CvodeAdaptor.hpp

/*

Copyright (C) University of Oxford, 2005-2009

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 _CVODEADAPTOR_HPP_
#define _CVODEADAPTOR_HPP_

#include <boost/serialization/access.hpp>
#include <boost/serialization/base_object.hpp>

#include "AbstractIvpOdeSolver.hpp"
#include "OdeSolution.hpp"

// CVODE headers
#include <cvode/cvode.h>
#include <nvector/nvector_serial.h>
#include <sundials/sundials_nvector.h>
#include <cvode/cvode_dense.h>

// Needs to be included last
#include <boost/serialization/export.hpp>

int CvodeRhsAdaptor(realtype t, N_Vector y, N_Vector ydot, void *pData);

int CvodeRootAdaptor(realtype t, N_Vector y, realtype *pGOut, void *pData);

// /**
//  * Jacobian computation adaptor function.
//  *
//  * If solving an AbstractOdeSystemWithAnalyticJacobian, this function
//  * can be used to allow CVODE to compute the Jacobian analytically.
//  *
//  * Note to self: can test using pSystem->GetUseAnalyticJacobian().
//  */
// int CvodeDenseJacobianAdaptor(long int numberOfStateVariables, DenseMat J,
//                               realtype t, N_Vector y, N_Vector fy,
//                               void *pData,
//                               N_Vector tmp1, N_Vector tmp2, N_Vector tmp3);

void CvodeErrorHandler(int errorCode, const char *module, const char *function,
                       char *message, void *pData);


typedef struct CvodeData_ {
    std::vector<realtype>* pY;
    AbstractOdeSystem* pSystem;
} CvodeData;

class CvodeAdaptor : public AbstractIvpOdeSolver
{
private:
    friend class boost::serialization::access;
    template<class Archive>
    void serialize(Archive & archive, const unsigned int version)
    {
        // This calls serialize on the base class - all member variables instantiated on construction or temporary.
        archive & boost::serialization::base_object<AbstractIvpOdeSolver>(*this);
        archive & mRelTol;
        archive & mAbsTol;
        // All other member variables given values on each call.
    }

    void *mpCvodeMem;

    N_Vector mInitialValues;

    CvodeData mData;

    double mRelTol;

    double mAbsTol;

    double mLastInternalStepSize;

    long int mMaxSteps;

    bool mCheckForRoots;

protected:

    void SetupCvode(AbstractOdeSystem* pOdeSystem,
                    std::vector<double>& rInitialY,
                    double startTime, double maxStep);

    void FreeCvodeMemory();

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

public:

    CvodeAdaptor(double relTol=1e-4, double absTol=1e-6);

    void SetTolerances(double relTol=1e-4, double absTol=1e-6);

    double GetRelativeTolerance();

    double GetAbsoluteTolerance();

    double GetLastStepSize();

    OdeSolution Solve(AbstractOdeSystem* pOdeSystem,
                      std::vector<double>& rYValues,
                      double startTime,
                      double endTime,
                      double maxStep,
                      double timeSampling);

    void Solve(AbstractOdeSystem* pOdeSystem,
               std::vector<double>& rYValues,
               double startTime,
               double endTime,
               double maxStep);

    void CheckForStoppingEvents();

    void SetMaxSteps(long int numSteps);

    long int GetMaxSteps();

};

BOOST_CLASS_EXPORT(CvodeAdaptor);

#endif // _CVODEADAPTOR_HPP_
#endif // CHASTE_CVODE

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