CorriasBuistICCModified.hpp

/*

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*/

#ifndef CorriasBuistICCModified_HPP_
#define CorriasBuistICCModified_HPP_

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

class CorriasBuistICCModified : public AbstractCardiacCell
{
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & boost::serialization::base_object<AbstractCardiacCell >(*this);
        archive &  mFractionOfVDDRInPU;
        archive &  mIP3Concentration;
        archive &  mScaleFactorSerca;
        archive &  mScaleFactorCarbonMonoxide;
    }

private:

    double mFractionOfVDDRInPU;
    double mIP3Concentration;
    double mScaleFactorSerca;
    double mScaleFactorCarbonMonoxide;

    /* Concentrations */
    double Ca_o;
    double Cl_o;
    double K_o;
    double Na_o;
    /* Nernst parameters */
    double R;
    double T;
    double F;
    double FoRT;
    double RToF;
    double  Cm ;
    double Asurf_in_cm_square;
    double  Asurf ;
    double  Cl_i  ;
    double  K_i   ;
    double  Na_i    ;
    double  P_cyto;
    double  Vol  ;
    double  fc ;
    double  fe  ;
    double  fm ;
    double  Q10Ca ;
    double  Q10K ;
    double  Q10Na  ;
    double  T_exp  ;
    double  G_max_BK  ;
    double  G_max_CaCl  ;
    double  G_max_ERG  ;
    double  G_max_Ltype ;
    double  G_max_NSCC  ;
    double  G_max_Na ;
    double  G_max_VDDR ;
    double  G_max_bk    ;
    double  G_max_kv11 ;
    double  J_max_PMCA  ;
    double  J_max_PMCA_PU ;
    double  J_ERleak   ;
    double  J_max_leak ;
    double  Jmax_IP3  ;
    double  Jmax_NaCa ;
    double  Jmax_serca   ;
    double  Jmax_uni    ;
    double  NaPerm_o_Kperm   ;
    double  L    ;
    double  P_ER  ;
    double  P_PU   ;
    double  P_mito ;
    double  b ;
    double  na ;
    double  K_Ca   ;
    double  K_Na ;
    double  K_act ;
    double  K_trans   ;
    double  k_serca ;
    double  conc   ;
    double  d_ACT   ;
    double  d_IP3 ;
    double  d_INH  ;
    double  tau_d_CaCl;
    double  tau_d_NSCC ;
    double  tauh;
    double  deltaPsi_B;
    double  deltaPsi_star;
    double  deltaPsi;

     //Calculated constants
     /* Volumes */
     double V_cyto;              
     double V_ER;                
     double V_MITO;              
     double V_PU;                
     /* Temperature corrections */
     double T_correction_Ca;     
     double T_correction_K;      
     double T_correction_Na;     
     double T_correction_BK;     
     /* Nernst potentials */
     double E_Na;                
     double E_K;                 
     double E_Cl;                
     double E_NSCC;              
     /* Activation gate time constants */
     double tau_d_ERG;           
     double tau_d_Ltype;         
     double tau_d_Na;            
     double tau_d_VDDR;          
     double tau_d_kv11;          
     /* Inactivation gate time constants */
     double tau_f_Ltype;         
     double tau_f_Na;            
     double tau_f_VDDR;          
     double tau_f_ca_Ltype;      
     double tau_f_kv11;          
     /* Speed ups */
     double e2FoRTdPsiMdPsiS;
     double ebFoRTdPsiMdPsiS;
public:
     CorriasBuistICCModified(boost::shared_ptr<AbstractIvpOdeSolver> pSolver, boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    ~CorriasBuistICCModified();

    void VerifyStateVariables();

    double GetIIonic(const std::vector<double>* pStateVariables=NULL);

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

    void SetFractionOfVDDRInPU(double fraction);

    void SetIP3Concentration(double concentration);

    void SetSercaPumpScaleFactor(double scaleFactor);

    void SetCarbonMonoxideScaleFactor(double scaleFactor);

    double GetCarbonMonoxideScaleFactor();
};


// Needs to be included last
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(CorriasBuistICCModified)

namespace boost
{
    namespace serialization
    {
        template<class Archive>
        inline void save_construct_data(
            Archive & ar, const CorriasBuistICCModified * t, const unsigned int fileVersion)
        {
            const boost::shared_ptr<AbstractIvpOdeSolver> p_solver = t->GetSolver();
            const boost::shared_ptr<AbstractStimulusFunction> p_stimulus = t->GetStimulusFunction();
            ar << p_solver;
            ar << p_stimulus;
        }

        template<class Archive>
        inline void load_construct_data(
            Archive & ar, CorriasBuistICCModified * t, const unsigned int fileVersion)
        {
            boost::shared_ptr<AbstractIvpOdeSolver> p_solver;
            boost::shared_ptr<AbstractStimulusFunction> p_stimulus;
            ar >> p_solver;
            ar >> p_stimulus;
            ::new(t)CorriasBuistICCModified(p_solver, p_stimulus);
        }

    }

}

#endif // CorriasBuistICCModified_HPP_