DTR.hpp

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#ifndef DTR_HPP
#define DTR_HPP
 
#include <deal.II/base/conditional_ostream.h>
#include <deal.II/base/quadrature_lib.h>
 
#include <deal.II/distributed/fully_distributed_tria.h>
 
#include <deal.II/dofs/dof_handler.h>
#include <deal.II/dofs/dof_tools.h>
 
#include <deal.II/fe/fe_q.h>
#include <deal.II/fe/fe_values.h>
#include <deal.II/fe/mapping_q1.h>
 
#include <deal.II/grid/grid_generator.h>
#include <deal.II/grid/grid_in.h>
#include <deal.II/grid/grid_out.h>
#include <deal.II/grid/tria.h>
#include <deal.II/grid/grid_tools.h>
 
#include <deal.II/lac/dynamic_sparsity_pattern.h>
#include <deal.II/lac/precondition.h>
#include <deal.II/lac/solver_cg.h>
#include <deal.II/lac/solver_gmres.h>
#include <deal.II/lac/trilinos_precondition.h>
#include <deal.II/lac/trilinos_sparse_matrix.h>
#include <deal.II/lac/vector.h>
 
#include <deal.II/numerics/data_out.h>
#include <deal.II/numerics/matrix_tools.h>
#include <deal.II/numerics/vector_tools.h>
#include <deal.II/base/timer.h>
 
#include <filesystem>
#include <fstream>
#include <iostream>
 
#include "problem_data.hpp"
 
static const std::string output_dir = "./output_mb/";
 
using namespace dealii;
 
class DTR
{
public:
  static constexpr unsigned int dim = 2;
 
  DTR(const unsigned int &r_, std::ofstream& dimension_time_file);
 
  DTR(const unsigned int &r_);
 
  void setup(unsigned int n_initial_refinements = 8);
 
  void assemble();
 
  void solve();
 
  void output() const;
 
  double compute_error(const VectorTools::NormType &norm_type) const;
 
protected:
  const std::string mesh_file_name;
 
  const unsigned int r;
 
  const unsigned int mpi_size;
 
  const unsigned int mpi_rank;
 
  problem_data::DiffusionCoefficient<dim> diffusion_coefficient;
 
  problem_data::ReactionCoefficient<dim> reaction_coefficient;
 
  problem_data::TransportCoefficient<dim> transport_coefficient;
 
  problem_data::ForcingTerm<dim> forcing_term;
 
  problem_data::DirichletBC1<dim> dirichletBC1;
 
  problem_data::DirichletBC2<dim> dirichletBC2;
 
  problem_data::NeumannBC1<dim> neumannBC1;
 
  problem_data::NeumannBC2<dim> neumannBC2;
 
  parallel::fullydistributed::Triangulation<dim> mesh;
 
  std::unique_ptr<FiniteElement<dim>> fe;
 
  std::unique_ptr<Quadrature<dim>> quadrature;
 
  std::unique_ptr<Quadrature<dim - 1>> quadrature_boundary;
 
  DoFHandler<dim> dof_handler;
 
  TrilinosWrappers::SparseMatrix system_matrix;
 
  TrilinosWrappers::MPI::Vector system_rhs;
 
  TrilinosWrappers::MPI::Vector solution;
 
  ConditionalOStream pcout;
 
  ConditionalOStream time_details;
 
  IndexSet locally_owned_dofs;
 
  double setup_time;
};
 
#endif