AbstractOdeSystem.hpp

/*

Copyright (C) University of Oxford, 2005-2010

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 <cassert>
#include <climits> // Work around a boost bug - see #1024.

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

#include "Exception.hpp"
#include "AbstractOdeSystemInformation.hpp"

class AbstractOdeSystem
{
    friend class TestAbstractOdeSystem;

    friend class boost::serialization::access;
private:
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        archive & mNumberOfStateVariables;
        archive & mUseAnalyticJacobian;
        archive & mStateVariables;
        archive & mParameters;

        // This is always set up by subclass constructors, and is essentially
        // 'static' data, so shouldn't go in the archive.
        //archive &mpSystemInfo;
    }

protected:

    unsigned mNumberOfStateVariables;

    std::vector<double> mStateVariables;

    std::vector<double> mParameters;

    boost::shared_ptr<AbstractOdeSystemInformation> mpSystemInfo;

    bool mUseAnalyticJacobian;

public:

    AbstractOdeSystem(unsigned numberOfStateVariables = 0);

    virtual ~AbstractOdeSystem();

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

    unsigned GetNumberOfStateVariables() const;


    unsigned GetNumberOfParameters() const;

    double GetParameter(unsigned index) const;

    void SetParameter(unsigned index, double value);

    const std::vector<std::string>& rGetParameterNames() const;

    const std::vector<std::string>& rGetParameterUnits() const;


    void SetInitialConditions(const std::vector<double>& rInitialConditions);

    void SetInitialConditionsComponent(unsigned index, double initialCondition);

    std::vector<double> GetInitialConditions() const;

    void SetStateVariables(const std::vector<double>& rStateVariables);

    void SetStateVariable(unsigned stateVariable, double newValue);

    std::vector<double>& rGetStateVariables();

    const std::vector<std::string>& rGetVariableNames() const;

    const std::vector<std::string>& rGetVariableUnits() const;

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

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

    bool GetUseAnalyticJacobian();

    unsigned GetStateVariableNumberByName(const std::string name) const;

    double GetStateVariableValueByNumber(unsigned varNumber) const;

    std::string GetStateVariableUnitsByNumber(unsigned varNumber) const;

    boost::shared_ptr<const AbstractOdeSystemInformation> GetSystemInformation() const;

protected:

    std::string DumpState(const std::string& rMessage,
                          std::vector<double> Y = std::vector<double>());
};

CLASS_IS_ABSTRACT(AbstractOdeSystem)


#endif //_ABSTRACTODESYSTEM_HPP_