TysonNovak2001OdeSystem.hpp

/*

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*/

#ifndef TYSONNOVAK2001ODESYSTEM_HPP_
#define TYSONNOVAK2001ODESYSTEM_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>

#include <cmath>
#include <iostream>

#include "AbstractOdeSystemWithAnalyticJacobian.hpp"

class TysonNovak2001OdeSystem : public AbstractOdeSystemWithAnalyticJacobian
{
private:

    double mK1;
    double mK2d;
    double mK2dd;
    double mK2ddd;
    double mCycB_threshold;
    double mK3d;
    double mK3dd;
    double mK4d;
    double mK4;
    double mJ3;
    double mJ4;
    double mK5d;
    double mK5dd;
    double mK6;
    double mJ5;
    unsigned mN;
    double mK7;
    double mK8;
    double mJ7;
    double mJ8;
    double mMad;
    double mK9;
    double mK10;
    double mK11;
    double mK12d;
    double mK12dd;
    double mK12ddd;
    double mKeq;
    double mK13;
    double mK14;
    double mK15d;
    double mK15dd;
    double mK16d;
    double mK16dd;
    double mJ15;
    double mJ16;
    double mMu;
    double mMstar;

    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractOdeSystem>(*this);
    }

public:

    TysonNovak2001OdeSystem(std::vector<double> stateVariables=std::vector<double>());

    ~TysonNovak2001OdeSystem();

    void Init();

    void EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY);

    bool CalculateStoppingEvent(double time, const std::vector<double>& rY);

    double CalculateRootFunction(double time, const std::vector<double>& rY);

    virtual void AnalyticJacobian(const std::vector<double>& rSolutionGuess, double** jacobian, double time, double timeStep);
};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(TysonNovak2001OdeSystem)

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const TysonNovak2001OdeSystem * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const std::vector<double>& state_variables = t->rGetConstStateVariables();
    ar & state_variables;
}

template<class Archive>
inline void load_construct_data(
    Archive & ar, TysonNovak2001OdeSystem * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    std::vector<double> state_variables;
    ar & state_variables;

    // Invoke inplace constructor to initialise instance
    ::new(t)TysonNovak2001OdeSystem(state_variables);
}
}
} // namespace ...

#endif /*TYSONNOVAK2001ODESYSTEM_HPP_*/