AbstractCvodeSystem.hpp

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*/
 
#ifdef CHASTE_CVODE
#ifndef _ABSTRACTCVODESYSTEM_HPP_
#define _ABSTRACTCVODESYSTEM_HPP_
 
#include <algorithm>
#include <memory>
#include <string>
#include <vector>
 
// This is only needed to prevent compilation errors on PETSc 2.2/Boost 1.33.1 combo
#include "UblasVectorInclude.hpp"
 
// Chaste includes
#include "AbstractParameterisedSystem.hpp"
#include "CvodeContextManager.hpp"
#include "Exception.hpp"
#include "OdeSolution.hpp"
#include "VectorHelperFunctions.hpp"
 
// Serialiazation
#include <boost/serialization/split_member.hpp>
#include <boost/serialization/vector.hpp>
#include "ChasteSerialization.hpp"
#include "ClassIsAbstract.hpp"
 
// CVODE headers
#include <nvector/nvector_serial.h>
 
#if CHASTE_SUNDIALS_VERSION >= 30000
#if CHASTE_SUNDIALS_VERSION < 70000
#include <cvode/cvode_direct.h> /* access to CVDls interface            */
#endif
#include <sundials/sundials_types.h> /* defs. of realtype, sunindextype      */
#include <sunlinsol/sunlinsol_dense.h> /* access to dense SUNLinearSolver      */
#include <sunmatrix/sunmatrix_dense.h> /* access to dense SUNMatrix            */
#else
#include <sundials/sundials_dense.h> /* definitions DlsMat DENSE_ELEM */
#endif
 
// CVODE changed their dense matrix type...
#if CHASTE_SUNDIALS_VERSION >= 30000
#define CHASTE_CVODE_DENSE_MATRIX SUNMatrix
#elif CHASTE_SUNDIALS_VERSION >= 20400
#define CHASTE_CVODE_DENSE_MATRIX DlsMat
#else
#define CHASTE_CVODE_DENSE_MATRIX DenseMat
#endif
 
// CVODE changed their way of referencing elements of a matrix. So we will copy their notation in examples.
#if CHASTE_SUNDIALS_VERSION >= 30000
#define IJth(A, i, j) SM_ELEMENT_D(A, i, j)
#else
#define IJth(A, i, j) DENSE_ELEM(A, i, j)
#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, const double& rTime,
                    const double& rStartTime, const double& rEndTime);
 
    N_Vector mLastSolutionState;
 
    double mLastSolutionTime;
 
    bool mForceReset;
 
    bool mForceMinimalReset;
 
#if CHASTE_SUNDIALS_VERSION >= 30000
    SUNMatrix mpSundialsDenseMatrix;
    SUNLinearSolver mpSundialsLinearSolver;
#endif
 
protected:
    bool mHasAnalyticJacobian;
 
    bool mUseAnalyticJacobian;
 
    double mRelTol;
 
    double mAbsTol;
 
    void* mpCvodeMem;
 
#if CHASTE_SUNDIALS_VERSION >= 60000
    std::shared_ptr<CvodeContextManager> mpSundialsContextManager;
#endif
 
    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(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);
 
    bool GetMinimalReset();
 
    bool GetForceReset();
 
    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