int main(int argc, char **argv) { SNES snes; /* nonlinear solver */ DM dm; /* problem definition */ Vec u, r; /* solution and residual */ AppCtx user; /* user-defined work context */ PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = PetscBagCreate(PETSC_COMM_WORLD, sizeof(Parameter), &user.bag);CHKERRQ(ierr); ierr = SetupParameters(&user);CHKERRQ(ierr); ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = DMSetApplicationContext(dm, &user);CHKERRQ(ierr); /* Setup problem */ ierr = PetscMalloc(2 * sizeof(void (*)(const PetscReal[], PetscScalar *, void *)), &user.exactFuncs);CHKERRQ(ierr); ierr = SetupDiscretization(dm, &user);CHKERRQ(ierr); ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = VecDuplicate(u, &r);CHKERRQ(ierr); ierr = DMPlexSetSNESLocalFEM(dm,&user,&user,&user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); { Parameter *param; void *ctxs[2]; ierr = PetscBagGetData(user.bag, (void **) ¶m);CHKERRQ(ierr); ctxs[0] = ctxs[1] = param; ierr = DMProjectFunction(dm, 0.0, user.exactFuncs, ctxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "Exact Solution");CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-exact_vec_view");CHKERRQ(ierr); } ierr = DMSNESCheckFromOptions(snes, u, NULL, NULL);CHKERRQ(ierr); ierr = VecSet(u, 0.0);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "Solution");CHKERRQ(ierr); ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-sol_vec_view");CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = PetscBagDestroy(&user.bag);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc, char **argv) { DM dm; SNES snes; Vec u, r; AppCtx user; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr); ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = PetscMalloc(3 * sizeof(void (*)()), &user.exactFuncs);CHKERRQ(ierr); ierr = SetupDiscretization(dm, &user);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "solution");CHKERRQ(ierr); ierr = VecDuplicate(u, &r);CHKERRQ(ierr); ierr = DMPlexSetSNESLocalFEM(dm,&user,&user,&user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = DMProjectFunction(dm, user.exactFuncs, NULL, INSERT_ALL_VALUES, u);CHKERRQ(ierr); ierr = DMSNESCheckFromOptions(snes, u, user.exactFuncs, NULL);CHKERRQ(ierr); if (user.runType == RUN_FULL) { PetscErrorCode (*initialGuess[3])(PetscInt dim, const PetscReal x[], PetscInt Nf, PetscScalar u[], void *ctx); PetscReal error; initialGuess[0] = zero; initialGuess[1] = zero; initialGuess[2] = zero; ierr = DMProjectFunction(dm, initialGuess, NULL, INSERT_VALUES, u);CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-initial_vec_view");CHKERRQ(ierr); ierr = DMComputeL2Diff(dm, user.exactFuncs, NULL, u, &error);CHKERRQ(ierr); if (error < 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} else {ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial L_2 Error: %g\n", error);CHKERRQ(ierr);} ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = DMComputeL2Diff(dm, user.exactFuncs, NULL, u, &error);CHKERRQ(ierr); if (error < 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "Final L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} else {ierr = PetscPrintf(PETSC_COMM_WORLD, "Final L_2 Error: %g\n", error);CHKERRQ(ierr);} } ierr = VecViewFromOptions(u, NULL, "-sol_vec_view");CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc, char **argv) { DM dm; /* Problem specification */ SNES snes; /* Nonlinear solver */ Vec u; /* Solutions */ AppCtx user; /* User-defined work context */ PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); /* Primal system */ ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = SetupFE(dm, user.dim, user.simplex, "displacement", SetupPrimalProblem, &user);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = VecSet(u, 0.0);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "displacement");CHKERRQ(ierr); ierr = DMPlexSetSNESLocalFEM(dm, &user, &user, &user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = DMSNESCheckFromOptions(snes, u, NULL, NULL);CHKERRQ(ierr); ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = SNESGetSolution(snes, &u);CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-displacement_view");CHKERRQ(ierr); /* Cleanup */ ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
static PetscErrorCode TestFieldProjection(DM dm, DM auxdm, DMLabel label, Vec la, const char name[], AppCtx *user) { PetscErrorCode (**afuncs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *); void (**funcs)(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]); Vec lx, lu; PetscInt Nf, f; PetscInt val[1] = {1}; char lname[PETSC_MAX_PATH_LEN]; PetscErrorCode ierr; PetscFunctionBeginUser; if (auxdm) { ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) auxdm);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) la);CHKERRQ(ierr); } ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); ierr = PetscMalloc2(Nf, &funcs, Nf, &afuncs);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) afuncs[f] = linear; funcs[0] = linear_vector; funcs[1] = linear_scalar; ierr = DMGetLocalVector(dm, &lu);CHKERRQ(ierr); ierr = PetscStrcpy(lname, "Local Field Input ");CHKERRQ(ierr); ierr = PetscStrcat(lname, name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) lu, lname);CHKERRQ(ierr); if (!label) {ierr = DMProjectFunctionLocal(dm, 0.0, afuncs, NULL, INSERT_VALUES, lu);CHKERRQ(ierr);} else {ierr = DMProjectFunctionLabelLocal(dm, 0.0, label, 1, val, 0, NULL, afuncs, NULL, INSERT_VALUES, lu);CHKERRQ(ierr);} ierr = VecViewFromOptions(lu, NULL, "-local_input_view");CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &lx);CHKERRQ(ierr); ierr = PetscStrcpy(lname, "Local Field ");CHKERRQ(ierr); ierr = PetscStrcat(lname, name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) lx, lname);CHKERRQ(ierr); if (!label) {ierr = DMProjectFieldLocal(dm, 0.0, lu, funcs, INSERT_VALUES, lx);CHKERRQ(ierr);} else {ierr = DMProjectFieldLabelLocal(dm, 0.0, label, 1, val, 0, NULL, lu, funcs, INSERT_VALUES, lx);CHKERRQ(ierr);} ierr = VecViewFromOptions(lx, NULL, "-local_field_view");CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &lx);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &lu);CHKERRQ(ierr); ierr = PetscFree2(funcs, afuncs);CHKERRQ(ierr); if (auxdm) { ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);CHKERRQ(ierr); } PetscFunctionReturn(0); }
/*@ MFNSolve - Solves the matrix function problem. Given a vector b, the vector x = f(alpha*A)*b is returned. Collective on MFN Input Parameters: + mfn - matrix function context obtained from MFNCreate() - b - the right hand side vector Output Parameter: . x - the solution (this may be the same vector as b, then b will be overwritten with the answer) Options Database Keys: + -mfn_view - print information about the solver used . -mfn_view_mat binary - save the matrix to the default binary viewer . -mfn_view_rhs binary - save right hand side vector to the default binary viewer - -mfn_view_solution binary - save computed solution vector to the default binary viewer Notes: The matrix A is specified with MFNSetOperator(). The function f is specified with MFNSetFunction(). The scalar alpha is specified with MFNSetScaleFactor(). Level: beginner .seealso: MFNCreate(), MFNSetUp(), MFNDestroy(), MFNSetTolerances(), MFNSetOperator(), MFNSetFunction(), MFNSetScaleFactor() @*/ PetscErrorCode MFNSolve(MFN mfn,Vec b,Vec x) { PetscErrorCode ierr; PetscBool flg; PetscViewer viewer; PetscViewerFormat format; PetscFunctionBegin; PetscValidHeaderSpecific(mfn,MFN_CLASSID,1); PetscValidHeaderSpecific(b,VEC_CLASSID,2); PetscCheckSameComm(mfn,1,b,2); if (b!=x) PetscValidHeaderSpecific(x,VEC_CLASSID,3); if (b!=x) PetscCheckSameComm(mfn,1,x,3); /* call setup */ ierr = MFNSetUp(mfn);CHKERRQ(ierr); mfn->its = 0; ierr = MFNMonitor(mfn,mfn->its,0);CHKERRQ(ierr); /* call solver */ ierr = PetscLogEventBegin(MFN_Solve,mfn,b,x,0);CHKERRQ(ierr); ierr = (*mfn->ops->solve)(mfn,b,x);CHKERRQ(ierr); ierr = PetscLogEventEnd(MFN_Solve,mfn,b,x,0);CHKERRQ(ierr); if (!mfn->reason) SETERRQ(PetscObjectComm((PetscObject)mfn),PETSC_ERR_PLIB,"Internal error, solver returned without setting converged reason"); if (mfn->errorifnotconverged && mfn->reason < 0) SETERRQ(PetscObjectComm((PetscObject)mfn),PETSC_ERR_NOT_CONVERGED,"MFNSolve has not converged"); /* various viewers */ ierr = MatViewFromOptions(mfn->A,((PetscObject)mfn)->prefix,"-mfn_view_mat");CHKERRQ(ierr); ierr = VecViewFromOptions(b,((PetscObject)mfn)->prefix,"-mfn_view_rhs");CHKERRQ(ierr); ierr = VecViewFromOptions(x,((PetscObject)mfn)->prefix,"-mfn_view_solution");CHKERRQ(ierr); ierr = PetscOptionsGetViewer(PetscObjectComm((PetscObject)mfn),((PetscObject)mfn)->prefix,"-mfn_view",&viewer,&format,&flg);CHKERRQ(ierr); if (flg && !PetscPreLoadingOn) { ierr = PetscViewerPushFormat(viewer,format);CHKERRQ(ierr); ierr = MFNView(mfn,viewer);CHKERRQ(ierr); ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } PetscFunctionReturn(0); }
static PetscErrorCode TestFunctionProjection(DM dm, DM auxdm, DMLabel label, Vec la, const char name[], AppCtx *user) { PetscErrorCode (**funcs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *); Vec x, lx; PetscInt Nf, f; PetscInt val[1] = {1}; char lname[PETSC_MAX_PATH_LEN]; PetscErrorCode ierr; PetscFunctionBeginUser; if (auxdm) { ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) auxdm);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) la);CHKERRQ(ierr); } ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); ierr = PetscMalloc1(Nf, &funcs);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) funcs[f] = linear; ierr = DMGetGlobalVector(dm, &x);CHKERRQ(ierr); ierr = PetscStrcpy(lname, "Function ");CHKERRQ(ierr); ierr = PetscStrcat(lname, name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) x, lname);CHKERRQ(ierr); if (!label) {ierr = DMProjectFunction(dm, 0.0, funcs, NULL, INSERT_VALUES, x);CHKERRQ(ierr);} else {ierr = DMProjectFunctionLabel(dm, 0.0, label, 1, val, 0, NULL, funcs, NULL, INSERT_VALUES, x);CHKERRQ(ierr);} ierr = VecViewFromOptions(x, NULL, "-func_view");CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dm, &x);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &lx);CHKERRQ(ierr); ierr = PetscStrcpy(lname, "Local Function ");CHKERRQ(ierr); ierr = PetscStrcat(lname, name);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) lx, lname);CHKERRQ(ierr); if (!label) {ierr = DMProjectFunctionLocal(dm, 0.0, funcs, NULL, INSERT_VALUES, lx);CHKERRQ(ierr);} else {ierr = DMProjectFunctionLabelLocal(dm, 0.0, label, 1, val, 0, NULL, funcs, NULL, INSERT_VALUES, lx);CHKERRQ(ierr);} ierr = VecViewFromOptions(lx, NULL, "-local_func_view");CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &lx);CHKERRQ(ierr); ierr = PetscFree(funcs);CHKERRQ(ierr); if (auxdm) { ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);CHKERRQ(ierr); } PetscFunctionReturn(0); }
int main(int argc, char** argv) { Mat Q; Vec v, a, se; KSP QRsolver; PC pc; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, NULL);if (ierr) return ierr; ierr = VecCreate(PETSC_COMM_WORLD, &v);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD, &Q);CHKERRQ(ierr); ierr = MatSetType(Q, MATDENSE);CHKERRQ(ierr); ierr = fill(Q, v);CHKERRQ(ierr); ierr = MatCreateVecs(Q, &a, NULL);CHKERRQ(ierr); ierr = KSPCreate(PETSC_COMM_WORLD, &QRsolver);CHKERRQ(ierr); ierr = KSPGetPC(QRsolver, &pc);CHKERRQ(ierr); ierr = PCSetType(pc, PCNONE);CHKERRQ(ierr); ierr = KSPSetType(QRsolver, KSPLSQR);CHKERRQ(ierr); ierr = KSPSetFromOptions(QRsolver);CHKERRQ(ierr); ierr = KSPSetOperators(QRsolver, Q, Q);CHKERRQ(ierr); ierr = MatViewFromOptions(Q, NULL, "-sys_view");CHKERRQ(ierr); ierr = VecViewFromOptions(a, NULL, "-rhs_view");CHKERRQ(ierr); ierr = KSPSolve(QRsolver, v, a);CHKERRQ(ierr); ierr = KSPLSQRGetStandardErrorVec(QRsolver, &se);CHKERRQ(ierr); if (se) { ierr = VecViewFromOptions(se, NULL, "-se_view");CHKERRQ(ierr); } ierr = KSPDestroy(&QRsolver);CHKERRQ(ierr); ierr = VecDestroy(&a);CHKERRQ(ierr); ierr = VecDestroy(&v);CHKERRQ(ierr); ierr = MatDestroy(&Q);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
static PetscErrorCode CreateAuxiliaryData(DM dm, DM *auxdm, Vec *la, AppCtx *user) { PetscErrorCode (**afuncs)(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *); PetscInt dim, Nf, f; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); ierr = PetscMalloc1(Nf, &afuncs);CHKERRQ(ierr); for (f = 0; f < Nf; ++f) afuncs[f] = linear; ierr = DMClone(dm, auxdm);CHKERRQ(ierr); ierr = SetupDiscretization(*auxdm, dim, user->cellSimplex, user);CHKERRQ(ierr); ierr = DMCreateLocalVector(*auxdm, la);CHKERRQ(ierr); ierr = DMProjectFunctionLocal(dm, 0.0, afuncs, NULL, INSERT_VALUES, *la);CHKERRQ(ierr); ierr = VecViewFromOptions(*la, NULL, "-local_aux_view");CHKERRQ(ierr); ierr = PetscFree(afuncs);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char **argv) { DM dm; Vec u; AppCtx ctx; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(PETSC_COMM_WORLD, &ctx);CHKERRQ(ierr); ierr = DMPlexCreateSphereMesh(PETSC_COMM_WORLD, ctx.dim, ctx.simplex, &dm);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) dm, "Sphere");CHKERRQ(ierr); ierr = DMSetFromOptions(dm);CHKERRQ(ierr); ierr = ProjectToUnitSphere(dm);CHKERRQ(ierr); ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); ierr = SetupSection(dm);CHKERRQ(ierr); ierr = DMGetGlobalVector(dm, &u);CHKERRQ(ierr); ierr = VecSet(u, 2);CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dm, &u);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
void PETSC_STDCALL vecviewfromoptions_(Vec vec, char *title, int *__ierr ){ *__ierr = VecViewFromOptions( (Vec)PetscToPointer((vec) ),title); }
int main(int argc, char **argv) { MPI_Comm comm; DM dm; Vec v, nv, rv, coord; PetscBool test_read = PETSC_FALSE, verbose = PETSC_FALSE, flg; PetscViewer hdf5Viewer; PetscInt dim = 2; PetscInt numFields = 1; PetscInt numBC = 0; PetscInt numComp[1] = {2}; PetscInt numDof[3] = {2, 0, 0}; PetscInt bcFields[1] = {0}; IS bcPoints[1] = {NULL}; PetscSection section; PetscReal norm; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, (char *) 0, help);CHKERRQ(ierr); comm = PETSC_COMM_WORLD; ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","Test Options","none");CHKERRQ(ierr); ierr = PetscOptionsBool("-test_read","Test reading from the HDF5 file","",PETSC_FALSE,&test_read,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-verbose","print the Vecs","",PETSC_FALSE,&verbose,NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-dim","the dimension of the problem","",2,&dim,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd(); ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, &dm);CHKERRQ(ierr); ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); numDof[0] = dim; ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcFields, bcPoints, NULL, NULL, §ion);CHKERRQ(ierr); ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr); ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr); ierr = DMSetUseNatural(dm, PETSC_TRUE);CHKERRQ(ierr); { DM dmDist; ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr); if (dmDist) { ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmDist; } } ierr = DMCreateGlobalVector(dm, &v);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) v, "V");CHKERRQ(ierr); ierr = DMGetCoordinates(dm, &coord);CHKERRQ(ierr); ierr = VecCopy(coord, v);CHKERRQ(ierr); if (verbose) { PetscInt size, bs; ierr = VecGetSize(v, &size);CHKERRQ(ierr); ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "==== original V in global ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr); ierr = VecView(v, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = DMCreateGlobalVector(dm, &nv);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) nv, "NV");CHKERRQ(ierr); ierr = DMPlexGlobalToNaturalBegin(dm, v, nv);CHKERRQ(ierr); ierr = DMPlexGlobalToNaturalEnd(dm, v, nv);CHKERRQ(ierr); if (verbose) { PetscInt size, bs; ierr = VecGetSize(nv, &size);CHKERRQ(ierr); ierr = VecGetBlockSize(nv, &bs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "==== V in natural ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr); ierr = VecView(nv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecViewFromOptions(v, NULL, "-global_vec_view");CHKERRQ(ierr); if (test_read) { ierr = DMCreateGlobalVector(dm, &rv);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) rv, "V");CHKERRQ(ierr); /* Test native read */ ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr); ierr = PetscViewerPushFormat(hdf5Viewer, PETSC_VIEWER_NATIVE);CHKERRQ(ierr); ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr); if (verbose) { PetscInt size, bs; ierr = VecGetSize(rv, &size);CHKERRQ(ierr); ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr); ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecEqual(rv, v, &flg);CHKERRQ(ierr); if (flg) { ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are equal\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are not equal\n\n");CHKERRQ(ierr); ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr); ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr); ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } /* Test raw read */ ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr); ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr); if (verbose) { PetscInt size, bs; ierr = VecGetSize(rv, &size);CHKERRQ(ierr); ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr); ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecEqual(rv, nv, &flg);CHKERRQ(ierr); if (flg) { ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are equal\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are not equal\n\n");CHKERRQ(ierr); ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr); ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr); ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = VecDestroy(&rv);CHKERRQ(ierr); } ierr = VecDestroy(&nv);CHKERRQ(ierr); ierr = VecDestroy(&v);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc, char **argv) { MPI_Comm comm; DM base, preForest, postForest; PetscInt dim = 2; PetscInt preCount, postCount; Vec preVec, postVecTransfer, postVecExact; PetscErrorCode (*funcs[1]) (PetscInt,PetscReal,const PetscReal [],PetscInt,PetscScalar [], void *) = {MultiaffineFunction}; void *ctxs[1] = {NULL}; const PetscInt cells[] = {3, 3, 3}; PetscReal diff, tol = PETSC_SMALL; PetscBool linear = PETSC_FALSE; PetscBool useFV = PETSC_FALSE; PetscDS ds; bc_func_ctx bcCtx; DMLabel adaptLabel; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; comm = PETSC_COMM_WORLD; ierr = PetscOptionsBegin(comm, "", "DMForestTransferVec() Test Options", "DMFOREST");CHKERRQ(ierr); ierr = PetscOptionsInt("-dim", "The dimension (2 or 3)", "ex2.c", dim, &dim, NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-linear","Transfer a simple linear function", "ex2.c", linear, &linear, NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-use_fv","Use a finite volume approximation", "ex2.c", useFV, &useFV, NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); if (linear) { funcs[0] = LinearFunction; } bcCtx.func = funcs[0]; bcCtx.dim = dim; bcCtx.Nf = 1; bcCtx.ctx = NULL; /* the base mesh */ ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &base);CHKERRQ(ierr); if (useFV) { PetscFV fv; PetscLimiter limiter; DM baseFV; ierr = DMPlexConstructGhostCells(base,NULL,NULL,&baseFV);CHKERRQ(ierr); ierr = DMDestroy(&base);CHKERRQ(ierr); base = baseFV; ierr = PetscFVCreate(comm, &fv);CHKERRQ(ierr); ierr = PetscFVSetSpatialDimension(fv,dim);CHKERRQ(ierr); ierr = PetscFVSetType(fv,PETSCFVLEASTSQUARES);CHKERRQ(ierr); ierr = PetscFVSetNumComponents(fv,1);CHKERRQ(ierr); ierr = PetscLimiterCreate(comm,&limiter);CHKERRQ(ierr); ierr = PetscLimiterSetType(limiter,PETSCLIMITERNONE);CHKERRQ(ierr); ierr = PetscFVSetLimiter(fv,limiter);CHKERRQ(ierr); ierr = PetscLimiterDestroy(&limiter);CHKERRQ(ierr); ierr = PetscFVSetFromOptions(fv);CHKERRQ(ierr); ierr = DMSetField(base,0,(PetscObject)fv);CHKERRQ(ierr); ierr = PetscFVDestroy(&fv);CHKERRQ(ierr); } else { PetscFE fe; ierr = PetscFECreateDefault(base,dim,1,PETSC_FALSE,NULL,PETSC_DEFAULT,&fe);CHKERRQ(ierr); ierr = DMSetField(base,0,(PetscObject)fe);CHKERRQ(ierr); ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); } { PetscDS prob; PetscInt comps[] = {0}; PetscInt ids[] = {1, 2, 3, 4, 5, 6}; ierr = DMGetDS(base,&prob);CHKERRQ(ierr); ierr = PetscDSAddBoundary(prob,PETSC_TRUE, "bc", "marker", 0, 1, comps, useFV ? (void(*)()) bc_func_fv : (void(*)()) funcs[0], 2 * dim, ids, useFV ? (void *) &bcCtx : NULL);CHKERRQ(ierr); } ierr = AddIdentityLabel(base);CHKERRQ(ierr); ierr = DMViewFromOptions(base,NULL,"-dm_base_view");CHKERRQ(ierr); /* the pre adaptivity forest */ ierr = DMCreate(comm,&preForest);CHKERRQ(ierr); ierr = DMSetType(preForest,(dim == 2) ? DMP4EST : DMP8EST);CHKERRQ(ierr); ierr = DMGetDS(base,&ds);CHKERRQ(ierr); ierr = DMSetDS(preForest,ds);CHKERRQ(ierr); ierr = DMForestSetBaseDM(preForest,base);CHKERRQ(ierr); ierr = DMForestSetMinimumRefinement(preForest,1);CHKERRQ(ierr); ierr = DMForestSetInitialRefinement(preForest,1);CHKERRQ(ierr); ierr = DMSetFromOptions(preForest);CHKERRQ(ierr); ierr = DMSetUp(preForest);CHKERRQ(ierr); ierr = DMViewFromOptions(preForest,NULL,"-dm_pre_view");CHKERRQ(ierr); /* the pre adaptivity field */ ierr = DMCreateGlobalVector(preForest,&preVec);CHKERRQ(ierr); ierr = DMProjectFunction(preForest,0.,funcs,ctxs,INSERT_VALUES,preVec);CHKERRQ(ierr); ierr = VecViewFromOptions(preVec,NULL,"-vec_pre_view");CHKERRQ(ierr); ierr = PetscObjectGetReference((PetscObject)preForest,&preCount);CHKERRQ(ierr); /* adapt */ ierr = CreateAdaptivityLabel(preForest,&adaptLabel);CHKERRQ(ierr); ierr = DMForestTemplate(preForest,comm,&postForest);CHKERRQ(ierr); ierr = DMForestSetMinimumRefinement(postForest,0);CHKERRQ(ierr); ierr = DMForestSetInitialRefinement(postForest,0);CHKERRQ(ierr); ierr = DMForestSetAdaptivityLabel(postForest,adaptLabel);CHKERRQ(ierr); ierr = DMLabelDestroy(&adaptLabel);CHKERRQ(ierr); ierr = DMSetUp(postForest);CHKERRQ(ierr); ierr = DMViewFromOptions(postForest,NULL,"-dm_post_view");CHKERRQ(ierr); /* transfer */ ierr = DMCreateGlobalVector(postForest,&postVecTransfer);CHKERRQ(ierr); ierr = DMForestTransferVec(preForest,preVec,postForest,postVecTransfer,PETSC_TRUE,0.0);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecTransfer,NULL,"-vec_post_transfer_view");CHKERRQ(ierr); /* the exact post adaptivity field */ ierr = DMCreateGlobalVector(postForest,&postVecExact);CHKERRQ(ierr); ierr = DMProjectFunction(postForest,0.,funcs,ctxs,INSERT_VALUES,postVecExact);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecExact,NULL,"-vec_post_exact_view");CHKERRQ(ierr); /* compare */ ierr = VecAXPY(postVecTransfer,-1.,postVecExact);CHKERRQ(ierr); ierr = VecViewFromOptions(postVecTransfer,NULL,"-vec_diff_view");CHKERRQ(ierr); ierr = VecNorm(postVecTransfer,NORM_2,&diff);CHKERRQ(ierr); /* output */ if (diff < tol) { ierr = PetscPrintf(comm,"DMForestTransferVec() passes.\n");CHKERRQ(ierr); } else { ierr = PetscPrintf(comm,"DMForestTransferVec() fails with error %g and tolerance %g\n",diff,tol);CHKERRQ(ierr); } /* disconnect preForest from postForest */ ierr = DMForestSetAdaptivityForest(postForest,NULL);CHKERRQ(ierr); ierr = PetscObjectGetReference((PetscObject)preForest,&postCount);CHKERRQ(ierr); if (postCount != preCount) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Adaptation not memory neutral: reference count increase from %d to %d\n",preCount,postCount); /* cleanup */ ierr = VecDestroy(&postVecExact);CHKERRQ(ierr); ierr = VecDestroy(&postVecTransfer);CHKERRQ(ierr); ierr = DMDestroy(&postForest);CHKERRQ(ierr); ierr = VecDestroy(&preVec);CHKERRQ(ierr); ierr = DMDestroy(&preForest);CHKERRQ(ierr); ierr = DMDestroy(&base);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **args) { User user; Mat A,S; PetscScalar *data,diag = 1.3; PetscReal tol = PETSC_SMALL; PetscInt i,j,m = PETSC_DECIDE,n = PETSC_DECIDE,M = 17,N = 15,s1,s2; PetscInt test, ntest = 2; PetscMPIInt rank,size; PetscBool nc = PETSC_FALSE, cong; PetscBool ronl = PETSC_TRUE; PetscBool randomize = PETSC_FALSE; PetscBool keep = PETSC_FALSE; PetscBool testzerorows = PETSC_TRUE, testdiagscale = PETSC_TRUE, testgetdiag = PETSC_TRUE; PetscBool testshift = PETSC_TRUE, testscale = PETSC_TRUE, testdup = PETSC_TRUE, testreset = PETSC_TRUE; PetscErrorCode ierr; ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-ml",&m,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-nl",&n,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-square_nc",&nc,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-rows_only",&ronl,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-randomize",&randomize,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_zerorows",&testzerorows,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_diagscale",&testdiagscale,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_getdiag",&testgetdiag,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_shift",&testshift,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_scale",&testscale,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_dup",&testdup,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-test_reset",&testreset,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-loop",&ntest,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-tol",&tol,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetScalar(NULL,NULL,"-diag",&diag,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-keep",&keep,NULL);CHKERRQ(ierr); /* This tests square matrices with different row/col layout */ if (nc && size > 1) { M = PetscMax(PetscMax(N,M),1); N = M; m = n = 0; if (rank == 0) { m = M-1; n = 1; } else if (rank == 1) { m = 1; n = N-1; } } ierr = MatCreateDense(PETSC_COMM_WORLD,m,n,M,N,NULL,&A);CHKERRQ(ierr); ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr); ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr); ierr = MatHasCongruentLayouts(A,&cong);CHKERRQ(ierr); ierr = MatGetOwnershipRange(A,&s1,NULL);CHKERRQ(ierr); s2 = 1; while (s2 < M) s2 *= 10; ierr = MatDenseGetArray(A,&data);CHKERRQ(ierr); for (j = 0; j < N; j++) { for (i = 0; i < m; i++) { data[j*m + i] = s2*j + i + s1 + 1; } } ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatConvert(A,MATAIJ,MAT_INPLACE_MATRIX,&A);CHKERRQ(ierr); ierr = MatSetOption(A,MAT_KEEP_NONZERO_PATTERN,keep);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)A,"initial");CHKERRQ(ierr); ierr = MatViewFromOptions(A,NULL,"-view_mat");CHKERRQ(ierr); ierr = PetscNew(&user);CHKERRQ(ierr); ierr = MatCreateShell(PETSC_COMM_WORLD,m,n,M,N,user,&S);CHKERRQ(ierr); ierr = MatShellSetOperation(S,MATOP_MULT,(void (*)(void))MatMult_User);CHKERRQ(ierr); ierr = MatShellSetOperation(S,MATOP_MULT_TRANSPOSE,(void (*)(void))MatMultTranspose_User);CHKERRQ(ierr); if (cong) { ierr = MatShellSetOperation(S,MATOP_GET_DIAGONAL,(void (*)(void))MatGetDiagonal_User);CHKERRQ(ierr); } ierr = MatDuplicate(A,MAT_COPY_VALUES,&user->B);CHKERRQ(ierr); /* Square and rows only scaling */ ronl = cong ? ronl : PETSC_TRUE; for (test = 0; test < ntest; test++) { PetscReal err; if (testzerorows) { Mat ST,B,C,BT,BTT; IS zr; Vec x = NULL, b1 = NULL, b2 = NULL; PetscInt *idxs = NULL, nr = 0; if (rank == (test%size)) { nr = 1; ierr = PetscMalloc1(nr,&idxs);CHKERRQ(ierr); if (test%2) { idxs[0] = (2*M - 1 - test/2)%M; } else { idxs[0] = (test/2)%M; } idxs[0] = PetscMax(idxs[0],0); } ierr = ISCreateGeneral(PETSC_COMM_WORLD,nr,idxs,PETSC_OWN_POINTER,&zr);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)zr,"ZR");CHKERRQ(ierr); ierr = ISViewFromOptions(zr,NULL,"-view_is");CHKERRQ(ierr); ierr = MatCreateVecs(A,&x,&b1);CHKERRQ(ierr); if (randomize) { ierr = VecSetRandom(x,NULL);CHKERRQ(ierr); ierr = VecSetRandom(b1,NULL);CHKERRQ(ierr); } else { ierr = VecSet(x,11.4);CHKERRQ(ierr); ierr = VecSet(b1,-14.2);CHKERRQ(ierr); } ierr = VecDuplicate(b1,&b2);CHKERRQ(ierr); ierr = VecCopy(b1,b2);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)b1,"A_B1");CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)b2,"A_B2");CHKERRQ(ierr); if (size > 1 && !cong) { /* MATMPIAIJ ZeroRows and ZeroRowsColumns are buggy in this case */ ierr = VecDestroy(&b1);CHKERRQ(ierr); } if (ronl) { ierr = MatZeroRowsIS(A,zr,diag,x,b1);CHKERRQ(ierr); ierr = MatZeroRowsIS(S,zr,diag,x,b2);CHKERRQ(ierr); } else { ierr = MatZeroRowsColumnsIS(A,zr,diag,x,b1);CHKERRQ(ierr); ierr = MatZeroRowsColumnsIS(S,zr,diag,x,b2);CHKERRQ(ierr); ierr = ISDestroy(&zr);CHKERRQ(ierr); /* Mix zerorows and zerorowscols */ nr = 0; idxs = NULL; if (!rank) { nr = 1; ierr = PetscMalloc1(nr,&idxs);CHKERRQ(ierr); if (test%2) { idxs[0] = (3*M - 2 - test/2)%M; } else { idxs[0] = (test/2+1)%M; } idxs[0] = PetscMax(idxs[0],0); } ierr = ISCreateGeneral(PETSC_COMM_WORLD,nr,idxs,PETSC_OWN_POINTER,&zr);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)zr,"ZR2");CHKERRQ(ierr); ierr = ISViewFromOptions(zr,NULL,"-view_is");CHKERRQ(ierr); ierr = MatZeroRowsIS(A,zr,diag*2.0+PETSC_SMALL,NULL,NULL);CHKERRQ(ierr); ierr = MatZeroRowsIS(S,zr,diag*2.0+PETSC_SMALL,NULL,NULL);CHKERRQ(ierr); } ierr = ISDestroy(&zr);CHKERRQ(ierr); if (b1) { Vec b; ierr = VecViewFromOptions(b1,NULL,"-view_b");CHKERRQ(ierr); ierr = VecViewFromOptions(b2,NULL,"-view_b");CHKERRQ(ierr); ierr = VecDuplicate(b1,&b);CHKERRQ(ierr); ierr = VecCopy(b1,b);CHKERRQ(ierr); ierr = VecAXPY(b,-1.0,b2);CHKERRQ(ierr); ierr = VecNorm(b,NORM_INFINITY,&err);CHKERRQ(ierr); if (err >= tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error b %g\n",test,(double)err);CHKERRQ(ierr); } ierr = VecDestroy(&b);CHKERRQ(ierr); } ierr = VecDestroy(&b1);CHKERRQ(ierr); ierr = VecDestroy(&b2);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = MatConvert(S,MATDENSE,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); ierr = MatCreateTranspose(S,&ST);CHKERRQ(ierr); ierr = MatComputeOperator(ST,MATDENSE,&BT);CHKERRQ(ierr); ierr = MatTranspose(BT,MAT_INITIAL_MATRIX,&BTT);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)B,"S");CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)BTT,"STT");CHKERRQ(ierr); ierr = MatConvert(A,MATDENSE,MAT_INITIAL_MATRIX,&C);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)C,"A");CHKERRQ(ierr); ierr = MatViewFromOptions(C,NULL,"-view_mat");CHKERRQ(ierr); ierr = MatViewFromOptions(B,NULL,"-view_mat");CHKERRQ(ierr); ierr = MatViewFromOptions(BTT,NULL,"-view_mat");CHKERRQ(ierr); ierr = MatAXPY(C,-1.0,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatNorm(C,NORM_FROBENIUS,&err);CHKERRQ(ierr); if (err >= tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error mat mult %g\n",test,(double)err);CHKERRQ(ierr); } ierr = MatConvert(A,MATDENSE,MAT_REUSE_MATRIX,&C);CHKERRQ(ierr); ierr = MatAXPY(C,-1.0,BTT,SAME_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatNorm(C,NORM_FROBENIUS,&err);CHKERRQ(ierr); if (err >= tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error mat mult transpose %g\n",test,(double)err);CHKERRQ(ierr); } ierr = MatDestroy(&ST);CHKERRQ(ierr); ierr = MatDestroy(&BTT);CHKERRQ(ierr); ierr = MatDestroy(&BT);CHKERRQ(ierr); ierr = MatDestroy(&B);CHKERRQ(ierr); ierr = MatDestroy(&C);CHKERRQ(ierr); } if (testdiagscale) { /* MatDiagonalScale() */ Vec vr,vl; ierr = MatCreateVecs(A,&vr,&vl);CHKERRQ(ierr); if (randomize) { ierr = VecSetRandom(vr,NULL);CHKERRQ(ierr); ierr = VecSetRandom(vl,NULL);CHKERRQ(ierr); } else { ierr = VecSet(vr,test%2 ? 0.15 : 1.0/0.15);CHKERRQ(ierr); ierr = VecSet(vl,test%2 ? -1.2 : 1.0/-1.2);CHKERRQ(ierr); } ierr = MatDiagonalScale(A,vl,vr);CHKERRQ(ierr); ierr = MatDiagonalScale(S,vl,vr);CHKERRQ(ierr); ierr = VecDestroy(&vr);CHKERRQ(ierr); ierr = VecDestroy(&vl);CHKERRQ(ierr); } if (testscale) { /* MatScale() */ ierr = MatScale(A,test%2 ? 1.4 : 1.0/1.4);CHKERRQ(ierr); ierr = MatScale(S,test%2 ? 1.4 : 1.0/1.4);CHKERRQ(ierr); } if (testshift && cong) { /* MatShift() : MATSHELL shift is broken when row/cols layout are not congruent and left/right scaling have been applied */ ierr = MatShift(A,test%2 ? -77.5 : 77.5);CHKERRQ(ierr); ierr = MatShift(S,test%2 ? -77.5 : 77.5);CHKERRQ(ierr); } if (testgetdiag && cong) { /* MatGetDiagonal() */ Vec dA,dS; ierr = MatCreateVecs(A,&dA,NULL);CHKERRQ(ierr); ierr = MatCreateVecs(S,&dS,NULL);CHKERRQ(ierr); ierr = MatGetDiagonal(A,dA);CHKERRQ(ierr); ierr = MatGetDiagonal(S,dS);CHKERRQ(ierr); ierr = VecAXPY(dA,-1.0,dS);CHKERRQ(ierr); ierr = VecNorm(dA,NORM_INFINITY,&err);CHKERRQ(ierr); if (err >= tol) { ierr = PetscPrintf(PETSC_COMM_WORLD,"[test %D] Error diag %g\n",test,(double)err);CHKERRQ(ierr); } ierr = VecDestroy(&dA);CHKERRQ(ierr); ierr = VecDestroy(&dS);CHKERRQ(ierr); } if (testdup && !test) { Mat A2, S2; ierr = MatDuplicate(A,MAT_COPY_VALUES,&A2);CHKERRQ(ierr); ierr = MatDuplicate(S,MAT_COPY_VALUES,&S2);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&S);CHKERRQ(ierr); A = A2; S = S2; } if (testreset && (ntest == 1 || test == ntest-2)) { /* reset MATSHELL */ ierr = MatAssemblyBegin(S,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(S,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* reset A */ ierr = MatCopy(user->B,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); } } ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = MatDestroy(&user->B);CHKERRQ(ierr); ierr = MatDestroy(&S);CHKERRQ(ierr); ierr = PetscFree(user);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc, char **argv) { DM dm; /* Problem specification */ DM dmAux; /* Material specification */ SNES snes; /* nonlinear solver */ Vec u,r; /* solution, residual vectors */ Mat A,J; /* Jacobian matrix */ MatNullSpace nullSpace; /* May be necessary for Neumann conditions */ AppCtx user; /* user-defined work context */ JacActionCtx userJ; /* context for Jacobian MF action */ PetscInt its; /* iterations for convergence */ PetscReal error = 0.0; /* L_2 error in the solution */ PetscInt numComponents; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr); ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = DMSetApplicationContext(dm, &user);CHKERRQ(ierr); user.fem.fe = user.fe; ierr = PetscFECreateDefault(dm, user.dim, 1, PETSC_TRUE, NULL, -1, &user.fe[0]);CHKERRQ(ierr); if (user.bcType != NEUMANN) { user.fem.feBd = NULL; user.feBd[0] = NULL; } else { user.fem.feBd = user.feBd; ierr = PetscFECreateDefault(dm, user.dim-1, 1, PETSC_TRUE, "bd_", -1, &user.feBd[0]);CHKERRQ(ierr); } ierr = PetscFEGetNumComponents(user.fe[0], &numComponents);CHKERRQ(ierr); ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *, void *)), &user.exactFuncs);CHKERRQ(ierr); ierr = SetupProblem(dm, &user);CHKERRQ(ierr); ierr = SetupSection(dm, &user);CHKERRQ(ierr); /* Setup Material */ ierr = DMClone(dm, &dmAux);CHKERRQ(ierr); ierr = DMPlexCopyCoordinates(dm, dmAux);CHKERRQ(ierr); if (user.variableCoefficient != COEFF_FIELD) { user.fem.feAux = NULL; user.feAux[0] = NULL; } else { PetscQuadrature q; user.fem.feAux = user.feAux; ierr = PetscFECreateDefault(dmAux, user.dim, 1, PETSC_TRUE, "mat_", -1, &user.feAux[0]);CHKERRQ(ierr); ierr = PetscFEGetQuadrature(user.fe[0], &q);CHKERRQ(ierr); ierr = PetscFESetQuadrature(user.feAux[0], q);CHKERRQ(ierr); } ierr = SetupMaterialSection(dmAux, &user);CHKERRQ(ierr); ierr = SetupMaterial(dm, dmAux, &user);CHKERRQ(ierr); ierr = DMDestroy(&dmAux);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "potential");CHKERRQ(ierr); ierr = VecDuplicate(u, &r);CHKERRQ(ierr); ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); if (user.jacobianMF) { PetscInt M, m, N, n; ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr); ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr); ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr); ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr); ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr); ierr = MatSetUp(A);CHKERRQ(ierr); #if 0 ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr); #endif userJ.dm = dm; userJ.J = J; userJ.user = &user; ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr); ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, NULL, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr); ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr); } else { A = J; } if (user.bcType == NEUMANN) { ierr = MatNullSpaceCreate(PetscObjectComm((PetscObject) dm), PETSC_TRUE, 0, NULL, &nullSpace);CHKERRQ(ierr); ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr); if (A != J) { ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr); } } ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*)) DMPlexComputeResidualFEM, &user);CHKERRQ(ierr); ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,void*)) DMPlexComputeJacobianFEM, &user);CHKERRQ(ierr); ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, NULL, INSERT_ALL_VALUES, u);CHKERRQ(ierr); if (user.checkpoint) { #if defined(PETSC_HAVE_HDF5) ierr = PetscViewerHDF5PushGroup(user.checkpoint, "/fields");CHKERRQ(ierr); ierr = VecLoad(u, user.checkpoint);CHKERRQ(ierr); ierr = PetscViewerHDF5PopGroup(user.checkpoint);CHKERRQ(ierr); #endif } ierr = PetscViewerDestroy(&user.checkpoint);CHKERRQ(ierr); if (user.showInitial) { Vec lv; ierr = DMGetLocalVector(dm, &lv);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, lv);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, lv);CHKERRQ(ierr); ierr = DMPrintLocalVec(dm, "Local function", 1.0e-10, lv);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &lv);CHKERRQ(ierr); } if (user.runType == RUN_FULL) { void (*initialGuess[numComponents])(const PetscReal x[], PetscScalar *, void *ctx); PetscInt c; for (c = 0; c < numComponents; ++c) initialGuess[c] = zero; ierr = DMPlexProjectFunction(dm, user.fe, initialGuess, NULL, INSERT_VALUES, u);CHKERRQ(ierr); if (user.debug) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr); ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, NULL, u, &error);CHKERRQ(ierr); if (error < 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);} if (user.showSolution) { ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr); ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } } else if (user.runType == RUN_PERF) { PetscReal res = 0.0; ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); } else { PetscReal res = 0.0; /* Check discretization error */ ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, NULL, u, &error);CHKERRQ(ierr); if (error < 1.0e-11) {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n");CHKERRQ(ierr);} else {ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);} /* Check residual */ ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr); /* Check Jacobian */ { Vec b; ierr = SNESComputeJacobian(snes, u, A, A);CHKERRQ(ierr); ierr = VecDuplicate(u, &b);CHKERRQ(ierr); ierr = VecSet(r, 0.0);CHKERRQ(ierr); ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr); ierr = MatMult(A, u, r);CHKERRQ(ierr); ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr); ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr); ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr); } } ierr = VecViewFromOptions(u, NULL, "-vec_view");CHKERRQ(ierr); if (user.bcType == NEUMANN) { ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr); } if (user.jacobianMF) { ierr = VecDestroy(&userJ.u);CHKERRQ(ierr); } if (A != J) {ierr = MatDestroy(&A);CHKERRQ(ierr);} ierr = PetscFEDestroy(&user.fe[0]);CHKERRQ(ierr); ierr = PetscFEDestroy(&user.feBd[0]);CHKERRQ(ierr); ierr = PetscFEDestroy(&user.feAux[0]);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc, char **argv) { DM dm; /* Problem specification */ SNES snes; /* Nonlinear solver */ Vec u; /* Solutions */ AppCtx user; /* User-defined work context */ PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr); /* Primal system */ ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); ierr = SetupDiscretization(dm, "potential", SetupPrimalProblem, &user);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr); ierr = VecSet(u, 0.0);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "potential");CHKERRQ(ierr); ierr = DMPlexSetSNESLocalFEM(dm, &user, &user, &user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr); ierr = SNESGetSolution(snes, &u);CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-potential_view");CHKERRQ(ierr); if (user.spectral) { PetscInt planeDir[2] = {0, 1}; PetscReal planeCoord[2] = {0., 1.}; ierr = ComputeSpectral(dm, u, 2, planeDir, planeCoord, &user);CHKERRQ(ierr); } /* Adjoint system */ if (user.adjoint) { DM dmAdj; SNES snesAdj; Vec uAdj; ierr = SNESCreate(PETSC_COMM_WORLD, &snesAdj);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) snesAdj, "adjoint_");CHKERRQ(ierr); ierr = DMClone(dm, &dmAdj);CHKERRQ(ierr); ierr = SNESSetDM(snesAdj, dmAdj);CHKERRQ(ierr); ierr = SetupDiscretization(dmAdj, "adjoint", SetupAdjointProblem, &user);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dmAdj, &uAdj);CHKERRQ(ierr); ierr = VecSet(uAdj, 0.0);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) uAdj, "adjoint");CHKERRQ(ierr); ierr = DMPlexSetSNESLocalFEM(dmAdj, &user, &user, &user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snesAdj);CHKERRQ(ierr); ierr = SNESSolve(snesAdj, NULL, uAdj);CHKERRQ(ierr); ierr = SNESGetSolution(snesAdj, &uAdj);CHKERRQ(ierr); ierr = VecViewFromOptions(uAdj, NULL, "-adjoint_view");CHKERRQ(ierr); /* Error representation */ { DM dmErr, dmErrAux, dms[2]; Vec errorEst, errorL2, uErr, uErrLoc, uAdjLoc, uAdjProj; IS *subis; PetscReal errorEstTot, errorL2Norm, errorL2Tot; PetscInt N, i; PetscErrorCode (*funcs[1])(PetscInt, PetscReal, const PetscReal [], PetscInt, PetscScalar *, void *) = {trig_u}; void (*identity[1])(PetscInt, PetscInt, PetscInt, const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], const PetscInt[], const PetscInt[], const PetscScalar[], const PetscScalar[], const PetscScalar[], PetscReal, const PetscReal[], PetscInt, const PetscScalar[], PetscScalar[]) = {f0_identityaux_u}; void *ctxs[1] = {0}; ctxs[0] = &user; ierr = DMClone(dm, &dmErr);CHKERRQ(ierr); ierr = SetupDiscretization(dmErr, "error", SetupErrorProblem, &user);CHKERRQ(ierr); ierr = DMGetGlobalVector(dmErr, &errorEst);CHKERRQ(ierr); ierr = DMGetGlobalVector(dmErr, &errorL2);CHKERRQ(ierr); /* Compute auxiliary data (solution and projection of adjoint solution) */ ierr = DMGetLocalVector(dmAdj, &uAdjLoc);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dmAdj, uAdj, INSERT_VALUES, uAdjLoc);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dmAdj, uAdj, INSERT_VALUES, uAdjLoc);CHKERRQ(ierr); ierr = DMGetGlobalVector(dm, &uAdjProj);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "dmAux", (PetscObject) dmAdj);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", (PetscObject) uAdjLoc);CHKERRQ(ierr); ierr = DMProjectField(dm, 0.0, u, identity, INSERT_VALUES, uAdjProj);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "dmAux", NULL);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dm, "A", NULL);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dmAdj, &uAdjLoc);CHKERRQ(ierr); /* Attach auxiliary data */ dms[0] = dm; dms[1] = dm; ierr = DMCreateSuperDM(dms, 2, &subis, &dmErrAux);CHKERRQ(ierr); if (0) { PetscSection sec; ierr = DMGetSection(dms[0], &sec);CHKERRQ(ierr); ierr = PetscSectionView(sec, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMGetSection(dms[1], &sec);CHKERRQ(ierr); ierr = PetscSectionView(sec, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = DMGetSection(dmErrAux, &sec);CHKERRQ(ierr); ierr = PetscSectionView(sec, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); } ierr = DMViewFromOptions(dmErrAux, NULL, "-dm_err_view");CHKERRQ(ierr); ierr = ISViewFromOptions(subis[0], NULL, "-super_is_view");CHKERRQ(ierr); ierr = ISViewFromOptions(subis[1], NULL, "-super_is_view");CHKERRQ(ierr); ierr = DMGetGlobalVector(dmErrAux, &uErr);CHKERRQ(ierr); ierr = VecViewFromOptions(u, NULL, "-map_vec_view");CHKERRQ(ierr); ierr = VecViewFromOptions(uAdjProj, NULL, "-map_vec_view");CHKERRQ(ierr); ierr = VecViewFromOptions(uErr, NULL, "-map_vec_view");CHKERRQ(ierr); ierr = VecISCopy(uErr, subis[0], SCATTER_FORWARD, u);CHKERRQ(ierr); ierr = VecISCopy(uErr, subis[1], SCATTER_FORWARD, uAdjProj);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dm, &uAdjProj);CHKERRQ(ierr); for (i = 0; i < 2; ++i) {ierr = ISDestroy(&subis[i]);CHKERRQ(ierr);} ierr = PetscFree(subis);CHKERRQ(ierr); ierr = DMGetLocalVector(dmErrAux, &uErrLoc);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, uErr, INSERT_VALUES, uErrLoc);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, uErr, INSERT_VALUES, uErrLoc);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmErrAux, &uErr);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dmAdj, "dmAux", (PetscObject) dmErrAux);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dmAdj, "A", (PetscObject) uErrLoc);CHKERRQ(ierr); /* Compute cellwise error estimate */ ierr = VecSet(errorEst, 0.0);CHKERRQ(ierr); ierr = DMPlexComputeCellwiseIntegralFEM(dmAdj, uAdj, errorEst, &user);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dmAdj, "dmAux", NULL);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject) dmAdj, "A", NULL);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dmErrAux, &uErrLoc);CHKERRQ(ierr); ierr = DMDestroy(&dmErrAux);CHKERRQ(ierr); /* Plot cellwise error vector */ ierr = VecViewFromOptions(errorEst, NULL, "-error_view");CHKERRQ(ierr); /* Compute ratio of estimate (sum over cells) with actual L_2 error */ ierr = DMComputeL2Diff(dm, 0.0, funcs, ctxs, u, &errorL2Norm);CHKERRQ(ierr); ierr = DMPlexComputeL2DiffVec(dm, 0.0, funcs, ctxs, u, errorL2);CHKERRQ(ierr); ierr = VecViewFromOptions(errorL2, NULL, "-l2_error_view");CHKERRQ(ierr); ierr = VecNorm(errorL2, NORM_INFINITY, &errorL2Tot);CHKERRQ(ierr); ierr = VecNorm(errorEst, NORM_INFINITY, &errorEstTot);CHKERRQ(ierr); ierr = VecGetSize(errorEst, &N);CHKERRQ(ierr); ierr = VecPointwiseDivide(errorEst, errorEst, errorL2);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) errorEst, "Error ratio");CHKERRQ(ierr); ierr = VecViewFromOptions(errorEst, NULL, "-error_ratio_view");CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "N: %D L2 error: %g Error Ratio: %g/%g = %g\n", N, (double) errorL2Norm, (double) errorEstTot, (double) PetscSqrtReal(errorL2Tot), (double) errorEstTot/PetscSqrtReal(errorL2Tot));CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmErr, &errorEst);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(dmErr, &errorL2);CHKERRQ(ierr); ierr = DMDestroy(&dmErr);CHKERRQ(ierr); } ierr = DMDestroy(&dmAdj);CHKERRQ(ierr); ierr = VecDestroy(&uAdj);CHKERRQ(ierr); ierr = SNESDestroy(&snesAdj);CHKERRQ(ierr); } /* Cleanup */ ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
static PetscErrorCode ComputeSpectral(DM dm, Vec u, PetscInt numPlanes, const PetscInt planeDir[], const PetscReal planeCoord[], AppCtx *user) { MPI_Comm comm; PetscSection coordSection, section; Vec coordinates, uloc; const PetscScalar *coords, *array; PetscInt p; PetscMPIInt size, rank; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = DMGetLocalVector(dm, &uloc);CHKERRQ(ierr); ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, uloc);CHKERRQ(ierr); ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, uloc);CHKERRQ(ierr); ierr = DMPlexInsertBoundaryValues(dm, PETSC_TRUE, uloc, 0.0, NULL, NULL, NULL);CHKERRQ(ierr); ierr = VecViewFromOptions(uloc, NULL, "-sol_view");CHKERRQ(ierr); ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); ierr = VecGetArrayRead(uloc, &array);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr); ierr = VecGetArrayRead(coordinates, &coords);CHKERRQ(ierr); for (p = 0; p < numPlanes; ++p) { DMLabel label; char name[PETSC_MAX_PATH_LEN]; Mat F; Vec x, y; IS stratum; PetscReal *ray, *gray; PetscScalar *rvals, *svals, *gsvals; PetscInt *perm, *nperm; PetscInt n, N, i, j, off, offu; const PetscInt *points; ierr = PetscSNPrintf(name, PETSC_MAX_PATH_LEN, "spectral_plane_%D", p);CHKERRQ(ierr); ierr = DMGetLabel(dm, name, &label);CHKERRQ(ierr); ierr = DMLabelGetStratumIS(label, 1, &stratum);CHKERRQ(ierr); ierr = ISGetLocalSize(stratum, &n);CHKERRQ(ierr); ierr = ISGetIndices(stratum, &points);CHKERRQ(ierr); ierr = PetscMalloc2(n, &ray, n, &svals);CHKERRQ(ierr); for (i = 0; i < n; ++i) { ierr = PetscSectionGetOffset(coordSection, points[i], &off);CHKERRQ(ierr); ierr = PetscSectionGetOffset(section, points[i], &offu);CHKERRQ(ierr); ray[i] = PetscRealPart(coords[off+((planeDir[p]+1)%2)]); svals[i] = array[offu]; } /* Gather the ray data to proc 0 */ if (size > 1) { PetscMPIInt *cnt, *displs, p; ierr = PetscCalloc2(size, &cnt, size, &displs);CHKERRQ(ierr); ierr = MPI_Gather(&n, 1, MPIU_INT, cnt, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); for (p = 1; p < size; ++p) displs[p] = displs[p-1] + cnt[p-1]; N = displs[size-1] + cnt[size-1]; ierr = PetscMalloc2(N, &gray, N, &gsvals);CHKERRQ(ierr); ierr = MPI_Gatherv(ray, n, MPIU_REAL, gray, cnt, displs, MPIU_REAL, 0, comm);CHKERRQ(ierr); ierr = MPI_Gatherv(svals, n, MPIU_SCALAR, gsvals, cnt, displs, MPIU_SCALAR, 0, comm);CHKERRQ(ierr); ierr = PetscFree2(cnt, displs);CHKERRQ(ierr); } else { N = n; gray = ray; gsvals = svals; } if (!rank) { /* Sort point along ray */ ierr = PetscMalloc2(N, &perm, N, &nperm);CHKERRQ(ierr); for (i = 0; i < N; ++i) {perm[i] = i;} ierr = PetscSortRealWithPermutation(N, gray, perm);CHKERRQ(ierr); /* Count duplicates and squish mapping */ nperm[0] = perm[0]; for (i = 1, j = 1; i < N; ++i) { if (PetscAbsReal(gray[perm[i]] - gray[perm[i-1]]) > PETSC_SMALL) nperm[j++] = perm[i]; } /* Create FFT structs */ ierr = MatCreateFFT(PETSC_COMM_SELF, 1, &j, MATFFTW, &F);CHKERRQ(ierr); ierr = MatCreateVecs(F, &x, &y);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) y, name);CHKERRQ(ierr); ierr = VecGetArray(x, &rvals);CHKERRQ(ierr); for (i = 0, j = 0; i < N; ++i) { if (i > 0 && PetscAbsReal(gray[perm[i]] - gray[perm[i-1]]) < PETSC_SMALL) continue; rvals[j] = gsvals[nperm[j]]; ++j; } ierr = PetscFree2(perm, nperm);CHKERRQ(ierr); if (size > 1) {ierr = PetscFree2(gray, gsvals);CHKERRQ(ierr);} ierr = VecRestoreArray(x, &rvals);CHKERRQ(ierr); /* Do FFT along the ray */ ierr = MatMult(F, x, y);CHKERRQ(ierr); /* Chop FFT */ ierr = VecChop(y, PETSC_SMALL);CHKERRQ(ierr); ierr = VecViewFromOptions(x, NULL, "-real_view");CHKERRQ(ierr); ierr = VecViewFromOptions(y, NULL, "-fft_view");CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&y);CHKERRQ(ierr); ierr = MatDestroy(&F);CHKERRQ(ierr); } ierr = ISRestoreIndices(stratum, &points);CHKERRQ(ierr); ierr = ISDestroy(&stratum);CHKERRQ(ierr); ierr = PetscFree2(ray, svals);CHKERRQ(ierr); } ierr = VecRestoreArrayRead(coordinates, &coords);CHKERRQ(ierr); ierr = VecRestoreArrayRead(uloc, &array);CHKERRQ(ierr); ierr = DMRestoreLocalVector(dm, &uloc);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char **argv) { AppCtx ctx; DM dm; TS ts; Vec u, r; PetscReal t = 0.0; PetscReal L2error = 0.0; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, help); CHKERRQ(ierr); ierr = ProcessOptions(PETSC_COMM_WORLD, &ctx); CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &dm, &ctx); CHKERRQ(ierr); ierr = DMSetApplicationContext(dm, &ctx); CHKERRQ(ierr); ierr = PetscMalloc1(1, &ctx.exactFuncs); CHKERRQ(ierr); ierr = SetupDiscretization(dm, &ctx); CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u); CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "temperature"); CHKERRQ(ierr); ierr = VecDuplicate(u, &r); CHKERRQ(ierr); ierr = TSCreate(PETSC_COMM_WORLD, &ts); CHKERRQ(ierr); ierr = TSSetDM(ts, dm); CHKERRQ(ierr); ierr = DMTSSetBoundaryLocal(dm, DMPlexTSComputeBoundary, &ctx); CHKERRQ(ierr); ierr = DMTSSetIFunctionLocal(dm, DMPlexTSComputeIFunctionFEM, &ctx); CHKERRQ(ierr); ierr = DMTSSetIJacobianLocal(dm, DMPlexTSComputeIJacobianFEM, &ctx); CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER); CHKERRQ(ierr); ierr = TSSetFromOptions(ts); CHKERRQ(ierr); ierr = DMProjectFunction(dm, t, ctx.exactFuncs, NULL, INSERT_ALL_VALUES, u); CHKERRQ(ierr); ierr = TSSolve(ts, u); CHKERRQ(ierr); ierr = TSGetTime(ts, &t); CHKERRQ(ierr); ierr = DMComputeL2Diff(dm, t, ctx.exactFuncs, NULL, u, &L2error); CHKERRQ(ierr); if (L2error < 1.0e-11) { ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n"); CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", L2error); CHKERRQ(ierr); } ierr = VecViewFromOptions(u, NULL, "-sol_vec_view"); CHKERRQ(ierr); ierr = VecDestroy(&u); CHKERRQ(ierr); ierr = VecDestroy(&r); CHKERRQ(ierr); ierr = TSDestroy(&ts); CHKERRQ(ierr); ierr = DMDestroy(&dm); CHKERRQ(ierr); ierr = PetscFree(ctx.exactFuncs); CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc, char **argv) { Vec vec, tagged, untagged; VecScatter taggedScatter, untaggedScatter; PetscInt bs; PetscInt n, nloc, nint, i, j, k, localStart, localEnd, ntagged, nuntagged; MPI_Comm comm; VecTagger tagger; PetscScalar *array; PetscRandom rand; VecTaggerBox *defaultBox; VecTaggerBox *boxes; IS is, isBlockGlobal, isComp; PetscErrorCode ierr; ierr = PetscInitialize(&argc,&argv,NULL,help);if (ierr) return ierr; n = 10.; bs = 1; comm = PETSC_COMM_WORLD; ierr = PetscOptionsBegin(comm, "" , "VecTagger Test Options", "Vec");CHKERRQ(ierr); ierr = PetscOptionsInt("-bs","The block size of the vector","ex1.c",bs,&bs,NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-n","The size of the vector (in blocks)","ex1.c",n,&n,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = PetscRandomCreate(comm,&rand);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr); ierr = VecCreate(comm,&vec);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)vec,"Vec to Tag");CHKERRQ(ierr); ierr = VecSetBlockSize(vec,bs);CHKERRQ(ierr); ierr = VecSetSizes(vec,PETSC_DECIDE,n);CHKERRQ(ierr); ierr = VecSetUp(vec);CHKERRQ(ierr); ierr = VecGetLocalSize(vec,&nloc);CHKERRQ(ierr); ierr = VecGetArray(vec,&array);CHKERRQ(ierr); for (i = 0; i < nloc; i++) { PetscScalar val; ierr = PetscRandomGetValue(rand,&val);CHKERRQ(ierr); array[i] = val; } ierr = VecRestoreArray(vec,&array);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr); ierr = VecViewFromOptions(vec,NULL,"-vec_view");CHKERRQ(ierr); ierr = VecTaggerCreate(comm,&tagger);CHKERRQ(ierr); ierr = VecTaggerSetBlockSize(tagger,bs);CHKERRQ(ierr); ierr = VecTaggerSetType(tagger,VECTAGGERABSOLUTE);CHKERRQ(ierr); ierr = PetscMalloc1(bs,&defaultBox);CHKERRQ(ierr); for (i = 0; i < bs; i++) { #if !defined(PETSC_USE_COMPLEX) defaultBox[i].min = 0.1; defaultBox[i].max = 1.5; #else defaultBox[i].min = PetscCMPLX(0.1,0.1); defaultBox[i].max = PetscCMPLX(1.5,1.5); #endif } ierr = VecTaggerAbsoluteSetBox(tagger,defaultBox);CHKERRQ(ierr); ierr = PetscFree(defaultBox);CHKERRQ(ierr); ierr = VecTaggerSetFromOptions(tagger);CHKERRQ(ierr); ierr = VecTaggerSetUp(tagger);CHKERRQ(ierr); ierr = PetscObjectViewFromOptions((PetscObject)tagger,NULL,"-vec_tagger_view");CHKERRQ(ierr); ierr = VecTaggerGetBlockSize(tagger,&bs);CHKERRQ(ierr); ierr = VecTaggerComputeBoxes(tagger,vec,&nint,&boxes); if (ierr && ierr != PETSC_ERR_SUP) CHKERRQ(ierr); else { PetscViewer viewer = NULL; ierr = PetscOptionsGetViewer(comm,NULL,NULL,"-vec_tagger_boxes_view",&viewer,NULL,NULL);CHKERRQ(ierr); if (viewer) { PetscBool iascii; ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);CHKERRQ(ierr); if (iascii) { ierr = PetscViewerASCIIPrintf(viewer,"Num boxes: %D\n",nint);CHKERRQ(ierr); ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); for (i = 0, k = 0; i < nint; i++) { ierr = PetscViewerASCIIPrintf(viewer,"%D: ",i);CHKERRQ(ierr); for (j = 0; j < bs; j++, k++) { if (j) {ierr = PetscViewerASCIIPrintf(viewer," x ");CHKERRQ(ierr);} #if !defined(PETSC_USE_COMPLEX) ierr = PetscViewerASCIIPrintf(viewer,"[%g,%g]",(double)boxes[k].min,(double)boxes[k].max);CHKERRQ(ierr); #else ierr = PetscViewerASCIIPrintf(viewer,"[%g+%gi,%g+%gi]",(double)PetscRealPart(boxes[k].min),(double)PetscImaginaryPart(boxes[k].min),(double)PetscRealPart(boxes[k].max),(double)PetscImaginaryPart(boxes[k].max));CHKERRQ(ierr); #endif } ierr = PetscViewerASCIIPrintf(viewer,"\n");CHKERRQ(ierr); } ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); } } ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = PetscFree(boxes);CHKERRQ(ierr); } ierr = VecTaggerComputeIS(tagger,vec,&is);CHKERRQ(ierr); ierr = ISGetBlockGlobalIS(is,vec,bs,&isBlockGlobal);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)isBlockGlobal,"Tagged IS (block global)");CHKERRQ(ierr); ierr = ISViewFromOptions(isBlockGlobal,NULL,"-tagged_is_view");CHKERRQ(ierr); ierr = VecGetOwnershipRange(vec,&localStart,&localEnd);CHKERRQ(ierr); ierr = ISComplement(isBlockGlobal,localStart,localEnd,&isComp);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)isComp,"Untagged IS (global)");CHKERRQ(ierr); ierr = ISViewFromOptions(isComp,NULL,"-untagged_is_view");CHKERRQ(ierr); ierr = ISGetLocalSize(isBlockGlobal,&ntagged);CHKERRQ(ierr); ierr = ISGetLocalSize(isComp,&nuntagged);CHKERRQ(ierr); ierr = VecCreate(comm,&tagged);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)tagged,"Tagged selection");CHKERRQ(ierr); ierr = VecSetSizes(tagged,ntagged,PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetUp(tagged);CHKERRQ(ierr); ierr = VecCreate(comm,&untagged);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject)untagged,"Untagged selection");CHKERRQ(ierr); ierr = VecSetSizes(untagged,nuntagged,PETSC_DETERMINE);CHKERRQ(ierr); ierr = VecSetUp(untagged);CHKERRQ(ierr); ierr = VecScatterCreate(vec,isBlockGlobal,tagged,NULL,&taggedScatter);CHKERRQ(ierr); ierr = VecScatterCreate(vec,isComp,untagged,NULL,&untaggedScatter);CHKERRQ(ierr); ierr = VecScatterBegin(taggedScatter,vec,tagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(taggedScatter,vec,tagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterBegin(untaggedScatter,vec,untagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(untaggedScatter,vec,untagged,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecViewFromOptions(tagged,NULL,"-tagged_vec_view");CHKERRQ(ierr); ierr = VecViewFromOptions(untagged,NULL,"-untagged_vec_view");CHKERRQ(ierr); ierr = VecScatterDestroy(&untaggedScatter);CHKERRQ(ierr); ierr = VecScatterDestroy(&taggedScatter);CHKERRQ(ierr); ierr = VecDestroy(&untagged);CHKERRQ(ierr); ierr = VecDestroy(&tagged);CHKERRQ(ierr); ierr = ISDestroy(&isComp);CHKERRQ(ierr); ierr = ISDestroy(&isBlockGlobal);CHKERRQ(ierr); ierr = ISDestroy(&is);CHKERRQ(ierr); ierr = VecTaggerDestroy(&tagger);CHKERRQ(ierr); ierr = VecDestroy(&vec);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }