TysonNovak2001OdeSystem.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#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 BOOST_PFTO 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_*/

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