reactioncoordinate.h

#pragma once

#include "core.h"

namespace Faunus {

class Space;

namespace ReactionCoordinate {

class ReactionCoordinateBase
{
  protected:
    std::function<double()> function = nullptr; 
  public:
    explicit ReactionCoordinateBase(const json& j); 
    double resolution = 0.0;    
    double minimum_value = 0.0; 
    double maximum_value = 0.0; 
    std::string name;           

    double operator()();                  
    virtual void _to_json(json& j) const; 
    [[nodiscard]] bool
    inRange(double coord) const; 
    virtual ~ReactionCoordinateBase() = default;
};

void to_json(json& j, const ReactionCoordinateBase&
                          reaction_coordinate); 

std::unique_ptr<ReactionCoordinateBase>
createReactionCoordinate(const json&,
                         const Space&); 

class SystemProperty : public ReactionCoordinateBase
{
  protected:
    std::string property;

  public:
    SystemProperty(const json& j, const Space& spc);
    void _to_json(json& j) const override;
};

class AtomProperty : public ReactionCoordinateBase
{
  protected:
    size_t index; // atom index
    Point dir = {0.0, 0.0, 0.0};

  public:
    std::string property;
    AtomProperty(const json& j, const Space& spc);
    void _to_json(json& j) const override;
};

struct MoleculeProperty : public ReactionCoordinateBase
{
  private:
    size_t index; 
    Point direction = {0.0, 0.0, 0.0};
    std::vector<size_t> indexes;
    std::string property;

    void selectAngleWithVector(const json& j, const Space& spc);
    void selectRinner(const json& j, const Space& spc);
    void selectMinimumGroupDistance(const json& j, const Space& spc);
    void selectMassCenterDistance(const json& j, const Space& spc);
    void selectDipoleAngle(const json& j, const Space& spc, Geometry::BoundaryFunction& b);
    void selectGyrationRadius(const Space& spc);
    void selectAtomAtomDistance(const json& j, const Space& spc);
    void selectMassCenterDistanceZ(const json& j, const Space& spc);
    void selectLengthOverRadiusRatio(const json& j, const Space& spc);

  public:
    MoleculeProperty(const json& j, const Space& spc);
    void _to_json(json& j) const override;
};

} // namespace ReactionCoordinate
} // namespace Faunus