AbstractCvodeSystem.hpp

/*

Copyright (c) 2005-2015, 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.

*/

#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>
#include <sundials/sundials_dense.h> /* definitions DlsMat DENSE_ELEM */

// CVODE changed their dense matrix type...
#if CHASTE_SUNDIALS_VERSION >= 20400
#define CHASTE_CVODE_DENSE_MATRIX DlsMat
#else
#define CHASTE_CVODE_DENSE_MATRIX DenseMat
#endif

class AbstractCvodeSystem : public AbstractParameterisedSystem<N_Vector>
{
private:
    friend class TestAbstractCvodeSystem;

    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;

        if (version >= 1u)
        {
            archive & mHasAnalyticJacobian;
        }

        // 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 & mForceReset;
        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;

        // This is pretty much what the code was saying before.
        mHasAnalyticJacobian = mUseAnalyticJacobian;
        if (version >= 1u)
        {   // Overwrite if it has been archived though
            archive & mHasAnalyticJacobian;
        }

        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 & mForceReset;
        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 mForceReset;

    bool mForceMinimalReset;

protected:

    bool mHasAnalyticJacobian;

    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,
                                      const N_Vector y,
                                      N_Vector ydot)=0;


    virtual void EvaluateAnalyticJacobian(long int N, realtype time, N_Vector y, N_Vector ydot,
                                          CHASTE_CVODE_DENSE_MATRIX jacobian,
                                          N_Vector tmp1, N_Vector tmp2, N_Vector tmp3)
    {
        EXCEPTION("No analytic Jacobian has been defined for this system.");
    }

    void SetForceReset(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();


    /* NB This needs making into a doxygen comment if you bring the method back in.
     *
     * 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);

    bool GetUseAnalyticJacobian() const;

    bool HasAnalyticJacobian() const;

    void ForceUseOfNumericalJacobian(bool useNumericalJacobian = true);

// The following method may be useful to identify problems with the Analytic Jacobians, if anything goes wrong,
// but #1795 seems to have got these working OK, so commented out for now.

//    /*
//     * Compare the calculated analytic jacobian to a numerical approximation, and throw if it looks silly.
//     *
//     * @param time  the current time
//     * @param y  the current state variables
//     * @param jacobian  the analytic jacobian matrix
//     * @param tmp1  working memory of the correct size provided by CVODE for temporary calculations
//     * @param tmp2  working memory of the correct size provided by CVODE for temporary calculations
//     * @param tmp3  working memory of the correct size provided by CVODE for temporary calculations
//     */
//    void CheckAnalyticJacobian(realtype time, N_Vector y, N_Vector ydot,
//                               CHASTE_CVODE_DENSE_MATRIX jacobian,
//                               N_Vector tmp1, N_Vector tmp2, N_Vector tmp3);

};

CLASS_IS_ABSTRACT(AbstractCvodeSystem)
 BOOST_CLASS_VERSION(AbstractCvodeSystem, 1u)

#endif //_ABSTRACTCVODESYSTEM_HPP_
#endif // CHASTE_CVODE