AbstractCvodeSystem.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/>.

*/

#ifdef CHASTE_CVODE
#ifndef _ABSTRACTCVODESYSTEM_HPP_
#define _ABSTRACTCVODESYSTEM_HPP_

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

// This is only needed to prevent compilation errors on PETSc 2.2/Boost 1.33.1 combo
#include "UblasVectorInclude.hpp"

// Chaste includes
#include "OdeSolution.hpp"
#include "AbstractParameterisedSystem.hpp"
#include "Exception.hpp"

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

// CVODE headers
#include <nvector/nvector_serial.h>

class AbstractCvodeSystem : public AbstractParameterisedSystem<N_Vector>
{
private:
    void SetupCvode(N_Vector initialConditions,
                    realtype tStart,
                    realtype maxDt);

    void RecordStoppingPoint(double stopTime);

    void FreeCvodeMemory();

    void CvodeError(int flag, const char * msg);

    N_Vector mLastSolutionState;

    double mLastSolutionTime;

    bool mAutoReset;

protected:

    bool mUseAnalyticJacobian;

    double mRelTol;

    double mAbsTol;

    void* mpCvodeMem;

    long int mMaxSteps;

    double mLastInternalStepSize;

    void Init();

public:

    AbstractCvodeSystem(unsigned numberOfStateVariables);

    virtual ~AbstractCvodeSystem();

    virtual void EvaluateYDerivatives(realtype time,
                                      N_Vector y,
                                      N_Vector ydot)=0;

    void SetAutoReset(bool autoReset);

    void ResetSolver();

    OdeSolution Solve(realtype tStart,
                      realtype tEnd,
                      realtype maxDt,
                      realtype tSamp);

    void Solve(realtype tStart,
               realtype tEnd,
               realtype maxDt);

    void SetMaxSteps(long int numSteps);

    long int GetMaxSteps();

    void SetTolerances(double relTol=1e-5, double absTol=1e-7);

    double GetRelativeTolerance();

    double GetAbsoluteTolerance();

    double GetLastStepSize();


//    /**
//     * An alternative approach to stopping events; currently only useful with CVODE.
//     * CVODE can search for roots (zeros) of this function while solving the ODE system,
//     * and home in on them to find sign transitions to high precision.
//     *
//     * The default implementation here fakes a root function using CalculateStoppingEvent.
//     *
//     * @param time  the current time
//     * @param rY  the current values of the state variables
//     */
//    virtual double CalculateRootFunction(double time, const std::vector<double>& rY);
//
//    /**
//     * Get whether an analytic Jacobian is used.
//     *
//     * @return mUseAnalyticJacobian
//     */
//    bool GetUseAnalyticJacobian();

//    /**
//     * \todo move to AbstractParameterisedSystem? (1540)
//     *
//     * @return const reference to the state variables in the ODE system (used in archiving).
//     */
//    const std::vector<double>& rGetConstStateVariables() const;

};

//CLASS_IS_ABSTRACT(AbstractCvodeSystem)

#endif //_ABSTRACTCVODESYSTEM_HPP_
#endif // CHASTE_CVODE