/* ------------------------------------------------------------------------
 *
 * SPDX-License-Identifier: LGPL-2.1-or-later
 * Copyright (C) 2000 - 2024 by the deal.II authors
 *
 * This file is part of the deal.II library.
 *
 * Part of the source code is dual licensed under Apache-2.0 WITH
 * LLVM-exception OR LGPL-2.1-or-later. Detailed license information
 * governing the source code and code contributions can be found in
 * LICENSE.md and CONTRIBUTING.md at the top level directory of deal.II.
 *
 * ------------------------------------------------------------------------
 */
 
 
 
#include <deal.II/base/quadrature_lib.h>
 
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/dofs/dof_tools.h>
 
#include <deal.II/fe/fe_values.h>
 
#include <deal.II/grid/tria.h>
#include <deal.II/grid/grid_generator.h>
 
#include <deal.II/lac/dynamic_sparsity_pattern.h>
#include <deal.II/lac/full_matrix.h>
#include <deal.II/lac/precondition.h>
#include <deal.II/lac/solver_cg.h>
#include <deal.II/lac/sparse_matrix.h>
#include <deal.II/lac/vector.h>
 
#include <deal.II/numerics/data_out.h>
#include <deal.II/numerics/vector_tools.h>
 
#include <fstream>
 
#include <deal.II/fe/fe_q.h>
#include <deal.II/grid/grid_out.h>
 
 
#include <deal.II/lac/affine_constraints.h>
 
#include <deal.II/grid/grid_refinement.h>
 
#include <deal.II/numerics/error_estimator.h>
 
using namespace dealii;
 
 
 
template <int dim>
class Step6
{
public:
  Step6();
 
  void run();
 
private:
  void setup_system();
  void assemble_system();
  void solve();
  void refine_grid();
  void output_results(const unsigned int cycle) const;
 
  Triangulation<dim> triangulation;
 
  const FE_Q<dim> fe;
  DoFHandler<dim> dof_handler;
 
 
  AffineConstraints<double> constraints;
 
  SparseMatrix<double> system_matrix;
  SparsityPattern      sparsity_pattern;
 
  Vector<double> solution;
  Vector<double> system_rhs;
};
 
 
 
template <int dim>
double coefficient(const Point<dim> &p)
{
  if (p.square() < 0.5 * 0.5)
    return 20;
  else
    return 1;
}
 
 
 
 
 
template <int dim>
Step6<dim>::Step6()
  : fe(/* polynomial degree = */ 2)
  , dof_handler(triangulation)
{}
 
 
 
 
template <int dim>
void Step6<dim>::setup_system()
{
  dof_handler.distribute_dofs(fe);
 
  solution.reinit(dof_handler.n_dofs());
  system_rhs.reinit(dof_handler.n_dofs());
 
  constraints.clear();
  DoFTools::make_hanging_node_constraints(dof_handler, constraints);
 
 
  VectorTools::interpolate_boundary_values(dof_handler,
                                           types::boundary_id(0),
                                           Functions::ZeroFunction<dim>(),
                                           constraints);
 
  constraints.close();
 
  DynamicSparsityPattern dsp(dof_handler.n_dofs());
  DoFTools::make_sparsity_pattern(dof_handler,
                                  dsp,
                                  constraints,
                                  /*keep_constrained_dofs = */ false);
 
  sparsity_pattern.copy_from(dsp);
 
  system_matrix.reinit(sparsity_pattern);
}
 
 
 
template <int dim>
void Step6<dim>::assemble_system()
{
  const QGauss<dim> quadrature_formula(fe.degree + 1);
 
  FEValues<dim> fe_values(fe,
                          quadrature_formula,
                          update_values | update_gradients |
                            update_quadrature_points | update_JxW_values);
 
  const unsigned int dofs_per_cell = fe.n_dofs_per_cell();
 
  FullMatrix<double> cell_matrix(dofs_per_cell, dofs_per_cell);
  Vector<double>     cell_rhs(dofs_per_cell);
 
  std::vector<types::global_dof_index> local_dof_indices(dofs_per_cell);
 
  for (const auto &cell : dof_handler.active_cell_iterators())
    {
      fe_values.reinit(cell);
 
      cell_matrix = 0;
      cell_rhs    = 0;
 
      for (const unsigned int q_index : fe_values.quadrature_point_indices())
        {
          const double current_coefficient =
            coefficient(fe_values.quadrature_point(q_index));
          for (const unsigned int i : fe_values.dof_indices())
            {
              for (const unsigned int j : fe_values.dof_indices())
                cell_matrix(i, j) +=
                  (current_coefficient *              // a(x_q)
                   fe_values.shape_grad(i, q_index) * // grad phi_i(x_q)
                   fe_values.shape_grad(j, q_index) * // grad phi_j(x_q)
                   fe_values.JxW(q_index));           // dx
 
              cell_rhs(i) += (fe_values.shape_value(i, q_index) * // phi_i(x_q)
                              1.0 *                               // f(x)
                              fe_values.JxW(q_index));            // dx
            }
        }
 
      cell->get_dof_indices(local_dof_indices);
      constraints.distribute_local_to_global(
        cell_matrix, cell_rhs, local_dof_indices, system_matrix, system_rhs);
    }
}
 
 
 
 
template <int dim>
void Step6<dim>::solve()
{
  SolverControl            solver_control(1000, 1e-6 * system_rhs.l2_norm());
  SolverCG<Vector<double>> solver(solver_control);
 
  PreconditionSSOR<SparseMatrix<double>> preconditioner;
  preconditioner.initialize(system_matrix, 1.2);
 
  solver.solve(system_matrix, solution, system_rhs, preconditioner);
 
  constraints.distribute(solution);
}
 
 
 
template <int dim>
void Step6<dim>::refine_grid()
{
  Vector<float> estimated_error_per_cell(triangulation.n_active_cells());
 
  KellyErrorEstimator<dim>::estimate(dof_handler,
                                     QGauss<dim - 1>(fe.degree + 1),
                                     {},
                                     solution,
                                     estimated_error_per_cell);
 
  GridRefinement::refine_and_coarsen_fixed_number(triangulation,
                                                  estimated_error_per_cell,
                                                  0.3,
                                                  0.03);
 
  triangulation.execute_coarsening_and_refinement();
}
 
 
 
template <int dim>
void Step6<dim>::output_results(const unsigned int cycle) const
{
  {
    GridOut               grid_out;
    std::ofstream         output("grid-" + std::to_string(cycle) + ".gnuplot");
    GridOutFlags::Gnuplot gnuplot_flags(false, 5);
    grid_out.set_flags(gnuplot_flags);
    MappingQ<dim> mapping(3);
    grid_out.write_gnuplot(triangulation, output, &mapping);
  }
 
  {
    DataOut<dim> data_out;
    data_out.attach_dof_handler(dof_handler);
    data_out.add_data_vector(solution, "solution");
    data_out.build_patches();
 
    std::ofstream output("solution-" + std::to_string(cycle) + ".vtu");
    data_out.write_vtu(output);
  }
}
 
 
 
template <int dim>
void Step6<dim>::run()
{
  for (unsigned int cycle = 0; cycle < 8; ++cycle)
    {
      std::cout << "Cycle " << cycle << ':' << std::endl;
 
      if (cycle == 0)
        {
          GridGenerator::hyper_ball(triangulation);
          triangulation.refine_global(1);
        }
      else
        refine_grid();
 
 
      std::cout << "   Number of active cells:       "
                << triangulation.n_active_cells() << std::endl;
 
      setup_system();
 
      std::cout << "   Number of degrees of freedom: " << dof_handler.n_dofs()
                << std::endl;
 
      assemble_system();
      solve();
      output_results(cycle);
    }
}
 
 
 
int main()
{
  cout << "\n";
  cout << "step-6():\n";
  cout << "  dealii example code.\n";
  cout << "\n";

  try
    {
      Step6<2> laplace_problem_2d;
      laplace_problem_2d.run();
    }
  catch (std::exception &exc)
    {
      std::cerr << std::endl
                << std::endl
                << "----------------------------------------------------"
                << std::endl;
      std::cerr << "Exception on processing: " << std::endl
                << exc.what() << std::endl
                << "Aborting!" << std::endl
                << "----------------------------------------------------"
                << std::endl;
 
      return 1;
    }
  catch (...)
    {
      std::cerr << std::endl
                << std::endl
                << "----------------------------------------------------"
                << std::endl;
      std::cerr << "Unknown exception!" << std::endl
                << "Aborting!" << std::endl
                << "----------------------------------------------------"
                << std::endl;
      return 1;
    }


  cout << "\n";
  cout << "step-6():\n";
  cout << "  Normal end of execution.\n";

  return 0;
}