spatial_mesh.h

#ifndef _SPATIAL_MESH_H_
#define _SPATIAL_MESH_H_

#include <math.h>
#include <stdlib.h>
#include <iostream>
#include <iomanip>
#include <boost/multi_array.hpp>
#include <hdf5.h>
#include <hdf5_hl.h>
#include "config.h"
#include "vec3d.h"


class Spatial_mesh {
  public:
    double x_volume_size, y_volume_size, z_volume_size;
    double x_cell_size, y_cell_size, z_cell_size;
    int x_n_nodes, y_n_nodes, z_n_nodes;
    boost::multi_array<Vec3d, 3> node_coordinates;
    boost::multi_array<double, 3> charge_density;
    boost::multi_array<double, 3> potential;
    boost::multi_array<Vec3d, 3> electric_field;
  public:
    Spatial_mesh( Config &conf );
    Spatial_mesh( hid_t h5_spat_mesh_group );
    void clear_old_density_values();
    void set_boundary_conditions( Config &conf );
    bool is_potential_equal_on_boundaries();
    void print();
    void write_to_file( hid_t hdf5_file_id );
    virtual ~Spatial_mesh();
    double node_number_to_coordinate_x( int i );
    double node_number_to_coordinate_y( int j );
    double node_number_to_coordinate_z( int k );
  private:
    // init
    void check_correctness_of_related_config_fields( Config &conf );
    void init_x_grid( Config &conf );
    void init_y_grid( Config &conf );
    void init_z_grid( Config &conf );
    void allocate_ongrid_values();
    void fill_node_coordinates();
    void set_boundary_conditions( const double phi_left, const double phi_right,
				  const double phi_top, const double phi_bottom,
				  const double phi_near, const double phi_far );
    // print
    void print_grid();
    void print_ongrid_values();
    // write hdf5
    void write_hdf5_attributes( hid_t group_id );
    void write_hdf5_ongrid_values( hid_t group_id );
    int n_of_elements_to_write_for_each_process_for_1d_dataset( int total_elements );
    int data_offset_for_each_process_for_1d_dataset( int total_elements );
    void hdf5_status_check( herr_t status );
    // config check
    void grid_x_size_gt_zero( Config &conf );
    void grid_x_step_gt_zero_le_grid_x_size( Config &conf );
    void grid_y_size_gt_zero( Config &conf );
    void grid_y_step_gt_zero_le_grid_y_size( Config &conf );
    void grid_z_size_gt_zero( Config &conf );
    void grid_z_step_gt_zero_le_grid_z_size( Config &conf );
    void check_and_exit_if_not( const bool &should_be, const std::string &message );
};

#endif /* _SPATIAL_MESH_H_ */