CorriasBuistSMCModified.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 CorriasBuistSMCModified_HPP_
#define CorriasBuistSMCModified_HPP_


#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include "AbstractCardiacCell.hpp"
#include "AbstractStimulusFunction.hpp"
class CorriasBuistSMCModified : 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);
    }

private:

    double mScaleFactorCarbonMonoxide;

    bool mFakeIccStimulusPresent;

    double Cm;
    double Asurf_in_cm_square;
    double Asurf;
    double VolCell;
    double hCa;
    double sCa;
    /* concentrations */
    double Ki;       
    double Nai;        
    double ACh;       
    double CaiRest;     
    /* maximum conductances*/
    double gLVA_max;                  // (0.18 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gCaL_max;                  // (65.0 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gBK_max;                  // (45.7 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gKb_max;                   // (0.0144 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gKA_max;                   // (9.0  nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gKr_max;                   // (35.0 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gNa_max;                    // (3.0  nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gnsCC_max;                 // (50.0 nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double gcouple;           // 1.3 nS * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2
    double JCaExt_max;     
    /* Temperature corrections */
    double Q10Ca;         
    double Q10K;          //1.365
    double Q10Na;        
    double Texp;       
    double T_correct_Ca ;
    double T_correct_K ;  
    double T_correct_Na;
    double T_correct_gBK;   // (nS) * 1e-6 (mS/nS) / Asurf (mm2) = mS/mm2

    /* Nernst potentials */
    double EK;                  
    double ENa ;               
    double EnsCC;                          
    double Ca_o;         
    double K_o;          
    double Na_o;         
    /* Nernst parameters */
    double R;    
    double T;       
    double F;     
    double FoRT;     
    double RToF;    
public:

    CorriasBuistSMCModified(boost::shared_ptr<AbstractIvpOdeSolver> pSolver, boost::shared_ptr<AbstractStimulusFunction> pIntracellularStimulus);

    ~CorriasBuistSMCModified();

    void VerifyStateVariables();

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

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


    void SetFakeIccStimulusPresent(bool present);

    bool GetFakeIccStimulusPresent();

    double SetCarbonMonoxideScaleFactor();

    void SetCarbonMonoxideScaleFactor(double scaleFactor);

    double GetCarbonMonoxideScaleFactor();

};


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

namespace boost
{
    namespace serialization
    {
        template<class Archive>
        inline void save_construct_data(
            Archive & ar, const CorriasBuistSMCModified * 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, CorriasBuistSMCModified * 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)CorriasBuistSMCModified(p_solver, p_stimulus);
        }

    }

}

#endif // CorriasBuistSMCModified_HPP_