#include <cassert>
#include <vector>
#include <nvector/nvector_serial.h>

Include dependency graph for VectorHelperFunctions.hpp:

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Functions
template<typename VECTOR >
double	GetVectorComponent (const VECTOR &rVec, unsigned index)
template<typename VECTOR >
void	SetVectorComponent (VECTOR &rVec, unsigned index, double value)
template<typename VECTOR >
unsigned	GetVectorSize (const VECTOR &rVec)
template<typename VECTOR >
void	InitialiseEmptyVector (VECTOR &rVec)
template<typename VECTOR >
void	CreateVectorIfEmpty (VECTOR &rVec, unsigned size)
template<typename VECTOR >
VECTOR	CreateEmptyVector ()
template<typename VECTOR >
bool	IsEmptyVector (VECTOR &rVec)
template<typename VECTOR >
void	DeleteVector (VECTOR &rVec)
template<typename VECTOR >
VECTOR	CopyVector (VECTOR &rVec)
template<typename VECTOR >
void	CopyToStdVector (const VECTOR &rSrc, std::vector< double > &rDest)
template<typename VECTOR >
void	CopyFromStdVector (const std::vector< double > &rSrc, VECTOR &rDest)
template<>
double	GetVectorComponent (const std::vector< double > &rVec, unsigned index)
template<>
void	SetVectorComponent (std::vector< double > &rVec, unsigned index, double value)
template<>
unsigned	GetVectorSize (const std::vector< double > &rVec)
template<>
void	InitialiseEmptyVector (std::vector< double > &rVec)
template<>
void	CreateVectorIfEmpty (std::vector< double > &rVec, unsigned size)
template<>
std::vector< double >	CreateEmptyVector ()
template<>
bool	IsEmptyVector (std::vector< double > &rVec)
template<>
void	DeleteVector (std::vector< double > &rVec)
template<>
std::vector< double >	CopyVector (std::vector< double > &rVec)
template<>
void	CopyToStdVector (const std::vector< double > &rSrc, std::vector< double > &rDest)
template<>
void	CopyFromStdVector (const std::vector< double > &rSrc, std::vector< double > &rDest)
template<>
double	GetVectorComponent (const N_Vector &rVec, unsigned index)
template<>
void	SetVectorComponent (N_Vector &rVec, unsigned index, double value)
template<>
unsigned	GetVectorSize (const N_Vector &rVec)
template<>
void	InitialiseEmptyVector (N_Vector &rVec)
template<>
void	CreateVectorIfEmpty (N_Vector &rVec, unsigned size)
template<>
bool	IsEmptyVector (N_Vector &rVec)
template<>
void	DeleteVector (N_Vector &rVec)
template<>
N_Vector	CopyVector (N_Vector &rVec)
template<>
void	CopyToStdVector (const N_Vector &rSrc, std::vector< double > &rDest)
template<>
void	CopyFromStdVector (const std::vector< double > &rSrc, N_Vector &rDest)
std::vector< double >	MakeStdVec (N_Vector v)
N_Vector	MakeNVector (const std::vector< double > &rSrc)

Detailed Description

A selection of helper functions to be able to access std::vector<double> and CVODE's N_Vector types using the same interface. These are used by AbstractParameterisedSystem and some tests.

Definition in file VectorHelperFunctions.hpp.

Function Documentation

template<typename VECTOR >

void CopyFromStdVector	(	const std::vector< double > &	rSrc,
		VECTOR &	rDest
	)		`[inline]`

A helper function to copy a std::vector<double> into a VECTOR.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rSrc	source vector
rDest	destination vector; must exist and be the correct size

Referenced by AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), AbstractCvodeSystem::load(), MakeNVector(), and OdeSolution::rGetDerivedQuantities().

template<>

void CopyFromStdVector	(	const std::vector< double > &	rSrc,
		std::vector< double > &	rDest
	)		`[inline]`

Specialisation for std::vector<double>.

Parameters:

rSrc
rDest

Definition at line 293 of file VectorHelperFunctions.hpp.

template<>

void CopyFromStdVector	(	const std::vector< double > &	rSrc,
		N_Vector &	rDest
	)		`[inline]`

A helper function to copy a std::vector<double> into an N_Vector.

Parameters:

rSrc	source vector
rDest	destination vector; must exist and be the correct size

Definition at line 444 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

void CopyToStdVector	(	const VECTOR &	rSrc,
		std::vector< double > &	rDest
	)		`[inline]`

A helper function to copy a VECTOR into a std::vector<double>.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rSrc	source vector
rDest	destination vector; will be resized and filled

Referenced by AbstractCvodeCell::GetStdVecStateVariables(), MakeStdVec(), OdeSolution::rGetDerivedQuantities(), SteadyStateRunner::RunToSteadyStateImplementation(), and AbstractParameterisedSystem< VECTOR >::SetDefaultInitialConditions().

template<>

void CopyToStdVector	(	const std::vector< double > &	rSrc,
		std::vector< double > &	rDest
	)		`[inline]`

Specialisation for std::vector<double>.

Parameters:

rSrc
rDest

Definition at line 282 of file VectorHelperFunctions.hpp.

template<>

void CopyToStdVector	(	const N_Vector &	rSrc,
		std::vector< double > &	rDest
	)		`[inline]`

A helper function to copy an N_Vector into a std::vector<double>.

Parameters:

rSrc	source vector
rDest	destination vector; will be resized and filled

Definition at line 422 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

VECTOR CopyVector ( VECTOR & rVec ) [inline]

Helper function to create a fresh copy of a vector.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rVec	the vector to copy

Referenced by AbstractParameterisedSystem< VECTOR >::GetStateVariables().

template<>

std::vector<double> CopyVector ( std::vector< double > & rVec ) [inline]

Specialisation for std::vector<double>.

Parameters:

rVec

Definition at line 271 of file VectorHelperFunctions.hpp.

template<>

N_Vector CopyVector ( N_Vector & rVec ) [inline]

Specialisation for CVODE's N_Vector type.

Parameters:

rVec

Definition at line 400 of file VectorHelperFunctions.hpp.

template<>

N_Vector CreateEmptyVector ( ) [inline]

Specialisation for std::vector<double>.

Specialisation for CVODE's N_Vector type.

Definition at line 242 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

VECTOR CreateEmptyVector ( ) [inline]

Helper function to create a new empty/unset vector, useful for defining a default parameter value.

Returns:: a new vector

Specialisation for std::vector<double>.

Specialisation for CVODE's N_Vector type.

Definition at line 242 of file VectorHelperFunctions.hpp.

template<>

void CreateVectorIfEmpty	(	std::vector< double > &	rVec,
		unsigned	size
	)		`[inline]`

Specialisation for std::vector<double>.

Parameters:

rVec
size

Definition at line 230 of file VectorHelperFunctions.hpp.

template<>

void CreateVectorIfEmpty	(	N_Vector &	rVec,
		unsigned	size
	)		`[inline]`

Specialisation for CVODE's N_Vector type.

Parameters:

rVec
size

Definition at line 354 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

void CreateVectorIfEmpty	(	VECTOR &	rVec,
		unsigned	size
	)		`[inline]`

If the given vector is empty, set it to have a particular size, allocating memory if necessary. It is a no-op if the vector is non-empty.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rVec	the empty vector
size	the size to create it as

Referenced by AbstractParameterisedSystem< VECTOR >::CheckParametersOnLoad(), AbstractParameterisedSystem< VECTOR >::GetInitialConditions(), MakeNVector(), CvodeAdaptor::RecordStoppingPoint(), AbstractCvodeSystem::RecordStoppingPoint(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().

template<typename VECTOR >

void DeleteVector ( VECTOR & rVec ) [inline]

Helper function to delete a vector.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rVec	the vector

Referenced by AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), AbstractCvodeSystem::Init(), CvodeAdaptor::ResetSolver(), AbstractCvodeSystem::ResetSolver(), AbstractParameterisedSystem< VECTOR >::ResetToInitialConditions(), OdeSolution::rGetDerivedQuantities(), AbstractCvodeCell::SetStateVariables(), CvodeAdaptor::SetupCvode(), CvodeAdaptor::Solve(), AbstractCvodeSystem::~AbstractCvodeSystem(), and CvodeAdaptor::~CvodeAdaptor().

template<>

void DeleteVector ( std::vector< double > & rVec ) [inline]

Specialisation for std::vector<double>.

Parameters:

rVec

Definition at line 262 of file VectorHelperFunctions.hpp.

template<>

void DeleteVector ( N_Vector & rVec ) [inline]

Specialisation for CVODE's N_Vector type.

Parameters:

rVec

Definition at line 386 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

double GetVectorComponent	(	const VECTOR &	rVec,
		unsigned	index
	)		`[inline]`

Helper function to get a vector component.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rVec	the vector to access
index	the index of the component to get

Referenced by AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), AbstractParameterisedSystem< VECTOR >::GetParameter(), AbstractParameterisedSystem< VECTOR >::GetStateMessage(), AbstractParameterisedSystem< VECTOR >::GetStateVariable(), CvodeAdaptor::RecordStoppingPoint(), AbstractCvodeSystem::RecordStoppingPoint(), AbstractParameterisedSystem< VECTOR >::SetStateVariables(), CvodeAdaptor::SetupCvode(), and AbstractCvodeSystem::SetupCvode().

template<>

double GetVectorComponent	(	const N_Vector &	rVec,
		unsigned	index
	)		`[inline]`

Specialisation for CVODE's N_Vector type.

Parameters:

rVec
index

Definition at line 308 of file VectorHelperFunctions.hpp.

template<>

double GetVectorComponent	(	const std::vector< double > &	rVec,
		unsigned	index
	)		`[inline]`

Specialisation for std::vector<double>.

Parameters:

rVec
index

Definition at line 186 of file VectorHelperFunctions.hpp.

template<>

unsigned GetVectorSize ( const N_Vector & rVec ) [inline]

Specialisation for CVODE's N_Vector type.

Parameters:

rVec

Definition at line 332 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

unsigned GetVectorSize ( const VECTOR & rVec ) [inline]

Helper function to determine a vector's size.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rVec	the vector

Returns:: its size

Referenced by AbstractParameterisedSystem< VECTOR >::CheckParametersOnLoad(), AbstractParameterisedSystem< VECTOR >::GetAnyVariable(), AbstractParameterisedSystem< VECTOR >::GetParameter(), AbstractParameterisedSystem< VECTOR >::GetStateMessage(), CvodeAdaptor::RecordStoppingPoint(), AbstractParameterisedSystem< VECTOR >::SetAnyVariable(), AbstractParameterisedSystem< VECTOR >::SetDefaultInitialConditions(), AbstractParameterisedSystem< VECTOR >::SetParameter(), AbstractParameterisedSystem< VECTOR >::SetStateVariables(), and CvodeAdaptor::SetupCvode().

template<>

unsigned GetVectorSize ( const std::vector< double > & rVec ) [inline]

Specialisation for std::vector<double>.

Parameters:

rVec

Definition at line 210 of file VectorHelperFunctions.hpp.

template<>

void InitialiseEmptyVector ( std::vector< double > & rVec ) [inline]

Specialisation for std::vector<double>.

Parameters:

rVec

Definition at line 220 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

void InitialiseEmptyVector ( VECTOR & rVec ) [inline]

Helper function to initialise a vector to be empty/unset.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rVec	the vector

Referenced by AbstractParameterisedSystem< VECTOR >::AbstractParameterisedSystem(), and AbstractParameterisedSystem< VECTOR >::GetInitialConditions().

template<>

void InitialiseEmptyVector ( N_Vector & rVec ) [inline]

Specialisation for CVODE's N_Vector type.

Parameters:

rVec

Definition at line 343 of file VectorHelperFunctions.hpp.

template<>

bool IsEmptyVector ( N_Vector & rVec ) [inline]

Specialisation for CVODE's N_Vector type.

Parameters:

rVec

Definition at line 376 of file VectorHelperFunctions.hpp.

template<>

bool IsEmptyVector ( std::vector< double > & rVec ) [inline]

Specialisation for std::vector<double>.

Parameters:

rVec

Definition at line 252 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

bool IsEmptyVector ( VECTOR & rVec ) [inline]

Helper function to test whether a vector is empty/unset.

Parameters:

rVec	the vector

N_Vector MakeNVector ( const std::vector< double > & rSrc ) [inline]

Make an N_Vector from a standard vector

Parameters:

rSrc	a std::vector to copy the entries from

Returns:: an N_Vector of the entries from the std::vector.

Definition at line 480 of file VectorHelperFunctions.hpp.

References CopyFromStdVector(), and CreateVectorIfEmpty().

Referenced by AbstractCvodeCell::SetStateVariables().

std::vector<double> MakeStdVec ( N_Vector v ) [inline]

Make a standard vector from an N_Vector

Parameters:

v	A CVODE N_Vector to copy the entries from

Returns:: a std::vector of the entries of the N_Vector.

Definition at line 467 of file VectorHelperFunctions.hpp.

References CopyToStdVector().

Referenced by AbstractCvodeSystem::save(), and AbstractCvodeSystem::Solve().

template<>

void SetVectorComponent	(	std::vector< double > &	rVec,
		unsigned	index,
		double	value
	)		`[inline]`

Specialisation for std::vector<double>.

Parameters:

rVec
index
value

Definition at line 199 of file VectorHelperFunctions.hpp.

template<>

void SetVectorComponent	(	N_Vector &	rVec,
		unsigned	index,
		double	value
	)		`[inline]`

Specialisation for CVODE's N_Vector type.

Parameters:

rVec
index
value

Definition at line 321 of file VectorHelperFunctions.hpp.

template<typename VECTOR >

void SetVectorComponent	(	VECTOR &	rVec,
		unsigned	index,
		double	value
	)		`[inline]`

Helper function to set a vector component.

This isn't a member so that we can specialise it without having to specialise the whole class.

Parameters:

rVec	the vector to modify
index	the index of the component to set
value	the new value

Referenced by AbstractParameterisedSystem< VECTOR >::CheckParametersOnLoad(), CvodeAdaptor::RecordStoppingPoint(), AbstractCvodeSystem::RecordStoppingPoint(), AbstractParameterisedSystem< VECTOR >::SetAnyVariable(), AbstractParameterisedSystem< VECTOR >::SetParameter(), AbstractParameterisedSystem< VECTOR >::SetStateVariable(), and AbstractParameterisedSystem< VECTOR >::SetStateVariables().