CvodeAdaptor.hpp

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*/
 
#ifdef CHASTE_CVODE
#ifndef _CVODEADAPTOR_HPP_
#define _CVODEADAPTOR_HPP_
 
#include <memory>
#include <vector>
 
#include <boost/serialization/base_object.hpp>
#include "ChasteSerialization.hpp"
 
#include "AbstractIvpOdeSolver.hpp"
#include "CvodeContextManager.hpp"
#include "OdeSolution.hpp"
 
// CVODE headers
#include <cvode/cvode.h>
#include <nvector/nvector_serial.h>
 
#if CHASTE_SUNDIALS_VERSION >= 30000
#include <sunlinsol/sunlinsol_dense.h> /* access to dense SUNLinearSolver      */
#include <sunmatrix/sunmatrix_dense.h> /* access to dense SUNMatrix            */
#endif
 
#if CHASTE_SUNDIALS_VERSION >= 70000
#define realtype sunrealtype
#endif
 
#if CHASTE_SUNDIALS_VERSION >= 70000
void CvodeErrorHandler(int errorCode, const char* module, const char* function,
                       const char* message, SUNErrCode errCode, void* pData, SUNContext sunContext);
#else
void CvodeErrorHandler(int errorCode, const char* module, const char* function,
                       char* message, void* pData);
#endif
// Note: declared here since it's also used by AbstractCvodeCell.
 
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)
    {
        archive& boost::serialization::base_object<AbstractIvpOdeSolver>(*this);
        archive& mRelTol;
        archive& mAbsTol;
        archive& mLastInternalStepSize;
        archive& mMaxSteps;
        archive& mCheckForRoots;
        // All other member variables given values on each call.
    }
 
    void* mpCvodeMem;
 
#if CHASTE_SUNDIALS_VERSION >= 60000
    std::shared_ptr<CvodeContextManager> mpSundialsContextManager;
#endif
 
    CvodeData mData;
 
    double mRelTol;
 
    double mAbsTol;
 
    double mLastInternalStepSize;
 
    long int mMaxSteps;
 
    bool mCheckForRoots;
 
    N_Vector mLastSolutionState;
 
    double mLastSolutionTime;
 
    bool mForceReset;
 
    bool mForceMinimalReset;
 
#if CHASTE_SUNDIALS_VERSION >= 30000
    SUNMatrix mpSundialsDenseMatrix;
    SUNLinearSolver mpSundialsLinearSolver;
#endif
 
    void RecordStoppingPoint(double stopTime, N_Vector yEnd);
 
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);
 
    ~CvodeAdaptor();
 
    void SetTolerances(double relTol = 1e-4, double absTol = 1e-6);
 
    double GetRelativeTolerance();
 
    double GetAbsoluteTolerance();
 
    double GetLastStepSize();
 
    void SetForceReset(bool autoReset);
 
    void SetMinimalReset(bool minimalReset);
 
    void ResetSolver();
 
    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();
};
 
#include "SerializationExportWrapper.hpp"
CHASTE_CLASS_EXPORT(CvodeAdaptor)
 
#endif // _CVODEADAPTOR_HPP_
#endif // CHASTE_CVODE