AbstractCardiacCell.hpp

/*

Copyright (c) 2005-2018, University of Oxford.
All rights reserved.

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.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*/

#ifndef ABSTRACTCARDIACCELL_HPP_
#define ABSTRACTCARDIACCELL_HPP_

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

        // For version 2 and above these move into AbstractCardiacCellInterface
        // (AbstractCardiacCellInterface serialization moved to 1 at the same time as this moved to 2).
        if (version <= 1)
        {
            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;
            }
        }

        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();


    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 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);

    //  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, 2)

#endif /*ABSTRACTCARDIACCELL_HPP_*/