AbstractCvodeCell.hpp

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*/
 
#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_