#include <AveragingVessel.h>

Inheritance diagram for PLMD::vesselbase::AveragingVessel:

Public Member Functions
	AveragingVessel (const vesselbase::VesselOptions &)
	Constructor.

bool	applyForce (std::vector< double > &forces) override
	Retrieve the forces on the quantities in the vessel.

virtual void	calculate (const unsigned &current, MultiValue &myvals, std::vector< double > &buffer, std::vector< unsigned > &der_list) const =0
	Calculate the part of the vessel that is done in the loop.

void	checkRead ()
	Check that readin was fine.

virtual void	clear ()
	Clear all the data stored on the grid.

virtual std::string	description ()=0
	Return a description of the vessel contents.

void	finish (const std::vector< double > &) override
	Copy data from an accumulated buffer into the grid.

std::string	getLabel () const
	Return the label.

std::string	getName () const
	Return the name.

double	getNorm () const

virtual void	prepare ()
	Do something before the loop.

virtual void	reset ()
	Reset the grid so that it is cleared at start of next time it is calculated.

virtual void	resize ()=0
	Reset the size of the buffers.

virtual void	setBufferStart (unsigned &start)
	Set the start of the buffer.

void	setNorm (const double &snorm)
	Functions for dealing with normalisation constant.

virtual MultiValue &	transformDerivatives (const unsigned &current, MultiValue &myvals, MultiValue &bvals)
	This is replaced in bridges so we can transform the derivatives.

bool	wasreset () const
	Was the grid cleared on the last step.

Static Public Member Functions
static void	registerKeywords (Keywords &keys)
	keywords

static std::string	transformName (const std::string &name)
	Convert the name to the label of the component.

Protected Member Functions
void	addDataElement (const unsigned &myelem, const double &value)
	Add some value to an element of the data array.

void	error (const std::string &errmsg)
	Report an error.

ActionWithVessel *	getAction () const
	Return a pointer to the action we are working in.

std::string	getAllInput ()
	This returns the whole input line (it is used for less_than/more_than/between)

double	getDataElement (const unsigned &myelem) const
	Get the value of one of the data element.

double	getNLTolerance () const
	Return the value of the neighbor list tolerance.

int	getNumericalLabel () const
	Return the numerical label.

unsigned	getSizeOfBuffer () const
	Return the size of the buffer.

double	getTolerance () const
	Return the value of the tolerance.

bool	noAverage () const
	Are we averaging the data.

template<class T>
void	parse (const std::string &key, T &t)
	Parse something from the input.

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag.

template<class T>
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector.

void	resizeBuffer (const unsigned &n)
	Set the size of the data buffer.

void	setDataElement (const unsigned &myelem, const double &value)
	Set an element of the data array.

void	setDataSize (const unsigned &size)
	Set the size of the data vector.

Protected Attributes
unsigned	bufstart
	The start of this Vessel's buffer in buffer in the underlying ActionWithVessel.

Private Attributes
ActionWithVessel *	action
	The action that this vessel is created within.

unsigned	bufsize
	The number of elements in this vessel's buffered data.

std::vector< double >	data
	The data that is being averaged.

bool	finished_read
	This just checks we have done checkRead.

const PLMD::Keywords &	keywords
	The keywords.

std::vector< std::string >	line
	Directive line.

std::string	mylabel
	The label for the vessel for referencing.

std::string	myname
	The keyword for the vessel in the input file.

const int	numlab
	The numerical label for this object.

bool	unormalised
	Are we outputting unormalised data.

bool	wascleared
	The grid was recently cleared and bounds can be set.

Constructor & Destructor Documentation

◆ AveragingVessel()

PLMD::vesselbase::AveragingVessel::AveragingVessel ( const vesselbase::VesselOptions & vo )

explicit

Constructor.

Member Function Documentation

◆ addDataElement()

void PLMD::vesselbase::AveragingVessel::addDataElement	(	const unsigned &	myelem,
		const double &	value )

inlineprotected

Add some value to an element of the data array.

◆ applyForce()

bool PLMD::vesselbase::AveragingVessel::applyForce ( std::vector< double > & forces )

inlineoverridevirtual

Retrieve the forces on the quantities in the vessel.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::gridtools::GridVessel.

◆ calculate()

virtual void PLMD::vesselbase::Vessel::calculate	(	const unsigned &	current,
		MultiValue &	myvals,
		std::vector< double > &	buffer,
		std::vector< unsigned > &	der_list ) const

pure virtualinherited

Calculate the part of the vessel that is done in the loop.

Implemented in PLMD::analysis::AverageVessel, PLMD::crystallization::GradientVessel, PLMD::crystallization::VectorMean, PLMD::crystallization::VectorSum, PLMD::gridtools::GridVessel, PLMD::gridtools::HistogramOnGrid, PLMD::mapping::SpathVessel, PLMD::vesselbase::BridgeVessel, PLMD::vesselbase::FunctionVessel, PLMD::vesselbase::Moments, PLMD::vesselbase::OrderingVessel, PLMD::vesselbase::ShortcutVessel, and PLMD::vesselbase::StoreDataVessel.

◆ checkRead()

void PLMD::vesselbase::Vessel::checkRead ( )

inherited

Check that readin was fine.

◆ clear()

void PLMD::vesselbase::AveragingVessel::clear ( )

virtual

Clear all the data stored on the grid.

◆ description()

virtual std::string PLMD::vesselbase::Vessel::description ( )

pure virtualinherited

Return a description of the vessel contents.

Implemented in PLMD::analysis::AverageVessel, PLMD::gridtools::GridVessel, PLMD::mapping::TrigonometricPathVessel, PLMD::vesselbase::BridgeVessel, PLMD::vesselbase::Moments, PLMD::vesselbase::ShortcutVessel, PLMD::vesselbase::StoreDataVessel, and PLMD::vesselbase::ValueVessel.

◆ error()

void PLMD::vesselbase::Vessel::error ( const std::string & errmsg )

protectedinherited

Report an error.

◆ finish()

void PLMD::vesselbase::AveragingVessel::finish ( const std::vector< double > & buffer )

overridevirtual

Copy data from an accumulated buffer into the grid.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::gridtools::GridVessel, and PLMD::gridtools::HistogramOnGrid.

◆ getAction()

ActionWithVessel * PLMD::vesselbase::Vessel::getAction ( ) const

inlineprotectedinherited

Return a pointer to the action we are working in.

◆ getAllInput()

std::string PLMD::vesselbase::Vessel::getAllInput ( )

protectedinherited

This returns the whole input line (it is used for less_than/more_than/between)

◆ getDataElement()

double PLMD::vesselbase::AveragingVessel::getDataElement ( const unsigned & myelem ) const

inlineprotected

Get the value of one of the data element.

◆ getLabel()

std::string PLMD::vesselbase::Vessel::getLabel ( ) const

inherited

Return the label.

◆ getName()

std::string PLMD::vesselbase::Vessel::getName ( ) const

inherited

Return the name.

◆ getNLTolerance()

double PLMD::vesselbase::Vessel::getNLTolerance ( ) const

inlineprotectedinherited

Return the value of the neighbor list tolerance.

◆ getNorm()

double PLMD::vesselbase::AveragingVessel::getNorm ( ) const

inline

◆ getNumericalLabel()

int PLMD::vesselbase::Vessel::getNumericalLabel ( ) const

inlineprotectedinherited

Return the numerical label.

◆ getSizeOfBuffer()

unsigned PLMD::vesselbase::Vessel::getSizeOfBuffer ( ) const

inlineprotectedinherited

Return the size of the buffer.

◆ getTolerance()

double PLMD::vesselbase::Vessel::getTolerance ( ) const

inlineprotectedinherited

Return the value of the tolerance.

◆ noAverage()

bool PLMD::vesselbase::AveragingVessel::noAverage ( ) const

inlineprotected

Are we averaging the data.

◆ parse()

template<class T>

void PLMD::vesselbase::Vessel::parse	(	const std::string &	key,
		T &	t )

protectedinherited

Parse something from the input.

◆ parseFlag()

void PLMD::vesselbase::Vessel::parseFlag	(	const std::string &	key,
		bool &	t )

protectedinherited

Parse one keyword as boolean flag.

◆ parseVector()

template<class T>

void PLMD::vesselbase::Vessel::parseVector	(	const std::string &	key,
		std::vector< T > &	t )

protectedinherited

Parse one keyword as std::vector.

◆ prepare()

virtual void PLMD::vesselbase::Vessel::prepare ( )

inlinevirtualinherited

Do something before the loop.

Reimplemented in PLMD::mapping::SpathVessel, and PLMD::vesselbase::BridgeVessel.

◆ registerKeywords()

void PLMD::vesselbase::AveragingVessel::registerKeywords ( Keywords & keys )

static

keywords

◆ reset()

void PLMD::vesselbase::AveragingVessel::reset ( )

virtual

Reset the grid so that it is cleared at start of next time it is calculated.

◆ resize()

virtual void PLMD::vesselbase::Vessel::resize ( )

pure virtualinherited

Reset the size of the buffers.

Implemented in PLMD::analysis::AverageVessel, PLMD::crystallization::GradientVessel, PLMD::crystallization::VectorMean, PLMD::crystallization::VectorSum, PLMD::gridtools::GridVessel, PLMD::mapping::TrigonometricPathVessel, PLMD::vesselbase::BridgeVessel, PLMD::vesselbase::FunctionVessel, PLMD::vesselbase::Moments, PLMD::vesselbase::OrderingVessel, PLMD::vesselbase::ShortcutVessel, and PLMD::vesselbase::StoreDataVessel.

◆ resizeBuffer()

void PLMD::vesselbase::Vessel::resizeBuffer ( const unsigned & n )

inlineprotectedinherited

Set the size of the data buffer.

◆ setBufferStart()

void PLMD::vesselbase::Vessel::setBufferStart ( unsigned & start )

inlinevirtualinherited

Set the start of the buffer.

Reimplemented in PLMD::vesselbase::BridgeVessel.

◆ setDataElement()

void PLMD::vesselbase::AveragingVessel::setDataElement	(	const unsigned &	myelem,
		const double &	value )

inlineprotected

Set an element of the data array.

◆ setDataSize()

void PLMD::vesselbase::AveragingVessel::setDataSize ( const unsigned & size )

protected

Set the size of the data vector.

◆ setNorm()

void PLMD::vesselbase::AveragingVessel::setNorm ( const double & snorm )

inline

Functions for dealing with normalisation constant.

◆ transformDerivatives()

MultiValue & PLMD::vesselbase::Vessel::transformDerivatives	(	const unsigned &	current,
		MultiValue &	myvals,
		MultiValue &	bvals )

inlinevirtualinherited

This is replaced in bridges so we can transform the derivatives.

Reimplemented in PLMD::vesselbase::BridgeVessel.

◆ transformName()

std::string PLMD::vesselbase::Vessel::transformName ( const std::string & name )

staticinherited

Convert the name to the label of the component.

◆ wasreset()

bool PLMD::vesselbase::AveragingVessel::wasreset ( ) const

Was the grid cleared on the last step.

Member Data Documentation

◆ action

ActionWithVessel* PLMD::vesselbase::Vessel::action

privateinherited

The action that this vessel is created within.

◆ bufsize

unsigned PLMD::vesselbase::Vessel::bufsize

privateinherited

The number of elements in this vessel's buffered data.

◆ bufstart

unsigned PLMD::vesselbase::Vessel::bufstart

protectedinherited

The start of this Vessel's buffer in buffer in the underlying ActionWithVessel.

◆ data

std::vector<double> PLMD::vesselbase::AveragingVessel::data

private

The data that is being averaged.

◆ finished_read

bool PLMD::vesselbase::Vessel::finished_read

privateinherited

This just checks we have done checkRead.

◆ keywords

const PLMD::Keywords& PLMD::vesselbase::Vessel::keywords

privateinherited

The keywords.

◆ line

std::vector<std::string> PLMD::vesselbase::Vessel::line

privateinherited

Directive line.

This line is progressively erased during vessel construction so as to check if all the present keywords are correct.

◆ mylabel

std::string PLMD::vesselbase::Vessel::mylabel

privateinherited

The label for the vessel for referencing.

◆ myname

std::string PLMD::vesselbase::Vessel::myname

privateinherited

The keyword for the vessel in the input file.

◆ numlab

const int PLMD::vesselbase::Vessel::numlab

privateinherited

The numerical label for this object.

◆ unormalised

bool PLMD::vesselbase::AveragingVessel::unormalised

private

Are we outputting unormalised data.

◆ wascleared

bool PLMD::vesselbase::AveragingVessel::wascleared

private

The grid was recently cleared and bounds can be set.

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

vesselbase/AveragingVessel.h
vesselbase/AveragingVessel.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Constructor & Destructor Documentation

◆ AveragingVessel()

Member Function Documentation

◆ addDataElement()

◆ applyForce()

◆ calculate()

◆ checkRead()

◆ clear()

◆ description()

◆ error()

◆ finish()

◆ getAction()

◆ getAllInput()

◆ getDataElement()

◆ getLabel()

◆ getName()

◆ getNLTolerance()

◆ getNorm()

◆ getNumericalLabel()

◆ getSizeOfBuffer()

◆ getTolerance()

◆ noAverage()

◆ parse()

◆ parseFlag()

◆ parseVector()

◆ prepare()

◆ registerKeywords()

◆ reset()

◆ resize()

◆ resizeBuffer()

◆ setBufferStart()

◆ setDataElement()

◆ setDataSize()

◆ setNorm()

◆ transformDerivatives()

◆ transformName()

◆ wasreset()

Member Data Documentation

◆ action

◆ bufsize

◆ bufstart

◆ data

◆ finished_read

◆ keywords

◆ line

◆ mylabel

◆ myname

◆ numlab

◆ unormalised

◆ wascleared