AbstractCardiacCell.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 ABSTRACTCARDIACCELL_HPP_
#define ABSTRACTCARDIACCELL_HPP_

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

// This is only needed to prevent compilation errors on PETSc 2.2/Boost 1.33.1 combo
#include "UblasVectorInclude.hpp"

#include "AbstractCardiacCellInterface.hpp"
#include "AbstractOdeSystem.hpp"
#include "AbstractIvpOdeSolver.hpp"
#include "AbstractStimulusFunction.hpp"

#include <vector>

typedef enum _CellModelState
{
    STATE_UNSET = 0,
    FAST_VARS_ONLY,
    ALL_VARS
} CellModelState;

class AbstractCardiacCell : public AbstractCardiacCellInterface, public AbstractOdeSystem
{
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // This calls serialize on the base class.
        archive & boost::serialization::base_object<AbstractOdeSystem>(*this);
        if (version > 0)
        {
            archive & boost::serialization::base_object<AbstractCardiacCellInterface>(*this);
        }
        archive & mDt;
        archive & this->mSetVoltageDerivativeToZero;
        if (version > 0)
        {
            // Note that when loading a version 0 archive, this will be initialised to
            // false by our constructor.  So we should get a consistent (wrong) answer
            // with previous versions of Chaste when in tissue.
            archive & this->mIsUsedInTissue;
            archive & this->mHasDefaultStimulusFromCellML;
        }
        // archive & mVoltageIndex; - always set by constructor - called by concrete class
        // archive & mpOdeSolver; - always set by constructor - called by concrete class
        // archive & mpIntracellularStimulus; - always set by constructor - called by concrete class
        if (version == 0)
        {
            CheckForArchiveFix();
        }
        // Paranoia check
        assert(this->mParameters.size() == this->rGetParameterNames().size());
    }

    void CheckForArchiveFix();

protected:
    double mDt;

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

    virtual ~AbstractCardiacCell();

    void Init();

    void SetTimestep(double dt);

    virtual void SolveAndUpdateState(double tStart, double tEnd);

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

    virtual void ComputeExceptVoltage(double tStart, double tEnd);

    void SetVoltage(double voltage);

    double GetVoltage();

    virtual double GetIntracellularCalciumConcentration();

    virtual void SetStretch(double stretch)
    {
    }

//    /**
//     *  Empty method which can be over-ridden in concrete cell class which should
//     *  go through the current state vector and go range checking on the values
//     *  (eg check that concentrations are positive and gating variables are between
//     *  zero and one). This method is called in the ComputeExceptVoltage method.
//     */
//    virtual void VerifyStateVariables()
//    {
//        for(std::set<unsigned>::iterator iter = mGatingVariableIndices.begin();
//            iter != mGatingVariableIndices.end();
//            ++iter)
//        {
//            double value = mStateVariables[*iter];
//            if(value<0.0)
//            {
//                std::stringstream error;
//                error << "State variable " << *iter << ", a gating variable, has gone negative";
//                EXCEPTION(DumpState(error.str()));
//            }
//            if(value>1.0)
//            {
//                std::stringstream error;
//                error << "State variable " << *iter << ", a gating variable, has become greater than one";
//                EXCEPTION(DumpState(error.str()));
//            }
//        }
//
//        for(std::set<unsigned>::iterator iter = mConcentrationIndices.begin();
//            iter != mConcentrationIndices.end();
//            ++iter)
//        {
//            if(mStateVariables[*iter] < 0.0)
//            {
//                std::stringstream error;
//                error << "State variable " << *iter << ", a concentration, has gone negative";
//                EXCEPTION(DumpState(error.str()));
//            }
//        }
//    }



    //  METHODS NEEDED BY FAST CARDIAC CELLS

    virtual void SetState(CellModelState state);

    virtual void SetSlowValues(const std::vector<double> &rSlowValues);

    virtual void GetSlowValues(std::vector<double>& rSlowValues);

    virtual bool IsFastOnly();

    virtual void AdjustOutOfRangeSlowValues(std::vector<double>& rSlowValues);

    virtual unsigned GetNumSlowValues();

};

CLASS_IS_ABSTRACT(AbstractCardiacCell)
BOOST_CLASS_VERSION(AbstractCardiacCell, 1)

#endif /*ABSTRACTCARDIACCELL_HPP_*/