#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::OdeSolution ( )

Public constructor - ensures data is empty to start with.

Definition at line 49 of file OdeSolution.cpp.

Member Function Documentation

◆ CalculateDerivedQuantitiesAndParameters()

template<typename VECTOR >

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

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 138 of file OdeSolution.cpp.

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

◆ GetAnyVariable()

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 111 of file OdeSolution.cpp.

References GetVariableAtIndex(), and mpOdeSystemInformation.

◆ GetNumberOfTimeSteps()

unsigned OdeSolution::GetNumberOfTimeSteps ( ) const

Get the number of timesteps.

Returns: mNumberOfTimeSteps

Definition at line 56 of file OdeSolution.cpp.

References mNumberOfTimeSteps.

◆ GetSolverName()

std::string OdeSolution::GetSolverName ( )

inline

Returns: the ODE solver used to create these results

Definition at line 169 of file OdeSolution.hpp.

References mSolverName.

◆ GetVariableAtIndex()

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 75 of file OdeSolution.cpp.

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

Referenced by GetAnyVariable().

◆ rGetDerivedQuantities() [1/2]

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 179 of file OdeSolution.cpp.

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

◆ rGetDerivedQuantities() [2/2]

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 163 of file OdeSolution.cpp.

References mDerivedQuantities, mSolutions, and mTimes.

Referenced by CalculateDerivedQuantitiesAndParameters().

◆ rGetParameters()

template<typename VECTOR >

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

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 147 of file OdeSolution.cpp.

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

Referenced by CalculateDerivedQuantitiesAndParameters().

◆ rGetSolutions() [1/2]

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

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

Definition at line 126 of file OdeSolution.cpp.

References mSolutions.

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

◆ rGetSolutions() [2/2]

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 131 of file OdeSolution.cpp.

References mSolutions.

◆ rGetTimes() [1/2]

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

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

Definition at line 116 of file OdeSolution.cpp.

References mTimes.

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

◆ rGetTimes() [2/2]

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

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

Definition at line 121 of file OdeSolution.cpp.

References mTimes.

◆ SetNumberOfTimeSteps()

void OdeSolution::SetNumberOfTimeSteps ( unsigned numTimeSteps )

Set the number of timesteps.

Parameters

numTimeSteps the number of timesteps to use

Definition at line 62 of file OdeSolution.cpp.

References mNumberOfTimeSteps, mSolutions, and mTimes.

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

◆ SetOdeSystemInformation()

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 70 of file OdeSolution.cpp.

References mpOdeSystemInformation.

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

◆ SetSolverName()

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().

◆ WriteToFile()

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.

Definition at line 207 of file OdeSolution.cpp.

References ColumnDataWriter::AdvanceAlongUnlimitedDimension(), PetscTools::AmMaster(), ColumnDataWriter::Close(), ColumnDataWriter::DefineUnlimitedDimension(), ColumnDataWriter::DefineVariable(), ColumnDataWriter::EndDefineMode(), EXCEPTION, mDerivedQuantities, mParameters, mpOdeSystemInformation, mSolutions, mSolverName, mTimes, ColumnDataWriter::PutVariable(), and ColumnDataWriter::SetCommentForInfoFile().

Member Data Documentation

◆ mDerivedQuantities

std::vector<std::vector<double> > OdeSolution::mDerivedQuantities

private

Derived quantities at each timestep.

Definition at line 71 of file OdeSolution.hpp.

Referenced by GetVariableAtIndex(), rGetDerivedQuantities(), rGetDerivedQuantities(), and WriteToFile().

◆ mNumberOfTimeSteps

unsigned OdeSolution::mNumberOfTimeSteps

private

Variable for the number of timesteps.

Definition at line 62 of file OdeSolution.hpp.

Referenced by GetNumberOfTimeSteps(), and SetNumberOfTimeSteps().

◆ mParameters

std::vector<double> OdeSolution::mParameters

private

Parameters - these are currently assumed constant across all time

Definition at line 74 of file OdeSolution.hpp.

Referenced by GetVariableAtIndex(), rGetParameters(), and WriteToFile().

◆ mpOdeSystemInformation

boost::shared_ptr<const AbstractOdeSystemInformation> OdeSolution::mpOdeSystemInformation

private

Information about the concrete ODE system class.

Used to get names and units into the file output.

Definition at line 84 of file OdeSolution.hpp.

Referenced by CalculateDerivedQuantitiesAndParameters(), GetAnyVariable(), SetOdeSystemInformation(), and WriteToFile().

◆ mSolutions

std::vector<std::vector<double> > OdeSolution::mSolutions

private

Solutions for each variable at each timestep.

Definition at line 68 of file OdeSolution.hpp.

Referenced by GetVariableAtIndex(), rGetDerivedQuantities(), rGetDerivedQuantities(), rGetSolutions(), rGetSolutions(), SetNumberOfTimeSteps(), and WriteToFile().

◆ mSolverName

std::string OdeSolution::mSolverName

private

The ODE solver used to create these results

Definition at line 77 of file OdeSolution.hpp.

Referenced by GetSolverName(), SetSolverName(), and WriteToFile().

◆ mTimes

std::vector<double> OdeSolution::mTimes

private

A vector of times at each timestep.

Definition at line 65 of file OdeSolution.hpp.

Referenced by GetVariableAtIndex(), rGetDerivedQuantities(), rGetDerivedQuantities(), rGetTimes(), rGetTimes(), SetNumberOfTimeSteps(), and WriteToFile().

The documentation for this class was generated from the following files:

ode/src/common/OdeSolution.hpp
ode/src/common/OdeSolution.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OdeSolution()

Member Function Documentation

◆ CalculateDerivedQuantitiesAndParameters()

◆ GetAnyVariable()

◆ GetNumberOfTimeSteps()

◆ GetSolverName()

◆ GetVariableAtIndex()

◆ rGetDerivedQuantities() [1/2]

◆ rGetDerivedQuantities() [2/2]

◆ rGetParameters()

◆ rGetSolutions() [1/2]

◆ rGetSolutions() [2/2]

◆ rGetTimes() [1/2]

◆ rGetTimes() [2/2]

◆ SetNumberOfTimeSteps()

◆ SetOdeSystemInformation()

◆ SetSolverName()

◆ WriteToFile()

Member Data Documentation

◆ mDerivedQuantities

◆ mNumberOfTimeSteps

◆ mParameters

◆ mpOdeSystemInformation

◆ mSolutions

◆ mSolverName

◆ mTimes