AbstractOdeSystem.hpp

/*

Copyright (c) 2005-2015, 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 _ABSTRACTODESYSTEM_HPP_
#define _ABSTRACTODESYSTEM_HPP_

#include <vector>
#include <string>
#include <algorithm>


#include "ChasteSerialization.hpp"
#include "ChasteSerializationVersion.hpp"
#include <boost/serialization/split_member.hpp>
#include <boost/serialization/vector.hpp>
#include "ClassIsAbstract.hpp"

#include "AbstractParameterisedSystem.hpp"
#include "Exception.hpp"

class AbstractOdeSystem : public AbstractParameterisedSystem<std::vector<double> >
{
    friend class TestAbstractOdeSystem;

private:


    friend class boost::serialization::access;
    template<class Archive>
    void save(Archive & archive, const unsigned int version) const
    {
        // Despite the fact that 3 of these variables actually live in our base class,
        // we still archive them here to maintain backwards compatibility.
        // Since the N_Vector version of mStateVariables and mParameters needs converting
        // to a standard vector before archiving, this doesn't hurt too much.
        archive & mNumberOfStateVariables;
        archive & mUseAnalyticJacobian;
        archive & mStateVariables;
        archive & mParameters;

        if (version > 0)
        {
            archive & rGetParameterNames();
        }

        // This is always set up by subclass constructors, and is essentially
        // 'static' data, so shouldn't go in the archive.
        //archive &mpSystemInfo;
    }
    template<class Archive>
    void load(Archive & archive, const unsigned int version)
    {
        archive & mNumberOfStateVariables;
        archive & mUseAnalyticJacobian;
        archive & mStateVariables;
        std::vector<double> parameters;
        archive & parameters;

        if (version > 0)
        {
            std::vector<std::string> param_names;
            archive & param_names;

            CheckParametersOnLoad(parameters,param_names);
        }
        else
        {
            mParameters = parameters;
        }
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

protected:

    bool mUseAnalyticJacobian;

public:

    AbstractOdeSystem(unsigned numberOfStateVariables);

    virtual ~AbstractOdeSystem();

    virtual void EvaluateYDerivatives(double time, const std::vector<double>& rY,
                                      std::vector<double>& rDY)=0;

    virtual bool CalculateStoppingEvent(double time, const std::vector<double>& rY);

    virtual double CalculateRootFunction(double time, const std::vector<double>& rY);

    bool GetUseAnalyticJacobian();

    const std::vector<double>& rGetConstStateVariables() const;
};

CLASS_IS_ABSTRACT(AbstractOdeSystem)
BOOST_CLASS_VERSION(AbstractOdeSystem, 1u)

#endif //_ABSTRACTODESYSTEM_HPP_