AbstractParameterisedSystem.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 ABSTRACTPARAMETERISEDSYSTEM_HPP_
#define ABSTRACTPARAMETERISEDSYSTEM_HPP_

#include <vector>
#include <string>
#include <boost/shared_ptr.hpp>

#include "AbstractOdeSystemInformation.hpp"

class AbstractUntemplatedParameterisedSystem
{
public:
    AbstractUntemplatedParameterisedSystem(unsigned numberOfStateVariables);

    virtual ~AbstractUntemplatedParameterisedSystem();

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

    std::string GetSystemName() const;

    //
    // Attribute methods
    //

    unsigned GetNumberOfAttributes() const;

    bool HasAttribute(const std::string& rName) const;

    double GetAttribute(const std::string& rName) const;

    //
    // State variable methods
    //

    unsigned GetNumberOfStateVariables() const;

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

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

    unsigned GetStateVariableIndex(const std::string& rName) const;

    bool HasStateVariable(const std::string& rName) const;

    std::string GetStateVariableUnits(unsigned index) const;

    //
    // Parameter methods
    //

    unsigned GetNumberOfParameters() const;

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

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

    unsigned GetParameterIndex(const std::string& rName) const;

    bool HasParameter(const std::string& rName) const;

    std::string GetParameterUnits(unsigned index) const;

    //
    // Derived quantity methods
    //

    unsigned GetNumberOfDerivedQuantities() const;

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

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

    unsigned GetDerivedQuantityIndex(const std::string& rName) const;

    bool HasDerivedQuantity(const std::string& rName) const;

    std::string GetDerivedQuantityUnits(unsigned index) const;

    //
    // "Any variable" methods
    //

    unsigned GetAnyVariableIndex(const std::string& rName) const;

    bool HasAnyVariable(const std::string& rName) const;

    std::string GetAnyVariableUnits(unsigned index) const;

    std::string GetAnyVariableUnits(const std::string& rName) const;


protected:
    unsigned mNumberOfStateVariables;

    boost::shared_ptr<AbstractOdeSystemInformation> mpSystemInfo;

};


template<typename VECTOR>
class AbstractParameterisedSystem : public AbstractUntemplatedParameterisedSystem
{
friend class TestAbstractCvodeSystem;

private:
    std::string GetStateMessage(const std::string& message, VECTOR Y);

protected:
    VECTOR mStateVariables;

    VECTOR mParameters;

    std::string DumpState(const std::string& rMessage);

    std::string DumpState(const std::string& rMessage,
                          VECTOR Y);

public:
    AbstractParameterisedSystem(unsigned numberOfStateVariables);

    //
    // State variable methods
    //

    VECTOR& rGetStateVariables();

    VECTOR GetStateVariables();

    void SetStateVariables(const VECTOR& rStateVariables);

    double GetStateVariable(unsigned index) const;

    double GetStateVariable(const std::string& rName) const;

    void SetStateVariable(unsigned index, double newValue);

    void SetStateVariable(const std::string& rName, double newValue);

    virtual void VerifyStateVariables()
    {}

    //
    // Initial condition methods
    //

    void SetDefaultInitialConditions(const VECTOR& rInitialConditions);

    void SetDefaultInitialCondition(unsigned index, double initialCondition);

    VECTOR GetInitialConditions() const;

    void ResetToInitialConditions();

    //
    // Parameter methods
    //

    double GetParameter(unsigned index) const;

    double GetParameter(const std::string& rName) const;

    void SetParameter(const std::string& rName, double value);

    void SetParameter(unsigned index, double value);

    //
    // "Any variable" methods
    //

    double GetAnyVariable(unsigned index, double time=0.0,
                          VECTOR* pDerivedQuantities=NULL);

    double GetAnyVariable(const std::string& rName, double time=0.0,
                          VECTOR* pDerivedQuantities=NULL);

    void SetAnyVariable(unsigned index, double value);

    void SetAnyVariable(const std::string& rName, double value);

    //
    // Derived quantity methods
    //

    virtual VECTOR ComputeDerivedQuantities(double time,
                                            const VECTOR& rState);

    VECTOR ComputeDerivedQuantitiesFromCurrentState(double time);
};



#endif /*ABSTRACTPARAMETERISEDSYSTEM_HPP_*/