AbstractCvodeSystem.hpp

/*

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*/

#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"
#include "VectorHelperFunctions.hpp"

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

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

class AbstractCvodeSystem : public AbstractParameterisedSystem<N_Vector>
{
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,
        // this doesn't hurt
        archive & mNumberOfStateVariables;
        archive & mUseAnalyticJacobian;

        // Convert from N_Vector to std::vector for serialization
        const std::vector<double> state_vars = MakeStdVec(mStateVariables);
        archive & state_vars;
        const std::vector<double> params = MakeStdVec(mParameters);
        archive & params;
        archive & rGetParameterNames();

        archive & mLastSolutionTime;
        archive & mAutoReset;
        archive & mForceMinimalReset;
        archive & mRelTol;
        archive & mAbsTol;
        archive & mMaxSteps;
        archive & mLastInternalStepSize;

        // We don't bother archiving CVODE's internal data, because it is missing then we'll just
        // get a new solver being initialised after a save/load.


        // 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;

        std::vector<double> state_vars;
        archive & state_vars;
        CopyFromStdVector(state_vars,mStateVariables);

        std::vector<double> parameters;
        archive & parameters;

        std::vector<std::string> param_names;
        archive & param_names;
        archive & mLastSolutionTime;
        archive & mAutoReset;
        archive & mForceMinimalReset;
        archive & mRelTol;
        archive & mAbsTol;
        archive & mMaxSteps;
        archive & mLastInternalStepSize;

        // We don't bother archiving CVODE's internal data, because it is missing then we'll just
        // get a new solver being initialised after a save/load.

        // Do some checking on the parameters
        CheckParametersOnLoad(parameters,param_names);
    }
    BOOST_SERIALIZATION_SPLIT_MEMBER()

    
    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;

    bool mForceMinimalReset;

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 SetMinimalReset(bool minimalReset);

    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();

};

CLASS_IS_ABSTRACT(AbstractCvodeSystem)

#endif //_ABSTRACTCVODESYSTEM_HPP_
#endif // CHASTE_CVODE