Owen2011OxygenBasedCellCycleOdeSystem.hpp

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*/

#ifndef _OWEN2011OXYGENBASEDCELLCYCLEODESYSTEM_HPP_
#define _OWEN2011OXYGENBASEDCELLCYCLEODESYSTEM_HPP_

#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/shared_ptr.hpp>
#include <cmath>
#include "AbstractCellMutationState.hpp"
#include "CancerCellMutationState.hpp"
#include "AbstractOdeSystem.hpp"
#include "UnitCollection.hpp"

class Owen2011OxygenBasedCellCycleOdeSystem : public AbstractOdeSystem
{

private:

    units::quantity<unit::pressure> mCphi;

    units::quantity<unit::time> mTmin;

    units::quantity<unit::rate> mk7;

    units::quantity<unit::rate> mk7dash;

    units::quantity<unit::pressure> mCp53;

    units::quantity<unit::rate> mk8;

    units::quantity<unit::rate> mk8doubledash;

    units::quantity<unit::dimensionless> mJ5;

    units::quantity<unit::rate> mk8dash;

    units::quantity<unit::pressure> mCVEGF;

    units::quantity<unit::concentration> mOxygenConcentration;

    boost::shared_ptr<AbstractCellMutationState> pmMutationState;

    units::quantity<unit::time> mReferenceTimeScale;

    units::quantity<unit::concentration> mReferenceConcentrationScale;

    units::quantity<unit::solubility> mReferenceSolubility;


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

public:

    Owen2011OxygenBasedCellCycleOdeSystem(units::quantity<unit::concentration> oxygenConcentration,
                                             boost::shared_ptr<AbstractCellMutationState> mutation_state,
                                             std::vector<double> stateVariables=std::vector<double>());

    ~Owen2011OxygenBasedCellCycleOdeSystem();

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

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

    units::quantity<unit::concentration> GetOxygenConcentration() const;

    boost::shared_ptr<AbstractCellMutationState> GetMutationState() const;

    void SetMutationState(boost::shared_ptr<AbstractCellMutationState> pMutationState);

};

// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(Owen2011OxygenBasedCellCycleOdeSystem)

namespace boost
{
namespace serialization
{
template<class Archive>
inline void save_construct_data(
    Archive & ar, const Owen2011OxygenBasedCellCycleOdeSystem * t, const unsigned int file_version)
{
    // Save data required to construct instance
    const units::quantity<unit::concentration> oxygen_concentration = t->GetOxygenConcentration();
    ar & oxygen_concentration;

    const boost::shared_ptr<AbstractCellMutationState> mutation_state = t->GetMutationState();
    ar & mutation_state;

    const std::vector<double> state_variables = t->rGetConstStateVariables();
    ar & state_variables;
}

template<class Archive>
inline void load_construct_data(
    Archive & ar, Owen2011OxygenBasedCellCycleOdeSystem * t, const unsigned int file_version)
{
    // Retrieve data from archive required to construct new instance
    units::quantity<unit::concentration> oxygen_concentration;
    ar & oxygen_concentration;

    boost::shared_ptr<AbstractCellMutationState> mutation_state;
    ar & mutation_state;

    std::vector<double> state_variables;
    ar & state_variables;

    // Invoke inplace constructor to initialise instance
    ::new(t)Owen2011OxygenBasedCellCycleOdeSystem(oxygen_concentration, mutation_state, state_variables);
}
}
} // namespace ...

#endif /*_OWEN2011OXYGENBASEDCELLCYCLEODESYSTEM_HPP_*/