFunctionReturn(0); 1230 } 1231 1232 /*@C 1233 DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces 1234 1235 Input Parameters: 1236 + dm - The DM 1237 . fStart - The first face to include 1238 . fEnd - The first face to exclude 1239 . faceGeometry - A local vector with face geometry 1240 - cellGeometry - A local vector with cell geometry 1241 1242 Output Parameters: 1243 + Nface - The number of faces with field values 1244 . fgeom - The extract the face centroid and normal 1245 - vol - The cell volume 1246 1247 Level: developer 1248 1249 .seealso: DMPlexGetCellFields() 1250 @*/ 1251 PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol) 1252 { 1253 DM dmFace, dmCell; 1254 DMLabel ghostLabel; 1255 const PetscScalar *facegeom, *cellgeom; 1256 PetscInt dim, numFaces = fEnd - fStart, iface, face; 1257 PetscErrorCode ierr; 1258 1259 PetscFunctionBegin; 1260 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1261 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); 1262 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); 1263 PetscValidPointer(fgeom, 6); 1264 PetscValidPointer(vol, 7); 1265 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1266 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1267 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1268 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1269 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1270 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1271 ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); 1272 ierr = DMGetWorkArray(dm, numFaces*2, MPIU_SCALAR, vol);CHKERRQ(ierr); 1273 for (face = fStart, iface = 0; face < fEnd; ++face) { 1274 const PetscInt *cells; 1275 PetscFVFaceGeom *fg; 1276 PetscFVCellGeom *cgL, *cgR; 1277 PetscFVFaceGeom *fgeoml = *fgeom; 1278 PetscReal *voll = *vol; 1279 PetscInt ghost, d, nchild, nsupp; 1280 1281 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1282 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1283 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1284 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1285 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1286 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1287 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1288 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1289 for (d = 0; d < dim; ++d) { 1290 fgeoml[iface].centroid[d] = fg->centroid[d]; 1291 fgeoml[iface].normal[d] = fg->normal[d]; 1292 } 1293 voll[iface*2+0] = cgL->volume; 1294 voll[iface*2+1] = cgR->volume; 1295 ++iface; 1296 } 1297 *Nface = iface; 1298 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1299 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1300 PetscFunctionReturn(0); 1301 } 1302 1303 /*@C 1304 DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces 1305 1306 Input Parameters: 1307 + dm - The DM 1308 . fStart - The first face to include 1309 . fEnd - The first face to exclude 1310 . faceGeometry - A local vector with face geometry 1311 - cellGeometry - A local vector with cell geometry 1312 1313 Output Parameters: 1314 + Nface - The number of faces with field values 1315 . fgeom - The extract the face centroid and normal 1316 - vol - The cell volume 1317 1318 Level: developer 1319 1320 .seealso: DMPlexGetFaceFields() 1321 @*/ 1322 PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol) 1323 { 1324 PetscErrorCode ierr; 1325 1326 PetscFunctionBegin; 1327 ierr = PetscFree(*fgeom);CHKERRQ(ierr); 1328 ierr = DMRestoreWorkArray(dm, 0, MPIU_REAL, vol);CHKERRQ(ierr); 1329 PetscFunctionReturn(0); 1330 } 1331 1332 static PetscErrorCode ISIntersect_Caching(IS is1, IS is2, IS *isect) 1333 { 1334 PetscErrorCode ierr; 1335 1336 PetscFunctionBegin; 1337 *isect = NULL; 1338 if (is2 && is1) { 1339 char composeStr[33] = {0}; 1340 PetscObjectId is2id; 1341 1342 ierr = PetscObjectGetId((PetscObject)is2,&is2id);CHKERRQ(ierr); 1343 ierr = PetscSNPrintf(composeStr,32,"ISIntersect_Caching_%x",is2id);CHKERRQ(ierr); 1344 ierr = PetscObjectQuery((PetscObject) is1, composeStr, (PetscObject *) isect);CHKERRQ(ierr); 1345 if (*isect == NULL) { 1346 ierr = ISIntersect(is1, is2, isect);CHKERRQ(ierr); 1347 ierr = PetscObjectCompose((PetscObject) is1, composeStr, (PetscObject) *isect);CHKERRQ(ierr); 1348 } else { 1349 ierr = PetscObjectReference((PetscObject) *isect);CHKERRQ(ierr); 1350 } 1351 } 1352 PetscFunctionReturn(0); 1353 } 1354 1355 static PetscErrorCode DMPlexComputeBdResidual_Single_Internal(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF, DMField coordField, IS facetIS) 1356 { 1357 DM_Plex *mesh = (DM_Plex *) dm->data; 1358 DM plex = NULL, plexA = NULL; 1359 PetscDS prob, probAux = NULL; 1360 PetscSection section, sectionAux = NULL; 1361 Vec locA = NULL; 1362 PetscFEGeom *fgeom; 1363 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL; 1364 PetscInt v; 1365 PetscInt totDim, totDimAux = 0; 1366 PetscErrorCode ierr; 1367 1368 PetscFunctionBegin; 1369 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1370 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1371 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1372 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1373 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1374 if (locA) { 1375 DM dmAux; 1376 1377 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1378 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1379 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1380 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1381 ierr = DMGetDefaultSection(plexA, §ionAux);CHKERRQ(ierr); 1382 } 1383 for (v = 0; v < numValues; ++v) { 1384 PetscBool isAffine; 1385 PetscQuadrature qGeom = NULL; 1386 IS pointIS; 1387 const PetscInt *points; 1388 PetscInt numFaces, face, Nq; 1389 1390 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1391 if (!pointIS) continue; /* No points with that id on this process */ 1392 { 1393 IS isectIS; 1394 1395 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 1396 ierr = ISIntersect_Caching(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1397 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1398 pointIS = isectIS; 1399 } 1400 ierr = ISGetLocalSize(pointIS,&numFaces);CHKERRQ(ierr); 1401 ierr = ISGetIndices(pointIS,&points);CHKERRQ(ierr); 1402 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1403 ierr = DMFieldGetFEInvariance(coordField,pointIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 1404 if (isAffine) { 1405 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1406 } 1407 if (!qGeom) { 1408 PetscFE fe; 1409 1410 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1411 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1412 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1413 } 1414 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1415 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1416 for (face = 0; face < numFaces; ++face) { 1417 const PetscInt point = points[face], *support, *cone; 1418 PetscScalar *x = NULL; 1419 PetscInt i, coneSize, faceLoc; 1420 1421 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1422 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1423 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1424 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1425 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1426 fgeom->face[face][0] = faceLoc; 1427 ierr = DMPlexVecGetClosure(dm, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1428 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1429 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1430 if (locX_t) { 1431 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1432 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1433 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1434 } 1435 if (locA) { 1436 PetscInt subp; 1437 ierr = DMPlexGetSubpoint(plexA, support[0], &subp);CHKERRQ(ierr); 1438 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1439 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1440 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1441 } 1442 } 1443 ierr = PetscMemzero(elemVec, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1444 { 1445 PetscFE fe; 1446 PetscInt Nb; 1447 PetscFEGeom *chunkGeom = NULL; 1448 /* Conforming batches */ 1449 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1450 /* Remainder */ 1451 PetscInt Nr, offset; 1452 1453 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1454 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1455 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1456 /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */ 1457 blockSize = Nb; 1458 batchSize = numBlocks * blockSize; 1459 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1460 numChunks = numFaces / (numBatches*batchSize); 1461 Ne = numChunks*numBatches*batchSize; 1462 Nr = numFaces % (numBatches*batchSize); 1463 offset = numFaces - Nr; 1464 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1465 ierr = PetscFEIntegrateBdResidual(fe, prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1466 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1467 ierr = PetscFEIntegrateBdResidual(fe, prob, field, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1468 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1469 } 1470 for (face = 0; face < numFaces; ++face) { 1471 const PetscInt point = points[face], *support; 1472 1473 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);CHKERRQ(ierr);} 1474 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1475 ierr = DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1476 } 1477 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1478 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1479 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1480 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1481 ierr = PetscFree4(u, u_t, elemVec, a);CHKERRQ(ierr); 1482 } 1483 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1484 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1485 PetscFunctionReturn(0); 1486 } 1487 1488 PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF) 1489 { 1490 DMField coordField; 1491 DMLabel depthLabel; 1492 IS facetIS; 1493 PetscInt dim; 1494 PetscErrorCode ierr; 1495 1496 PetscFunctionBegin; 1497 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1498 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1499 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1500 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1501 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1502 PetscFunctionReturn(0); 1503 } 1504 1505 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1506 { 1507 PetscDS prob; 1508 PetscInt dim, numBd, bd; 1509 DMLabel depthLabel; 1510 DMField coordField = NULL; 1511 IS facetIS; 1512 PetscErrorCode ierr; 1513 1514 PetscFunctionBegin; 1515 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1516 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1517 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1518 ierr = DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);CHKERRQ(ierr); 1519 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1520 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1521 for (bd = 0; bd < numBd; ++bd) { 1522 DMBoundaryConditionType type; 1523 const char *bdLabel; 1524 DMLabel label; 1525 const PetscInt *values; 1526 PetscInt field, numValues; 1527 PetscObject obj; 1528 PetscClassId id; 1529 1530 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1531 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 1532 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1533 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1534 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1535 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1536 } 1537 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1538 PetscFunctionReturn(0); 1539 } 1540 1541 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1542 { 1543 DM_Plex *mesh = (DM_Plex *) dm->data; 1544 const char *name = "Residual"; 1545 DM dmAux = NULL; 1546 DM dmGrad = NULL; 1547 DMLabel ghostLabel = NULL; 1548 PetscDS prob = NULL; 1549 PetscDS probAux = NULL; 1550 PetscSection section = NULL; 1551 PetscBool useFEM = PETSC_FALSE; 1552 PetscBool useFVM = PETSC_FALSE; 1553 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1554 PetscFV fvm = NULL; 1555 PetscFVCellGeom *cgeomFVM = NULL; 1556 PetscFVFaceGeom *fgeomFVM = NULL; 1557 DMField coordField = NULL; 1558 Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1559 PetscScalar *u = NULL, *u_t, *a, *uL, *uR; 1560 IS chunkIS; 1561 const PetscInt *cells; 1562 PetscInt cStart, cEnd, numCells; 1563 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1564 PetscBool isAffine = PETSC_FALSE; 1565 PetscQuadrature affineQuad = NULL, *quads = NULL; 1566 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1567 PetscErrorCode ierr; 1568 1569 PetscFunctionBegin; 1570 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1571 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1572 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1573 /* FEM+FVM */ 1574 /* 1: Get sizes from dm and dmAux */ 1575 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1576 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1577 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1578 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1579 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1580 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1581 if (locA) { 1582 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1583 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1584 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1585 } 1586 /* 2: Get geometric data */ 1587 for (f = 0; f < Nf; ++f) { 1588 PetscObject obj; 1589 PetscClassId id; 1590 PetscBool fimp; 1591 1592 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1593 if (isImplicit != fimp) continue; 1594 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1595 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1596 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1597 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1598 } 1599 if (useFEM) { 1600 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1601 ierr = DMFieldGetFEInvariance(coordField,cellIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 1602 if (isAffine) { 1603 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 1604 if (affineQuad) { 1605 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1606 } 1607 } else { 1608 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1609 for (f = 0; f < Nf; ++f) { 1610 PetscObject obj; 1611 PetscClassId id; 1612 PetscBool fimp; 1613 1614 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1615 if (isImplicit != fimp) continue; 1616 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1617 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1618 if (id == PETSCFE_CLASSID) { 1619 PetscFE fe = (PetscFE) obj; 1620 1621 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1622 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 1623 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1624 } 1625 } 1626 } 1627 } 1628 if (useFVM) { 1629 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1630 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1631 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1632 /* Reconstruct and limit cell gradients */ 1633 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1634 if (dmGrad) { 1635 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1636 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1637 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1638 /* Communicate gradient values */ 1639 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1640 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1641 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1642 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1643 } 1644 /* Handle non-essential (e.g. outflow) boundary values */ 1645 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1646 } 1647 /* Loop over chunks */ 1648 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1649 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1650 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 1651 numCells = cEnd - cStart; 1652 numChunks = 1; 1653 cellChunkSize = numCells/numChunks; 1654 faceChunkSize = (fEnd - fStart)/numChunks; 1655 numChunks = PetscMin(1,numCells); 1656 for (chunk = 0; chunk < numChunks; ++chunk) { 1657 PetscScalar *elemVec, *fluxL, *fluxR; 1658 PetscReal *vol; 1659 PetscFVFaceGeom *fgeom; 1660 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1661 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face; 1662 1663 /* Extract field coefficients */ 1664 if (useFEM) { 1665 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 1666 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1667 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1668 ierr = PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1669 } 1670 if (useFVM) { 1671 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1672 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1673 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1674 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1675 ierr = PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1676 ierr = PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1677 } 1678 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1679 /* Loop over fields */ 1680 for (f = 0; f < Nf; ++f) { 1681 PetscObject obj; 1682 PetscClassId id; 1683 PetscBool fimp; 1684 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1685 1686 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1687 if (isImplicit != fimp) continue; 1688 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1689 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1690 if (id == PETSCFE_CLASSID) { 1691 PetscFE fe = (PetscFE) obj; 1692 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1693 PetscFEGeom *chunkGeom = NULL; 1694 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1695 PetscInt Nq, Nb; 1696 1697 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1698 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1699 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1700 blockSize = Nb; 1701 batchSize = numBlocks * blockSize; 1702 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1703 numChunks = numCells / (numBatches*batchSize); 1704 Ne = numChunks*numBatches*batchSize; 1705 Nr = numCells % (numBatches*batchSize); 1706 offset = numCells - Nr; 1707 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1708 /* 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) */ 1709 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1710 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1711 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1712 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 1713 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1714 } else if (id == PETSCFV_CLASSID) { 1715 PetscFV fv = (PetscFV) obj; 1716 1717 Ne = numFaces; 1718 /* Riemann solve over faces (need fields at face centroids) */ 1719 /* We need to evaluate FE fields at those coordinates */ 1720 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1721 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f); 1722 } 1723 /* Loop over domain */ 1724 if (useFEM) { 1725 /* Add elemVec to locX */ 1726 for (c = cS; c < cE; ++c) { 1727 const PetscInt cell = cells ? cells[c] : c; 1728 const PetscInt cind = c - cStart; 1729 1730 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1731 if (ghostLabel) { 1732 PetscInt ghostVal; 1733 1734 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1735 if (ghostVal > 0) continue; 1736 } 1737 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1738 } 1739 } 1740 if (useFVM) { 1741 PetscScalar *fa; 1742 PetscInt iface; 1743 1744 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1745 for (f = 0; f < Nf; ++f) { 1746 PetscFV fv; 1747 PetscObject obj; 1748 PetscClassId id; 1749 PetscInt foff, pdim; 1750 1751 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1752 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1753 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1754 if (id != PETSCFV_CLASSID) continue; 1755 fv = (PetscFV) obj; 1756 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1757 /* Accumulate fluxes to cells */ 1758 for (face = fS, iface = 0; face < fE; ++face) { 1759 const PetscInt *scells; 1760 PetscScalar *fL = NULL, *fR = NULL; 1761 PetscInt ghost, d, nsupp, nchild; 1762 1763 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1764 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1765 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1766 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1767 ierr = DMPlexGetSupport(dm, face, &scells);CHKERRQ(ierr); 1768 ierr = DMLabelGetValue(ghostLabel,scells[0],&ghost);CHKERRQ(ierr); 1769 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);CHKERRQ(ierr);} 1770 ierr = DMLabelGetValue(ghostLabel,scells[1],&ghost);CHKERRQ(ierr); 1771 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);CHKERRQ(ierr);} 1772 for (d = 0; d < pdim; ++d) { 1773 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1774 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1775 } 1776 ++iface; 1777 } 1778 } 1779 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1780 } 1781 /* Handle time derivative */ 1782 if (locX_t) { 1783 PetscScalar *x_t, *fa; 1784 1785 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1786 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1787 for (f = 0; f < Nf; ++f) { 1788 PetscFV fv; 1789 PetscObject obj; 1790 PetscClassId id; 1791 PetscInt pdim, d; 1792 1793 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1794 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1795 if (id != PETSCFV_CLASSID) continue; 1796 fv = (PetscFV) obj; 1797 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1798 for (c = cS; c < cE; ++c) { 1799 const PetscInt cell = cells ? cells[c] : c; 1800 PetscScalar *u_t, *r; 1801 1802 if (ghostLabel) { 1803 PetscInt ghostVal; 1804 1805 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 1806 if (ghostVal > 0) continue; 1807 } 1808 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1809 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1810 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1811 } 1812 } 1813 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1814 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1815 } 1816 if (useFEM) { 1817 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1818 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1819 } 1820 if (useFVM) { 1821 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1822 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1823 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1824 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1825 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1826 } 1827 } 1828 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 1829 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1830 1831 if (useFEM) { 1832 ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr); 1833 1834 if (isAffine) { 1835 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1836 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1837 } else { 1838 for (f = 0; f < Nf; ++f) { 1839 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1840 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 1841 } 1842 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1843 } 1844 } 1845 1846 /* FEM */ 1847 /* 1: Get sizes from dm and dmAux */ 1848 /* 2: Get geometric data */ 1849 /* 3: Handle boundary values */ 1850 /* 4: Loop over domain */ 1851 /* Extract coefficients */ 1852 /* Loop over fields */ 1853 /* Set tiling for FE*/ 1854 /* Integrate FE residual to get elemVec */ 1855 /* Loop over subdomain */ 1856 /* Loop over quad points */ 1857 /* Transform coords to real space */ 1858 /* Evaluate field and aux fields at point */ 1859 /* Evaluate residual at point */ 1860 /* Transform residual to real space */ 1861 /* Add residual to elemVec */ 1862 /* Loop over domain */ 1863 /* Add elemVec to locX */ 1864 1865 /* FVM */ 1866 /* Get geometric data */ 1867 /* If using gradients */ 1868 /* Compute gradient data */ 1869 /* Loop over domain faces */ 1870 /* Count computational faces */ 1871 /* Reconstruct cell gradient */ 1872 /* Loop over domain cells */ 1873 /* Limit cell gradients */ 1874 /* Handle boundary values */ 1875 /* Loop over domain faces */ 1876 /* Read out field, centroid, normal, volume for each side of face */ 1877 /* Riemann solve over faces */ 1878 /* Loop over domain faces */ 1879 /* Accumulate fluxes to cells */ 1880 /* TODO Change printFEM to printDisc here */ 1881 if (mesh->printFEM) { 1882 Vec locFbc; 1883 PetscInt pStart, pEnd, p, maxDof; 1884 PetscScalar *zeroes; 1885 1886 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1887 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1888 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1889 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1890 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1891 for (p = pStart; p < pEnd; p++) { 1892 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1893 } 1894 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1895 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1896 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1897 } 1898 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1899 PetscFunctionReturn(0); 1900 } 1901 1902 static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, PetscReal t, Vec F, void *user) 1903 { 1904 DM dmCh, dmAux; 1905 Vec A; 1906 DMField coordField = NULL; 1907 PetscDS prob, probCh, probAux = NULL; 1908 PetscSection section, sectionAux; 1909 PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL; 1910 PetscInt Nf, f, numCells, cStart, cEnd, c; 1911 PetscInt totDim, totDimAux = 0, diffCell = 0; 1912 PetscInt depth; 1913 PetscBool isAffine; 1914 IS cellIS; 1915 DMLabel depthLabel; 1916 PetscErrorCode ierr; 1917 1918 PetscFunctionBegin; 1919 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1920 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1921 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1922 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1923 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1924 numCells = cEnd - cStart; 1925 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);CHKERRQ(ierr); 1926 ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); 1927 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1928 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1929 if (dmAux) { 1930 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1931 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1932 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1933 } 1934 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 1935 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);CHKERRQ(ierr); 1936 ierr = PetscMalloc1(numCells*totDim,&elemVecCh);CHKERRQ(ierr); 1937 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1938 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1939 ierr = DMPlexGetDepth(dm,&depth);CHKERRQ(ierr); 1940 ierr = DMLabelGetStratumIS(depthLabel,depth,&cellIS);CHKERRQ(ierr); 1941 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1942 for (c = cStart; c < cEnd; ++c) { 1943 PetscScalar *x = NULL, *x_t = NULL; 1944 PetscInt i; 1945 1946 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1947 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1948 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1949 if (X_t) { 1950 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1951 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 1952 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1953 } 1954 if (dmAux) { 1955 DM dmAuxPlex; 1956 1957 ierr = DMSNESConvertPlex(dmAux,&dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 1958 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1959 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 1960 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1961 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 1962 } 1963 } 1964 for (f = 0; f < Nf; ++f) { 1965 PetscFE fe, feCh; 1966 PetscInt Nq, Nb; 1967 /* Conforming batches */ 1968 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1969 /* Remainder */ 1970 PetscInt Nr, offset; 1971 PetscQuadrature qGeom = NULL; 1972 PetscFEGeom *cgeomFEM, *chunkGeom = NULL; 1973 1974 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1975 ierr = PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);CHKERRQ(ierr); 1976 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1977 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1978 ierr = DMFieldGetFEInvariance(coordField,cellIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 1979 if (isAffine) { 1980 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 1981 } 1982 if (!qGeom) { 1983 ierr = PetscFEGetQuadrature(fe, &qGeom);CHKERRQ(ierr); 1984 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1985 } 1986 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1987 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 1988 blockSize = Nb; 1989 batchSize = numBlocks * blockSize; 1990 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1991 numChunks = numCells / (numBatches*batchSize); 1992 Ne = numChunks*numBatches*batchSize; 1993 Nr = numCells % (numBatches*batchSize); 1994 offset = numCells - Nr; 1995 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 1996 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1997 ierr = PetscFEIntegrateResidual(feCh, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVecCh);CHKERRQ(ierr); 1998 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1999 ierr = PetscFEIntegrateResidual(fe, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVec[offset*totDim]);CHKERRQ(ierr); 2000 ierr = PetscFEIntegrateResidual(feCh, prob, f, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, &elemVecCh[offset*totDim]);CHKERRQ(ierr); 2001 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); 2002 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2003 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2004 } 2005 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2006 for (c = cStart; c < cEnd; ++c) { 2007 PetscBool diff = PETSC_FALSE; 2008 PetscInt d; 2009 2010 for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;} 2011 if (diff) { 2012 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);CHKERRQ(ierr); 2013 ierr = DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);CHKERRQ(ierr); 2014 ierr = DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);CHKERRQ(ierr); 2015 ++diffCell; 2016 } 2017 if (diffCell > 9) break; 2018 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 2019 } 2020 ierr = PetscFree3(u,u_t,elemVec);CHKERRQ(ierr); 2021 ierr = PetscFree(elemVecCh);CHKERRQ(ierr); 2022 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 2023 PetscFunctionReturn(0); 2024 } 2025 2026 /*@ 2027 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 2028 2029 Input Parameters: 2030 + dm - The mesh 2031 . X - Local solution 2032 - user - The user context 2033 2034 Output Parameter: 2035 . F - Local output vector 2036 2037 Level: developer 2038 2039 .seealso: DMPlexComputeJacobianAction() 2040 @*/ 2041 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 2042 { 2043 PetscObject check; 2044 DM plex; 2045 IS cellIS; 2046 PetscInt depth; 2047 PetscErrorCode ierr; 2048 2049 PetscFunctionBegin; 2050 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2051 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2052 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2053 if (!cellIS) { 2054 ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr); 2055 } 2056 /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */ 2057 ierr = PetscObjectQuery((PetscObject) plex, "dmCh", &check);CHKERRQ(ierr); 2058 if (check) {ierr = DMPlexComputeResidualFEM_Check_Internal(plex, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 2059 else {ierr = DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 2060 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2061 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2062 PetscFunctionReturn(0); 2063 } 2064 2065 /*@ 2066 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 2067 2068 Input Parameters: 2069 + dm - The mesh 2070 - user - The user context 2071 2072 Output Parameter: 2073 . X - Local solution 2074 2075 Level: developer 2076 2077 .seealso: DMPlexComputeJacobianAction() 2078 @*/ 2079 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 2080 { 2081 DM plex; 2082 PetscErrorCode ierr; 2083 2084 PetscFunctionBegin; 2085 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2086 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 2087 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2088 PetscFunctionReturn(0); 2089 } 2090 2091 PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user) 2092 { 2093 DM_Plex *mesh = (DM_Plex *) dm->data; 2094 DM dmAux = NULL, plex = NULL; 2095 DMField coordField = NULL; 2096 PetscSection section, globalSection, subSection, sectionAux = NULL; 2097 PetscDS prob, probAux = NULL; 2098 DMLabel depth; 2099 Vec locA = NULL; 2100 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL; 2101 PetscInt dim, totDim, totDimAux, numBd, bd, Nf; 2102 PetscBool isMatISP; 2103 IS facetIS; 2104 PetscErrorCode ierr; 2105 2106 PetscFunctionBegin; 2107 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2108 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2109 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2110 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2111 if (isMatISP) { 2112 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2113 } 2114 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2115 ierr = DMLabelGetStratumIS(depth,dim-1,&facetIS);CHKERRQ(ierr); 2116 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2117 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2118 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2119 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 2120 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 2121 if (locA) { 2122 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 2123 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2124 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2125 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2126 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2127 } 2128 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2129 for (bd = 0; bd < numBd; ++bd) { 2130 DMBoundaryConditionType type; 2131 const char *bdLabel; 2132 DMLabel label; 2133 IS pointIS; 2134 const PetscInt *points; 2135 const PetscInt *values; 2136 PetscInt fieldI, fieldJ, numValues, v, numFaces, face, Nq; 2137 PetscObject obj; 2138 PetscBool isAffine; 2139 PetscFE fe; 2140 PetscClassId id; 2141 2142 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 2143 ierr = PetscDSGetDiscretization(prob, fieldI, &obj);CHKERRQ(ierr); 2144 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2145 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 2146 fe = (PetscFE) obj; 2147 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2148 for (v = 0; v < numValues; ++v) { 2149 PetscQuadrature qGeom = NULL; 2150 PetscFEGeom *fgeom; 2151 2152 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 2153 if (!pointIS) continue; /* No points with that id on this process */ 2154 { 2155 IS isectIS; 2156 2157 /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */ 2158 ierr = ISIntersect_Caching(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 2159 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2160 pointIS = isectIS; 2161 } 2162 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 2163 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2164 ierr = PetscMalloc3(numFaces*totDim,&u,locX_t ? numFaces*totDim : 0,&u_t,numFaces*totDim*totDim,&elemMat);CHKERRQ(ierr); 2165 if (locA) {ierr = PetscMalloc1(numFaces*totDimAux,&a);CHKERRQ(ierr);} 2166 ierr = DMFieldGetFEInvariance(coordField,pointIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 2167 if (isAffine) { 2168 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 2169 } 2170 if (!qGeom) { 2171 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 2172 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2173 } 2174 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2175 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 2176 for (face = 0; face < numFaces; ++face) { 2177 const PetscInt point = points[face], *support, *cone; 2178 PetscScalar *x = NULL; 2179 PetscInt i, coneSize, faceLoc; 2180 2181 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 2182 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 2183 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 2184 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 2185 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of support[0] %d", point, support[0]); 2186 fgeom->face[face][0] = faceLoc; 2187 ierr = DMPlexVecGetClosure(dm, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 2188 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 2189 ierr = DMPlexVecRestoreClosure(dm, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 2190 if (locX_t) { 2191 ierr = DMPlexVecGetClosure(dm, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 2192 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 2193 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 2194 } 2195 if (locA) { 2196 ierr = DMPlexVecGetClosure(plex, sectionAux, locA, support[0], NULL, &x);CHKERRQ(ierr); 2197 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 2198 ierr = DMPlexVecRestoreClosure(plex, sectionAux, locA, support[0], NULL, &x);CHKERRQ(ierr); 2199 } 2200 } 2201 ierr = PetscMemzero(elemMat, numFaces*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2202 { 2203 PetscFE fe; 2204 PetscInt Nb; 2205 /* Conforming batches */ 2206 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2207 /* Remainder */ 2208 PetscFEGeom *chunkGeom = NULL; 2209 PetscInt Nr, offset; 2210 2211 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2212 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2213 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2214 blockSize = Nb; 2215 batchSize = numBlocks * blockSize; 2216 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2217 numChunks = numFaces / (numBatches*batchSize); 2218 Ne = numChunks*numBatches*batchSize; 2219 Nr = numFaces % (numBatches*batchSize); 2220 offset = numFaces - Nr; 2221 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 2222 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2223 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2224 } 2225 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 2226 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2227 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Nr, chunkGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, a ? &a[offset*totDimAux] : NULL, t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 2228 } 2229 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 2230 } 2231 for (face = 0; face < numFaces; ++face) { 2232 const PetscInt point = points[face], *support; 2233 2234 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 2235 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 2236 if (!isMatISP) { 2237 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2238 } else { 2239 Mat lJ; 2240 2241 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2242 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2243 } 2244 } 2245 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 2246 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2247 ierr = PetscFree3(u,u_t,elemMat);CHKERRQ(ierr); 2248 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2249 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2250 if (locA) {ierr = PetscFree(a);CHKERRQ(ierr);} 2251 } 2252 } 2253 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 2254 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 2255 PetscFunctionReturn(0); 2256 } 2257 2258 /* 2259 We always assemble JacP, and if the matrix is different from Jac and two different sets of point functions are provided, we also assemble Jac 2260 2261 X - The local solution vector 2262 X_t - The local solution time derviative vector, or NULL 2263 */ 2264 PetscErrorCode DMPlexComputeJacobian_Patch_Internal(DM dm, PetscSection section, PetscSection globalSection, IS cellIS, 2265 PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP, void *ctx) 2266 { 2267 DM_Plex *mesh = (DM_Plex *) dm->data; 2268 const char *name = "Jacobian", *nameP = "JacobianPre"; 2269 DM dmAux = NULL; 2270 PetscDS prob, probAux = NULL; 2271 PetscSection sectionAux = NULL; 2272 Vec A; 2273 DMField coordField; 2274 PetscFEGeom *cgeomFEM; 2275 PetscQuadrature qGeom = NULL; 2276 Mat J = Jac, JP = JacP; 2277 PetscScalar *work, *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL, *elemMatP = NULL, *elemMatD = NULL; 2278 PetscBool hasJac, hasPrec, hasDyn, isAffine, assembleJac, isMatIS, isMatISP, *isFE, hasFV = PETSC_FALSE; 2279 const PetscInt *cells; 2280 PetscInt Nf, fieldI, fieldJ, numCells, cStart, cEnd, numChunks, chunkSize, chunk, totDim, totDimAux = 0, sz, wsz, off = 0, offCell = 0; 2281 PetscErrorCode ierr; 2282 2283 PetscFunctionBegin; 2284 CHKMEMQ; 2285 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2286 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2287 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2288 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2289 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2290 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2291 if (dmAux) { 2292 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 2293 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2294 } 2295 /* Get flags */ 2296 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2297 ierr = DMGetWorkArray(dm, Nf, MPIU_BOOL, &isFE);CHKERRQ(ierr); 2298 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2299 PetscObject disc; 2300 PetscClassId id; 2301 ierr = PetscDSGetDiscretization(prob, fieldI, &disc);CHKERRQ(ierr); 2302 ierr = PetscObjectGetClassId(disc, &id);CHKERRQ(ierr); 2303 if (id == PETSCFE_CLASSID) {isFE[fieldI] = PETSC_TRUE;} 2304 else if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; isFE[fieldI] = PETSC_FALSE;} 2305 } 2306 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2307 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2308 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2309 assembleJac = hasJac && hasPrec && (Jac != JacP) ? PETSC_TRUE : PETSC_FALSE; 2310 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2311 ierr = PetscObjectTypeCompare((PetscObject) Jac, MATIS, &isMatIS);CHKERRQ(ierr); 2312 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2313 /* Setup input data and temp arrays (should be DMGetWorkArray) */ 2314 if (isMatISP || isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &globalSection);CHKERRQ(ierr);} 2315 if (isMatIS) {ierr = MatISGetLocalMat(Jac, &J);CHKERRQ(ierr);} 2316 if (isMatISP) {ierr = MatISGetLocalMat(JacP, &JP);CHKERRQ(ierr);} 2317 if (hasFV) {ierr = MatSetOption(JP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr);} /* No allocated space for FV stuff, so ignore the zero entries */ 2318 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2319 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2320 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2321 if (probAux) {ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr);} 2322 CHKMEMQ; 2323 /* Compute batch sizes */ 2324 if (isFE[0]) { 2325 PetscFE fe; 2326 PetscQuadrature q; 2327 PetscInt numQuadPoints, numBatches, batchSize, numBlocks, blockSize, Nb; 2328 2329 ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);CHKERRQ(ierr); 2330 ierr = PetscFEGetQuadrature(fe, &q);CHKERRQ(ierr); 2331 ierr = PetscQuadratureGetData(q, NULL, NULL, &numQuadPoints, NULL, NULL);CHKERRQ(ierr); 2332 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2333 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2334 blockSize = Nb*numQuadPoints; 2335 batchSize = numBlocks * blockSize; 2336 chunkSize = numBatches * batchSize; 2337 numChunks = numCells / chunkSize + numCells % chunkSize; 2338 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2339 } else { 2340 chunkSize = numCells; 2341 numChunks = 1; 2342 } 2343 /* Get work space */ 2344 wsz = (((X?1:0) + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize; 2345 ierr = DMGetWorkArray(dm, wsz, MPIU_SCALAR, &work);CHKERRQ(ierr); 2346 ierr = PetscMemzero(work, wsz * sizeof(PetscScalar));CHKERRQ(ierr); 2347 off = 0; 2348 u = X ? (sz = chunkSize*totDim, off += sz, work+off-sz) : NULL; 2349 u_t = X_t ? (sz = chunkSize*totDim, off += sz, work+off-sz) : NULL; 2350 a = dmAux ? (sz = chunkSize*totDimAux, off += sz, work+off-sz) : NULL; 2351 elemMat = hasJac ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; 2352 elemMatP = hasPrec ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; 2353 elemMatD = hasDyn ? (sz = chunkSize*totDim*totDim, off += sz, work+off-sz) : NULL; 2354 if (off != wsz) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Error is workspace size %D should be %D", off, wsz); 2355 /* Setup geometry */ 2356 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2357 ierr = DMFieldGetFEInvariance(coordField, cellIS, NULL, &isAffine, NULL);CHKERRQ(ierr); 2358 if (isAffine) {ierr = DMFieldCreateDefaultQuadrature(coordField, cellIS, &qGeom);CHKERRQ(ierr);} 2359 if (!qGeom) { 2360 PetscFE fe; 2361 2362 ierr = PetscDSGetDiscretization(prob, 0, (PetscObject *) &fe);CHKERRQ(ierr); 2363 ierr = PetscFEGetQuadrature(fe, &qGeom);CHKERRQ(ierr); 2364 ierr = PetscObjectReference((PetscObject) qGeom);CHKERRQ(ierr); 2365 } 2366 ierr = DMSNESGetFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);CHKERRQ(ierr); 2367 /* Compute volume integrals */ 2368 if (assembleJac) {ierr = MatZeroEntries(J);CHKERRQ(ierr);} 2369 ierr = MatZeroEntries(JP);CHKERRQ(ierr); 2370 for (chunk = 0; chunk < numChunks; ++chunk, offCell += chunkSize) { 2371 const PetscInt Ncell = PetscMin(chunkSize, numCells - offCell); 2372 PetscInt c; 2373 2374 /* Extract values */ 2375 for (c = 0; c < Ncell; ++c) { 2376 const PetscInt cell = cells ? cells[c+offCell] : c+offCell; 2377 PetscScalar *x = NULL, *x_t = NULL; 2378 PetscInt i; 2379 2380 if (X) { 2381 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2382 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 2383 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2384 } 2385 if (X_t) { 2386 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2387 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 2388 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2389 } 2390 if (dmAux) { 2391 ierr = DMPlexVecGetClosure(dmAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2392 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 2393 ierr = DMPlexVecRestoreClosure(dmAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2394 } 2395 } 2396 CHKMEMQ; 2397 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2398 PetscFE fe; 2399 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2400 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2401 if (hasJac) {ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr);} 2402 if (hasPrec) {ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr);} 2403 if (hasDyn) {ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ncell, cgeomFEM, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr);} 2404 } 2405 /* For finite volume, add the identity */ 2406 if (!isFE[fieldI]) { 2407 PetscFV fv; 2408 PetscInt eOffset = 0, Nc, fc, foff; 2409 2410 ierr = PetscDSGetFieldOffset(prob, fieldI, &foff);CHKERRQ(ierr); 2411 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2412 ierr = PetscFVGetNumComponents(fv, &Nc);CHKERRQ(ierr); 2413 for (c = 0; c < chunkSize; ++c, eOffset += totDim*totDim) { 2414 for (fc = 0; fc < Nc; ++fc) { 2415 const PetscInt i = foff + fc; 2416 if (hasJac) {elemMat [eOffset+i*totDim+i] = 1.0;} 2417 if (hasPrec) {elemMatP[eOffset+i*totDim+i] = 1.0;} 2418 } 2419 } 2420 } 2421 } 2422 CHKMEMQ; 2423 /* Add contribution from X_t */ 2424 if (hasDyn) {for (c = 0; c < chunkSize*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 2425 /* Insert values into matrix */ 2426 for (c = 0; c < Ncell; ++c) { 2427 const PetscInt cell = cells ? cells[c+offCell] : c+offCell; 2428 if (mesh->printFEM > 1) { 2429 if (hasJac) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2430 if (hasPrec) {ierr = DMPrintCellMatrix(cell, nameP, totDim, totDim, &elemMatP[(c-cStart)*totDim*totDim]);CHKERRQ(ierr);} 2431 } 2432 if (assembleJac) {ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr);} 2433 ierr = DMPlexMatSetClosure(dm, section, globalSection, JP, cell, &elemMat[(c-cStart)*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2434 } 2435 CHKMEMQ; 2436 } 2437 /* Cleanup */ 2438 ierr = DMSNESRestoreFEGeom(coordField, cellIS, qGeom, PETSC_FALSE, &cgeomFEM);CHKERRQ(ierr); 2439 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2440 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2441 ierr = DMRestoreWorkArray(dm, Nf, MPIU_BOOL, &isFE);CHKERRQ(ierr); 2442 ierr = DMRestoreWorkArray(dm, ((1 + (X_t?1:0) + (dmAux?1:0))*totDim + ((hasJac?1:0) + (hasPrec?1:0) + (hasDyn?1:0))*totDim*totDim)*chunkSize, MPIU_SCALAR, &work);CHKERRQ(ierr); 2443 /* Compute boundary integrals */ 2444 /* ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, ctx);CHKERRQ(ierr); */ 2445 /* Assemble matrix */ 2446 if (assembleJac) {ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);} 2447 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2448 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2449 CHKMEMQ; 2450 PetscFunctionReturn(0); 2451 } 2452 2453 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 2454 { 2455 DM_Plex *mesh = (DM_Plex *) dm->data; 2456 const char *name = "Jacobian"; 2457 DM dmAux, plex; 2458 Vec A; 2459 DMField coordField; 2460 PetscDS prob, probAux = NULL; 2461 PetscSection section, globalSection, subSection, sectionAux; 2462 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 2463 const PetscInt *cells; 2464 PetscInt Nf, fieldI, fieldJ; 2465 PetscInt totDim, totDimAux, cStart, cEnd, numCells, c; 2466 PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE; 2467 PetscErrorCode ierr; 2468 2469 PetscFunctionBegin; 2470 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2471 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2472 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2473 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2474 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 2475 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2476 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2477 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2478 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2479 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2480 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2481 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2482 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2483 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2484 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2485 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2486 if (dmAux) { 2487 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2488 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2489 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2490 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2491 } 2492 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); 2493 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2494 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2495 for (c = cStart; c < cEnd; ++c) { 2496 const PetscInt cell = cells ? cells[c] : c; 2497 const PetscInt cind = c - cStart; 2498 PetscScalar *x = NULL, *x_t = NULL; 2499 PetscInt i; 2500 2501 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2502 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2503 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2504 if (X_t) { 2505 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2506 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2507 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2508 } 2509 if (dmAux) { 2510 ierr = DMPlexVecGetClosure(plex, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2511 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2512 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2513 } 2514 } 2515 if (hasJac) {ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2516 if (hasPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2517 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2518 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2519 PetscClassId id; 2520 PetscFE fe; 2521 PetscQuadrature qGeom = NULL; 2522 PetscInt Nb; 2523 /* Conforming batches */ 2524 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2525 /* Remainder */ 2526 PetscInt Nr, offset, Nq; 2527 PetscBool isAffine; 2528 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2529 2530 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2531 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 2532 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 2533 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2534 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2535 ierr = DMFieldGetFEInvariance(coordField,cellIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 2536 if (isAffine) { 2537 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 2538 } 2539 if (!qGeom) { 2540 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2541 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2542 } 2543 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2544 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2545 blockSize = Nb; 2546 batchSize = numBlocks * blockSize; 2547 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2548 numChunks = numCells / (numBatches*batchSize); 2549 Ne = numChunks*numBatches*batchSize; 2550 Nr = numCells % (numBatches*batchSize); 2551 offset = numCells - Nr; 2552 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2553 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2554 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2555 if (hasJac) { 2556 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2557 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 2558 } 2559 if (hasPrec) { 2560 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2561 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatP[offset*totDim*totDim]);CHKERRQ(ierr); 2562 } 2563 if (hasDyn) { 2564 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2565 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);CHKERRQ(ierr); 2566 } 2567 } 2568 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2569 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2570 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2571 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2572 } 2573 /* Add contribution from X_t */ 2574 if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 2575 if (hasFV) { 2576 PetscClassId id; 2577 PetscFV fv; 2578 PetscInt offsetI, NcI, NbI = 1, fc, f; 2579 2580 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2581 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2582 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 2583 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 2584 if (id != PETSCFV_CLASSID) continue; 2585 /* Put in the identity */ 2586 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 2587 for (c = cStart; c < cEnd; ++c) { 2588 const PetscInt cind = c - cStart; 2589 const PetscInt eOffset = cind*totDim*totDim; 2590 for (fc = 0; fc < NcI; ++fc) { 2591 for (f = 0; f < NbI; ++f) { 2592 const PetscInt i = offsetI + f*NcI+fc; 2593 if (hasPrec) { 2594 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 2595 elemMatP[eOffset+i*totDim+i] = 1.0; 2596 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 2597 } 2598 } 2599 } 2600 } 2601 /* No allocated space for FV stuff, so ignore the zero entries */ 2602 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 2603 } 2604 /* Insert values into matrix */ 2605 isMatIS = PETSC_FALSE; 2606 if (hasPrec && hasJac) { 2607 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr); 2608 } 2609 if (isMatIS && !subSection) { 2610 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2611 } 2612 for (c = cStart; c < cEnd; ++c) { 2613 const PetscInt cell = cells ? cells[c] : c; 2614 const PetscInt cind = c - cStart; 2615 2616 if (hasPrec) { 2617 if (hasJac) { 2618 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2619 if (!isMatIS) { 2620 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2621 } else { 2622 Mat lJ; 2623 2624 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2625 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2626 } 2627 } 2628 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2629 if (!isMatISP) { 2630 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2631 } else { 2632 Mat lJ; 2633 2634 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2635 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2636 } 2637 } else { 2638 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2639 if (!isMatISP) { 2640 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2641 } else { 2642 Mat lJ; 2643 2644 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2645 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2646 } 2647 } 2648 } 2649 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2650 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2651 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2652 if (dmAux) { 2653 ierr = PetscFree(a);CHKERRQ(ierr); 2654 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2655 } 2656 /* Compute boundary integrals */ 2657 ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);CHKERRQ(ierr); 2658 /* Assemble matrix */ 2659 if (hasJac && hasPrec) { 2660 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2661 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2662 } 2663 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2664 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2665 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2666 PetscFunctionReturn(0); 2667 } 2668 2669 /*@ 2670 DMPlexComputeJacobianAction - Form the local portion of the Jacobian action Z = J(X) Y at the local solution X using pointwise functions specified by the user. 2671 2672 Input Parameters: 2673 + dm - The mesh 2674 . cellIS - 2675 . t - The time 2676 . X_tShift - The multiplier for the Jacobian with repsect to X_t 2677 . X - Local solution vector 2678 . X_t - Time-derivative of the local solution vector 2679 . Y - Local input vector 2680 - user - The user context 2681 2682 Output Parameter: 2683 . Z - Local output vector 2684 2685 Note: 2686 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2687 like a GPU, or vectorize on a multicore machine. 2688 2689 Level: developer 2690 2691 .seealso: FormFunctionLocal() 2692 @*/ 2693 PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 2694 { 2695 DM_Plex *mesh = (DM_Plex *) dm->data; 2696 const char *name = "Jacobian"; 2697 DM dmAux, plex, plexAux = NULL; 2698 Vec A; 2699 PetscDS prob, probAux = NULL; 2700 PetscQuadrature quad; 2701 PetscSection section, globalSection, sectionAux; 2702 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2703 PetscInt Nf, fieldI, fieldJ; 2704 PetscInt totDim, totDimAux = 0; 2705 const PetscInt *cells; 2706 PetscInt cStart, cEnd, numCells, c; 2707 PetscBool hasDyn; 2708 DMField coordField; 2709 PetscErrorCode ierr; 2710 2711 PetscFunctionBegin; 2712 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2713 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 2714 if (!cellIS) { 2715 PetscInt depth; 2716 2717 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2718 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2719 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2720 } else { 2721 ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr); 2722 } 2723 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2724 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2725 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2726 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2727 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2728 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2729 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2730 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2731 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2732 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2733 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2734 if (dmAux) { 2735 ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr); 2736 ierr = DMGetDefaultSection(plexAux, §ionAux);CHKERRQ(ierr); 2737 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2738 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2739 } 2740 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2741 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); 2742 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2743 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2744 for (c = cStart; c < cEnd; ++c) { 2745 const PetscInt cell = cells ? cells[c] : c; 2746 const PetscInt cind = c - cStart; 2747 PetscScalar *x = NULL, *x_t = NULL; 2748 PetscInt i; 2749 2750 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2751 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2752 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2753 if (X_t) { 2754 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2755 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2756 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2757 } 2758 if (dmAux) { 2759 ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2760 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2761 ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2762 } 2763 ierr = DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2764 for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i]; 2765 ierr = DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2766 } 2767 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2768 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2769 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2770 PetscFE fe; 2771 PetscInt Nb; 2772 /* Conforming batches */ 2773 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2774 /* Remainder */ 2775 PetscInt Nr, offset, Nq; 2776 PetscQuadrature qGeom = NULL; 2777 PetscBool isAffine; 2778 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2779 2780 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2781 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2782 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2783 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2784 ierr = DMFieldGetFEInvariance(coordField,cellIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 2785 if (isAffine) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);} 2786 if (!qGeom) { 2787 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2788 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2789 } 2790 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2791 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2792 blockSize = Nb; 2793 batchSize = numBlocks * blockSize; 2794 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2795 numChunks = numCells / (numBatches*batchSize); 2796 Ne = numChunks*numBatches*batchSize; 2797 Nr = numCells % (numBatches*batchSize); 2798 offset = numCells - Nr; 2799 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2800 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2801 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2802 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2803 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMat[offset*totDim*totDim]);CHKERRQ(ierr); 2804 if (hasDyn) { 2805 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2806 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Nr, remGeom, &u[offset*totDim], u_t ? &u_t[offset*totDim] : NULL, probAux, &a[offset*totDimAux], t, X_tShift, &elemMatD[offset*totDim*totDim]);CHKERRQ(ierr); 2807 } 2808 } 2809 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2810 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2811 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2812 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2813 } 2814 if (hasDyn) { 2815 for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2816 } 2817 for (c = cStart; c < cEnd; ++c) { 2818 const PetscInt cell = cells ? cells[c] : c; 2819 const PetscInt cind = c - cStart; 2820 const PetscBLASInt M = totDim, one = 1; 2821 const PetscScalar a = 1.0, b = 0.0; 2822 2823 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one)); 2824 if (mesh->printFEM > 1) { 2825 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr); 2826 ierr = DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);CHKERRQ(ierr); 2827 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2828 } 2829 ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr); 2830 } 2831 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2832 if (mesh->printFEM) { 2833 ierr = PetscPrintf(PETSC_COMM_WORLD, "Z:\n");CHKERRQ(ierr); 2834 ierr = VecView(Z, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2835 } 2836 ierr = PetscFree(a);CHKERRQ(ierr); 2837 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2838 ierr = DMDestroy(&plexAux);CHKERRQ(ierr); 2839 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2840 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2841 PetscFunctionReturn(0); 2842 } 2843 2844 /*@ 2845 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2846 2847 Input Parameters: 2848 + dm - The mesh 2849 . X - Local input vector 2850 - user - The user context 2851 2852 Output Parameter: 2853 . Jac - Jacobian matrix 2854 2855 Note: 2856 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2857 like a GPU, or vectorize on a multicore machine. 2858 2859 Level: developer 2860 2861 .seealso: FormFunctionLocal() 2862 @*/ 2863 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2864 { 2865 DM plex; 2866 PetscDS prob; 2867 IS cellIS; 2868 PetscBool hasJac, hasPrec; 2869 PetscInt depth; 2870 PetscErrorCode ierr; 2871 2872 PetscFunctionBegin; 2873 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2874 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2875 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2876 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2877 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2878 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2879 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2880 if (hasJac && hasPrec) {ierr = MatZeroEntries(Jac);CHKERRQ(ierr);} 2881 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2882 ierr = DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2883 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2884 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2885 PetscFunctionReturn(0); 2886 } 2887 2888 /*@ 2889 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2890 2891 Input Parameters: 2892 + dm - The DM object 2893 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary()) 2894 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2895 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2896 2897 Level: developer 2898 @*/ 2899 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2900 { 2901 PetscErrorCode ierr; 2902 2903 PetscFunctionBegin; 2904 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2905 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2906 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2907 PetscFunctionReturn(0); 2908 } 2909 2910 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) 2911 { 2912 PetscDS prob; 2913 Mat J, M; 2914 Vec r, b; 2915 MatNullSpace nullSpace; 2916 PetscReal *error, res = 0.0; 2917 PetscInt numFields; 2918 PetscBool hasJac, hasPrec; 2919 PetscErrorCode ierr; 2920 2921 PetscFunctionBegin; 2922 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2923 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2924 /* TODO Null space for J */ 2925 /* Check discretization error */ 2926 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 2927 ierr = PetscMalloc1(PetscMax(1, numFields), &error);CHKERRQ(ierr); 2928 if (numFields > 1) { 2929 PetscInt f; 2930 2931 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs, ctxs, u, error);CHKERRQ(ierr); 2932 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: [");CHKERRQ(ierr); 2933 for (f = 0; f < numFields; ++f) { 2934 if (f) {ierr = PetscPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);} 2935 if (error[f] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "%g", (double)error[f]);CHKERRQ(ierr);} 2936 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "< 1.0e-11");CHKERRQ(ierr);} 2937 } 2938 ierr = PetscPrintf(PETSC_COMM_WORLD, "]\n");CHKERRQ(ierr); 2939 } else { 2940 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs, ctxs, u, &error[0]);CHKERRQ(ierr); 2941 if (error[0] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", (double)error[0]);CHKERRQ(ierr);} 2942 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} 2943 } 2944 ierr = PetscFree(error);CHKERRQ(ierr); 2945 /* Check residual */ 2946 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2947 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2948 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2949 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2950 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2951 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2952 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2953 /* Check Jacobian */ 2954 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2955 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2956 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2957 if (hasJac && hasPrec) { 2958 ierr = DMCreateMatrix(dm, &M);CHKERRQ(ierr); 2959 ierr = SNESComputeJacobian(snes, u, J, M);CHKERRQ(ierr); 2960 ierr = PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");CHKERRQ(ierr); 2961 ierr = MatViewFromOptions(M, NULL, "-mat_view");CHKERRQ(ierr); 2962 ierr = MatDestroy(&M);CHKERRQ(ierr); 2963 } else { 2964 ierr = SNESComputeJacobian(snes, u, J, J);CHKERRQ(ierr); 2965 } 2966 ierr = PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");CHKERRQ(ierr); 2967 ierr = MatViewFromOptions(J, NULL, "-mat_view");CHKERRQ(ierr); 2968 ierr = MatGetNullSpace(J, &nullSpace);CHKERRQ(ierr); 2969 if (nullSpace) { 2970 PetscBool isNull; 2971 ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr); 2972 if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2973 } 2974 ierr = VecDuplicate(u, &b);CHKERRQ(ierr); 2975 ierr = VecSet(r, 0.0);CHKERRQ(ierr); 2976 ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); 2977 ierr = MatMult(J, u, r);CHKERRQ(ierr); 2978 ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); 2979 ierr = VecDestroy(&b);CHKERRQ(ierr); 2980 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2981 ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2982 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2983 ierr = PetscObjectSetName((PetscObject) r, "Au - b = Au + F(0)");CHKERRQ(ierr); 2984 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"linear_res_");CHKERRQ(ierr); 2985 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2986 ierr = VecDestroy(&r);CHKERRQ(ierr); 2987 ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); 2988 ierr = MatDestroy(&J);CHKERRQ(ierr); 2989 PetscFunctionReturn(0); 2990 } 2991 2992 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2993 { 2994 DM dm; 2995 Vec sol; 2996 PetscBool check; 2997 PetscErrorCode ierr; 2998 2999 PetscFunctionBegin; 3000 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 3001 if (!check) PetscFunctionReturn(0); 3002 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 3003 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 3004 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 3005 ierr = DMSNESCheckFromOptions_Internal(snes, dm, u, sol, exactFuncs, ctxs);CHKERRQ(ierr); 3006 ierr = VecDestroy(&sol);CHKERRQ(ierr); 3007 PetscFunctionReturn(0); 3008 } 3009