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 **************************/ 826 827 828 /*@ 829 DMPlexSNESGetGeometryFVM - Return precomputed geometric data 830 831 Input Parameter: 832 . dm - The DM 833 834 Output Parameters: 835 + facegeom - The values precomputed from face geometry 836 . cellgeom - The values precomputed from cell geometry 837 - minRadius - The minimum radius over the mesh of an inscribed sphere in a cell 838 839 Level: developer 840 841 .seealso: DMPlexTSSetRHSFunctionLocal() 842 @*/ 843 PetscErrorCode DMPlexSNESGetGeometryFVM(DM dm, Vec *facegeom, Vec *cellgeom, PetscReal *minRadius) 844 { 845 DM plex; 846 PetscErrorCode ierr; 847 848 PetscFunctionBegin; 849 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 850 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 851 ierr = DMPlexGetDataFVM(plex, NULL, cellgeom, facegeom, NULL);CHKERRQ(ierr); 852 if (minRadius) {ierr = DMPlexGetMinRadius(plex, minRadius);CHKERRQ(ierr);} 853 ierr = DMDestroy(&plex);CHKERRQ(ierr); 854 PetscFunctionReturn(0); 855 } 856 857 /*@ 858 DMPlexSNESGetGradientDM - Return gradient data layout 859 860 Input Parameters: 861 + dm - The DM 862 - fv - The PetscFV 863 864 Output Parameter: 865 . dmGrad - The layout for gradient values 866 867 Level: developer 868 869 .seealso: DMPlexSNESGetGeometryFVM() 870 @*/ 871 PetscErrorCode DMPlexSNESGetGradientDM(DM dm, PetscFV fv, DM *dmGrad) 872 { 873 DM plex; 874 PetscBool computeGradients; 875 PetscErrorCode ierr; 876 877 PetscFunctionBegin; 878 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 879 PetscValidHeaderSpecific(fv,PETSCFV_CLASSID,2); 880 PetscValidPointer(dmGrad,3); 881 ierr = PetscFVGetComputeGradients(fv, &computeGradients);CHKERRQ(ierr); 882 if (!computeGradients) {*dmGrad = NULL; PetscFunctionReturn(0);} 883 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 884 ierr = DMPlexGetDataFVM(plex, fv, NULL, NULL, dmGrad);CHKERRQ(ierr); 885 ierr = DMDestroy(&plex);CHKERRQ(ierr); 886 PetscFunctionReturn(0); 887 } 888 889 /*@C 890 DMPlexGetCellFields - Retrieve the field values values for a chunk of cells 891 892 Input Parameters: 893 + dm - The DM 894 . cellIS - The cells to include 895 . locX - A local vector with the solution fields 896 . locX_t - A local vector with solution field time derivatives, or NULL 897 - locA - A local vector with auxiliary fields, or NULL 898 899 Output Parameters: 900 + u - The field coefficients 901 . u_t - The fields derivative coefficients 902 - a - The auxiliary field coefficients 903 904 Level: developer 905 906 .seealso: DMPlexGetFaceFields() 907 @*/ 908 PetscErrorCode DMPlexGetCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 909 { 910 DM plex, plexA = NULL; 911 PetscSection section, sectionAux; 912 PetscDS prob; 913 const PetscInt *cells; 914 PetscInt cStart, cEnd, numCells, totDim, totDimAux, c; 915 PetscErrorCode ierr; 916 917 PetscFunctionBegin; 918 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 919 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 920 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 921 if (locA) {PetscValidHeaderSpecific(locA, VEC_CLASSID, 6);} 922 PetscValidPointer(u, 7); 923 PetscValidPointer(u_t, 8); 924 PetscValidPointer(a, 9); 925 ierr = DMSNESConvertPlex(dm, &plex, PETSC_FALSE);CHKERRQ(ierr); 926 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 927 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 928 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 929 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 930 if (locA) { 931 DM dmAux; 932 PetscDS probAux; 933 934 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 935 ierr = DMSNESConvertPlex(dmAux, &plexA, PETSC_FALSE);CHKERRQ(ierr); 936 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 937 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 938 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 939 } 940 numCells = cEnd - cStart; 941 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u);CHKERRQ(ierr); 942 if (locX_t) {ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, u_t);CHKERRQ(ierr);} else {*u_t = NULL;} 943 if (locA) {ierr = DMGetWorkArray(dm, numCells*totDimAux, MPIU_SCALAR, a);CHKERRQ(ierr);} else {*a = NULL;} 944 for (c = cStart; c < cEnd; ++c) { 945 const PetscInt cell = cells ? cells[c] : c; 946 const PetscInt cind = c - cStart; 947 PetscScalar *x = NULL, *x_t = NULL, *ul = *u, *ul_t = *u_t, *al = *a; 948 PetscInt i; 949 950 ierr = DMPlexVecGetClosure(plex, section, locX, cell, NULL, &x);CHKERRQ(ierr); 951 for (i = 0; i < totDim; ++i) ul[cind*totDim+i] = x[i]; 952 ierr = DMPlexVecRestoreClosure(plex, section, locX, cell, NULL, &x);CHKERRQ(ierr); 953 if (locX_t) { 954 ierr = DMPlexVecGetClosure(plex, section, locX_t, cell, NULL, &x_t);CHKERRQ(ierr); 955 for (i = 0; i < totDim; ++i) ul_t[cind*totDim+i] = x_t[i]; 956 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, cell, NULL, &x_t);CHKERRQ(ierr); 957 } 958 if (locA) { 959 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, cell, NULL, &x);CHKERRQ(ierr); 960 for (i = 0; i < totDimAux; ++i) al[cind*totDimAux+i] = x[i]; 961 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, cell, NULL, &x);CHKERRQ(ierr); 962 } 963 } 964 ierr = DMDestroy(&plex);CHKERRQ(ierr); 965 if (locA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 966 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 967 PetscFunctionReturn(0); 968 } 969 970 /*@C 971 DMPlexRestoreCellFields - Restore the field values values for a chunk of cells 972 973 Input Parameters: 974 + dm - The DM 975 . cellIS - The cells to include 976 . locX - A local vector with the solution fields 977 . locX_t - A local vector with solution field time derivatives, or NULL 978 - locA - A local vector with auxiliary fields, or NULL 979 980 Output Parameters: 981 + u - The field coefficients 982 . u_t - The fields derivative coefficients 983 - a - The auxiliary field coefficients 984 985 Level: developer 986 987 .seealso: DMPlexGetFaceFields() 988 @*/ 989 PetscErrorCode DMPlexRestoreCellFields(DM dm, IS cellIS, Vec locX, Vec locX_t, Vec locA, PetscScalar **u, PetscScalar **u_t, PetscScalar **a) 990 { 991 PetscErrorCode ierr; 992 993 PetscFunctionBegin; 994 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u);CHKERRQ(ierr); 995 if (locX_t) {ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, u_t);CHKERRQ(ierr);} 996 if (locA) {ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, a);CHKERRQ(ierr);} 997 PetscFunctionReturn(0); 998 } 999 1000 /*@C 1001 DMPlexGetFaceFields - Retrieve the field values values for a chunk of faces 1002 1003 Input Parameters: 1004 + dm - The DM 1005 . fStart - The first face to include 1006 . fEnd - The first face to exclude 1007 . locX - A local vector with the solution fields 1008 . locX_t - A local vector with solution field time derivatives, or NULL 1009 . faceGeometry - A local vector with face geometry 1010 . cellGeometry - A local vector with cell geometry 1011 - locaGrad - A local vector with field gradients, or NULL 1012 1013 Output Parameters: 1014 + Nface - The number of faces with field values 1015 . uL - The field values at the left side of the face 1016 - uR - The field values at the right side of the face 1017 1018 Level: developer 1019 1020 .seealso: DMPlexGetCellFields() 1021 @*/ 1022 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) 1023 { 1024 DM dmFace, dmCell, dmGrad = NULL; 1025 PetscSection section; 1026 PetscDS prob; 1027 DMLabel ghostLabel; 1028 const PetscScalar *facegeom, *cellgeom, *x, *lgrad; 1029 PetscBool *isFE; 1030 PetscInt dim, Nf, f, Nc, numFaces = fEnd - fStart, iface, face; 1031 PetscErrorCode ierr; 1032 1033 PetscFunctionBegin; 1034 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1035 PetscValidHeaderSpecific(locX, VEC_CLASSID, 4); 1036 if (locX_t) {PetscValidHeaderSpecific(locX_t, VEC_CLASSID, 5);} 1037 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 6); 1038 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 7); 1039 if (locGrad) {PetscValidHeaderSpecific(locGrad, VEC_CLASSID, 8);} 1040 PetscValidPointer(uL, 9); 1041 PetscValidPointer(uR, 10); 1042 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1043 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1044 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1045 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1046 ierr = PetscDSGetTotalComponents(prob, &Nc);CHKERRQ(ierr); 1047 ierr = PetscMalloc1(Nf, &isFE);CHKERRQ(ierr); 1048 for (f = 0; f < Nf; ++f) { 1049 PetscObject obj; 1050 PetscClassId id; 1051 1052 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1053 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1054 if (id == PETSCFE_CLASSID) {isFE[f] = PETSC_TRUE;} 1055 else if (id == PETSCFV_CLASSID) {isFE[f] = PETSC_FALSE;} 1056 else {isFE[f] = PETSC_FALSE;} 1057 } 1058 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1059 ierr = VecGetArrayRead(locX, &x);CHKERRQ(ierr); 1060 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1061 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1062 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1063 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1064 if (locGrad) { 1065 ierr = VecGetDM(locGrad, &dmGrad);CHKERRQ(ierr); 1066 ierr = VecGetArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1067 } 1068 ierr = DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uL);CHKERRQ(ierr); 1069 ierr = DMGetWorkArray(dm, numFaces*Nc, MPIU_SCALAR, uR);CHKERRQ(ierr); 1070 /* Right now just eat the extra work for FE (could make a cell loop) */ 1071 for (face = fStart, iface = 0; face < fEnd; ++face) { 1072 const PetscInt *cells; 1073 PetscFVFaceGeom *fg; 1074 PetscFVCellGeom *cgL, *cgR; 1075 PetscScalar *xL, *xR, *gL, *gR; 1076 PetscScalar *uLl = *uL, *uRl = *uR; 1077 PetscInt ghost, nsupp, nchild; 1078 1079 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1080 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1081 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1082 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1083 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1084 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1085 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1086 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1087 for (f = 0; f < Nf; ++f) { 1088 PetscInt off; 1089 1090 ierr = PetscDSGetComponentOffset(prob, f, &off);CHKERRQ(ierr); 1091 if (isFE[f]) { 1092 const PetscInt *cone; 1093 PetscInt comp, coneSizeL, coneSizeR, faceLocL, faceLocR, ldof, rdof, d; 1094 1095 xL = xR = NULL; 1096 ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); 1097 ierr = DMPlexVecGetClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1098 ierr = DMPlexVecGetClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1099 ierr = DMPlexGetCone(dm, cells[0], &cone);CHKERRQ(ierr); 1100 ierr = DMPlexGetConeSize(dm, cells[0], &coneSizeL);CHKERRQ(ierr); 1101 for (faceLocL = 0; faceLocL < coneSizeL; ++faceLocL) if (cone[faceLocL] == face) break; 1102 ierr = DMPlexGetCone(dm, cells[1], &cone);CHKERRQ(ierr); 1103 ierr = DMPlexGetConeSize(dm, cells[1], &coneSizeR);CHKERRQ(ierr); 1104 for (faceLocR = 0; faceLocR < coneSizeR; ++faceLocR) if (cone[faceLocR] == face) break; 1105 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]); 1106 /* Check that FEM field has values in the right cell (sometimes its an FV ghost cell) */ 1107 /* TODO: this is a hack that might not be right for nonconforming */ 1108 if (faceLocL < coneSizeL) { 1109 ierr = EvaluateFaceFields(prob, f, faceLocL, xL, &uLl[iface*Nc+off]);CHKERRQ(ierr); 1110 if (rdof == ldof && faceLocR < coneSizeR) {ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr);} 1111 else {for(d = 0; d < comp; ++d) uRl[iface*Nc+off+d] = uLl[iface*Nc+off+d];} 1112 } 1113 else { 1114 ierr = EvaluateFaceFields(prob, f, faceLocR, xR, &uRl[iface*Nc+off]);CHKERRQ(ierr); 1115 ierr = PetscSectionGetFieldComponents(section, f, &comp);CHKERRQ(ierr); 1116 for(d = 0; d < comp; ++d) uLl[iface*Nc+off+d] = uRl[iface*Nc+off+d]; 1117 } 1118 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[0], &ldof, (PetscScalar **) &xL);CHKERRQ(ierr); 1119 ierr = DMPlexVecRestoreClosure(dm, section, locX, cells[1], &rdof, (PetscScalar **) &xR);CHKERRQ(ierr); 1120 } else { 1121 PetscFV fv; 1122 PetscInt numComp, c; 1123 1124 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fv);CHKERRQ(ierr); 1125 ierr = PetscFVGetNumComponents(fv, &numComp);CHKERRQ(ierr); 1126 ierr = DMPlexPointLocalFieldRead(dm, cells[0], f, x, &xL);CHKERRQ(ierr); 1127 ierr = DMPlexPointLocalFieldRead(dm, cells[1], f, x, &xR);CHKERRQ(ierr); 1128 if (dmGrad) { 1129 PetscReal dxL[3], dxR[3]; 1130 1131 ierr = DMPlexPointLocalRead(dmGrad, cells[0], lgrad, &gL);CHKERRQ(ierr); 1132 ierr = DMPlexPointLocalRead(dmGrad, cells[1], lgrad, &gR);CHKERRQ(ierr); 1133 DMPlex_WaxpyD_Internal(dim, -1, cgL->centroid, fg->centroid, dxL); 1134 DMPlex_WaxpyD_Internal(dim, -1, cgR->centroid, fg->centroid, dxR); 1135 for (c = 0; c < numComp; ++c) { 1136 uLl[iface*Nc+off+c] = xL[c] + DMPlex_DotD_Internal(dim, &gL[c*dim], dxL); 1137 uRl[iface*Nc+off+c] = xR[c] + DMPlex_DotD_Internal(dim, &gR[c*dim], dxR); 1138 } 1139 } else { 1140 for (c = 0; c < numComp; ++c) { 1141 uLl[iface*Nc+off+c] = xL[c]; 1142 uRl[iface*Nc+off+c] = xR[c]; 1143 } 1144 } 1145 } 1146 } 1147 ++iface; 1148 } 1149 *Nface = iface; 1150 ierr = VecRestoreArrayRead(locX, &x);CHKERRQ(ierr); 1151 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1152 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1153 if (locGrad) { 1154 ierr = VecRestoreArrayRead(locGrad, &lgrad);CHKERRQ(ierr); 1155 } 1156 ierr = PetscFree(isFE);CHKERRQ(ierr); 1157 PetscFunctionReturn(0); 1158 } 1159 1160 /*@C 1161 DMPlexRestoreFaceFields - Restore the field values values for a chunk of faces 1162 1163 Input Parameters: 1164 + dm - The DM 1165 . fStart - The first face to include 1166 . fEnd - The first face to exclude 1167 . locX - A local vector with the solution fields 1168 . locX_t - A local vector with solution field time derivatives, or NULL 1169 . faceGeometry - A local vector with face geometry 1170 . cellGeometry - A local vector with cell geometry 1171 - locaGrad - A local vector with field gradients, or NULL 1172 1173 Output Parameters: 1174 + Nface - The number of faces with field values 1175 . uL - The field values at the left side of the face 1176 - uR - The field values at the right side of the face 1177 1178 Level: developer 1179 1180 .seealso: DMPlexGetFaceFields() 1181 @*/ 1182 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) 1183 { 1184 PetscErrorCode ierr; 1185 1186 PetscFunctionBegin; 1187 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uL);CHKERRQ(ierr); 1188 ierr = DMRestoreWorkArray(dm, 0, MPIU_SCALAR, uR);CHKERRQ(ierr); 1189 PetscFunctionReturn(0); 1190 } 1191 1192 /*@C 1193 DMPlexGetFaceGeometry - Retrieve the geometric values for a chunk of faces 1194 1195 Input Parameters: 1196 + dm - The DM 1197 . fStart - The first face to include 1198 . fEnd - The first face to exclude 1199 . faceGeometry - A local vector with face geometry 1200 - cellGeometry - A local vector with cell geometry 1201 1202 Output Parameters: 1203 + Nface - The number of faces with field values 1204 . fgeom - The extract the face centroid and normal 1205 - vol - The cell volume 1206 1207 Level: developer 1208 1209 .seealso: DMPlexGetCellFields() 1210 @*/ 1211 PetscErrorCode DMPlexGetFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol) 1212 { 1213 DM dmFace, dmCell; 1214 DMLabel ghostLabel; 1215 const PetscScalar *facegeom, *cellgeom; 1216 PetscInt dim, numFaces = fEnd - fStart, iface, face; 1217 PetscErrorCode ierr; 1218 1219 PetscFunctionBegin; 1220 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1221 PetscValidHeaderSpecific(faceGeometry, VEC_CLASSID, 4); 1222 PetscValidHeaderSpecific(cellGeometry, VEC_CLASSID, 5); 1223 PetscValidPointer(fgeom, 6); 1224 PetscValidPointer(vol, 7); 1225 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1226 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1227 ierr = VecGetDM(faceGeometry, &dmFace);CHKERRQ(ierr); 1228 ierr = VecGetArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1229 ierr = VecGetDM(cellGeometry, &dmCell);CHKERRQ(ierr); 1230 ierr = VecGetArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1231 ierr = PetscMalloc1(numFaces, fgeom);CHKERRQ(ierr); 1232 ierr = DMGetWorkArray(dm, numFaces*2, MPIU_SCALAR, vol);CHKERRQ(ierr); 1233 for (face = fStart, iface = 0; face < fEnd; ++face) { 1234 const PetscInt *cells; 1235 PetscFVFaceGeom *fg; 1236 PetscFVCellGeom *cgL, *cgR; 1237 PetscFVFaceGeom *fgeoml = *fgeom; 1238 PetscReal *voll = *vol; 1239 PetscInt ghost, d, nchild, nsupp; 1240 1241 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1242 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1243 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1244 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1245 ierr = DMPlexPointLocalRead(dmFace, face, facegeom, &fg);CHKERRQ(ierr); 1246 ierr = DMPlexGetSupport(dm, face, &cells);CHKERRQ(ierr); 1247 ierr = DMPlexPointLocalRead(dmCell, cells[0], cellgeom, &cgL);CHKERRQ(ierr); 1248 ierr = DMPlexPointLocalRead(dmCell, cells[1], cellgeom, &cgR);CHKERRQ(ierr); 1249 for (d = 0; d < dim; ++d) { 1250 fgeoml[iface].centroid[d] = fg->centroid[d]; 1251 fgeoml[iface].normal[d] = fg->normal[d]; 1252 } 1253 voll[iface*2+0] = cgL->volume; 1254 voll[iface*2+1] = cgR->volume; 1255 ++iface; 1256 } 1257 *Nface = iface; 1258 ierr = VecRestoreArrayRead(faceGeometry, &facegeom);CHKERRQ(ierr); 1259 ierr = VecRestoreArrayRead(cellGeometry, &cellgeom);CHKERRQ(ierr); 1260 PetscFunctionReturn(0); 1261 } 1262 1263 /*@C 1264 DMPlexRestoreFaceGeometry - Restore the field values values for a chunk of faces 1265 1266 Input Parameters: 1267 + dm - The DM 1268 . fStart - The first face to include 1269 . fEnd - The first face to exclude 1270 . faceGeometry - A local vector with face geometry 1271 - cellGeometry - A local vector with cell geometry 1272 1273 Output Parameters: 1274 + Nface - The number of faces with field values 1275 . fgeom - The extract the face centroid and normal 1276 - vol - The cell volume 1277 1278 Level: developer 1279 1280 .seealso: DMPlexGetFaceFields() 1281 @*/ 1282 PetscErrorCode DMPlexRestoreFaceGeometry(DM dm, PetscInt fStart, PetscInt fEnd, Vec faceGeometry, Vec cellGeometry, PetscInt *Nface, PetscFVFaceGeom **fgeom, PetscReal **vol) 1283 { 1284 PetscErrorCode ierr; 1285 1286 PetscFunctionBegin; 1287 ierr = PetscFree(*fgeom);CHKERRQ(ierr); 1288 ierr = DMRestoreWorkArray(dm, 0, MPIU_REAL, vol);CHKERRQ(ierr); 1289 PetscFunctionReturn(0); 1290 } 1291 1292 static PetscErrorCode ISIntersect_Caching(IS is1, IS is2, IS *isect) 1293 { 1294 PetscErrorCode ierr; 1295 1296 PetscFunctionBegin; 1297 *isect = NULL; 1298 if (is2 && is1) { 1299 char composeStr[33] = {0}; 1300 PetscObjectId is2id; 1301 1302 ierr = PetscObjectGetId((PetscObject)is2,&is2id);CHKERRQ(ierr); 1303 ierr = PetscSNPrintf(composeStr,32,"ISIntersect_Caching_%x",is2id);CHKERRQ(ierr); 1304 ierr = PetscObjectQuery((PetscObject) is1, composeStr, (PetscObject *) isect);CHKERRQ(ierr); 1305 if (*isect == NULL) { 1306 ierr = ISIntersect(is1, is2, isect);CHKERRQ(ierr); 1307 ierr = PetscObjectCompose((PetscObject) is1, composeStr, (PetscObject) *isect);CHKERRQ(ierr); 1308 } else { 1309 ierr = PetscObjectReference((PetscObject) *isect);CHKERRQ(ierr); 1310 } 1311 } 1312 PetscFunctionReturn(0); 1313 } 1314 1315 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) 1316 { 1317 DM_Plex *mesh = (DM_Plex *) dm->data; 1318 DM plex = NULL, plexA = NULL; 1319 PetscDS prob, probAux = NULL; 1320 PetscSection section, sectionAux = NULL; 1321 Vec locA = NULL; 1322 PetscFEGeom *fgeom; 1323 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemVec = NULL; 1324 PetscInt v; 1325 PetscInt totDim, totDimAux = 0; 1326 PetscErrorCode ierr; 1327 1328 PetscFunctionBegin; 1329 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 1330 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1331 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1332 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1333 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1334 if (locA) { 1335 DM dmAux; 1336 1337 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1338 ierr = DMConvert(dmAux, DMPLEX, &plexA);CHKERRQ(ierr); 1339 ierr = DMGetDS(plexA, &probAux);CHKERRQ(ierr); 1340 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1341 ierr = DMGetDefaultSection(plexA, §ionAux);CHKERRQ(ierr); 1342 } 1343 for (v = 0; v < numValues; ++v) { 1344 PetscBool isAffine; 1345 PetscQuadrature qGeom = NULL; 1346 IS pointIS; 1347 const PetscInt *points; 1348 PetscInt numFaces, face, Nq; 1349 1350 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 1351 if (!pointIS) continue; /* No points with that id on this process */ 1352 { 1353 IS isectIS; 1354 1355 /* TODO: Special cases of ISIntersect where it is quick to check a priori if one is a superset of the other */ 1356 ierr = ISIntersect_Caching(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 1357 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1358 pointIS = isectIS; 1359 } 1360 ierr = ISGetLocalSize(pointIS,&numFaces);CHKERRQ(ierr); 1361 ierr = ISGetIndices(pointIS,&points);CHKERRQ(ierr); 1362 ierr = PetscMalloc4(numFaces*totDim, &u, locX_t ? numFaces*totDim : 0, &u_t, numFaces*totDim, &elemVec, locA ? numFaces*totDimAux : 0, &a);CHKERRQ(ierr); 1363 ierr = DMFieldGetFEInvariance(coordField,pointIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 1364 if (isAffine) { 1365 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 1366 } 1367 if (!qGeom) { 1368 PetscFE fe; 1369 1370 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1371 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 1372 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1373 } 1374 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1375 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1376 for (face = 0; face < numFaces; ++face) { 1377 const PetscInt point = points[face], *support, *cone; 1378 PetscScalar *x = NULL; 1379 PetscInt i, coneSize, faceLoc; 1380 1381 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 1382 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 1383 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 1384 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 1385 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %D in cone of support[0] %D", point, support[0]); 1386 fgeom->face[face][0] = faceLoc; 1387 ierr = DMPlexVecGetClosure(dm, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1388 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 1389 ierr = DMPlexVecRestoreClosure(plex, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 1390 if (locX_t) { 1391 ierr = DMPlexVecGetClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1392 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 1393 ierr = DMPlexVecRestoreClosure(plex, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 1394 } 1395 if (locA) { 1396 PetscInt subp; 1397 ierr = DMPlexGetSubpoint(plexA, support[0], &subp);CHKERRQ(ierr); 1398 ierr = DMPlexVecGetClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1399 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 1400 ierr = DMPlexVecRestoreClosure(plexA, sectionAux, locA, subp, NULL, &x);CHKERRQ(ierr); 1401 } 1402 } 1403 ierr = PetscMemzero(elemVec, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1404 { 1405 PetscFE fe; 1406 PetscInt Nb; 1407 PetscFEGeom *chunkGeom = NULL; 1408 /* Conforming batches */ 1409 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1410 /* Remainder */ 1411 PetscInt Nr, offset; 1412 1413 ierr = PetscDSGetDiscretization(prob, field, (PetscObject *) &fe);CHKERRQ(ierr); 1414 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1415 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1416 /* TODO: documentation is unclear about what is going on with these numbers: how should Nb / Nq factor in ? */ 1417 blockSize = Nb; 1418 batchSize = numBlocks * blockSize; 1419 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1420 numChunks = numFaces / (numBatches*batchSize); 1421 Ne = numChunks*numBatches*batchSize; 1422 Nr = numFaces % (numBatches*batchSize); 1423 offset = numFaces - Nr; 1424 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 1425 ierr = PetscFEIntegrateBdResidual(fe, prob, field, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1426 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1427 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); 1428 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 1429 } 1430 for (face = 0; face < numFaces; ++face) { 1431 const PetscInt point = points[face], *support; 1432 1433 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(point, "BdResidual", totDim, &elemVec[face*totDim]);CHKERRQ(ierr);} 1434 ierr = DMPlexGetSupport(plex, point, &support);CHKERRQ(ierr); 1435 ierr = DMPlexVecSetClosure(plex, NULL, locF, support[0], &elemVec[face*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1436 } 1437 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 1438 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1439 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 1440 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 1441 ierr = PetscFree4(u, u_t, elemVec, a);CHKERRQ(ierr); 1442 } 1443 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 1444 if (plexA) {ierr = DMDestroy(&plexA);CHKERRQ(ierr);} 1445 PetscFunctionReturn(0); 1446 } 1447 1448 PetscErrorCode DMPlexComputeBdResidualSingle(DM dm, PetscReal t, DMLabel label, PetscInt numValues, const PetscInt values[], PetscInt field, Vec locX, Vec locX_t, Vec locF) 1449 { 1450 DMField coordField; 1451 DMLabel depthLabel; 1452 IS facetIS; 1453 PetscInt dim; 1454 PetscErrorCode ierr; 1455 1456 PetscFunctionBegin; 1457 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1458 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1459 ierr = DMLabelGetStratumIS(depthLabel, dim-1, &facetIS);CHKERRQ(ierr); 1460 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1461 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1462 PetscFunctionReturn(0); 1463 } 1464 1465 PetscErrorCode DMPlexComputeBdResidual_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1466 { 1467 PetscDS prob; 1468 PetscInt dim, numBd, bd; 1469 DMLabel depthLabel; 1470 DMField coordField = NULL; 1471 IS facetIS; 1472 PetscErrorCode ierr; 1473 1474 PetscFunctionBegin; 1475 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1476 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1477 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1478 ierr = DMLabelGetStratumIS(depthLabel,dim - 1,&facetIS);CHKERRQ(ierr); 1479 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 1480 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1481 for (bd = 0; bd < numBd; ++bd) { 1482 DMBoundaryConditionType type; 1483 const char *bdLabel; 1484 DMLabel label; 1485 const PetscInt *values; 1486 PetscInt field, numValues; 1487 PetscObject obj; 1488 PetscClassId id; 1489 1490 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &field, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 1491 ierr = PetscDSGetDiscretization(prob, field, &obj);CHKERRQ(ierr); 1492 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1493 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 1494 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 1495 ierr = DMPlexComputeBdResidual_Single_Internal(dm, t, label, numValues, values, field, locX, locX_t, locF, coordField, facetIS);CHKERRQ(ierr); 1496 } 1497 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 1498 PetscFunctionReturn(0); 1499 } 1500 1501 PetscErrorCode DMPlexComputeResidual_Internal(DM dm, IS cellIS, PetscReal time, Vec locX, Vec locX_t, PetscReal t, Vec locF, void *user) 1502 { 1503 DM_Plex *mesh = (DM_Plex *) dm->data; 1504 const char *name = "Residual"; 1505 DM dmAux = NULL; 1506 DM dmGrad = NULL; 1507 DMLabel ghostLabel = NULL; 1508 PetscDS prob = NULL; 1509 PetscDS probAux = NULL; 1510 PetscSection section = NULL; 1511 PetscBool useFEM = PETSC_FALSE; 1512 PetscBool useFVM = PETSC_FALSE; 1513 PetscBool isImplicit = (locX_t || time == PETSC_MIN_REAL) ? PETSC_TRUE : PETSC_FALSE; 1514 PetscFV fvm = NULL; 1515 PetscFVCellGeom *cgeomFVM = NULL; 1516 PetscFVFaceGeom *fgeomFVM = NULL; 1517 DMField coordField = NULL; 1518 Vec locA, cellGeometryFVM = NULL, faceGeometryFVM = NULL, grad, locGrad = NULL; 1519 PetscScalar *u = NULL, *u_t, *a, *uL, *uR; 1520 IS chunkIS; 1521 const PetscInt *cells; 1522 PetscInt cStart, cEnd, numCells; 1523 PetscInt Nf, f, totDim, totDimAux, numChunks, cellChunkSize, faceChunkSize, chunk, fStart, fEnd; 1524 PetscBool isAffine = PETSC_FALSE; 1525 PetscQuadrature affineQuad = NULL, *quads = NULL; 1526 PetscFEGeom *affineGeom = NULL, **geoms = NULL; 1527 PetscErrorCode ierr; 1528 1529 PetscFunctionBegin; 1530 ierr = PetscLogEventBegin(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1531 /* TODO The places where we have to use isFE are probably the member functions for the PetscDisc class */ 1532 /* TODO The FVM geometry is over-manipulated. Make the precalc functions return exactly what we need */ 1533 /* FEM+FVM */ 1534 /* 1: Get sizes from dm and dmAux */ 1535 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1536 ierr = DMGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr); 1537 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1538 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 1539 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1540 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 1541 if (locA) { 1542 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 1543 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1544 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1545 } 1546 /* 2: Get geometric data */ 1547 for (f = 0; f < Nf; ++f) { 1548 PetscObject obj; 1549 PetscClassId id; 1550 PetscBool fimp; 1551 1552 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1553 if (isImplicit != fimp) continue; 1554 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1555 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1556 if (id == PETSCFE_CLASSID) {useFEM = PETSC_TRUE;} 1557 if (id == PETSCFV_CLASSID) {useFVM = PETSC_TRUE; fvm = (PetscFV) obj;} 1558 } 1559 if (useFEM) { 1560 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1561 ierr = DMFieldGetFEInvariance(coordField,cellIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 1562 if (isAffine) { 1563 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&affineQuad);CHKERRQ(ierr); 1564 if (affineQuad) { 1565 ierr = DMSNESGetFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1566 } 1567 } else { 1568 ierr = PetscCalloc2(Nf,&quads,Nf,&geoms);CHKERRQ(ierr); 1569 for (f = 0; f < Nf; ++f) { 1570 PetscObject obj; 1571 PetscClassId id; 1572 PetscBool fimp; 1573 1574 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1575 if (isImplicit != fimp) continue; 1576 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1577 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1578 if (id == PETSCFE_CLASSID) { 1579 PetscFE fe = (PetscFE) obj; 1580 1581 ierr = PetscFEGetQuadrature(fe, &quads[f]);CHKERRQ(ierr); 1582 ierr = PetscObjectReference((PetscObject)quads[f]);CHKERRQ(ierr); 1583 ierr = DMSNESGetFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1584 } 1585 } 1586 } 1587 } 1588 if (useFVM) { 1589 ierr = DMPlexSNESGetGeometryFVM(dm, &faceGeometryFVM, &cellGeometryFVM, NULL);CHKERRQ(ierr); 1590 ierr = VecGetArrayRead(faceGeometryFVM, (const PetscScalar **) &fgeomFVM);CHKERRQ(ierr); 1591 ierr = VecGetArrayRead(cellGeometryFVM, (const PetscScalar **) &cgeomFVM);CHKERRQ(ierr); 1592 /* Reconstruct and limit cell gradients */ 1593 ierr = DMPlexSNESGetGradientDM(dm, fvm, &dmGrad);CHKERRQ(ierr); 1594 if (dmGrad) { 1595 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1596 ierr = DMGetGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1597 ierr = DMPlexReconstructGradients_Internal(dm, fvm, fStart, fEnd, faceGeometryFVM, cellGeometryFVM, locX, grad);CHKERRQ(ierr); 1598 /* Communicate gradient values */ 1599 ierr = DMGetLocalVector(dmGrad, &locGrad);CHKERRQ(ierr); 1600 ierr = DMGlobalToLocalBegin(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1601 ierr = DMGlobalToLocalEnd(dmGrad, grad, INSERT_VALUES, locGrad);CHKERRQ(ierr); 1602 ierr = DMRestoreGlobalVector(dmGrad, &grad);CHKERRQ(ierr); 1603 } 1604 /* Handle non-essential (e.g. outflow) boundary values */ 1605 ierr = DMPlexInsertBoundaryValues(dm, PETSC_FALSE, locX, time, faceGeometryFVM, cellGeometryFVM, locGrad);CHKERRQ(ierr); 1606 } 1607 /* Loop over chunks */ 1608 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1609 ierr = DMPlexGetHeightStratum(dm, 1, &fStart, &fEnd);CHKERRQ(ierr); 1610 if (useFEM) {ierr = ISCreate(PETSC_COMM_SELF, &chunkIS);CHKERRQ(ierr);} 1611 numCells = cEnd - cStart; 1612 numChunks = 1; 1613 cellChunkSize = numCells/numChunks; 1614 faceChunkSize = (fEnd - fStart)/numChunks; 1615 numChunks = PetscMin(1,numCells); 1616 for (chunk = 0; chunk < numChunks; ++chunk) { 1617 PetscScalar *elemVec, *fluxL, *fluxR; 1618 PetscReal *vol; 1619 PetscFVFaceGeom *fgeom; 1620 PetscInt cS = cStart+chunk*cellChunkSize, cE = PetscMin(cS+cellChunkSize, cEnd), numCells = cE - cS, c; 1621 PetscInt fS = fStart+chunk*faceChunkSize, fE = PetscMin(fS+faceChunkSize, fEnd), numFaces = 0, face; 1622 1623 /* Extract field coefficients */ 1624 if (useFEM) { 1625 ierr = ISGetPointSubrange(chunkIS, cS, cE, cells);CHKERRQ(ierr); 1626 ierr = DMPlexGetCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1627 ierr = DMGetWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1628 ierr = PetscMemzero(elemVec, numCells*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1629 } 1630 if (useFVM) { 1631 ierr = DMPlexGetFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1632 ierr = DMPlexGetFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1633 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1634 ierr = DMGetWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1635 ierr = PetscMemzero(fluxL, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1636 ierr = PetscMemzero(fluxR, numFaces*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 1637 } 1638 /* TODO We will interlace both our field coefficients (u, u_t, uL, uR, etc.) and our output (elemVec, fL, fR). I think this works */ 1639 /* Loop over fields */ 1640 for (f = 0; f < Nf; ++f) { 1641 PetscObject obj; 1642 PetscClassId id; 1643 PetscBool fimp; 1644 PetscInt numChunks, numBatches, batchSize, numBlocks, blockSize, Ne, Nr, offset; 1645 1646 ierr = PetscDSGetImplicit(prob, f, &fimp);CHKERRQ(ierr); 1647 if (isImplicit != fimp) continue; 1648 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1649 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1650 if (id == PETSCFE_CLASSID) { 1651 PetscFE fe = (PetscFE) obj; 1652 PetscFEGeom *geom = affineGeom ? affineGeom : geoms[f]; 1653 PetscFEGeom *chunkGeom = NULL; 1654 PetscQuadrature quad = affineQuad ? affineQuad : quads[f]; 1655 PetscInt Nq, Nb; 1656 1657 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1658 ierr = PetscQuadratureGetData(quad, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1659 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1660 blockSize = Nb; 1661 batchSize = numBlocks * blockSize; 1662 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1663 numChunks = numCells / (numBatches*batchSize); 1664 Ne = numChunks*numBatches*batchSize; 1665 Nr = numCells % (numBatches*batchSize); 1666 offset = numCells - Nr; 1667 /* Integrate FE residual to get elemVec (need fields at quadrature points) */ 1668 /* 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) */ 1669 ierr = PetscFEGeomGetChunk(geom,0,offset,&chunkGeom);CHKERRQ(ierr); 1670 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1671 ierr = PetscFEGeomGetChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1672 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); 1673 ierr = PetscFEGeomRestoreChunk(geom,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1674 } else if (id == PETSCFV_CLASSID) { 1675 PetscFV fv = (PetscFV) obj; 1676 1677 Ne = numFaces; 1678 /* Riemann solve over faces (need fields at face centroids) */ 1679 /* We need to evaluate FE fields at those coordinates */ 1680 ierr = PetscFVIntegrateRHSFunction(fv, prob, f, Ne, fgeom, vol, uL, uR, fluxL, fluxR);CHKERRQ(ierr); 1681 } else SETERRQ1(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_WRONG, "Unknown discretization type for field %d", f); 1682 } 1683 /* Loop over domain */ 1684 if (useFEM) { 1685 /* Add elemVec to locX */ 1686 for (c = cS; c < cE; ++c) { 1687 const PetscInt cell = cells ? cells[c] : c; 1688 const PetscInt cind = c - cStart; 1689 1690 if (mesh->printFEM > 1) {ierr = DMPrintCellVector(cell, name, totDim, &elemVec[cind*totDim]);CHKERRQ(ierr);} 1691 if (ghostLabel) { 1692 PetscInt ghostVal; 1693 1694 ierr = DMLabelGetValue(ghostLabel,cell,&ghostVal);CHKERRQ(ierr); 1695 if (ghostVal > 0) continue; 1696 } 1697 ierr = DMPlexVecSetClosure(dm, section, locF, cell, &elemVec[cind*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1698 } 1699 } 1700 if (useFVM) { 1701 PetscScalar *fa; 1702 PetscInt iface; 1703 1704 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1705 for (f = 0; f < Nf; ++f) { 1706 PetscFV fv; 1707 PetscObject obj; 1708 PetscClassId id; 1709 PetscInt foff, pdim; 1710 1711 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1712 ierr = PetscDSGetFieldOffset(prob, f, &foff);CHKERRQ(ierr); 1713 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1714 if (id != PETSCFV_CLASSID) continue; 1715 fv = (PetscFV) obj; 1716 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1717 /* Accumulate fluxes to cells */ 1718 for (face = fS, iface = 0; face < fE; ++face) { 1719 const PetscInt *scells; 1720 PetscScalar *fL = NULL, *fR = NULL; 1721 PetscInt ghost, d, nsupp, nchild; 1722 1723 ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr); 1724 ierr = DMPlexGetSupportSize(dm, face, &nsupp);CHKERRQ(ierr); 1725 ierr = DMPlexGetTreeChildren(dm, face, &nchild, NULL);CHKERRQ(ierr); 1726 if (ghost >= 0 || nsupp > 2 || nchild > 0) continue; 1727 ierr = DMPlexGetSupport(dm, face, &scells);CHKERRQ(ierr); 1728 ierr = DMLabelGetValue(ghostLabel,scells[0],&ghost);CHKERRQ(ierr); 1729 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[0], f, fa, &fL);CHKERRQ(ierr);} 1730 ierr = DMLabelGetValue(ghostLabel,scells[1],&ghost);CHKERRQ(ierr); 1731 if (ghost <= 0) {ierr = DMPlexPointLocalFieldRef(dm, scells[1], f, fa, &fR);CHKERRQ(ierr);} 1732 for (d = 0; d < pdim; ++d) { 1733 if (fL) fL[d] -= fluxL[iface*totDim+foff+d]; 1734 if (fR) fR[d] += fluxR[iface*totDim+foff+d]; 1735 } 1736 ++iface; 1737 } 1738 } 1739 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1740 } 1741 /* Handle time derivative */ 1742 if (locX_t) { 1743 PetscScalar *x_t, *fa; 1744 1745 ierr = VecGetArray(locF, &fa);CHKERRQ(ierr); 1746 ierr = VecGetArray(locX_t, &x_t);CHKERRQ(ierr); 1747 for (f = 0; f < Nf; ++f) { 1748 PetscFV fv; 1749 PetscObject obj; 1750 PetscClassId id; 1751 PetscInt pdim, d; 1752 1753 ierr = PetscDSGetDiscretization(prob, f, &obj);CHKERRQ(ierr); 1754 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 1755 if (id != PETSCFV_CLASSID) continue; 1756 fv = (PetscFV) obj; 1757 ierr = PetscFVGetNumComponents(fv, &pdim);CHKERRQ(ierr); 1758 for (c = cS; c < cE; ++c) { 1759 const PetscInt cell = cells ? cells[c] : c; 1760 PetscScalar *u_t, *r; 1761 1762 if (ghostLabel) { 1763 PetscInt ghostVal; 1764 1765 ierr = DMLabelGetValue(ghostLabel, cell, &ghostVal);CHKERRQ(ierr); 1766 if (ghostVal > 0) continue; 1767 } 1768 ierr = DMPlexPointLocalFieldRead(dm, cell, f, x_t, &u_t);CHKERRQ(ierr); 1769 ierr = DMPlexPointLocalFieldRef(dm, cell, f, fa, &r);CHKERRQ(ierr); 1770 for (d = 0; d < pdim; ++d) r[d] += u_t[d]; 1771 } 1772 } 1773 ierr = VecRestoreArray(locX_t, &x_t);CHKERRQ(ierr); 1774 ierr = VecRestoreArray(locF, &fa);CHKERRQ(ierr); 1775 } 1776 if (useFEM) { 1777 ierr = DMPlexRestoreCellFields(dm, chunkIS, locX, locX_t, locA, &u, &u_t, &a);CHKERRQ(ierr); 1778 ierr = DMRestoreWorkArray(dm, numCells*totDim, MPIU_SCALAR, &elemVec);CHKERRQ(ierr); 1779 } 1780 if (useFVM) { 1781 ierr = DMPlexRestoreFaceFields(dm, fS, fE, locX, locX_t, faceGeometryFVM, cellGeometryFVM, locGrad, &numFaces, &uL, &uR);CHKERRQ(ierr); 1782 ierr = DMPlexRestoreFaceGeometry(dm, fS, fE, faceGeometryFVM, cellGeometryFVM, &numFaces, &fgeom, &vol);CHKERRQ(ierr); 1783 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxL);CHKERRQ(ierr); 1784 ierr = DMRestoreWorkArray(dm, numFaces*totDim, MPIU_SCALAR, &fluxR);CHKERRQ(ierr); 1785 if (dmGrad) {ierr = DMRestoreLocalVector(dmGrad, &locGrad);CHKERRQ(ierr);} 1786 } 1787 } 1788 if (useFEM) {ierr = ISDestroy(&chunkIS);CHKERRQ(ierr);} 1789 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 1790 1791 if (useFEM) { 1792 ierr = DMPlexComputeBdResidual_Internal(dm, locX, locX_t, t, locF, user);CHKERRQ(ierr); 1793 1794 if (isAffine) { 1795 ierr = DMSNESRestoreFEGeom(coordField,cellIS,affineQuad,PETSC_FALSE,&affineGeom);CHKERRQ(ierr); 1796 ierr = PetscQuadratureDestroy(&affineQuad);CHKERRQ(ierr); 1797 } else { 1798 for (f = 0; f < Nf; ++f) { 1799 ierr = DMSNESRestoreFEGeom(coordField,cellIS,quads[f],PETSC_FALSE,&geoms[f]);CHKERRQ(ierr); 1800 ierr = PetscQuadratureDestroy(&quads[f]);CHKERRQ(ierr); 1801 } 1802 ierr = PetscFree2(quads,geoms);CHKERRQ(ierr); 1803 } 1804 } 1805 1806 /* FEM */ 1807 /* 1: Get sizes from dm and dmAux */ 1808 /* 2: Get geometric data */ 1809 /* 3: Handle boundary values */ 1810 /* 4: Loop over domain */ 1811 /* Extract coefficients */ 1812 /* Loop over fields */ 1813 /* Set tiling for FE*/ 1814 /* Integrate FE residual to get elemVec */ 1815 /* Loop over subdomain */ 1816 /* Loop over quad points */ 1817 /* Transform coords to real space */ 1818 /* Evaluate field and aux fields at point */ 1819 /* Evaluate residual at point */ 1820 /* Transform residual to real space */ 1821 /* Add residual to elemVec */ 1822 /* Loop over domain */ 1823 /* Add elemVec to locX */ 1824 1825 /* FVM */ 1826 /* Get geometric data */ 1827 /* If using gradients */ 1828 /* Compute gradient data */ 1829 /* Loop over domain faces */ 1830 /* Count computational faces */ 1831 /* Reconstruct cell gradient */ 1832 /* Loop over domain cells */ 1833 /* Limit cell gradients */ 1834 /* Handle boundary values */ 1835 /* Loop over domain faces */ 1836 /* Read out field, centroid, normal, volume for each side of face */ 1837 /* Riemann solve over faces */ 1838 /* Loop over domain faces */ 1839 /* Accumulate fluxes to cells */ 1840 /* TODO Change printFEM to printDisc here */ 1841 if (mesh->printFEM) { 1842 Vec locFbc; 1843 PetscInt pStart, pEnd, p, maxDof; 1844 PetscScalar *zeroes; 1845 1846 ierr = VecDuplicate(locF,&locFbc);CHKERRQ(ierr); 1847 ierr = VecCopy(locF,locFbc);CHKERRQ(ierr); 1848 ierr = PetscSectionGetChart(section,&pStart,&pEnd);CHKERRQ(ierr); 1849 ierr = PetscSectionGetMaxDof(section,&maxDof);CHKERRQ(ierr); 1850 ierr = PetscCalloc1(maxDof,&zeroes);CHKERRQ(ierr); 1851 for (p = pStart; p < pEnd; p++) { 1852 ierr = VecSetValuesSection(locFbc,section,p,zeroes,INSERT_BC_VALUES);CHKERRQ(ierr); 1853 } 1854 ierr = PetscFree(zeroes);CHKERRQ(ierr); 1855 ierr = DMPrintLocalVec(dm, name, mesh->printTol, locFbc);CHKERRQ(ierr); 1856 ierr = VecDestroy(&locFbc);CHKERRQ(ierr); 1857 } 1858 ierr = PetscLogEventEnd(DMPLEX_ResidualFEM,dm,0,0,0);CHKERRQ(ierr); 1859 PetscFunctionReturn(0); 1860 } 1861 1862 static PetscErrorCode DMPlexComputeResidualFEM_Check_Internal(DM dm, Vec X, Vec X_t, PetscReal t, Vec F, void *user) 1863 { 1864 DM dmCh, dmAux; 1865 Vec A; 1866 DMField coordField = NULL; 1867 PetscDS prob, probCh, probAux = NULL; 1868 PetscSection section, sectionAux; 1869 PetscScalar *elemVec, *elemVecCh, *u, *u_t, *a = NULL; 1870 PetscInt Nf, f, numCells, cStart, cEnd, c; 1871 PetscInt totDim, totDimAux = 0, diffCell = 0; 1872 PetscInt depth; 1873 PetscBool isAffine; 1874 IS cellIS; 1875 DMLabel depthLabel; 1876 PetscErrorCode ierr; 1877 1878 PetscFunctionBegin; 1879 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1880 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1881 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 1882 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 1883 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1884 numCells = cEnd - cStart; 1885 ierr = PetscObjectQuery((PetscObject) dm, "dmCh", (PetscObject *) &dmCh);CHKERRQ(ierr); 1886 ierr = DMGetDS(dmCh, &probCh);CHKERRQ(ierr); 1887 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 1888 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 1889 if (dmAux) { 1890 ierr = DMGetDefaultSection(dmAux, §ionAux);CHKERRQ(ierr); 1891 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 1892 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 1893 } 1894 ierr = VecSet(F, 0.0);CHKERRQ(ierr); 1895 ierr = PetscMalloc3(numCells*totDim,&u,X_t ? numCells*totDim : 0,&u_t,numCells*totDim,&elemVec);CHKERRQ(ierr); 1896 ierr = PetscMalloc1(numCells*totDim,&elemVecCh);CHKERRQ(ierr); 1897 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 1898 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1899 ierr = DMPlexGetDepth(dm,&depth);CHKERRQ(ierr); 1900 ierr = DMLabelGetStratumIS(depthLabel,depth,&cellIS);CHKERRQ(ierr); 1901 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 1902 for (c = cStart; c < cEnd; ++c) { 1903 PetscScalar *x = NULL, *x_t = NULL; 1904 PetscInt i; 1905 1906 ierr = DMPlexVecGetClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1907 for (i = 0; i < totDim; ++i) u[c*totDim+i] = x[i]; 1908 ierr = DMPlexVecRestoreClosure(dm, section, X, c, NULL, &x);CHKERRQ(ierr); 1909 if (X_t) { 1910 ierr = DMPlexVecGetClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1911 for (i = 0; i < totDim; ++i) u_t[c*totDim+i] = x_t[i]; 1912 ierr = DMPlexVecRestoreClosure(dm, section, X_t, c, NULL, &x_t);CHKERRQ(ierr); 1913 } 1914 if (dmAux) { 1915 DM dmAuxPlex; 1916 1917 ierr = DMSNESConvertPlex(dmAux,&dmAuxPlex, PETSC_FALSE);CHKERRQ(ierr); 1918 ierr = DMPlexVecGetClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1919 for (i = 0; i < totDimAux; ++i) a[c*totDimAux+i] = x[i]; 1920 ierr = DMPlexVecRestoreClosure(dmAuxPlex, sectionAux, A, c, NULL, &x);CHKERRQ(ierr); 1921 ierr = DMDestroy(&dmAuxPlex);CHKERRQ(ierr); 1922 } 1923 } 1924 for (f = 0; f < Nf; ++f) { 1925 PetscFE fe, feCh; 1926 PetscInt Nq, Nb; 1927 /* Conforming batches */ 1928 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 1929 /* Remainder */ 1930 PetscInt Nr, offset; 1931 PetscQuadrature qGeom = NULL; 1932 PetscFEGeom *cgeomFEM, *chunkGeom = NULL; 1933 1934 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1935 ierr = PetscDSGetDiscretization(probCh, f, (PetscObject *) &feCh);CHKERRQ(ierr); 1936 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 1937 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 1938 ierr = DMFieldGetFEInvariance(coordField,cellIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 1939 if (isAffine) { 1940 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 1941 } 1942 if (!qGeom) { 1943 ierr = PetscFEGetQuadrature(fe, &qGeom);CHKERRQ(ierr); 1944 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 1945 } 1946 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 1947 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 1948 blockSize = Nb; 1949 batchSize = numBlocks * blockSize; 1950 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 1951 numChunks = numCells / (numBatches*batchSize); 1952 Ne = numChunks*numBatches*batchSize; 1953 Nr = numCells % (numBatches*batchSize); 1954 offset = numCells - Nr; 1955 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 1956 ierr = PetscFEIntegrateResidual(fe, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVec);CHKERRQ(ierr); 1957 ierr = PetscFEIntegrateResidual(feCh, prob, f, Ne, chunkGeom, u, u_t, probAux, a, t, elemVecCh);CHKERRQ(ierr); 1958 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1959 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); 1960 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); 1961 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&chunkGeom);CHKERRQ(ierr); 1962 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 1963 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 1964 } 1965 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 1966 for (c = cStart; c < cEnd; ++c) { 1967 PetscBool diff = PETSC_FALSE; 1968 PetscInt d; 1969 1970 for (d = 0; d < totDim; ++d) if (PetscAbsScalar(elemVec[c*totDim+d] - elemVecCh[c*totDim+d]) > 1.0e-7) {diff = PETSC_TRUE;break;} 1971 if (diff) { 1972 ierr = PetscPrintf(PetscObjectComm((PetscObject) dm), "Different cell %d\n", c);CHKERRQ(ierr); 1973 ierr = DMPrintCellVector(c, "Residual", totDim, &elemVec[c*totDim]);CHKERRQ(ierr); 1974 ierr = DMPrintCellVector(c, "Check Residual", totDim, &elemVecCh[c*totDim]);CHKERRQ(ierr); 1975 ++diffCell; 1976 } 1977 if (diffCell > 9) break; 1978 ierr = DMPlexVecSetClosure(dm, section, F, c, &elemVec[c*totDim], ADD_ALL_VALUES);CHKERRQ(ierr); 1979 } 1980 ierr = PetscFree3(u,u_t,elemVec);CHKERRQ(ierr); 1981 ierr = PetscFree(elemVecCh);CHKERRQ(ierr); 1982 if (dmAux) {ierr = PetscFree(a);CHKERRQ(ierr);} 1983 PetscFunctionReturn(0); 1984 } 1985 1986 /*@ 1987 DMPlexSNESComputeResidualFEM - Form the local residual F from the local input X using pointwise functions specified by the user 1988 1989 Input Parameters: 1990 + dm - The mesh 1991 . X - Local solution 1992 - user - The user context 1993 1994 Output Parameter: 1995 . F - Local output vector 1996 1997 Level: developer 1998 1999 .seealso: DMPlexComputeJacobianAction() 2000 @*/ 2001 PetscErrorCode DMPlexSNESComputeResidualFEM(DM dm, Vec X, Vec F, void *user) 2002 { 2003 PetscObject check; 2004 DM plex; 2005 IS cellIS; 2006 PetscInt depth; 2007 PetscErrorCode ierr; 2008 2009 PetscFunctionBegin; 2010 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2011 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2012 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2013 if (!cellIS) { 2014 ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr); 2015 } 2016 /* The dmCh is used to check two mathematically equivalent discretizations for computational equivalence */ 2017 ierr = PetscObjectQuery((PetscObject) plex, "dmCh", &check);CHKERRQ(ierr); 2018 if (check) {ierr = DMPlexComputeResidualFEM_Check_Internal(plex, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 2019 else {ierr = DMPlexComputeResidual_Internal(plex, cellIS, PETSC_MIN_REAL, X, NULL, 0.0, F, user);CHKERRQ(ierr);} 2020 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2021 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2022 PetscFunctionReturn(0); 2023 } 2024 2025 /*@ 2026 DMPlexSNESComputeBoundaryFEM - Form the boundary values for the local input X 2027 2028 Input Parameters: 2029 + dm - The mesh 2030 - user - The user context 2031 2032 Output Parameter: 2033 . X - Local solution 2034 2035 Level: developer 2036 2037 .seealso: DMPlexComputeJacobianAction() 2038 @*/ 2039 PetscErrorCode DMPlexSNESComputeBoundaryFEM(DM dm, Vec X, void *user) 2040 { 2041 DM plex; 2042 PetscErrorCode ierr; 2043 2044 PetscFunctionBegin; 2045 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2046 ierr = DMPlexInsertBoundaryValues(plex, PETSC_TRUE, X, PETSC_MIN_REAL, NULL, NULL, NULL);CHKERRQ(ierr); 2047 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2048 PetscFunctionReturn(0); 2049 } 2050 2051 PetscErrorCode DMPlexComputeBdJacobian_Internal(DM dm, Vec locX, Vec locX_t, PetscReal t, PetscReal X_tShift, Mat Jac, Mat JacP, void *user) 2052 { 2053 DM_Plex *mesh = (DM_Plex *) dm->data; 2054 DM dmAux = NULL, plex = NULL; 2055 DMField coordField = NULL; 2056 PetscSection section, globalSection, subSection, sectionAux = NULL; 2057 PetscDS prob, probAux = NULL; 2058 DMLabel depth; 2059 Vec locA = NULL; 2060 PetscScalar *u = NULL, *u_t = NULL, *a = NULL, *elemMat = NULL; 2061 PetscInt dim, totDim, totDimAux, numBd, bd, Nf; 2062 PetscBool isMatISP; 2063 IS facetIS; 2064 PetscErrorCode ierr; 2065 2066 PetscFunctionBegin; 2067 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 2068 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2069 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2070 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2071 if (isMatISP) { 2072 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2073 } 2074 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 2075 ierr = DMLabelGetStratumIS(depth,dim-1,&facetIS);CHKERRQ(ierr); 2076 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2077 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 2078 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2079 ierr = PetscDSGetNumBoundary(prob, &numBd);CHKERRQ(ierr); 2080 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &locA);CHKERRQ(ierr); 2081 if (locA) { 2082 ierr = VecGetDM(locA, &dmAux);CHKERRQ(ierr); 2083 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2084 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2085 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2086 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2087 } 2088 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2089 for (bd = 0; bd < numBd; ++bd) { 2090 DMBoundaryConditionType type; 2091 const char *bdLabel; 2092 DMLabel label; 2093 IS pointIS; 2094 const PetscInt *points; 2095 const PetscInt *values; 2096 PetscInt fieldI, fieldJ, numValues, v, numFaces, face, Nq; 2097 PetscObject obj; 2098 PetscBool isAffine; 2099 PetscFE fe; 2100 PetscClassId id; 2101 2102 ierr = PetscDSGetBoundary(prob, bd, &type, NULL, &bdLabel, &fieldI, NULL, NULL, NULL, &numValues, &values, NULL);CHKERRQ(ierr); 2103 ierr = PetscDSGetDiscretization(prob, fieldI, &obj);CHKERRQ(ierr); 2104 ierr = PetscObjectGetClassId(obj, &id);CHKERRQ(ierr); 2105 if ((id != PETSCFE_CLASSID) || (type & DM_BC_ESSENTIAL)) continue; 2106 fe = (PetscFE) obj; 2107 ierr = DMGetLabel(dm, bdLabel, &label);CHKERRQ(ierr); 2108 for (v = 0; v < numValues; ++v) { 2109 PetscQuadrature qGeom = NULL; 2110 PetscFEGeom *fgeom; 2111 2112 ierr = DMLabelGetStratumIS(label, values[v], &pointIS);CHKERRQ(ierr); 2113 if (!pointIS) continue; /* No points with that id on this process */ 2114 { 2115 IS isectIS; 2116 2117 /* TODO: Special cases of ISIntersect where it is quick to check a prior if one is a superset of the other */ 2118 ierr = ISIntersect_Caching(facetIS,pointIS,&isectIS);CHKERRQ(ierr); 2119 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2120 pointIS = isectIS; 2121 } 2122 ierr = ISGetLocalSize(pointIS, &numFaces);CHKERRQ(ierr); 2123 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 2124 ierr = PetscMalloc3(numFaces*totDim,&u,locX_t ? numFaces*totDim : 0,&u_t,numFaces*totDim*totDim,&elemMat);CHKERRQ(ierr); 2125 if (locA) {ierr = PetscMalloc1(numFaces*totDimAux,&a);CHKERRQ(ierr);} 2126 ierr = DMFieldGetFEInvariance(coordField,pointIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 2127 if (isAffine) { 2128 ierr = DMFieldCreateDefaultQuadrature(coordField,pointIS,&qGeom);CHKERRQ(ierr); 2129 } 2130 if (!qGeom) { 2131 ierr = PetscFEGetFaceQuadrature(fe, &qGeom);CHKERRQ(ierr); 2132 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2133 } 2134 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2135 ierr = DMSNESGetFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 2136 for (face = 0; face < numFaces; ++face) { 2137 const PetscInt point = points[face], *support, *cone; 2138 PetscScalar *x = NULL; 2139 PetscInt i, coneSize, faceLoc; 2140 2141 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 2142 ierr = DMPlexGetConeSize(dm, support[0], &coneSize);CHKERRQ(ierr); 2143 ierr = DMPlexGetCone(dm, support[0], &cone);CHKERRQ(ierr); 2144 for (faceLoc = 0; faceLoc < coneSize; ++faceLoc) if (cone[faceLoc] == point) break; 2145 if (faceLoc == coneSize) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Could not find face %d in cone of support[0] %d", point, support[0]); 2146 fgeom->face[face][0] = faceLoc; 2147 ierr = DMPlexVecGetClosure(dm, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 2148 for (i = 0; i < totDim; ++i) u[face*totDim+i] = x[i]; 2149 ierr = DMPlexVecRestoreClosure(dm, section, locX, support[0], NULL, &x);CHKERRQ(ierr); 2150 if (locX_t) { 2151 ierr = DMPlexVecGetClosure(dm, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 2152 for (i = 0; i < totDim; ++i) u_t[face*totDim+i] = x[i]; 2153 ierr = DMPlexVecRestoreClosure(dm, section, locX_t, support[0], NULL, &x);CHKERRQ(ierr); 2154 } 2155 if (locA) { 2156 ierr = DMPlexVecGetClosure(plex, sectionAux, locA, support[0], NULL, &x);CHKERRQ(ierr); 2157 for (i = 0; i < totDimAux; ++i) a[face*totDimAux+i] = x[i]; 2158 ierr = DMPlexVecRestoreClosure(plex, sectionAux, locA, support[0], NULL, &x);CHKERRQ(ierr); 2159 } 2160 } 2161 ierr = PetscMemzero(elemMat, numFaces*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2162 { 2163 PetscFE fe; 2164 PetscInt Nb; 2165 /* Conforming batches */ 2166 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2167 /* Remainder */ 2168 PetscFEGeom *chunkGeom = NULL; 2169 PetscInt Nr, offset; 2170 2171 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2172 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2173 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2174 blockSize = Nb; 2175 batchSize = numBlocks * blockSize; 2176 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2177 numChunks = numFaces / (numBatches*batchSize); 2178 Ne = numChunks*numBatches*batchSize; 2179 Nr = numFaces % (numBatches*batchSize); 2180 offset = numFaces - Nr; 2181 ierr = PetscFEGeomGetChunk(fgeom,0,offset,&chunkGeom);CHKERRQ(ierr); 2182 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2183 ierr = PetscFEIntegrateBdJacobian(fe, prob, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2184 } 2185 ierr = PetscFEGeomGetChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 2186 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2187 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); 2188 } 2189 ierr = PetscFEGeomRestoreChunk(fgeom,offset,numFaces,&chunkGeom);CHKERRQ(ierr); 2190 } 2191 for (face = 0; face < numFaces; ++face) { 2192 const PetscInt point = points[face], *support; 2193 2194 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(point, "BdJacobian", totDim, totDim, &elemMat[face*totDim*totDim]);CHKERRQ(ierr);} 2195 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 2196 if (!isMatISP) { 2197 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2198 } else { 2199 Mat lJ; 2200 2201 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2202 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, support[0], &elemMat[face*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2203 } 2204 } 2205 ierr = DMSNESRestoreFEGeom(coordField,pointIS,qGeom,PETSC_TRUE,&fgeom);CHKERRQ(ierr); 2206 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2207 ierr = PetscFree3(u,u_t,elemMat);CHKERRQ(ierr); 2208 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 2209 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 2210 if (locA) {ierr = PetscFree(a);CHKERRQ(ierr);} 2211 } 2212 } 2213 ierr = ISDestroy(&facetIS);CHKERRQ(ierr); 2214 if (plex) {ierr = DMDestroy(&plex);CHKERRQ(ierr);} 2215 PetscFunctionReturn(0); 2216 } 2217 2218 PetscErrorCode DMPlexComputeJacobian_Internal(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Mat Jac, Mat JacP,void *user) 2219 { 2220 DM_Plex *mesh = (DM_Plex *) dm->data; 2221 const char *name = "Jacobian"; 2222 DM dmAux, plex; 2223 Vec A; 2224 DMField coordField; 2225 PetscDS prob, probAux = NULL; 2226 PetscSection section, globalSection, subSection, sectionAux; 2227 PetscScalar *elemMat, *elemMatP, *elemMatD, *u, *u_t, *a = NULL; 2228 const PetscInt *cells; 2229 PetscInt Nf, fieldI, fieldJ; 2230 PetscInt totDim, totDimAux, cStart, cEnd, numCells, c; 2231 PetscBool isMatIS, isMatISP, hasJac, hasPrec, hasDyn, hasFV = PETSC_FALSE; 2232 PetscErrorCode ierr; 2233 2234 PetscFunctionBegin; 2235 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2236 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2237 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatISP);CHKERRQ(ierr); 2238 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2239 if (isMatISP) {ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr);} 2240 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2241 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2242 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2243 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2244 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2245 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2246 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2247 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2248 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2249 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2250 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2251 if (dmAux) { 2252 ierr = DMConvert(dmAux, DMPLEX, &plex);CHKERRQ(ierr); 2253 ierr = DMGetDefaultSection(plex, §ionAux);CHKERRQ(ierr); 2254 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2255 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2256 } 2257 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); 2258 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2259 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2260 for (c = cStart; c < cEnd; ++c) { 2261 const PetscInt cell = cells ? cells[c] : c; 2262 const PetscInt cind = c - cStart; 2263 PetscScalar *x = NULL, *x_t = NULL; 2264 PetscInt i; 2265 2266 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2267 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2268 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2269 if (X_t) { 2270 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2271 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2272 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2273 } 2274 if (dmAux) { 2275 ierr = DMPlexVecGetClosure(plex, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2276 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2277 ierr = DMPlexVecRestoreClosure(plex, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2278 } 2279 } 2280 if (hasJac) {ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2281 if (hasPrec) {ierr = PetscMemzero(elemMatP, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2282 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2283 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2284 PetscClassId id; 2285 PetscFE fe; 2286 PetscQuadrature qGeom = NULL; 2287 PetscInt Nb; 2288 /* Conforming batches */ 2289 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2290 /* Remainder */ 2291 PetscInt Nr, offset, Nq; 2292 PetscBool isAffine; 2293 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2294 2295 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2296 ierr = PetscObjectGetClassId((PetscObject) fe, &id);CHKERRQ(ierr); 2297 if (id == PETSCFV_CLASSID) {hasFV = PETSC_TRUE; continue;} 2298 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2299 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2300 ierr = DMFieldGetFEInvariance(coordField,cellIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 2301 if (isAffine) { 2302 ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr); 2303 } 2304 if (!qGeom) { 2305 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2306 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2307 } 2308 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2309 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2310 blockSize = Nb; 2311 batchSize = numBlocks * blockSize; 2312 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2313 numChunks = numCells / (numBatches*batchSize); 2314 Ne = numChunks*numBatches*batchSize; 2315 Nr = numCells % (numBatches*batchSize); 2316 offset = numCells - Nr; 2317 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2318 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2319 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2320 if (hasJac) { 2321 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2322 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); 2323 } 2324 if (hasPrec) { 2325 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_PRE, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatP);CHKERRQ(ierr); 2326 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); 2327 } 2328 if (hasDyn) { 2329 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2330 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); 2331 } 2332 } 2333 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2334 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2335 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2336 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2337 } 2338 /* Add contribution from X_t */ 2339 if (hasDyn) {for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c];} 2340 if (hasFV) { 2341 PetscClassId id; 2342 PetscFV fv; 2343 PetscInt offsetI, NcI, NbI = 1, fc, f; 2344 2345 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2346 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fv);CHKERRQ(ierr); 2347 ierr = PetscDSGetFieldOffset(prob, fieldI, &offsetI);CHKERRQ(ierr); 2348 ierr = PetscObjectGetClassId((PetscObject) fv, &id);CHKERRQ(ierr); 2349 if (id != PETSCFV_CLASSID) continue; 2350 /* Put in the identity */ 2351 ierr = PetscFVGetNumComponents(fv, &NcI);CHKERRQ(ierr); 2352 for (c = cStart; c < cEnd; ++c) { 2353 const PetscInt cind = c - cStart; 2354 const PetscInt eOffset = cind*totDim*totDim; 2355 for (fc = 0; fc < NcI; ++fc) { 2356 for (f = 0; f < NbI; ++f) { 2357 const PetscInt i = offsetI + f*NcI+fc; 2358 if (hasPrec) { 2359 if (hasJac) {elemMat[eOffset+i*totDim+i] = 1.0;} 2360 elemMatP[eOffset+i*totDim+i] = 1.0; 2361 } else {elemMat[eOffset+i*totDim+i] = 1.0;} 2362 } 2363 } 2364 } 2365 } 2366 /* No allocated space for FV stuff, so ignore the zero entries */ 2367 ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_TRUE);CHKERRQ(ierr); 2368 } 2369 /* Insert values into matrix */ 2370 isMatIS = PETSC_FALSE; 2371 if (hasPrec && hasJac) { 2372 ierr = PetscObjectTypeCompare((PetscObject) JacP, MATIS, &isMatIS);CHKERRQ(ierr); 2373 } 2374 if (isMatIS && !subSection) { 2375 ierr = DMPlexGetSubdomainSection(dm, &subSection);CHKERRQ(ierr); 2376 } 2377 for (c = cStart; c < cEnd; ++c) { 2378 const PetscInt cell = cells ? cells[c] : c; 2379 const PetscInt cind = c - cStart; 2380 2381 if (hasPrec) { 2382 if (hasJac) { 2383 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2384 if (!isMatIS) { 2385 ierr = DMPlexMatSetClosure(dm, section, globalSection, Jac, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2386 } else { 2387 Mat lJ; 2388 2389 ierr = MatISGetLocalMat(Jac,&lJ);CHKERRQ(ierr); 2390 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2391 } 2392 } 2393 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMatP[cind*totDim*totDim]);CHKERRQ(ierr);} 2394 if (!isMatISP) { 2395 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2396 } else { 2397 Mat lJ; 2398 2399 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2400 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMatP[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2401 } 2402 } else { 2403 if (mesh->printFEM > 1) {ierr = DMPrintCellMatrix(cell, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr);} 2404 if (!isMatISP) { 2405 ierr = DMPlexMatSetClosure(dm, section, globalSection, JacP, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2406 } else { 2407 Mat lJ; 2408 2409 ierr = MatISGetLocalMat(JacP,&lJ);CHKERRQ(ierr); 2410 ierr = DMPlexMatSetClosure(dm, section, subSection, lJ, cell, &elemMat[cind*totDim*totDim], ADD_VALUES);CHKERRQ(ierr); 2411 } 2412 } 2413 } 2414 ierr = ISRestorePointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2415 if (hasFV) {ierr = MatSetOption(JacP, MAT_IGNORE_ZERO_ENTRIES, PETSC_FALSE);CHKERRQ(ierr);} 2416 ierr = PetscFree5(u,u_t,elemMat,elemMatP,elemMatD);CHKERRQ(ierr); 2417 if (dmAux) { 2418 ierr = PetscFree(a);CHKERRQ(ierr); 2419 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2420 } 2421 /* Compute boundary integrals */ 2422 ierr = DMPlexComputeBdJacobian_Internal(dm, X, X_t, t, X_tShift, Jac, JacP, user);CHKERRQ(ierr); 2423 /* Assemble matrix */ 2424 if (hasJac && hasPrec) { 2425 ierr = MatAssemblyBegin(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2426 ierr = MatAssemblyEnd(Jac, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2427 } 2428 ierr = MatAssemblyBegin(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2429 ierr = MatAssemblyEnd(JacP, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 2430 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2431 PetscFunctionReturn(0); 2432 } 2433 2434 /*@ 2435 DMPlexComputeJacobianAction - Form the local portion of the Jacobian action Z = J(X) Y at the local solution X using pointwise functions specified by the user. 2436 2437 Input Parameters: 2438 + dm - The mesh 2439 . cellIS - 2440 . t - The time 2441 . X_tShift - The multiplier for the Jacobian with repsect to X_t 2442 . X - Local solution vector 2443 . X_t - Time-derivative of the local solution vector 2444 . Y - Local input vector 2445 - user - The user context 2446 2447 Output Parameter: 2448 . Z - Local output vector 2449 2450 Note: 2451 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2452 like a GPU, or vectorize on a multicore machine. 2453 2454 Level: developer 2455 2456 .seealso: FormFunctionLocal() 2457 @*/ 2458 PetscErrorCode DMPlexComputeJacobianAction(DM dm, IS cellIS, PetscReal t, PetscReal X_tShift, Vec X, Vec X_t, Vec Y, Vec Z, void *user) 2459 { 2460 DM_Plex *mesh = (DM_Plex *) dm->data; 2461 const char *name = "Jacobian"; 2462 DM dmAux, plex, plexAux = NULL; 2463 Vec A; 2464 PetscDS prob, probAux = NULL; 2465 PetscQuadrature quad; 2466 PetscSection section, globalSection, sectionAux; 2467 PetscScalar *elemMat, *elemMatD, *u, *u_t, *a = NULL, *y, *z; 2468 PetscInt Nf, fieldI, fieldJ; 2469 PetscInt totDim, totDimAux = 0; 2470 const PetscInt *cells; 2471 PetscInt cStart, cEnd, numCells, c; 2472 PetscBool hasDyn; 2473 DMField coordField; 2474 PetscErrorCode ierr; 2475 2476 PetscFunctionBegin; 2477 ierr = PetscLogEventBegin(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2478 ierr = DMSNESConvertPlex(dm, &plex, PETSC_TRUE);CHKERRQ(ierr); 2479 if (!cellIS) { 2480 PetscInt depth; 2481 2482 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2483 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2484 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2485 } else { 2486 ierr = PetscObjectReference((PetscObject) cellIS);CHKERRQ(ierr); 2487 } 2488 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 2489 ierr = DMGetDefaultGlobalSection(dm, &globalSection);CHKERRQ(ierr); 2490 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2491 ierr = PetscDSGetTotalDimension(prob, &totDim);CHKERRQ(ierr); 2492 ierr = PetscDSHasDynamicJacobian(prob, &hasDyn);CHKERRQ(ierr); 2493 hasDyn = hasDyn && (X_tShift != 0.0) ? PETSC_TRUE : PETSC_FALSE; 2494 ierr = PetscSectionGetNumFields(section, &Nf);CHKERRQ(ierr); 2495 ierr = ISGetLocalSize(cellIS, &numCells);CHKERRQ(ierr); 2496 ierr = ISGetPointRange(cellIS, &cStart, &cEnd, &cells);CHKERRQ(ierr); 2497 ierr = PetscObjectQuery((PetscObject) dm, "dmAux", (PetscObject *) &dmAux);CHKERRQ(ierr); 2498 ierr = PetscObjectQuery((PetscObject) dm, "A", (PetscObject *) &A);CHKERRQ(ierr); 2499 if (dmAux) { 2500 ierr = DMConvert(dmAux, DMPLEX, &plexAux);CHKERRQ(ierr); 2501 ierr = DMGetDefaultSection(plexAux, §ionAux);CHKERRQ(ierr); 2502 ierr = DMGetDS(dmAux, &probAux);CHKERRQ(ierr); 2503 ierr = PetscDSGetTotalDimension(probAux, &totDimAux);CHKERRQ(ierr); 2504 } 2505 ierr = VecSet(Z, 0.0);CHKERRQ(ierr); 2506 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); 2507 if (dmAux) {ierr = PetscMalloc1(numCells*totDimAux, &a);CHKERRQ(ierr);} 2508 ierr = DMGetCoordinateField(dm, &coordField);CHKERRQ(ierr); 2509 for (c = cStart; c < cEnd; ++c) { 2510 const PetscInt cell = cells ? cells[c] : c; 2511 const PetscInt cind = c - cStart; 2512 PetscScalar *x = NULL, *x_t = NULL; 2513 PetscInt i; 2514 2515 ierr = DMPlexVecGetClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2516 for (i = 0; i < totDim; ++i) u[cind*totDim+i] = x[i]; 2517 ierr = DMPlexVecRestoreClosure(dm, section, X, cell, NULL, &x);CHKERRQ(ierr); 2518 if (X_t) { 2519 ierr = DMPlexVecGetClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2520 for (i = 0; i < totDim; ++i) u_t[cind*totDim+i] = x_t[i]; 2521 ierr = DMPlexVecRestoreClosure(dm, section, X_t, cell, NULL, &x_t);CHKERRQ(ierr); 2522 } 2523 if (dmAux) { 2524 ierr = DMPlexVecGetClosure(plexAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2525 for (i = 0; i < totDimAux; ++i) a[cind*totDimAux+i] = x[i]; 2526 ierr = DMPlexVecRestoreClosure(plexAux, sectionAux, A, cell, NULL, &x);CHKERRQ(ierr); 2527 } 2528 ierr = DMPlexVecGetClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2529 for (i = 0; i < totDim; ++i) y[cind*totDim+i] = x[i]; 2530 ierr = DMPlexVecRestoreClosure(dm, section, Y, cell, NULL, &x);CHKERRQ(ierr); 2531 } 2532 ierr = PetscMemzero(elemMat, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr); 2533 if (hasDyn) {ierr = PetscMemzero(elemMatD, numCells*totDim*totDim * sizeof(PetscScalar));CHKERRQ(ierr);} 2534 for (fieldI = 0; fieldI < Nf; ++fieldI) { 2535 PetscFE fe; 2536 PetscInt Nb; 2537 /* Conforming batches */ 2538 PetscInt numChunks, numBatches, numBlocks, Ne, blockSize, batchSize; 2539 /* Remainder */ 2540 PetscInt Nr, offset, Nq; 2541 PetscQuadrature qGeom = NULL; 2542 PetscBool isAffine; 2543 PetscFEGeom *cgeomFEM, *chunkGeom = NULL, *remGeom = NULL; 2544 2545 ierr = PetscDSGetDiscretization(prob, fieldI, (PetscObject *) &fe);CHKERRQ(ierr); 2546 ierr = PetscFEGetQuadrature(fe, &quad);CHKERRQ(ierr); 2547 ierr = PetscFEGetDimension(fe, &Nb);CHKERRQ(ierr); 2548 ierr = PetscFEGetTileSizes(fe, NULL, &numBlocks, NULL, &numBatches);CHKERRQ(ierr); 2549 ierr = DMFieldGetFEInvariance(coordField,cellIS,NULL,&isAffine,NULL);CHKERRQ(ierr); 2550 if (isAffine) {ierr = DMFieldCreateDefaultQuadrature(coordField,cellIS,&qGeom);CHKERRQ(ierr);} 2551 if (!qGeom) { 2552 ierr = PetscFEGetQuadrature(fe,&qGeom);CHKERRQ(ierr); 2553 ierr = PetscObjectReference((PetscObject)qGeom);CHKERRQ(ierr); 2554 } 2555 ierr = PetscQuadratureGetData(qGeom, NULL, NULL, &Nq, NULL, NULL);CHKERRQ(ierr); 2556 ierr = DMSNESGetFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2557 blockSize = Nb; 2558 batchSize = numBlocks * blockSize; 2559 ierr = PetscFESetTileSizes(fe, blockSize, numBlocks, batchSize, numBatches);CHKERRQ(ierr); 2560 numChunks = numCells / (numBatches*batchSize); 2561 Ne = numChunks*numBatches*batchSize; 2562 Nr = numCells % (numBatches*batchSize); 2563 offset = numCells - Nr; 2564 ierr = PetscFEGeomGetChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2565 ierr = PetscFEGeomGetChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2566 for (fieldJ = 0; fieldJ < Nf; ++fieldJ) { 2567 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMat);CHKERRQ(ierr); 2568 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); 2569 if (hasDyn) { 2570 ierr = PetscFEIntegrateJacobian(fe, prob, PETSCFE_JACOBIAN_DYN, fieldI, fieldJ, Ne, chunkGeom, u, u_t, probAux, a, t, X_tShift, elemMatD);CHKERRQ(ierr); 2571 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); 2572 } 2573 } 2574 ierr = PetscFEGeomRestoreChunk(cgeomFEM,offset,numCells,&remGeom);CHKERRQ(ierr); 2575 ierr = PetscFEGeomRestoreChunk(cgeomFEM,0,offset,&chunkGeom);CHKERRQ(ierr); 2576 ierr = DMSNESRestoreFEGeom(coordField,cellIS,qGeom,PETSC_FALSE,&cgeomFEM);CHKERRQ(ierr); 2577 ierr = PetscQuadratureDestroy(&qGeom);CHKERRQ(ierr); 2578 } 2579 if (hasDyn) { 2580 for (c = 0; c < numCells*totDim*totDim; ++c) elemMat[c] += X_tShift*elemMatD[c]; 2581 } 2582 for (c = cStart; c < cEnd; ++c) { 2583 const PetscInt cell = cells ? cells[c] : c; 2584 const PetscInt cind = c - cStart; 2585 const PetscBLASInt M = totDim, one = 1; 2586 const PetscScalar a = 1.0, b = 0.0; 2587 2588 PetscStackCallBLAS("BLASgemv", BLASgemv_("N", &M, &M, &a, &elemMat[cind*totDim*totDim], &M, &y[cind*totDim], &one, &b, z, &one)); 2589 if (mesh->printFEM > 1) { 2590 ierr = DMPrintCellMatrix(c, name, totDim, totDim, &elemMat[cind*totDim*totDim]);CHKERRQ(ierr); 2591 ierr = DMPrintCellVector(c, "Y", totDim, &y[cind*totDim]);CHKERRQ(ierr); 2592 ierr = DMPrintCellVector(c, "Z", totDim, z);CHKERRQ(ierr); 2593 } 2594 ierr = DMPlexVecSetClosure(dm, section, Z, cell, z, ADD_VALUES);CHKERRQ(ierr); 2595 } 2596 ierr = PetscFree6(u,u_t,elemMat,elemMatD,y,z);CHKERRQ(ierr); 2597 if (mesh->printFEM) { 2598 ierr = PetscPrintf(PETSC_COMM_WORLD, "Z:\n");CHKERRQ(ierr); 2599 ierr = VecView(Z, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 2600 } 2601 ierr = PetscFree(a);CHKERRQ(ierr); 2602 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2603 ierr = DMDestroy(&plexAux);CHKERRQ(ierr); 2604 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2605 ierr = PetscLogEventEnd(DMPLEX_JacobianFEM,dm,0,0,0);CHKERRQ(ierr); 2606 PetscFunctionReturn(0); 2607 } 2608 2609 /*@ 2610 DMPlexSNESComputeJacobianFEM - Form the local portion of the Jacobian matrix J at the local solution X using pointwise functions specified by the user. 2611 2612 Input Parameters: 2613 + dm - The mesh 2614 . X - Local input vector 2615 - user - The user context 2616 2617 Output Parameter: 2618 . Jac - Jacobian matrix 2619 2620 Note: 2621 We form the residual one batch of elements at a time. This allows us to offload work onto an accelerator, 2622 like a GPU, or vectorize on a multicore machine. 2623 2624 Level: developer 2625 2626 .seealso: FormFunctionLocal() 2627 @*/ 2628 PetscErrorCode DMPlexSNESComputeJacobianFEM(DM dm, Vec X, Mat Jac, Mat JacP,void *user) 2629 { 2630 DM plex; 2631 PetscDS prob; 2632 IS cellIS; 2633 PetscBool hasJac, hasPrec; 2634 PetscInt depth; 2635 PetscErrorCode ierr; 2636 2637 PetscFunctionBegin; 2638 ierr = DMSNESConvertPlex(dm,&plex,PETSC_TRUE);CHKERRQ(ierr); 2639 ierr = DMPlexGetDepth(plex, &depth);CHKERRQ(ierr); 2640 ierr = DMGetStratumIS(plex, "dim", depth, &cellIS);CHKERRQ(ierr); 2641 if (!cellIS) {ierr = DMGetStratumIS(plex, "depth", depth, &cellIS);CHKERRQ(ierr);} 2642 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2643 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2644 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2645 if (hasJac && hasPrec) {ierr = MatZeroEntries(Jac);CHKERRQ(ierr);} 2646 ierr = MatZeroEntries(JacP);CHKERRQ(ierr); 2647 ierr = DMPlexComputeJacobian_Internal(plex, cellIS, 0.0, 0.0, X, NULL, Jac, JacP, user);CHKERRQ(ierr); 2648 ierr = ISDestroy(&cellIS);CHKERRQ(ierr); 2649 ierr = DMDestroy(&plex);CHKERRQ(ierr); 2650 PetscFunctionReturn(0); 2651 } 2652 2653 /*@ 2654 DMPlexSetSNESLocalFEM - Use DMPlex's internal FEM routines to compute SNES boundary values, residual, and Jacobian. 2655 2656 Input Parameters: 2657 + dm - The DM object 2658 . boundaryctx - the user context that will be passed to pointwise evaluation of boundary values (see PetscDSAddBoundary()) 2659 . residualctx - the user context that will be passed to pointwise evaluation of finite element residual computations (see PetscDSSetResidual()) 2660 - jacobianctx - the user context that will be passed to pointwise evaluation of finite element Jacobian construction (see PetscDSSetJacobian()) 2661 2662 Level: developer 2663 @*/ 2664 PetscErrorCode DMPlexSetSNESLocalFEM(DM dm, void *boundaryctx, void *residualctx, void *jacobianctx) 2665 { 2666 PetscErrorCode ierr; 2667 2668 PetscFunctionBegin; 2669 ierr = DMSNESSetBoundaryLocal(dm,DMPlexSNESComputeBoundaryFEM,boundaryctx);CHKERRQ(ierr); 2670 ierr = DMSNESSetFunctionLocal(dm,DMPlexSNESComputeResidualFEM,residualctx);CHKERRQ(ierr); 2671 ierr = DMSNESSetJacobianLocal(dm,DMPlexSNESComputeJacobianFEM,jacobianctx);CHKERRQ(ierr); 2672 PetscFunctionReturn(0); 2673 } 2674 2675 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) 2676 { 2677 PetscDS prob; 2678 Mat J, M; 2679 Vec r, b; 2680 MatNullSpace nullSpace; 2681 PetscReal *error, res = 0.0; 2682 PetscInt numFields; 2683 PetscBool hasJac, hasPrec; 2684 PetscErrorCode ierr; 2685 2686 PetscFunctionBegin; 2687 ierr = VecDuplicate(u, &r);CHKERRQ(ierr); 2688 ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); 2689 /* TODO Null space for J */ 2690 /* Check discretization error */ 2691 ierr = DMGetNumFields(dm, &numFields);CHKERRQ(ierr); 2692 ierr = PetscMalloc1(PetscMax(1, numFields), &error);CHKERRQ(ierr); 2693 if (numFields > 1) { 2694 PetscInt f; 2695 2696 ierr = DMComputeL2FieldDiff(dm, 0.0, exactFuncs, ctxs, u, error);CHKERRQ(ierr); 2697 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: [");CHKERRQ(ierr); 2698 for (f = 0; f < numFields; ++f) { 2699 if (f) {ierr = PetscPrintf(PETSC_COMM_WORLD, ", ");CHKERRQ(ierr);} 2700 if (error[f] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "%g", (double)error[f]);CHKERRQ(ierr);} 2701 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "< 1.0e-11");CHKERRQ(ierr);} 2702 } 2703 ierr = PetscPrintf(PETSC_COMM_WORLD, "]\n");CHKERRQ(ierr); 2704 } else { 2705 ierr = DMComputeL2Diff(dm, 0.0, exactFuncs, ctxs, u, &error[0]);CHKERRQ(ierr); 2706 if (error[0] >= 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", (double)error[0]);CHKERRQ(ierr);} 2707 else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} 2708 } 2709 ierr = PetscFree(error);CHKERRQ(ierr); 2710 /* Check residual */ 2711 ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); 2712 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2713 ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2714 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2715 ierr = PetscObjectSetName((PetscObject) r, "Initial Residual");CHKERRQ(ierr); 2716 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"res_");CHKERRQ(ierr); 2717 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2718 /* Check Jacobian */ 2719 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 2720 ierr = PetscDSHasJacobian(prob, &hasJac);CHKERRQ(ierr); 2721 ierr = PetscDSHasJacobianPreconditioner(prob, &hasPrec);CHKERRQ(ierr); 2722 if (hasJac && hasPrec) { 2723 ierr = DMCreateMatrix(dm, &M);CHKERRQ(ierr); 2724 ierr = SNESComputeJacobian(snes, u, J, M);CHKERRQ(ierr); 2725 ierr = PetscObjectSetOptionsPrefix((PetscObject) M, "jacpre_");CHKERRQ(ierr); 2726 ierr = MatViewFromOptions(M, NULL, "-mat_view");CHKERRQ(ierr); 2727 ierr = MatDestroy(&M);CHKERRQ(ierr); 2728 } else { 2729 ierr = SNESComputeJacobian(snes, u, J, J);CHKERRQ(ierr); 2730 } 2731 ierr = PetscObjectSetOptionsPrefix((PetscObject) J, "jac_");CHKERRQ(ierr); 2732 ierr = MatViewFromOptions(J, NULL, "-mat_view");CHKERRQ(ierr); 2733 ierr = MatGetNullSpace(J, &nullSpace);CHKERRQ(ierr); 2734 if (nullSpace) { 2735 PetscBool isNull; 2736 ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr); 2737 if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid."); 2738 } 2739 ierr = VecDuplicate(u, &b);CHKERRQ(ierr); 2740 ierr = VecSet(r, 0.0);CHKERRQ(ierr); 2741 ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); 2742 ierr = MatMult(J, u, r);CHKERRQ(ierr); 2743 ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); 2744 ierr = VecDestroy(&b);CHKERRQ(ierr); 2745 ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); 2746 ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", (double)res);CHKERRQ(ierr); 2747 ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); 2748 ierr = PetscObjectSetName((PetscObject) r, "Au - b = Au + F(0)");CHKERRQ(ierr); 2749 ierr = PetscObjectSetOptionsPrefix((PetscObject)r,"linear_res_");CHKERRQ(ierr); 2750 ierr = VecViewFromOptions(r, NULL, "-vec_view");CHKERRQ(ierr); 2751 ierr = VecDestroy(&r);CHKERRQ(ierr); 2752 ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); 2753 ierr = MatDestroy(&J);CHKERRQ(ierr); 2754 PetscFunctionReturn(0); 2755 } 2756 2757 PetscErrorCode DMSNESCheckFromOptions(SNES snes, Vec u, PetscErrorCode (**exactFuncs)(PetscInt dim, PetscReal time, const PetscReal x[], PetscInt Nf, PetscScalar *u, void *ctx), void **ctxs) 2758 { 2759 DM dm; 2760 Vec sol; 2761 PetscBool check; 2762 PetscErrorCode ierr; 2763 2764 PetscFunctionBegin; 2765 ierr = PetscOptionsHasName(((PetscObject)snes)->options,((PetscObject)snes)->prefix, "-dmsnes_check", &check);CHKERRQ(ierr); 2766 if (!check) PetscFunctionReturn(0); 2767 ierr = SNESGetDM(snes, &dm);CHKERRQ(ierr); 2768 ierr = VecDuplicate(u, &sol);CHKERRQ(ierr); 2769 ierr = SNESSetSolution(snes, sol);CHKERRQ(ierr); 2770 ierr = DMSNESCheckFromOptions_Internal(snes, dm, u, sol, exactFuncs, ctxs);CHKERRQ(ierr); 2771 ierr = VecDestroy(&sol);CHKERRQ(ierr); 2772 PetscFunctionReturn(0); 2773 } 2774