AbstractOdeSystem.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 _ABSTRACTODESYSTEM_HPP_
#define _ABSTRACTODESYSTEM_HPP_

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


#include "ChasteSerialization.hpp"
#include <boost/serialization/split_member.hpp>
#include <boost/serialization/vector.hpp>
#include <boost/serialization/version.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 AbstractParameterisedSystem doesn't get checkpointed yet,
        // this doesn't hurt.
        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;

            if (mParameters.size() != rGetParameterNames().size())
            {
                // Subclass constructor didn't give default values, so we need the archive to provide them all
                if (param_names.size() != rGetParameterNames().size())
                {
                    EXCEPTION("Number of ODE parameters in archive does not match number in class.");
                }
                mParameters.resize(rGetParameterNames().size());
            }

            // Check whether the archive specifies parameters that don't appear in this class,
            // and create a map from archive index to local index
            std::vector<unsigned> index_map(param_names.size());
            for (unsigned i=0; i<param_names.size(); ++i)
            {
                index_map[i] = find(rGetParameterNames().begin(), rGetParameterNames().end(), param_names[i])
                               - rGetParameterNames().begin();
                if (index_map[i] == rGetParameterNames().size())
                {
                    EXCEPTION("Archive specifies a parameter '" + param_names[i] + "' which does not appear in this class.");
                }
            }

            for (unsigned i=0; i<param_names.size(); ++i)
            {
                mParameters[index_map[i]] = parameters[i];
            }
        }
        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_