diffusion.hpp

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#ifndef DIFFUSION_HPP
#define DIFFUSION_HPP

#include "sml.hpp"
#include "grid.hpp"
#include "magnetic_field.hpp"
#include "electric_field.hpp"
#include "domain_decomposition.hpp"
#include "velocity_grid.hpp"
#include "plasma.hpp"
#include "vgrid_distribution.hpp"
#include "source.hpp"
#include "smoothing.hpp"
#include "diag_f0_df.hpp"
#include "boundary.hpp"
#include "xgc_io.hpp"

extern "C" void initialize_diffusion(int* bd, int is_update);

class Diffusion : public Source{
    double inner_psi_bound; 
    double outer_psi_bound; 

    Boundary bndry; 
    bool use_smoothing; 

    bool update_on; 
    StepTrigger step_trigger_update; 

    XGC_IO_Stream diffusion_update_stream; 

    public:

    bool is_triggered_update(int step) const{
        return step_trigger_update.is_triggered(step);
    }

     int trigger_count_update(int step) const{
         return step_trigger_update.trigger_count(step);
     }

    Diffusion(){}

    Diffusion(NLReader::NamelistReader& nlr, const MagneticField<DeviceType>& magnetic_field, const Grid<DeviceType>& grid);

    void init(NLReader::NamelistReader& nlr, const MagneticField<DeviceType>& magnetic_field, const Grid<DeviceType>& grid);

    void apply(const Simulation<DeviceType>& sml, const Grid<DeviceType>& grid, const MagneticField<DeviceType>& magnetic_field,
              ElectricField<DeviceType>& electric_field,
              const DomainDecomposition<DeviceType>& pol_decomp, const VelocityGrid& vgrid, Plasma& plasma, Smoothing& smoothing,
              DiagF0DF& diag_f0_df, const Moments& moments,
              const VGridDistribution<DeviceType>& f0_f, VGridDistribution<HostType>& f0_df0g,
              double dt);

    void update(const Plasma& plasma, const DomainDecomposition<DeviceType>& pol_decomp, const Grid<DeviceType>& grid);
};

#endif