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Goldbeter1991OdeSystem.hpp
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Goldbeter1991OdeSystem.hpp
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/*
Copyright (c) 2005-2024, 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 GOLDBETER1991ODESYSTEM_HPP_
#define GOLDBETER1991ODESYSTEM_HPP_
#include "ChasteSerialization.hpp"
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/shared_ptr.hpp>
#include <cmath>
#include <iostream>
#include "AbstractOdeSystem.hpp"
/**
* Goldbeter 1991 System
*/
class Goldbeter1991OdeSystem : public AbstractOdeSystem
{
private:
friend class boost::serialization::access;
/**
* Serialize the object and its member variables.
*
* @param archive the archive
* @param version the current version of this class
*/
template<class Archive>
void serialize(Archive & archive, const unsigned int version)
{
archive & boost::serialization::base_object<AbstractOdeSystem>(*this);
}
///\todo extract model parameters as member variables
public:
/**
* Default constructor.
*
* @param stateVariables optional initial conditions for state variables (only used in archiving)
*/
Goldbeter1991OdeSystem(std::vector<double> stateVariables=std::vector<double>());
/**
* Destructor.
*/
~Goldbeter1991OdeSystem();
/**
* Compute the RHS of the Collier et al. system of ODEs.
*
* Returns a vector representing the RHS of the ODEs at each time step, y' = [y1' ... yn'].
* An ODE solver will call this function repeatedly to solve for y = [y1 ... yn].
*
* @param time used to evaluate the RHS.
* @param rY value of the solution vector used to evaluate the RHS.
* @param rDY filled in with the resulting derivatives (using Collier et al. system of equations).
*/
void EvaluateYDerivatives(double time, const std::vector<double>& rY, std::vector<double>& rDY);
};
// Declare identifier for the serializer
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(Goldbeter1991OdeSystem)
namespace boost
{
namespace serialization
{
/**
* Serialize information required to construct a Goldbeter1991OdeSystem.
*/
template<class Archive>
inline void save_construct_data(
Archive & ar, const Goldbeter1991OdeSystem * t, const unsigned int file_version)
{
const std::vector<double>& state_variables = t->rGetConstStateVariables();
ar & state_variables;
}
/**
* De-serialize constructor parameters and initialise a Goldbeter1991OdeSystem.
*/
template<class Archive>
inline void load_construct_data(
Archive & ar, Goldbeter1991OdeSystem * t, const unsigned int file_version)
{
std::vector<double> state_variables;
ar & state_variables;
// Invoke inplace constructor to initialise instance
::new(t)Goldbeter1991OdeSystem(state_variables);
}
}
} // namespace ...
#endif /* GOLDBETER1991ODESYSTEM_HPP_ */