Functions
void	write_output (EquationSystems &es, unsigned int t_step, std::string solution_type, FEMParameters &param)

void	set_system_parameters (HeatSystem &system, FEMParameters &param)

int	main (int argc, char **argv)

Function Documentation

◆ main()

int main	(	int	argc,
		char **	argv
	)

Definition at line 337 of file adjoints_ex5.C.

{
  // Skip adaptive examples on a non-adaptive libMesh build
#ifndef LIBMESH_ENABLE_AMR
  libmesh_ignore(argc, argv);
  libmesh_example_requires(false, "--enable-amr");
#else
  // Skip this 2D example if libMesh was compiled as 1D-only.
  libmesh_example_requires(2 <= LIBMESH_DIM, "2D support");
 
  // We use Dirichlet boundary conditions here
#ifndef LIBMESH_ENABLE_DIRICHLET
  libmesh_example_requires(false, "--enable-dirichlet");
#endif
 
  // Initialize libMesh.
  LibMeshInit init (argc, argv);
 
  // This doesn't converge with Trilinos for some reason...
  libmesh_example_requires(libMesh::default_solver_package() == PETSC_SOLVERS, "--enable-petsc");
 
  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.");
  }
  GetPot infile("general.in");
 
  // But allow the command line to override it.
  infile.parse_command_line(argc, argv);
 
  // Read in parameters from the input file
  FEMParameters param(init.comm());
  param.read(infile);
 
  // Create a mesh with the given dimension, distributed
  // across the default MPI communicator.
  Mesh mesh(init.comm(), cast_int<unsigned char>(param.dimension));
 
  // And an object to refine it
  auto mesh_refinement = std::make_unique<MeshRefinement>(mesh);
 
  // And an EquationSystems to run on it
  EquationSystems equation_systems (mesh);
 
  libMesh::out << "Building mesh" << std::endl;
 
  // Build a unit square
  ElemType elemtype;
 
  if (param.elementtype == "tri" ||
      param.elementtype == "unstructured")
    elemtype = TRI3;
  else
    elemtype = QUAD4;
 
  MeshTools::Generation::build_square (mesh, param.coarsegridx, param.coarsegridy,
                                       param.domain_xmin, param.domain_xmin + param.domain_edge_width,
                                       param.domain_ymin, param.domain_ymin + param.domain_edge_length,
                                       elemtype);
 
  libMesh::out << "Building system" << std::endl;
 
  HeatSystem & system = equation_systems.add_system<HeatSystem> ("HeatSystem");
 
  set_system_parameters(system, param);
 
  libMesh::out << "Initializing systems" << std::endl;
 
  // Initialize the system
  equation_systems.init ();
 
  // Refine the grid again if requested
  for (unsigned int i=0; i != param.extrarefinements; ++i)
    {
      mesh_refinement->uniformly_refine(1);
      equation_systems.reinit();
    }
 
  libMesh::out << "Setting primal initial conditions" << std::endl;
 
  read_initial_parameters();
 
  system.project_solution(initial_value, initial_grad,
                          equation_systems.parameters);
 
  // Output the H1 norm of the initial conditions
  libMesh::out << "|U("
               << system.time
               << ")|= "
               << system.calculate_norm(*system.solution, 0, H1)
               << std::endl
               << std::endl;
 
  // Tell system that we have two qois
  system.init_qois(1);
 
  // Add the adjoint vectors (and the old adjoint vectors) to system
  system.time_solver->init_adjoints();
 
  // Close up any resources initial.C needed
  finish_initialization();
 
  // Plot the initial conditions
  write_output(equation_systems, 0, "primal", param);
 
  // Print information about the mesh and system to the screen.
  mesh.print_info();
  equation_systems.print_info();
 
  // In optimized mode we catch any solver errors, so that we can
  // write the proper footers before closing.  In debug mode we just
  // let the exception throw so that gdb can grab it.
#if defined(NDEBUG) && defined(LIBMESH_ENABLE_EXCEPTIONS)
  try
#endif
    {
      // Now we begin the timestep loop to compute the time-accurate
      // solution of the equations.
      for (unsigned int t_step=param.initial_timestep;
           t_step != param.initial_timestep + param.n_timesteps; ++t_step)
        {
          // A pretty update message
          libMesh::out << " Solving time step "
                       << t_step
                       << ", time = "
                       << system.time
                       << std::endl;
 
          // Solve the forward problem at time t, to obtain the solution at time t + dt
          system.solve();
 
 
          // Output the H1 norm of the computed solution
          libMesh::out << "|U("
                      << system.time + system.time_solver->last_completed_timestep_size()
                      << ")|= "
                      << system.calculate_norm(*system.solution, 0, H1)
                      << std::endl;
 
          // Advance to the next timestep in a transient problem
          libMesh::out << "Advancing timestep" << std::endl << std::endl;
          system.time_solver->advance_timestep();
 
          // Write out this timestep
          write_output(equation_systems, t_step+1, "primal", param);
        }
      // End timestep loop
 
 
      // Now we will solve the backwards in time adjoint problem
      libMesh::out << std::endl << "Solving the adjoint problem" << std::endl;
 
      // We need to tell the library that it needs to project the adjoint, so
      // MemorySolutionHistory knows it has to save it
 
      const std::string & adjoint_solution_name0 = "adjoint_solution0";
      const std::string & old_adjoint_solution_name0 = "_old_adjoint_solution0";
      // Tell the library to project the adjoint vector, and hence, memory solution history to
      // save it
      system.set_vector_preservation(adjoint_solution_name0, true);
      system.set_vector_preservation(old_adjoint_solution_name0, true);
 
      libMesh::out << "Setting adjoint initial conditions Z("
                   << system.time
                   << ")"
                   <<std::endl;
 
      // The first thing we have to do is to apply the adjoint initial
      // condition. The user should supply these. Here they are specified
      // in the functions adjoint_initial_value and adjoint_initial_gradient
      system.project_vector(adjoint_initial_value,
                            adjoint_initial_grad,
                            equation_systems.parameters,
                            system.get_adjoint_solution(0));
 
      // Since we have specified an adjoint solution for the current
      // time (T), set the adjoint_already_solved boolean to true, so
      // we dont solve unnecessarily in the adjoint sensitivity method
      system.set_adjoint_already_solved(true);
 
      Real Z_norm = system.calculate_norm(system.get_adjoint_solution(), 0, H1);
 
      libMesh::out << "|Z("
                   << system.time
                   << ")|= "
                   << Z_norm
                   << std::endl
                   << std::endl;
 
      // Call the adjoint advance timestep here to save the adjoint
      // initial conditions to disk
      system.time_solver->adjoint_advance_timestep();
 
      Real Z_old_norm = system.calculate_norm(system.get_vector(old_adjoint_solution_name0), 0, H1);
 
      // Make sure that we have copied the old adjoint solution properly
      libmesh_assert(Z_norm == Z_old_norm);
 
      libMesh::out << "|Z_old("
                       << system.time + (system.time_solver->last_completed_timestep_size())/((param.timesolver_tolerance) ? 2.0 : 1.0)
                       << ")|= "
                       << Z_old_norm
                       << std::endl
                       << std::endl;
 
      write_output(equation_systems, param.n_timesteps, "dual", param);
 
      // Now that the adjoint initial condition is set, we will start the
      // backwards in time adjoint integration
 
      // For loop stepping backwards in time
      for (unsigned int t_step=param.initial_timestep;
           t_step != param.initial_timestep + param.n_timesteps; ++t_step)
        {
          //A pretty update message
          libMesh::out << " Solving adjoint time step "
                       << t_step
                       << ", time = "
                       << system.time
                       << std::endl;
 
          // Output the H1 norm of the retrieved primal solution from the last call
          // to adjoint_advance_timestep
          libMesh::out << "|U("
                       << system.time
                       << ")|= "
                       << system.calculate_norm(*system.solution, 0, H1)
                       << std::endl;
 
          libMesh::out << "|U("
                         << system.time - (system.time_solver->last_completed_timestep_size())/((param.timesolver_tolerance) ? 2.0 : 1.0)
                         << ")|= "
                         << system.calculate_norm(system.get_vector("_old_nonlinear_solution"), 0, H1)
                         << std::endl;
 
          system.set_adjoint_already_solved(false);
 
          system.adjoint_solve();
 
          Z_norm = system.calculate_norm(system.get_adjoint_solution(), 0, H1);
 
          libMesh::out << "|Z("
                       << system.time
                       << ")|= "
                       << Z_norm
                       << std::endl
                       << std::endl;
 
          // 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);
 
          libMesh::out << "Saving adjoint and retrieving primal solutions at time t=" << system.time - system.deltat << std::endl;
 
          // The adjoint_advance_timestep function calls the retrieve and store
          // function of the memory_solution_history class via the
          // memory_solution_history object we declared earlier.  The
          // retrieve function sets the system primal vectors to their
          // values at the current time instance.
          system.time_solver->adjoint_advance_timestep();
 
          Z_old_norm = system.calculate_norm(system.get_vector(old_adjoint_solution_name0), 0, H1);
 
          // Make sure that we have copied the old adjoint solution properly
          libmesh_assert(Z_norm == Z_old_norm);
 
          libMesh::out << "|Z_old("
                       << system.time + (system.time_solver->last_completed_timestep_size())/((param.timesolver_tolerance) ? 2.0 : 1.0)
                       << ")|= "
                       << Z_old_norm
                       << std::endl
                       << std::endl;
 
          // 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, param.n_timesteps - (t_step + 1), "dual", param);
 
          // Swap back
          primal_solution.swap(dual_solution_0);
        }
      // End adjoint timestep loop
 
      // Now that we have computed both the primal and adjoint solutions, we compute the sensitivities to the parameter p
      // dQ/dp = int_{0}^{T} partialQ/partialp - partialR/partialp(u,z;p) dt
      // The quantity partialQ/partialp - partialR/partialp(u,z;p) is evaluated internally by the ImplicitSystem::adjoint_qoi_parameter_sensitivity function.
      // This sensitivity evaluation is called internally by an overloaded TimeSolver::integrate_adjoint_sensitivity method which we call below.
 
      // Reset the time
      system.time = 0.0;
 
      // Prepare the quantities we need to pass to TimeSolver::integrate_adjoint_sensitivity
      QoISet qois;
 
      qois.add_indices({0});
      qois.set_weight(0, 1.0);
 
      // A SensitivityData object
      SensitivityData sensitivities(qois, system, system.get_parameter_vector());
 
      // Accumulator for the time integrated total sensitivity
      Number total_sensitivity = 0.0;
 
      // Retrieve the primal and adjoint solutions at the current timestep
      system.time_solver->retrieve_timestep();
 
      Z_old_norm = system.calculate_norm(system.get_vector(old_adjoint_solution_name0), 0, H1);
 
      // Assert that the old adjoint values match hard coded numbers for 1st timestep or 1st half time step from the adjoint solve
      if(param.timesolver_tolerance)
      {
        libmesh_error_msg_if(std::abs(Z_old_norm - (2.23366)) >= 2.e-4,
                             "Mismatch in expected Z0_old norm for the 1st half timestep!");
       }
      else
      {
        libmesh_error_msg_if(std::abs(Z_old_norm - (2.23627)) >= 2.e-4,
                             "Mismatch in expected Z0_old norm for the 1st timestep!");
      }
 
      // A pretty update message
      libMesh::out << "Retrieved, "
               << "time = "
               << system.time
               << std::endl;
 
      libMesh::out << "|U("
                   << system.time
                   << ")|= "
                   << system.calculate_norm(*system.solution, 0, H1)
                   << std::endl;
 
      libMesh::out << "|U_old("
                   << system.time
                   << ")|= "
                   << system.calculate_norm(system.get_vector("_old_nonlinear_solution"), 0, H1)
                   << std::endl;
 
      libMesh::out << "|Z("
                   << system.time
                   << ")|= "
                   << system.calculate_norm(system.get_adjoint_solution(0), 0, H1)
                   << std::endl
                   << std::endl;
 
      libMesh::out << "|Z_old("
                       << system.time + (system.time_solver->last_completed_timestep_size())/((param.timesolver_tolerance) ? 2.0 : 1.0)
                       << ")|= "
                       << system.calculate_norm(system.get_vector(old_adjoint_solution_name0), 0, H1)
                       << std::endl
                       << std::endl;
 
      // Now we begin the timestep loop to compute the time-accurate
      // adjoint sensitivities
      for (unsigned int t_step=param.initial_timestep;
           t_step != param.initial_timestep + param.n_timesteps; ++t_step)
        {
          // Call the postprocess function which we have overloaded to compute
          // accumulate the perturbed residuals
          system.time_solver->integrate_adjoint_sensitivity(qois, system.get_parameter_vector(), sensitivities);
 
          // A pretty update message
          libMesh::out << "Retrieved, "
               << "time = "
               << system.time
               << std::endl;
 
          libMesh::out << "|U("
                   << system.time
                   << ")|= "
                   << system.calculate_norm(*system.solution, 0, H1)
                   << std::endl;
 
          libMesh::out << "|U_old("
                   << system.time
                   << ")|= "
                   << system.calculate_norm(system.get_vector("_old_nonlinear_solution"), 0, H1)
                   << std::endl;
 
          libMesh::out << "|Z("
                   << system.time
                   << ")|= "
                   << system.calculate_norm(system.get_adjoint_solution(0), 0, H1)
                   << std::endl
                   << std::endl;
 
          libMesh::out << "|Z_old("
                   << system.time
                   << ")|= "
                   << system.calculate_norm(system.get_vector(old_adjoint_solution_name0), 0, H1)
                   << std::endl
                   << std::endl;
 
          // Add the contribution of the current timestep to the total sensitivity
          total_sensitivity += sensitivities[0][0];
        }
 
      // Print it out
      libMesh::out << "Sensitivity of QoI 0 w.r.t parameter 0 is: "
                   << total_sensitivity
                   << std::endl;
 
      // Hard coded test to ensure that the actual numbers we are
      // getting are what they should be
      // The 2e-4 tolerance is chosen to ensure success even with
      // 32-bit floats
      if(param.timesolver_tolerance)
      {
        libmesh_error_msg_if(std::abs(system.time - (1.0089)) >= 2.e-4,
                             "Mismatch in end time reached by adaptive timestepper!");
 
        libmesh_error_msg_if(std::abs(total_sensitivity - 4.87767) >= 3.e-3,
                             "Mismatch in sensitivity gold value!");
      }
      else
      {
        libmesh_error_msg_if(std::abs(total_sensitivity - 4.83551) >= 2.e-4,
                             "Mismatch in sensitivity gold value!");
      }
    }
#if defined(NDEBUG) && defined(LIBMESH_ENABLE_EXCEPTIONS)
  catch (...)
    {
      libMesh::err << '[' << mesh.processor_id()
                   << "] Caught exception; exiting early." << std::endl;
    }
#endif
 
  libMesh::err << '[' << mesh.processor_id()
               << "] Completing output."
               << std::endl;
 
  // All done.
  return 0;
 
#endif // LIBMESH_ENABLE_AMR
}

◆ set_system_parameters()

void set_system_parameters	(	HeatSystem &	system,
		FEMParameters &	param
	)

Definition at line 179 of file adjoints_ex5.C.

{
  // Use the prescribed FE type
  system.fe_family() = param.fe_family[0];
  system.fe_order() = param.fe_order[0];
 
  // Use analytical jacobians?
  system.analytic_jacobians() = param.analytic_jacobians;
 
  // Verify analytic jacobians against numerical ones?
  system.verify_analytic_jacobians = param.verify_analytic_jacobians;
  system.numerical_jacobian_h = param.numerical_jacobian_h;
 
  // 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;
  system.print_element_jacobians = param.print_element_jacobians;
  system.print_element_residuals = param.print_element_residuals;
 
  // Solve this as a time-dependent or steady system
  if (param.transient)
    {
      std::unique_ptr<UnsteadySolver> innersolver;
      if (param.timesolver_core == "euler2")
        {
          auto euler2solver = std::make_unique<Euler2Solver>(system);
          euler2solver->theta = param.timesolver_theta;
          innersolver = std::move(euler2solver);
        }
      else if (param.timesolver_core == "euler")
        {
          auto eulersolver = std::make_unique<EulerSolver>(system);
          eulersolver->theta = param.timesolver_theta;
          innersolver = std::move(eulersolver);
        }
      else
        libmesh_error_msg("This example (and unsteady adjoints in libMesh) only support Backward Euler and explicit methods.");
 
      if (param.timesolver_tolerance)
        {
          system.time_solver = std::make_unique<TwostepTimeSolver>(system);
          auto timesolver = cast_ptr<TwostepTimeSolver *>(system.time_solver.get());
 
          timesolver->max_growth       = param.timesolver_maxgrowth;
          timesolver->target_tolerance = param.timesolver_tolerance;
          timesolver->upper_tolerance  = param.timesolver_upper_tolerance;
          timesolver->component_norm   = SystemNorm(param.timesolver_norm);
          timesolver->core_time_solver = std::move(innersolver);
 
          // The Memory/File Solution History object we will set the system SolutionHistory object to
          if(param.solution_history_type == "memory")
          {
            MemorySolutionHistory heatsystem_solution_history(system);
            system.time_solver->set_solution_history(heatsystem_solution_history);
          }
          else if (param.solution_history_type == "file")
          {
            FileSolutionHistory heatsystem_solution_history(system);
            system.time_solver->set_solution_history(heatsystem_solution_history);
          }
          else
            libmesh_error_msg("Unrecognized solution history type: " << param.solution_history_type);
        }
      else
      {
        system.time_solver = std::move(innersolver);
 
        // The Memory/File Solution History object we will set the system SolutionHistory object to
        if(param.solution_history_type == "memory")
        {
          MemorySolutionHistory heatsystem_solution_history(system);
          system.time_solver->set_solution_history(heatsystem_solution_history);
        }
        else if (param.solution_history_type == "file")
        {
          FileSolutionHistory heatsystem_solution_history(system);
          system.time_solver->set_solution_history(heatsystem_solution_history);
        }
        else
          libmesh_error_msg("Unrecognized solution history type: " << param.solution_history_type);
      }
    }
  else // !param.transient
    system.time_solver = std::make_unique<SteadySolver>(system);
 
  system.time_solver->reduce_deltat_on_diffsolver_failure = param.deltat_reductions;
  system.time_solver->quiet = param.time_solver_quiet;
 
 #ifdef LIBMESH_ENABLE_DIRICHLET
  // Create any Dirichlet boundary conditions
  typedef
    std::map<boundary_id_type, FunctionBase<Number> *>::
    const_iterator Iter;
 
  for (Iter i = param.dirichlet_conditions.begin();
       i != param.dirichlet_conditions.end(); ++i)
    {
      boundary_id_type b = i->first;
      FunctionBase<Number> *f = i->second;
 
      system.get_dof_map().add_dirichlet_boundary(DirichletBoundary({b},
                                                                    param.dirichlet_condition_variables[b],
                                                                    f));
 
      libMesh::out << "Added Dirichlet boundary " << b << " for variables ";
      for (std::size_t vi=0; vi != param.dirichlet_condition_variables[b].size(); ++vi)
        libMesh::out << param.dirichlet_condition_variables[b][vi];
      libMesh::out << std::endl;
    }
 #endif // LIBMESH_ENABLE_DIRICHLET
 
  // Set the time stepping options
  system.deltat = param.deltat;
 
  // And the integration options
  system.extra_quadrature_order = param.extra_quadrature_order;
 
  // And the 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->verbose                     = param.solver_verbose;
      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;
    }
}

Referenced by main().

◆ write_output()

void write_output	(	EquationSystems &	es,
		unsigned int	t_step,
		std::string	solution_type,
		FEMParameters &	param
	)

Definition at line 122 of file adjoints_ex5.C.

{
  // Ignore parameters when there are no output formats available.
  libmesh_ignore(es, t_step, solution_type, param);
 
#ifdef LIBMESH_HAVE_GMV
  if (param.output_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
                    << t_step;
 
      GMVIO(mesh).write_equation_systems(file_name_gmv.str(), es);
    }
#endif
 
#ifdef LIBMESH_HAVE_EXODUS_API
  if (param.output_exodus)
    {
      MeshBase & mesh = es.get_mesh();
 
      // We write out one file per timestep. The files are named in
      // the following way:
      // foo.e
      // foo.e-s002
      // foo.e-s003
      // ...
      // so that, if you open the first one with Paraview, it actually
      // opens the entire sequence of adapted files.
      std::ostringstream file_name_exodus;
 
      file_name_exodus << solution_type << ".e";
      if (t_step > 0)
        file_name_exodus << "-s"
                         << std::setw(3)
                         << std::setfill('0')
                         << std::right
                         << t_step + 1;
 
      // TODO: Get the current time from the System...
      ExodusII_IO(mesh).write_timestep(file_name_exodus.str(),
                                       es,
                                       1,
                                       /*time=*/t_step + 1);
    }
#endif
}

References mesh, FEMParameters::output_exodus, and FEMParameters::output_gmv.

Referenced by main().

Functions

Function Documentation

◆ main()

◆ set_system_parameters()

◆ write_output()