#include <Vessel.h>

Inheritance diagram for PLMD::vesselbase::Vessel:

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...

void	zero ()
	Set all the buffer elements to zero. More...

void	addToBufferElement (const unsigned &i, const double &val)
	Add something to the ith element in the buffer. More...

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

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

virtual bool	calculate ()=0
	Calculate the part of the vessel that is done in the loop. More...

virtual void	finish ()=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...

virtual unsigned	getNumberOfTerms ()=0
	Retrieve the number of terms we need to accumulate. More...

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

void	setBufferElement (const unsigned &i, const double &val)
	Set the value of the ith element in the buffer. More...

double	getBufferElement (const unsigned &i) const
	Get the value in the ith element of the buffer. More...

void	stashBuffers ()
	Store everything that is the buffers. More...

void	setBufferFromStash ()
	Add the contents of the stash to the buffer. More...

Protected Attributes
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...

std::vector< double >	stash
	Something to store the buffer if this is required. More...

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

Detailed Description

Definition at line 75 of file Vessel.h.

Constructor & Destructor Documentation

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

The constructor.

Definition at line 57 of file Vessel.cpp.

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

inlinevirtual

Virtual destructor needed for proper inheritance.

Definition at line 141 of file Vessel.h.

Member Function Documentation

void PLMD::vesselbase::Vessel::addToBufferElement	(	const unsigned &	i,
		const double &	val
	)

inline

Add something to the ith element in the buffer.

Definition at line 252 of file Vessel.h.

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::FunctionVessel, PLMD::vesselbase::BridgeVessel, PLMD::multicolvar::StoreCentralAtomsVessel, PLMD::vesselbase::ShortcutVessel, and PLMD::multicolvar::Moments.

virtual bool PLMD::vesselbase::Vessel::calculate ( )

pure virtual

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

Implemented in PLMD::multicolvar::StoreColvarVessel, PLMD::vesselbase::BridgeVessel, PLMD::multicolvar::StoreCentralAtomsVessel, PLMD::multicolvar::DHEnergy, PLMD::vesselbase::ShortcutVessel, PLMD::vesselbase::Between, PLMD::vesselbase::MoreThan, PLMD::vesselbase::LessThan, PLMD::vesselbase::Min, PLMD::vesselbase::Mean, and PLMD::vesselbase::Sum.

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

Check that readin was fine.

Definition at line 111 of file Vessel.cpp.

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

pure virtual

Return a description of the vessel contents.

Implemented in PLMD::vesselbase::FunctionVessel, PLMD::vesselbase::BridgeVessel, PLMD::multicolvar::StoreCentralAtomsVessel, PLMD::multicolvar::Moments, and PLMD::vesselbase::ShortcutVessel.

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

protected

Report an error.

Definition at line 122 of file Vessel.cpp.

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

pure virtual

Complete the calculation once the loop is finished.

Implemented in PLMD::multicolvar::StoreColvarVessel, PLMD::vesselbase::BridgeVessel, PLMD::multicolvar::StoreCentralAtomsVessel, PLMD::multicolvar::DHEnergy, PLMD::vesselbase::ShortcutVessel, PLMD::vesselbase::Between, PLMD::vesselbase::MoreThan, PLMD::vesselbase::LessThan, PLMD::vesselbase::Min, PLMD::vesselbase::Mean, and PLMD::vesselbase::Sum.

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

inlineprotected

Return a pointer to the action we are working in.

Definition at line 236 of file Vessel.h.

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

protected

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

Definition at line 84 of file Vessel.cpp.

double PLMD::vesselbase::Vessel::getBufferElement ( const unsigned & i ) const

inlineprotected

Get the value in the ith element of the buffer.

Definition at line 258 of file Vessel.h.

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

Return the label.

Definition at line 80 of file Vessel.cpp.

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

Return the name.

Definition at line 76 of file Vessel.cpp.

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

inlineprotected

Return the value of the neighbor list tolerance.

Definition at line 231 of file Vessel.h.

virtual unsigned PLMD::vesselbase::Vessel::getNumberOfTerms ( )

pure virtual

Retrieve the number of terms we need to accumulate.

Implemented in PLMD::vesselbase::FunctionVessel, PLMD::multicolvar::StoreColvarVessel, PLMD::vesselbase::BridgeVessel, PLMD::multicolvar::StoreCentralAtomsVessel, and PLMD::vesselbase::ShortcutVessel.

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

inlineprotected

Return the numerical label.

Definition at line 216 of file Vessel.h.

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

inlineprotected

Return the value of the tolerance.

Definition at line 226 of file Vessel.h.

template<class T >

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

protected

Parse something from the input.

Definition at line 169 of file Vessel.h.

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

protected

Parse one keyword as boolean flag.

Definition at line 93 of file Vessel.cpp.

template<class T >

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

protected

Parse one keyword as std::vector.

Definition at line 184 of file Vessel.h.

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

inlinevirtual

Do something before the loop.

Reimplemented in PLMD::vesselbase::BridgeVessel.

Definition at line 155 of file Vessel.h.

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

static

Reserve any keywords for this particular vessel.

Definition at line 53 of file Vessel.cpp.

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

pure virtual

Reset the size of the buffers.

Implemented in PLMD::vesselbase::FunctionVessel, PLMD::multicolvar::StoreColvarVessel, PLMD::vesselbase::BridgeVessel, PLMD::multicolvar::StoreCentralAtomsVessel, and PLMD::vesselbase::ShortcutVessel.

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

inlineprotected

Set the size of the data buffer.

Definition at line 221 of file Vessel.h.

void PLMD::vesselbase::Vessel::setBufferElement	(	const unsigned &	i,
		const double &	val
	)

inlineprotected

Set the value of the ith element in the buffer.

Definition at line 246 of file Vessel.h.

void PLMD::vesselbase::Vessel::setBufferFromStash ( )

protected

Add the contents of the stash to the buffer.

Definition at line 133 of file Vessel.cpp.

void PLMD::vesselbase::Vessel::stashBuffers ( )

protected

Store everything that is the buffers.

Definition at line 128 of file Vessel.cpp.

void PLMD::vesselbase::Vessel::zero ( )

inline

Set all the buffer elements to zero.

Definition at line 241 of file Vessel.h.

Friends And Related Function Documentation

friend class ActionWithVessel

friend

Definition at line 76 of file Vessel.h.

Member Data Documentation

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

private

The action that this vessel is created within.

Definition at line 85 of file Vessel.h.

unsigned PLMD::vesselbase::Vessel::bufsize

private

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

Definition at line 91 of file Vessel.h.

unsigned PLMD::vesselbase::Vessel::bufstart

private

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

Definition at line 89 of file Vessel.h.

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

protected

A copy of the communicator.

Definition at line 102 of file Vessel.h.

bool PLMD::vesselbase::Vessel::finished_read

private

This just checks we have done checkRead.

Definition at line 99 of file Vessel.h.

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

private

The keywords.

Definition at line 97 of file Vessel.h.

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.

Definition at line 95 of file Vessel.h.

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

Reference to the log on which to output details.

Definition at line 135 of file Vessel.h.

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

private

The label for the vessel for referencing.

Definition at line 81 of file Vessel.h.

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

private

The keyword for the vessel in the input file.

Definition at line 79 of file Vessel.h.

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

private

The numerical label for this object.

Definition at line 83 of file Vessel.h.

std::vector<double> PLMD::vesselbase::Vessel::stash

private

Something to store the buffer if this is required.

Definition at line 87 of file Vessel.h.

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

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation