AbstractCvodeCell.hpp

/*

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*/

#ifdef CHASTE_CVODE
#ifndef _ABSTRACTCVODECELL_HPP_
#define _ABSTRACTCVODECELL_HPP_

// Serialization headers
#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/shared_ptr.hpp>
#include <boost/serialization/shared_ptr.hpp>

// Chaste headers
#include "AbstractOdeSystemInformation.hpp"
#include "AbstractStimulusFunction.hpp"
#include "AbstractIvpOdeSolver.hpp"
#include "AbstractCvodeSystem.hpp"
#include "AbstractCardiacCellInterface.hpp"
#include "VectorHelperFunctions.hpp"


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

protected:
    double mMaxDt;

public:
    AbstractCvodeCell(boost::shared_ptr<AbstractIvpOdeSolver> pSolver,
                      unsigned numberOfStateVariables,
                      unsigned voltageIndex,
                      boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    virtual ~AbstractCvodeCell();

    double GetVoltage();

    void SetVoltage(double voltage);

    void SetMaxTimestep(double maxDt);

    void SetTimestep(double maxDt);

    double GetTimestep();

    virtual void SolveAndUpdateState(double tStart, double tEnd);

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

    void ComputeExceptVoltage(double tStart, double tEnd);

    void SetVoltageDerivativeToZero(bool clamp=true);

    unsigned GetNumberOfStateVariables() const;

    unsigned GetNumberOfParameters() const;

    std::vector<double> GetStdVecStateVariables();

    const std::vector<std::string>& rGetStateVariableNames() const;

    void SetStateVariables(const std::vector<double>& rVariables);

    void SetStateVariables(const N_Vector& rVariables);

    void SetStateVariable(unsigned index, double newValue);

    void SetStateVariable(const std::string& rName, double newValue);

    double GetAnyVariable(const std::string& rName, double time=0.0);

    double GetParameter(const std::string& rParameterName);

    double GetParameter(unsigned parameterIndex);

    void SetParameter(const std::string& rParameterName, double value);
};

CLASS_IS_ABSTRACT(AbstractCvodeCell)

#endif // _ABSTRACTCVODECELL_HPP_
#endif // CHASTE_CVODE