AbstractGeneralizedRushLarsenCardiacCell.hpp

/*

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*/

#ifndef ABSTRACTGENERALIZEDRUSHLARSENCARDIACCELL_HPP_
#define ABSTRACTGENERALIZEDRUSHLARSENCARDIACCELL_HPP_

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

/*
Megan E. Marsh, Raymond J. Spiteri
Numerical Simulation Laboratory
University of Saskatchewan
December 2011
Partial support provided by research grants from the National
Science and Engineering Research Council (NSERC) of Canada
and the MITACS/Mprime Canadian Network of Centres of Excellence.
*/

class AbstractGeneralizedRushLarsenCardiacCell : public AbstractCardiacCell
{
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // This calls serialize on the base class.
        archive & boost::serialization::base_object<AbstractCardiacCell>(*this);
    }

public:
    AbstractGeneralizedRushLarsenCardiacCell(
            unsigned numberOfStateVariables,
            unsigned voltageIndex,
            boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    virtual ~AbstractGeneralizedRushLarsenCardiacCell();

    OdeSolution Compute(double tStart, double tEnd, double tSamp=0.0);

    void ComputeExceptVoltage(double tStart, double tEnd);

    void SolveAndUpdateState(double tStart, double tEnd);


    bool HasAnalyticJacobian() const;

    void ForceUseOfNumericalJacobian(bool useNumericalJacobian = true);


private:
#define COVERAGE_IGNORE

    void EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY)
    {
        NEVER_REACHED;
    }
#undef COVERAGE_IGNORE

protected:
    virtual void ComputeOneStepExceptVoltage(double time)=0;

    virtual void UpdateTransmembranePotential(double time)=0;

    std::vector<double> mPartialF;

    std::vector<double> mEvalF;

    std::vector<double> mYInit;

    bool mHasAnalyticJacobian;
};

CLASS_IS_ABSTRACT(AbstractGeneralizedRushLarsenCardiacCell)

#endif // ABSTRACTGENERALIZEDRUSHLARSENCARDIACCELL_HPP_