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