#include <Vessel.h>

Inheritance diagram for PLMD::vesselbase::Vessel:

[legend]

Public Member Functions
	Vessel (const VesselOptions &da)
	The constructor. More...

virtual	~Vessel ()
	Virtual destructor needed for proper inheritance. 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 std::string	description ()=0
	Return a description of the vessel contents. 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...

virtual bool	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. More...

virtual void	finish (const std::vector< double > &)=0
	Complete the calculation once the loop is finished. More...

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

virtual bool	applyForce (std::vector< double > &forces)=0
	Retrieve the forces on the quantities in the vessel. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)
	Reserve any keywords for this particular vessel. More...

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

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

const int	numlab
	The numerical label for this object. More...

ActionWithVessel *	action
	The action that this vessel is created within. More...

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

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

const PLMD::Keywords &	keywords
	The keywords. More...

bool	finished_read
	This just checks we have done checkRead. More...

Friends
class	ActionWithVessel

Constructor & Destructor Documentation

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

explicit

The constructor.

virtual PLMD::vesselbase::Vessel::~Vessel ( )

inlinevirtual

Virtual destructor needed for proper inheritance.

Member Function Documentation

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

pure virtual

Retrieve the forces on the quantities in the vessel.

Implemented in PLMD::vesselbase::StoreDataVessel, PLMD::vesselbase::BridgeVessel, PLMD::vesselbase::ValueVessel, PLMD::vesselbase::Moments, and PLMD::vesselbase::ShortcutVessel.

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

pure virtual

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

Implemented in PLMD::vesselbase::StoreDataVessel, PLMD::vesselbase::BridgeVessel, PLMD::vesselbase::FunctionVessel, PLMD::multicolvar::AdjacencyMatrixVessel, PLMD::crystallisation::GradientVessel, PLMD::vesselbase::OrderingVessel, PLMD::vesselbase::ShortcutVessel, PLMD::crystallization::VectorMean, PLMD::crystallization::VectorSum, and PLMD::mapping::SpathVessel.

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

Check that readin was fine.

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

pure virtual

Return a description of the vessel contents.

Implemented in PLMD::vesselbase::StoreDataVessel, PLMD::vesselbase::BridgeVessel, PLMD::vesselbase::ValueVessel, PLMD::vesselbase::Moments, and PLMD::vesselbase::ShortcutVessel.

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

protected

Report an error.

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

pure virtual

Complete the calculation once the loop is finished.

Implemented in PLMD::vesselbase::StoreDataVessel, PLMD::vesselbase::BridgeVessel, PLMD::vesselbase::FunctionVessel, PLMD::multicolvar::AdjacencyMatrixVessel, PLMD::crystallisation::GradientVessel, PLMD::vesselbase::Moments, PLMD::vesselbase::OrderingVessel, PLMD::vesselbase::ShortcutVessel, PLMD::crystallization::VectorMean, and PLMD::crystallization::VectorSum.

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

inlineprotected

Return a pointer to the action we are working in.

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

protected

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

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

Return the label.

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

Return the name.

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

inlineprotected

Return the value of the neighbor list tolerance.

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

inlineprotected

Return the numerical label.

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

inlineprotected

Return the value of the tolerance.

template<class T >

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

protected

Parse something from the input.

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

protected

Parse one keyword as boolean flag.

template<class T >

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

protected

Parse one keyword as std::vector.

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

inlinevirtual

Do something before the loop.

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

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

static

Reserve any keywords for this particular vessel.

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

pure virtual

Reset the size of the buffers.

Implemented in PLMD::vesselbase::StoreDataVessel, PLMD::vesselbase::FunctionVessel, PLMD::vesselbase::BridgeVessel, PLMD::crystallisation::GradientVessel, PLMD::vesselbase::Moments, PLMD::vesselbase::OrderingVessel, PLMD::vesselbase::ShortcutVessel, PLMD::crystallization::VectorMean, and PLMD::crystallization::VectorSum.

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

inlineprotected

Set the size of the data buffer.

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

inlinevirtual

Set the start of the buffer.

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

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

inlinevirtual

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 )

static

Convert the name to the label of the component.

Friends And Related Function Documentation

friend class ActionWithVessel

friend

Member Data Documentation

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

private

The action that this vessel is created within.

unsigned PLMD::vesselbase::Vessel::bufsize

private

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

unsigned PLMD::vesselbase::Vessel::bufstart

protected

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

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

protected

A copy of the communicator.

bool PLMD::vesselbase::Vessel::finished_read

private

This just checks we have done checkRead.

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

private

The keywords.

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

private

Directive line.

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

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

Reference to the log on which to output details.

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

private

The label for the vessel for referencing.

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

private

The keyword for the vessel in the input file.

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

private

The numerical label for this object.

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

vesselbase/Vessel.h
vesselbase/Vessel.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation