#include <OrderingVessel.h>

Inheritance diagram for PLMD::vesselbase::OrderingVessel:

[legend]

Public Member Functions
	OrderingVessel (const VesselOptions &da)

void	resize ()
	Reset the size of the buffers. More...

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

void	finish (const std::vector< double > &buffer)
	Complete the calculation once the loop is finished. More...

virtual bool	compare (const double &, const double &)=0

std::string	description ()
	Return a description of the vessel contents. More...

virtual std::string	value_descriptor ()=0

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

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

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

void	checkRead ()
	Check that readin was fine. More...

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

virtual void	prepare ()
	Do something before the loop. More...

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

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

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

Public Attributes
Log &	log
	Reference to the log on which to output details. More...

Protected Member Functions
Value *	getFinalValue () const

void	setOutputValue (const double &val)
	Set the final value. More...

int	getNumericalLabel () const
	Return the numerical label. More...

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

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

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

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

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

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

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

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

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

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

Communicator &	comm
	A copy of the communicator. More...

Private Attributes
StoreDataVessel *	mydata

Constructor & Destructor Documentation

PLMD::vesselbase::OrderingVessel::OrderingVessel ( const VesselOptions & da )

explicit

Member Function Documentation

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

virtualinherited

Retrieve the forces on the quantities in the vessel.

Implements PLMD::vesselbase::Vessel.

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

inlinevirtual

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

Implements PLMD::vesselbase::Vessel.

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

inherited

Check that readin was fine.

virtual bool PLMD::vesselbase::OrderingVessel::compare	(	const double &	,
		const double &
	)

pure virtual

Implemented in PLMD::vesselbase::Highest, and PLMD::vesselbase::Lowest.

std::string PLMD::vesselbase::ValueVessel::description ( )

virtualinherited

Return a description of the vessel contents.

Implements PLMD::vesselbase::Vessel.

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

protectedinherited

Report an error.

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

virtual

Complete the calculation once the loop is finished.

Implements PLMD::vesselbase::Vessel.

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

inlineprotectedinherited

Return a pointer to the action we are working in.

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

protectedinherited

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

Value * PLMD::vesselbase::ValueVessel::getFinalValue ( ) const

inlineprotectedinherited

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

inherited

Return the label.

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

inherited

Return the name.

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

inlineprotectedinherited

Return the value of the neighbor list tolerance.

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

inlineprotectedinherited

Return the numerical label.

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

inlineprotectedinherited

Return the value of the tolerance.

template<class T >

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

protectedinherited

Parse something from the input.

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

protectedinherited

Parse one keyword as boolean flag.

template<class T >

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

protectedinherited

Parse one keyword as std::vector.

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

inlinevirtualinherited

Do something before the loop.

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

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

static

void PLMD::vesselbase::OrderingVessel::resize ( )

virtual

Reset the size of the buffers.

Implements PLMD::vesselbase::Vessel.

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

inlineprotectedinherited

Set the size of the data buffer.

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

inlinevirtualinherited

Set the start of the buffer.

Reimplemented in PLMD::vesselbase::BridgeVessel, and PLMD::multicolvar::AdjacencyMatrixVessel.

void PLMD::vesselbase::ValueVessel::setOutputValue ( const double & val )

inlineprotectedinherited

Set the final value.

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.

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

staticinherited

Convert the name to the label of the component.

virtual std::string PLMD::vesselbase::ValueVessel::value_descriptor ( )

pure virtualinherited

Implemented in PLMD::crystallisation::GradientVessel, PLMD::vesselbase::LessThan, PLMD::crystallization::VectorMean, PLMD::crystallization::VectorSum, PLMD::mapping::SpathVessel, PLMD::vesselbase::Between, PLMD::vesselbase::MoreThan, PLMD::mapping::ZpathVessel, PLMD::vesselbase::Max, PLMD::vesselbase::Min, PLMD::mapping::AltMin, PLMD::vesselbase::Mean, PLMD::vesselbase::Highest, PLMD::vesselbase::Lowest, and PLMD::vesselbase::Sum.

Member Data Documentation

unsigned PLMD::vesselbase::Vessel::bufstart

protectedinherited

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

Communicator& PLMD::vesselbase::Vessel::comm

protectedinherited

A copy of the communicator.

Log& PLMD::vesselbase::Vessel::log

inherited

Reference to the log on which to output details.

StoreDataVessel* PLMD::vesselbase::OrderingVessel::mydata

private

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

vesselbase/OrderingVessel.h
vesselbase/OrderingVessel.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation