#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<>
N_Vector	CreateEmptyVector ()

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

◆ CopyFromStdVector() [1/3]

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 471 of file VectorHelperFunctions.hpp.

◆ CopyFromStdVector() [2/3]

template<>

void CopyFromStdVector	(	const std::vector< double > &	rSrc,
		std::vector< double > &	rDest
	)

inline

Specialisation for std::vector<double>.

Parameters

rSrc
rDest

Definition at line 310 of file VectorHelperFunctions.hpp.

◆ CopyFromStdVector() [3/3]

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 AbstractCvodeSystem::load(), MakeNVector(), and OdeSolution::rGetDerivedQuantities().

◆ CopyToStdVector() [1/3]

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 448 of file VectorHelperFunctions.hpp.

◆ CopyToStdVector() [2/3]

template<>

void CopyToStdVector	(	const std::vector< double > &	rSrc,
		std::vector< double > &	rDest
	)

inline

Specialisation for std::vector<double>.

Parameters

rSrc
rDest

Definition at line 299 of file VectorHelperFunctions.hpp.

◆ CopyToStdVector() [3/3]

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().

◆ CopyVector() [1/3]

template<>

N_Vector CopyVector ( N_Vector & rVec )

inline

Specialisation for CVODE's N_Vector type.

Parameters

rVec

Returns: copy

Definition at line 426 of file VectorHelperFunctions.hpp.

◆ CopyVector() [2/3]

template<>

std::vector< double > CopyVector ( std::vector< double > & rVec )

inline

Specialisation for std::vector<double>.

Parameters

rVec

Returns: copy

Definition at line 288 of file VectorHelperFunctions.hpp.

◆ CopyVector() [3/3]

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

Returns: A copy

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

◆ CreateEmptyVector() [1/3]

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

◆ CreateEmptyVector() [2/3]

template<>

std::vector< double > CreateEmptyVector ( )

inline

Specialisation for std::vector<double>.

Returns: empty vector

Definition at line 257 of file VectorHelperFunctions.hpp.

◆ CreateEmptyVector() [3/3]

template<>

N_Vector CreateEmptyVector ( )

inline

Specialisation for CVODE's N_Vector type.

Returns: empty vector

Definition at line 390 of file VectorHelperFunctions.hpp.

◆ CreateVectorIfEmpty() [1/3]

template<>

void CreateVectorIfEmpty	(	N_Vector &	rVec,
		unsigned	size
	)

inline

Specialisation for CVODE's N_Vector type.

Parameters

rVec
size

Definition at line 373 of file VectorHelperFunctions.hpp.

◆ CreateVectorIfEmpty() [2/3]

template<>

void CreateVectorIfEmpty	(	std::vector< double > &	rVec,
		unsigned	size
	)

inline

Specialisation for std::vector<double>.

Parameters

rVec
size

Definition at line 244 of file VectorHelperFunctions.hpp.

◆ CreateVectorIfEmpty() [3/3]

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(), MakeNVector(), AbstractCvodeSystem::RecordStoppingPoint(), and CvodeAdaptor::RecordStoppingPoint().

◆ DeleteVector() [1/3]

template<>

void DeleteVector ( N_Vector & rVec )

inline

Specialisation for CVODE's N_Vector type.

Parameters

rVec

Definition at line 411 of file VectorHelperFunctions.hpp.

◆ DeleteVector() [2/3]

template<>

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

inline

Specialisation for std::vector<double>.

Parameters

rVec

Definition at line 278 of file VectorHelperFunctions.hpp.

◆ DeleteVector() [3/3]

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 AbstractCvodeSystem::~AbstractCvodeSystem(), CvodeAdaptor::~CvodeAdaptor(), AbstractCvodeSystem::Init(), AbstractCvodeSystem::ResetSolver(), CvodeAdaptor::ResetSolver(), OdeSolution::rGetDerivedQuantities(), AbstractCvodeCell::SetStateVariables(), CvodeAdaptor::SetupCvode(), CvodeAdaptor::Solve(), and CvodeAdaptor::Solve().

◆ GetVectorComponent() [1/3]

template<>

double GetVectorComponent	(	const N_Vector &	rVec,
		unsigned	index
	)

inline

Specialisation for CVODE's N_Vector type.

Parameters

rVec
index

Returns: the vector component

Definition at line 326 of file VectorHelperFunctions.hpp.

◆ GetVectorComponent() [2/3]

template<>

double GetVectorComponent	(	const std::vector< double > &	rVec,
		unsigned	index
	)

inline

Specialisation for std::vector<double>.

Parameters

rVec
index

Returns: vector component

Definition at line 199 of file VectorHelperFunctions.hpp.

◆ GetVectorComponent() [3/3]

template<typename VECTOR >

double GetVectorComponent	(	const VECTOR &	rVec,
		unsigned	index
	)

inline

Returns: The vector component 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(), AbstractCvodeSystem::RecordStoppingPoint(), CvodeAdaptor::RecordStoppingPoint(), CvodeAdaptor::SetupCvode(), and AbstractCvodeSystem::SetupCvode().

◆ GetVectorSize() [1/3]

template<>

unsigned GetVectorSize ( const N_Vector & rVec )

inline

Specialisation for CVODE's N_Vector type.

Parameters

rVec

Returns: size

Definition at line 351 of file VectorHelperFunctions.hpp.

◆ GetVectorSize() [2/3]

template<>

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

inline

Specialisation for std::vector<double>.

Parameters

rVec

Returns: size

Definition at line 224 of file VectorHelperFunctions.hpp.

◆ GetVectorSize() [3/3]

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< N_Vector >::GetParameter(), AbstractParameterisedSystem< VECTOR >::GetParameter(), AbstractParameterisedSystem< VECTOR >::GetStateMessage(), CvodeAdaptor::RecordStoppingPoint(), AbstractParameterisedSystem< VECTOR >::SetAnyVariable(), AbstractParameterisedSystem< VECTOR >::SetDefaultInitialConditions(), AbstractParameterisedSystem< VECTOR >::SetStateVariables(), and CvodeAdaptor::SetupCvode().

◆ InitialiseEmptyVector() [1/3]

template<>

void InitialiseEmptyVector ( N_Vector & rVec )

inline

Specialisation for CVODE's N_Vector type.

Parameters

rVec

Definition at line 362 of file VectorHelperFunctions.hpp.

◆ InitialiseEmptyVector() [2/3]

template<>

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

inline

Specialisation for std::vector<double>.

Parameters

rVec

Definition at line 234 of file VectorHelperFunctions.hpp.

◆ InitialiseEmptyVector() [3/3]

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().

◆ IsEmptyVector() [1/3]

template<>

bool IsEmptyVector ( N_Vector & rVec )

inline

Specialisation for CVODE's N_Vector type.

Parameters

rVec

Returns: true if empty

Definition at line 401 of file VectorHelperFunctions.hpp.

◆ IsEmptyVector() [2/3]

template<>

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

inline

Specialisation for std::vector<double>.

Parameters

rVec

Returns: true if empty

Definition at line 268 of file VectorHelperFunctions.hpp.

◆ IsEmptyVector() [3/3]

template<typename VECTOR >

bool IsEmptyVector ( VECTOR & rVec )

inline

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

Parameters

rVec	the vector

Returns: true if empty

◆ MakeNVector()

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 507 of file VectorHelperFunctions.hpp.

References CopyFromStdVector(), and CreateVectorIfEmpty().

Referenced by AbstractCvodeCell::SetStateVariables().

◆ MakeStdVec()

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 494 of file VectorHelperFunctions.hpp.

References CopyToStdVector().

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

◆ SetVectorComponent() [1/3]

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 339 of file VectorHelperFunctions.hpp.

◆ SetVectorComponent() [2/3]

template<>

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

inline

Specialisation for std::vector<double>.

Parameters

rVec
index
value

Definition at line 212 of file VectorHelperFunctions.hpp.

◆ SetVectorComponent() [3/3]

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< N_Vector >::CheckParametersOnLoad(), AbstractParameterisedSystem< N_Vector >::GetParameter(), AbstractCvodeSystem::RecordStoppingPoint(), CvodeAdaptor::RecordStoppingPoint(), AbstractParameterisedSystem< VECTOR >::SetAnyVariable(), and AbstractParameterisedSystem< VECTOR >::SetParameter().