adjoints_ex6.C File Reference

Go to the source code of this file.

Functions
void	write_output (EquationSystems &es, unsigned int a_step, std::string solution_type)
void	set_system_parameters (PoissonSystem &system, FEMParameters &param)
std::unique_ptr< MeshRefinement >	build_mesh_refinement (MeshBase &mesh, FEMParameters &param)
std::unique_ptr< AdjointRefinementEstimator >	build_adjoint_refinement_error_estimator (QoISet &qois)
int	main (int argc, char **argv)

Function Documentation

build_adjoint_refinement_error_estimator()

std::unique_ptr<AdjointRefinementEstimator> build_adjoint_refinement_error_estimator

(

QoISet &

qois

)

Definition at line 204 of file adjoints_ex6.C.

References libMesh::out.

Referenced by main().

{
  libMesh::out << "Computing the error estimate using the Adjoint Refinement Error Estimator\n" << std::endl;

  auto adjoint_refinement_estimator = std::make_unique<AdjointRefinementEstimator>();

  adjoint_refinement_estimator->qoi_set() = qois;

  // We enrich the FE space for the dual problem by doing 2 uniform h refinements
  adjoint_refinement_estimator->number_h_refinements = 2;

  return adjoint_refinement_estimator;
}

build_mesh_refinement()

std::unique_ptr<MeshRefinement> build_mesh_refinement	(	MeshBase &	mesh,
		FEMParameters &	param
	)

Definition at line 184 of file adjoints_ex6.C.

References FEMParameters::coarsen_fraction, FEMParameters::coarsen_threshold, FEMParameters::global_tolerance, mesh, FEMParameters::nelem_target, and FEMParameters::refine_fraction.

Referenced by main().

{
  auto mesh_refinement = std::make_unique<MeshRefinement>(mesh);
  mesh_refinement->coarsen_by_parents() = true;
  mesh_refinement->absolute_global_tolerance() = param.global_tolerance;
  mesh_refinement->nelem_target()      = param.nelem_target;
  mesh_refinement->refine_fraction()   = param.refine_fraction;
  mesh_refinement->coarsen_fraction()  = param.coarsen_fraction;
  mesh_refinement->coarsen_threshold() = param.coarsen_threshold;

  return mesh_refinement;
}

main()

int main	(	int	argc,
		char **	argv
	)

Definition at line 222 of file adjoints_ex6.C.

References libMesh::QoISet::add_indices(), libMesh::EquationSystems::add_system(), libMesh::DifferentiableSystem::adjoint_solve(), libMesh::MeshBase::all_second_order(), libMesh::DifferentiableQoI::assemble_qoi_sides, build_adjoint_refinement_error_estimator(), build_mesh_refinement(), libMesh::MeshTools::Generation::build_square(), libMesh::default_solver_package(), libMesh::err, libMesh::System::get_adjoint_solution(), libMesh::DifferentiableSystem::get_linear_solver(), PoissonSystem::get_QoI_value(), libMesh::TriangleWrapper::init(), libMesh::EquationSystems::init(), libMesh::INVALID_SOLVER_PACKAGE, mesh, libMesh::EquationSystems::n_active_dofs(), libMesh::MeshBase::n_active_elem(), libMesh::out, PoissonSystem::postprocess(), libMesh::DifferentiableSystem::postprocess_sides, libMesh::EquationSystems::print_info(), libMesh::MeshBase::print_info(), libMesh::ParallelObject::processor_id(), libMesh::QUAD4, FEMParameters::read(), libMesh::EquationSystems::reinit(), libMesh::LinearSolver< T >::reuse_preconditioner(), libMesh::System::set_adjoint_already_solved(), set_system_parameters(), libMesh::QoISet::set_weight(), libMesh::System::solution, libMesh::FEMSystem::solve(), libMesh::NumericVector< T >::swap(), libMesh::MeshRefinement::uniformly_refine(), and write_output().

{
  // Initialize libMesh.
  LibMeshInit init (argc, argv);

  // This example requires a linear solver package.
  libmesh_example_requires(libMesh::default_solver_package() != INVALID_SOLVER_PACKAGE,
                           "--enable-petsc, --enable-trilinos, or --enable-eigen");

  // Skip adaptive examples on a non-adaptive libMesh build
#ifndef LIBMESH_ENABLE_AMR
  libmesh_example_requires(false, "--enable-amr");
#else

  // We use Dirichlet boundary conditions here
#ifndef LIBMESH_ENABLE_DIRICHLET
  libmesh_example_requires(false, "--enable-dirichlet");
#endif

  libMesh::out << "Started " << argv[0] << std::endl;

  // Make sure the general input file exists, and parse it
  {
    std::ifstream i("general.in");
    libmesh_error_msg_if(!i, '[' << init.comm().rank() << "] Can't find general.in; exiting early.");
  }

  // Read in parameters from the input file
  GetPot infile("general.in");

  // But allow the command line to override it.
  infile.parse_command_line(argc, argv);

  FEMParameters param(init.comm());
  param.read(infile);

  // Skip this default-2D example if libMesh was compiled as 1D-only.
  libmesh_example_requires(2 <= LIBMESH_DIM, "2D support");

  // Create a mesh, with dimension to be overridden later, distributed
  // across the default MPI communicator.
  Mesh mesh(init.comm());

  // And an object to refine it
  std::unique_ptr<MeshRefinement> mesh_refinement =
    build_mesh_refinement(mesh, param);

  // And an EquationSystems to run on it
  EquationSystems equation_systems (mesh);

  libMesh::out << "Reading in and building the mesh" << std::endl;

  // Read in the mesh
  MeshTools::Generation::build_square
    (mesh, 2, 2,
     0.0, 1.0,
     0.0, 1.0,
     QUAD4);

  // Make all the elements of the mesh second order so we can compute
  // with a higher order basis
  mesh.all_second_order();

  // Create a mesh refinement object to do the initial uniform refinements
  // on the coarse grid read in from lshaped.xda
  MeshRefinement initial_uniform_refinements(mesh);
  initial_uniform_refinements.uniformly_refine(param.coarserefinements);

  libMesh::out << "Building system" << std::endl;

  // Build the FEMSystem
  PoissonSystem & system = equation_systems.add_system<PoissonSystem> ("PoissonSystem");

  // Set its parameters
  set_system_parameters(system, param);

  libMesh::out << "Initializing systems" << std::endl;

  equation_systems.init ();

  // Print information about the mesh and system to the screen.
  mesh.print_info();
  equation_systems.print_info();

  // Get a pointer to the linear solver object to be able to reuse preconditioner
  LinearSolver<Number> * linear_solver = system.get_linear_solver();

  {
    // Adaptively solve the timestep
    unsigned int a_step = 0;
    for (; a_step != param.max_adaptivesteps; ++a_step)
      {
        // We can't adapt to both a tolerance and a
        // target mesh size
        if (param.global_tolerance != 0.)
          libmesh_assert_equal_to (param.nelem_target, 0);
        // If we aren't adapting to a tolerance we need a
        // target mesh size
        else
          libmesh_assert_greater (param.nelem_target, 0);

        // Dont reuse preconditioners before the primal solve
        linear_solver->reuse_preconditioner(false);

        // Solve the forward problem
        system.solve();

        // Write out the computed primal solution
        write_output(equation_systems, a_step, "primal");

        // Declare a QoISet object, we need this object to set weights for our QoI error contributions
        QoISet qois;

        // Each index will correspond to a QoI
        qois.add_indices({0});

        // Set weights for each index, these will weight the contribution of each QoI in the final error
        // estimate to be used for flagging elements for refinement
        qois.set_weight(0, 1.0);

        // Make sure we get the contributions to the adjoint RHS from the sides
        system.assemble_qoi_sides = true;

        // We are about to solve the adjoint system, but before we do this we see the same preconditioner
        // flag to reuse the preconditioner from the forward solver
        linear_solver->reuse_preconditioner(param.reuse_preconditioner);

        // Solve the adjoint system. This takes the transpose of the stiffness matrix and then
        // solves the resulting system
        system.adjoint_solve();

        //Now that we have solved the adjoint, set the adjoint_already_solved boolean to true, so we dont solve unnecessarily in the error estimator
        system.set_adjoint_already_solved(true);

        // Get a pointer to the primal solution vector
        NumericVector<Number> & primal_solution = *system.solution;

        //Get a pointer to the solution vector of the adjoint problem for QoI 0
        NumericVector<Number> & dual_solution_0 = system.get_adjoint_solution(0);

        //Swap the primal and dual solutions so we can write out the adjoint solution
        primal_solution.swap(dual_solution_0);
        write_output(equation_systems, a_step, "adjoint_0");

        //Swap back
        primal_solution.swap(dual_solution_0);

        libMesh::out << "Adaptive step " << a_step << ", we have " << mesh.n_active_elem()
                     << " active elements and "
                     << equation_systems.n_active_dofs()
                     << " active dofs." << std::endl ;

        // Postprocess, compute the approximate QoIs and write them out to the console
        libMesh::out << "Postprocessing: " << std::endl;
        system.postprocess_sides = true;
        system.postprocess();

        Number QoI_0_computed = system.get_QoI_value("computed", 0);
        Number QoI_0_exact = system.get_QoI_value("exact", 0);

        libMesh::out << "The computed QoI 0 is " << std::setprecision(17)
                     << QoI_0_computed << std::endl;
        libMesh::out << "The relative error in QoI 0 is " << std::setprecision(17)
                     << std::abs(QoI_0_computed - QoI_0_exact) << std::endl; // / std::abs(QoI_0_exact)

        // We will declare an error vector for passing to the adjoint refinement error estimator
        ErrorVector QoI_elementwise_error;

        // Build an adjoint refinement error estimator object
        std::unique_ptr<AdjointRefinementEstimator> adjoint_refinement_error_estimator =
          build_adjoint_refinement_error_estimator(qois);

        // Estimate the error in each element using the Adjoint Refinement estimator
        adjoint_refinement_error_estimator->estimate_error(system, QoI_elementwise_error);

        // Print out the computed error estimate, note that we access the global error estimates
        // using an accessor function, right now sum(QoI_elementwise_error) != global_QoI_error_estimate
        libMesh::out << "The computed relative error in QoI 0 is " << std::setprecision(17)
                     << std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(0)) << std::endl; // / std::abs(QoI_0_exact)

        // Also print out effectivity indices (estimated error/true error)
        libMesh::out << "The effectivity index for the computed error in QoI 0 is " << std::setprecision(17)
                     << std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(0)) /
          std::abs(QoI_0_computed - QoI_0_exact) << std::endl;

        // For refinement purposes we need to sort by error
        // *magnitudes*, but AdjointRefinement gives us signed errors.
        if (!param.refine_uniformly)
          for (std::size_t i=0; i<QoI_elementwise_error.size(); i++)
            if (QoI_elementwise_error[i] != 0.)
              QoI_elementwise_error[i] = std::abs(QoI_elementwise_error[i]);

        // We have to refine either based on reaching an error tolerance or
        // a number of elements target, which should be verified above
        // Otherwise we flag elements by error tolerance or nelem target

        // Uniform refinement
        if (param.refine_uniformly)
          {
            mesh_refinement->uniformly_refine(1);
          }
        // Adaptively refine based on reaching an error tolerance
        else if (param.global_tolerance >= 0. && param.nelem_target == 0.)
          {
            mesh_refinement->flag_elements_by_error_tolerance (QoI_elementwise_error);

            mesh_refinement->refine_and_coarsen_elements();
          }
        // Adaptively refine based on reaching a target number of elements
        else
          {
            if (mesh.n_active_elem() >= param.nelem_target)
              {
                libMesh::out << "We reached the target number of elements.\n" << std::endl;
                break;
              }

            mesh_refinement->flag_elements_by_nelem_target (QoI_elementwise_error);

            mesh_refinement->refine_and_coarsen_elements();
          }

        // Dont forget to reinit the system after each adaptive refinement!
        equation_systems.reinit();

        libMesh::out << "Refined mesh to "
                     << mesh.n_active_elem()
                     << " active elements and "
                     << equation_systems.n_active_dofs()
                     << " active dofs." << std::endl;
      }

    // On the last adaptive step, dont refine elements and check regressions via asserts
    if (a_step == param.max_adaptivesteps)
      {
        linear_solver->reuse_preconditioner(false);
        system.solve();

        write_output(equation_systems, a_step, "primal");

        NumericVector<Number> & primal_solution = *system.solution;

        QoISet qois;
        std::vector<unsigned int> qoi_indices;

        qoi_indices.push_back(0);
        qois.add_indices(qoi_indices);

        qois.set_weight(0, 1.0);

        system.assemble_qoi_sides = true;

        linear_solver->reuse_preconditioner(param.reuse_preconditioner);
        system.adjoint_solve();
        system.set_adjoint_already_solved(true);

        NumericVector<Number> & dual_solution_0 = system.get_adjoint_solution(0);

        primal_solution.swap(dual_solution_0);
        write_output(equation_systems, a_step, "adjoint_0");

        primal_solution.swap(dual_solution_0);

        libMesh::out << "Adaptive step " << a_step << ", we have " << mesh.n_active_elem()
                     << " active elements and "
                     << equation_systems.n_active_dofs()
                     << " active dofs." << std::endl ;

        libMesh::out << "Postprocessing: " << std::endl;
        system.postprocess_sides = true;
        system.postprocess();

        Number QoI_0_computed = system.get_QoI_value("computed", 0);
        Number QoI_0_exact = system.get_QoI_value("exact", 0);

        libMesh::out << "The computed QoI 0 is " << std::setprecision(17)
                     << QoI_0_computed << std::endl;
        libMesh::out << "The relative error in QoI 0 is " << std::setprecision(17)
                     << std::abs(QoI_0_computed - QoI_0_exact) << std::endl; // / std::abs(QoI_0_exact)


        // We will declare an error vector for passing to the adjoint
        // refinement error estimator Right now, only the first entry
        // of this vector will be filled (with the global QoI error
        // estimate) Later, each entry of the vector will contain
        // elementwise error that the user can sum to get the total
        // error
        ErrorVector QoI_elementwise_error;

        // Build an adjoint refinement error estimator object
        std::unique_ptr<AdjointRefinementEstimator> adjoint_refinement_error_estimator =
          build_adjoint_refinement_error_estimator(qois);

        // Estimate the error in each element using the Adjoint Refinement estimator
        adjoint_refinement_error_estimator->estimate_error(system, QoI_elementwise_error);

        // Print out the computed error estimate, note that we access
        // the global error estimates using an accessor function,
        // right now sum(QoI_elementwise_error) != global_QoI_error_estimate
        libMesh::out << "The computed relative error in QoI 0 is " << std::setprecision(17)
                     << std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(0)) << std::endl; // / std::abs(QoI_0_exact)

        // Also print out effectivity indices (estimated error/true error)
        libMesh::out << "The effectivity index for the computed error in QoI 0 is " << std::setprecision(17)
                     << std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(0)) /
          std::abs(QoI_0_computed - QoI_0_exact) << std::endl;

        // Hard coded assert to ensure that the actual numbers we are getting are what they should be

        // The effectivity index isn't exactly reproducible at single precision
        // libmesh_assert_less(std::abs(std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(0)) / std::abs(QoI_0_computed - QoI_0_exact) - 0.84010976704434637), 1.e-5);
        // libmesh_assert_less(std::abs(std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(1)) / std::abs(QoI_1_computed - QoI_1_exact) - 0.48294428289950514), 1.e-5);

        // But the effectivity indices should always be sane
        // libmesh_assert_less(std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(0)) / std::abs(QoI_0_computed - QoI_0_exact), 2.5);
        // libmesh_assert_greater(std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(0)) / std::abs(QoI_0_computed - QoI_0_exact), .4);
        // libmesh_assert_less(std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(1)) / std::abs(QoI_1_computed - QoI_1_exact), 2.5);
        // libmesh_assert_greater(std::abs(adjoint_refinement_error_estimator->get_global_QoI_error_estimate(1)) / std::abs(QoI_1_computed - QoI_1_exact), .4);

        // And the computed errors should still be low
        // libmesh_assert_less(std::abs(QoI_0_computed - QoI_0_exact), 2e-4);
        // libmesh_assert_less(std::abs(QoI_1_computed - QoI_1_exact), 2e-4);
      }
  }

  libMesh::err << '[' << mesh.processor_id()
               << "] Completing output." << std::endl;

#endif // #ifndef LIBMESH_ENABLE_AMR

  // All done.
  return 0;
}

set_system_parameters()

void set_system_parameters	(	PoissonSystem &	system,
		FEMParameters &	param
	)

Definition at line 122 of file adjoints_ex6.C.

References PoissonSystem::analytic_jacobians(), FEMParameters::analytic_jacobians, FEMParameters::constrain_in_solver, PoissonSystem::fe_family(), FEMParameters::fe_family, PoissonSystem::fe_order(), FEMParameters::fe_order, FEMParameters::initial_linear_tolerance, FEMParameters::linear_tolerance_multiplier, FEMParameters::max_linear_iterations, FEMParameters::max_nonlinear_iterations, FEMParameters::min_step_length, FEMParameters::minimum_linear_tolerance, FEMParameters::print_jacobian_norms, libMesh::DifferentiableSystem::print_jacobian_norms, FEMParameters::print_jacobians, libMesh::DifferentiableSystem::print_jacobians, FEMParameters::print_residual_norms, libMesh::DifferentiableSystem::print_residual_norms, FEMParameters::print_residuals, libMesh::DifferentiableSystem::print_residuals, FEMParameters::print_solution_norms, libMesh::DifferentiableSystem::print_solution_norms, FEMParameters::print_solutions, libMesh::DifferentiableSystem::print_solutions, FEMParameters::relative_residual_tolerance, FEMParameters::relative_step_tolerance, FEMParameters::require_residual_reduction, libMesh::DifferentiableSystem::set_constrain_in_solver(), FEMParameters::solver_quiet, libMesh::DifferentiableSystem::time_solver, FEMParameters::use_petsc_snes, FEMParameters::verify_analytic_jacobians, and libMesh::FEMSystem::verify_analytic_jacobians.

Referenced by main().

{
  // Use analytical jacobians?
  system.analytic_jacobians() = param.analytic_jacobians;

  // Verify analytic jacobians against numerical ones?
  system.verify_analytic_jacobians = param.verify_analytic_jacobians;

  // Use the prescribed FE type
  system.fe_family() = param.fe_family[0];
  system.fe_order() = param.fe_order[0];

  // More desperate debugging options
  system.print_solution_norms = param.print_solution_norms;
  system.print_solutions      = param.print_solutions;
  system.print_residual_norms = param.print_residual_norms;
  system.print_residuals      = param.print_residuals;
  system.print_jacobian_norms = param.print_jacobian_norms;
  system.print_jacobians      = param.print_jacobians;

  // No transient time solver
  system.time_solver = std::make_unique<SteadySolver>(system);

  // Nonlinear solver options
  if (param.use_petsc_snes)
  {
#ifdef LIBMESH_HAVE_PETSC
    system.time_solver->diff_solver() = std::make_unique<PetscDiffSolver>(system);
#else
    libmesh_error_msg("This example requires libMesh to be compiled with PETSc support.");
#endif
  }
  else
  {
    system.time_solver->diff_solver() = std::make_unique<NewtonSolver>(system);
    auto solver = cast_ptr<NewtonSolver*>(system.time_solver->diff_solver().get());

    solver->quiet                       = param.solver_quiet;
    solver->max_nonlinear_iterations    = param.max_nonlinear_iterations;
    solver->minsteplength               = param.min_step_length;
    solver->relative_step_tolerance     = param.relative_step_tolerance;
    solver->relative_residual_tolerance = param.relative_residual_tolerance;
    solver->require_residual_reduction  = param.require_residual_reduction;
    solver->linear_tolerance_multiplier = param.linear_tolerance_multiplier;
    if (system.time_solver->reduce_deltat_on_diffsolver_failure)
      {
        solver->continue_after_max_iterations = true;
        solver->continue_after_backtrack_failure = true;
      }
    system.set_constrain_in_solver(param.constrain_in_solver);

    // And the linear solver options
    solver->max_linear_iterations       = param.max_linear_iterations;
    solver->initial_linear_tolerance    = param.initial_linear_tolerance;
    solver->minimum_linear_tolerance    = param.minimum_linear_tolerance;
  }
}

write_output()

void write_output	(	EquationSystems &	es,
		unsigned int	a_step,
		std::string	solution_type
	)

Definition at line 98 of file adjoints_ex6.C.

References libMesh::EquationSystems::get_mesh(), libMesh::libmesh_ignore(), mesh, and libMesh::MeshOutput< MT >::write_equation_systems().

Referenced by main().

{
  // Avoid unused variable warnings in the --disable-gmv configuration
  libmesh_ignore(es, a_step, solution_type);

#ifdef LIBMESH_HAVE_GMV
  MeshBase & mesh = es.get_mesh();

  std::ostringstream file_name_gmv;
  file_name_gmv << solution_type
                << ".out.gmv."
                << std::setw(2)
                << std::setfill('0')
                << std::right
                << a_step;

  GMVIO(mesh).write_equation_systems
    (file_name_gmv.str(), es);
#endif
}