CorriasBuistICCModified.hpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 2.1 of the License, or
(at your option) any later version.

Chaste is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/

#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_