Inheritance diagram for PLMD::mapping::SpathVessel:

Public Member Functions
	SpathVessel (const vesselbase::VesselOptions &da)

std::string	value_descriptor ()

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

bool	calculate (const unsigned &current, MultiValue &myvals, std::vector< double > &buffer, std::vector< unsigned > &der_index) const
	Do the calcualtion. More...

virtual void	resize ()
	This does the resizing of the buffer. More...

virtual double	calcTransform (const double &val, double &df) const
	Do any transformations of the value that are required. More...

virtual void	finish (const std::vector< double > &buffer)
	Finish the calculation of the quantity. More...

virtual double	finalTransform (const double &val, double &dv)
	Finish with any transforms required. More...

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

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 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 void	reserveKeyword (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
bool	diffweight
	Are the derivatives differentiable. More...

bool	norm
	Are we normalising by the weight. More...

bool	usetol
	Are we using the tolerance. More...

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
bool	foundoneclose

unsigned	mycoordnumber

Mapping *	mymap

Constructor & Destructor Documentation

PLMD::mapping::SpathVessel::SpathVessel ( const vesselbase::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.

double PLMD::vesselbase::FunctionVessel::calcTransform	(	const double &	val,
		double &	df
	)		const

virtualinherited

Do any transformations of the value that are required.

Reimplemented in PLMD::vesselbase::LessThan, PLMD::vesselbase::Between, PLMD::vesselbase::MoreThan, PLMD::mapping::ZpathVessel, PLMD::vesselbase::Max, PLMD::vesselbase::Min, PLMD::mapping::AltMin, PLMD::vesselbase::Mean, and PLMD::vesselbase::Sum.

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

virtual

Do the calcualtion.

Reimplemented from PLMD::vesselbase::FunctionVessel.

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

inherited

Check that readin was fine.

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.

double PLMD::vesselbase::FunctionVessel::finalTransform	(	const double &	val,
		double &	dv
	)

virtualinherited

Finish with any transforms required.

Reimplemented in PLMD::mapping::ZpathVessel, PLMD::vesselbase::Max, PLMD::vesselbase::Min, and PLMD::mapping::AltMin.

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

virtualinherited

Finish the calculation of the quantity.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::crystallisation::GradientVessel, PLMD::crystallization::VectorMean, and PLMD::crystallization::VectorSum.

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.

void PLMD::mapping::SpathVessel::prepare ( )

virtual

Do something before the loop.

Reimplemented from PLMD::vesselbase::Vessel.

void PLMD::mapping::SpathVessel::registerKeywords ( Keywords & keys )

static

void PLMD::mapping::SpathVessel::reserveKeyword ( Keywords & keys )

static

void PLMD::vesselbase::FunctionVessel::resize ( )

virtualinherited

This does the resizing of the buffer.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::crystallisation::GradientVessel, PLMD::crystallization::VectorMean, and PLMD::crystallization::VectorSum.

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.

std::string PLMD::mapping::SpathVessel::value_descriptor ( )

virtual

Implements PLMD::vesselbase::ValueVessel.

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.

bool PLMD::vesselbase::FunctionVessel::diffweight

protectedinherited

Are the derivatives differentiable.

bool PLMD::mapping::SpathVessel::foundoneclose

private

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

inherited

Reference to the log on which to output details.

unsigned PLMD::mapping::SpathVessel::mycoordnumber

private

Mapping* PLMD::mapping::SpathVessel::mymap

private

bool PLMD::vesselbase::FunctionVessel::norm

protectedinherited

Are we normalising by the weight.

bool PLMD::vesselbase::FunctionVessel::usetol

protectedinherited

Are we using the tolerance.

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

mapping/SpathVessel.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