OdeSolution Class Reference

#include <OdeSolution.hpp>

Collaboration diagram for OdeSolution:

Public Member Functions
	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)
std::string	GetSolverName ()
template<typename VECTOR >
void	CalculateDerivedQuantitiesAndParameters (AbstractParameterisedSystem< VECTOR > *pOdeSystem)
std::vector< std::vector < double > > &	rGetDerivedQuantities (AbstractParameterisedSystem< std::vector< double > > *pOdeSystem)
std::vector< std::vector < double > > &	rGetDerivedQuantities (AbstractParameterisedSystem< N_Vector > *pOdeSystem)
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)
Private Attributes
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

Detailed Description

A class that that stores the output data from solving a system of ODEs, and allows us to save it to file.

Definition at line 58 of file OdeSolution.hpp.

Constructor & Destructor Documentation

OdeSolution::OdeSolution ( )

Public constructor - ensures data is empty to start with.

Definition at line 45 of file OdeSolution.cpp.

Member Function Documentation

template<typename VECTOR >

void OdeSolution::CalculateDerivedQuantitiesAndParameters ( AbstractParameterisedSystem< VECTOR > * pOdeSystem ) [inline]

Calculate the derived quantities and store them and the current parameters for printing/accessing.

Parameters:

pOdeSystem

the ODE system which was solved to generate this solution object

Definition at line 134 of file OdeSolution.cpp.

References AbstractUntemplatedParameterisedSystem::GetSystemInformation(), mpOdeSystemInformation, rGetDerivedQuantities(), and rGetParameters().

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

Returns:: the values of a state variable, parameter or derived quantity with a given name in the ODE system for each output timestep.

Parameters:

rName

the name of the variable to extract

Definition at line 107 of file OdeSolution.cpp.

References GetVariableAtIndex(), and mpOdeSystemInformation.

unsigned OdeSolution::GetNumberOfTimeSteps ( ) const

Get the number of timesteps.

Returns:: mNumberOfTimeSteps

Definition at line 52 of file OdeSolution.cpp.

References mNumberOfTimeSteps.

std::string OdeSolution::GetSolverName ( ) [inline]

Returns:: the ODE solver used to create these results

Definition at line 169 of file OdeSolution.hpp.

References mSolverName.

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

Returns:: the values of a state variable, parameter or derived quantity with a given index in the ODE system at each output timestep. The index is that given by AbstractOdeSystemInformation::GetAnyVariableIndex, which for state variables (the most common case) is equal to their index within the state variable vector.

Parameters:

index

the index of the variable in the system

Definition at line 71 of file OdeSolution.cpp.

References EXCEPTION, mDerivedQuantities, mParameters, mSolutions, and mTimes.

Referenced by GetAnyVariable().

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

Returns:: the derived quantities for this ODE system at each timestep.

Parameters:

pOdeSystem

the ODE system which was solved to generate this solution object

Returns:: A std::vector of vectors of derived quantities for each time step.

Definition at line 175 of file OdeSolution.cpp.

References AbstractParameterisedSystem< VECTOR >::ComputeDerivedQuantities(), CopyFromStdVector(), CopyToStdVector(), DeleteVector(), AbstractUntemplatedParameterisedSystem::GetNumberOfDerivedQuantities(), mDerivedQuantities, mSolutions, and mTimes.

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

Returns:: the derived quantities for this ODE system at each timestep.

Parameters:

pOdeSystem

the ODE system which was solved to generate this solution object

Returns:: A vector of vectors of derived quantities for each time step.

Definition at line 159 of file OdeSolution.cpp.

References mDerivedQuantities, mSolutions, and mTimes.

Referenced by CalculateDerivedQuantitiesAndParameters().

template<typename VECTOR >

std::vector< double > & OdeSolution::rGetParameters ( AbstractParameterisedSystem< VECTOR > * pOdeSystem ) [inline]

This method currently assumes that mParameters is constant through time. This may not be the case when using modifiers.

Parameters:

pOdeSystem

The ODE system which was solved to generate this solution object.

Returns:: A vector of the current system parameters.

Definition at line 143 of file OdeSolution.cpp.

References AbstractUntemplatedParameterisedSystem::GetNumberOfParameters(), AbstractParameterisedSystem< VECTOR >::GetParameter(), and mParameters.

Referenced by CalculateDerivedQuantitiesAndParameters().

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

Returns:: the values of the solution to the ODE system at each timestep.; mSolutions.

Definition at line 127 of file OdeSolution.cpp.

References mSolutions.

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

Returns:: the values of the solution to the ODE system at each timestep.; mSolutions.

Definition at line 122 of file OdeSolution.cpp.

References mSolutions.

Referenced by AbstractRushLarsenCardiacCell::Compute(), AbstractGeneralizedRushLarsenCardiacCell::Compute(), AbstractBackwardEulerCardiacCell< 0u >::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::Compute(), RungeKuttaFehlbergIvpOdeSolver::InternalSolve(), CvodeAdaptor::Solve(), AbstractOneStepIvpOdeSolver::Solve(), and AbstractCvodeSystem::Solve().

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

Returns:: the times at which the solution to the ODE system is stored.; mTimes.

Definition at line 117 of file OdeSolution.cpp.

References mTimes.

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

Returns:: the times at which the solution to the ODE system is stored.; mTimes.

Definition at line 112 of file OdeSolution.cpp.

References mTimes.

Referenced by AbstractRushLarsenCardiacCell::Compute(), AbstractGeneralizedRushLarsenCardiacCell::Compute(), AbstractBackwardEulerCardiacCell< 0u >::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::Compute(), RungeKuttaFehlbergIvpOdeSolver::InternalSolve(), CvodeAdaptor::Solve(), AbstractOneStepIvpOdeSolver::Solve(), and AbstractCvodeSystem::Solve().

void OdeSolution::SetNumberOfTimeSteps ( unsigned numTimeSteps )

Set the number of timesteps.

Parameters:

numTimeSteps

the number of timesteps to use

Definition at line 58 of file OdeSolution.cpp.

References mNumberOfTimeSteps, mSolutions, and mTimes.

Referenced by AbstractRushLarsenCardiacCell::Compute(), AbstractGeneralizedRushLarsenCardiacCell::Compute(), AbstractBackwardEulerCardiacCell< 0u >::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::Compute(), RungeKuttaFehlbergIvpOdeSolver::InternalSolve(), CvodeAdaptor::Solve(), AbstractOneStepIvpOdeSolver::Solve(), and AbstractCvodeSystem::Solve().

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

Set the ODE system information

Parameters:

pOdeSystemInfo

ODE system information (used to get the names and units of variables).

Definition at line 66 of file OdeSolution.cpp.

References mpOdeSystemInformation.

Referenced by AbstractRushLarsenCardiacCell::Compute(), AbstractGeneralizedRushLarsenCardiacCell::Compute(), AbstractBackwardEulerCardiacCell< 0u >::Compute(), AbstractBackwardEulerCardiacCell< SIZE >::Compute(), CvodeAdaptor::Solve(), AbstractOneStepIvpOdeSolver::Solve(), and AbstractCvodeSystem::Solve().

void OdeSolution::SetSolverName ( std::string solverName ) [inline]

Set the ODE solver used to create these results

Parameters:

solverName

solver used

Definition at line 163 of file OdeSolution.hpp.

References mSolverName.

Referenced by AbstractOneStepIvpOdeSolver::Solve().

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

Write the data to a file.

Parameters:

	directoryName	the directory in which to write the data to file
	baseResultsFilename	the name of the file in which to write the data
	timeUnits	name of the units of time used
	stepsPerRow	the solution to the ODE system is written to file every this number of timesteps (defaults to 1)
	cleanDirectory	whether to clean the directory (defaults to true)
	precision	the precision with which to write the data (i.e. exactly how many digits to display after the decimal point). Defaults to 8. Must be between 2 and 20 (inclusive).
	includeDerivedQuantities	whether to include parameters and derived quantities in the output.