actions.h

#pragma once

#include "geometry.h"
#include "space.h"

namespace Faunus {

namespace Energy {
class Hamiltonian;
class NonbondedBase;
} // namespace Energy
class XTCWriter;

struct SystemAction
{
    virtual void operator()(Space& space, Energy::Hamiltonian& hamiltonian) = 0;
    virtual ~SystemAction() = default;
};

class AngularScan : public SystemAction
{
    static constexpr std::string_view NAME = "angular scan"; 

    class EnergyAnalysis
    {
        double partition_sum = 0.0;      
        double energy_sum = 0.0;         
        Average<double> mean_exp_energy; 
      public:
        void clear();                               
        void add(double energy);                    
        [[nodiscard]] double getFreeEnergy() const; 
        [[nodiscard]] double getMeanEnergy() const; 
        void printLog() const;                      
    };

    struct Molecule
    {
        Space::GroupVector::size_type index; 
        std::vector<Point> ref_positions;    
        void initialize(const Space::GroupVector& groups,
                        int index); 
        ParticleVector getRotatedReference(const Space::GroupVector& groups,
                                           const Eigen::Quaterniond& q);
    };

    double zmin = 0;                
    double zmax = 0;                
    double dz = 0;                  
    double max_energy = pc::infty;  
    EnergyAnalysis energy_analysis; 

    std::pair<Molecule, Molecule> molecules; 
    std::unique_ptr<std::ostream> stream;    
    std::unique_ptr<XTCWriter> trajectory;   
    Geometry::TwobodyAngles angles;          

    void report(const Group& group1, const Group& group2, const Eigen::Quaterniond& q1,
                const Eigen::Quaterniond& q2, Energy::NonbondedBase& nonbonded);

  public:
    AngularScan(const json& input, const Space& spc);
    void operator()(Space& space, Energy::Hamiltonian& hamiltonian) override;
};

std::unique_ptr<SystemAction> createAction(std::string_view name, const json& properties,
                                           Space& spc);

std::vector<std::unique_ptr<SystemAction>> createActionList(const json& input, Space& spc);

} // namespace Faunus