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_