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