OdeSolution.hpp

/*

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*/


#ifndef _ODESOLUTION_HPP_
#define _ODESOLUTION_HPP_

#include <vector>
#include <string>
#include <cassert>
#include <boost/shared_ptr.hpp>

#include "AbstractOdeSystemInformation.hpp"
#include "AbstractParameterisedSystem.hpp"

#ifdef CHASTE_CVODE
// CVODE headers
#include <nvector/nvector_serial.h>
#endif // CHASTE_CVODE

class AbstractOdeSystem; // Avoid cyclic include issues

class OdeSolution
{
private:
    unsigned mNumberOfTimeSteps;

    std::vector<double> mTimes;

    std::vector<std::vector<double> > mSolutions;

    std::vector<std::vector<double> > mDerivedQuantities;

    std::vector<double> mParameters;

    std::string mSolverName;

    boost::shared_ptr<const AbstractOdeSystemInformation> mpOdeSystemInformation;

public:
    OdeSolution();

    unsigned GetNumberOfTimeSteps() const;

    void SetNumberOfTimeSteps(unsigned numTimeSteps);

    void SetOdeSystemInformation(boost::shared_ptr<const AbstractOdeSystemInformation> pOdeSystemInfo);

    std::vector<double> GetVariableAtIndex(unsigned index) const;

    std::vector<double> GetAnyVariable(const std::string& rName) const;

    std::vector<double>& rGetTimes();

    const std::vector<double>& rGetTimes() const;

    std::vector<std::vector<double> >& rGetSolutions();

    const std::vector<std::vector<double> >& rGetSolutions() const;


    void SetSolverName(std::string solverName)
    {
        mSolverName = solverName;
    }

    std::string GetSolverName()
    {
        return mSolverName;
    }

    template<typename VECTOR>
    void CalculateDerivedQuantitiesAndParameters(AbstractParameterisedSystem<VECTOR>* pOdeSystem);

    std::vector<std::vector<double> >& rGetDerivedQuantities(AbstractParameterisedSystem<std::vector<double> >* pOdeSystem);

#ifdef CHASTE_CVODE

    std::vector<std::vector<double> >& rGetDerivedQuantities(AbstractParameterisedSystem<N_Vector>* pOdeSystem);
#endif //CHASTE_CVODE

    template<typename VECTOR>
    std::vector<double>& rGetParameters(AbstractParameterisedSystem<VECTOR>* pOdeSystem);

    void WriteToFile(std::string directoryName,
                     std::string baseResultsFilename,
                     std::string timeUnits,
                     unsigned stepsPerRow=1,
                     bool cleanDirectory=true,
                     unsigned precision=8,
                     bool includeDerivedQuantities=false);
};


#endif //_ODESOLUTION_HPP_