Objects that inherit from FunctionVessel can be used (in tandem with PLMD::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\). More...

#include <FunctionVessel.h>

Inheritance diagram for PLMD::vesselbase::FunctionVessel:

[legend]

Public Member Functions
	FunctionVessel (const VesselOptions &)

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

bool	applyForce (std::vector< double > &forces)
	This applies all the forces. More...

std::string	description ()
	The description for the log. More...

virtual std::string	function_description ()=0
	The rest of the description of what we are calculating. More...

virtual unsigned	getNumberOfTerms ()
	Return number of terms. 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 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...

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

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

Protected Member Functions
bool	addValueUsingTolerance (const unsigned &jval, const double &val)
	Add some value to the accumulator if it is greater than tolerance. More...

void	addValueIgnoringTolerance (const unsigned &jval, const double &val)
	Add some value to the accumulator and ignore the tolerance. More...

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

double	getFinalValue (const unsigned &j)
	Get the nth value in the distribution. More...

void	mergeFinalDerivatives (const std::vector< double > &df)
	This does a combination of the product and chain rules. 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 ()
	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
bool	diffweight
	Are the derivatives differentiable. More...

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

Private Attributes
unsigned	nderivatives
	The number of derivatives. More...

Value *	final_value
	This is the pointer to the value we are creating. More...

Detailed Description

Objects that inherit from FunctionVessel can be used (in tandem with PLMD::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\).

They should take in a series of values and return one single value.

Definition at line 41 of file FunctionVessel.h.

Constructor & Destructor Documentation

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

Definition at line 33 of file FunctionVessel.cpp.

Member Function Documentation

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

inlineinherited

Add something to the ith element in the buffer.

Definition at line 252 of file Vessel.h.

void PLMD::vesselbase::FunctionVessel::addValueIgnoringTolerance	(	const unsigned &	jval,
		const double &	val
	)

inlineprotected

Add some value to the accumulator and ignore the tolerance.

Definition at line 83 of file FunctionVessel.h.

bool PLMD::vesselbase::FunctionVessel::addValueUsingTolerance	(	const unsigned &	jval,
		const double &	val
	)

inlineprotected

Add some value to the accumulator if it is greater than tolerance.

Definition at line 76 of file FunctionVessel.h.

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

virtual

This applies all the forces.

Implements PLMD::vesselbase::Vessel.

Definition at line 70 of file FunctionVessel.cpp.

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

pure virtualinherited

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 ( )

inherited

Check that readin was fine.

Definition at line 111 of file Vessel.cpp.

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

virtual

The description for the log.

Implements PLMD::vesselbase::Vessel.

Definition at line 50 of file FunctionVessel.cpp.

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

protectedinherited

Report an error.

Definition at line 122 of file Vessel.cpp.

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

pure virtualinherited

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.

virtual std::string PLMD::vesselbase::FunctionVessel::function_description ( )

pure virtual

The rest of the description of what we are calculating.

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

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

inlineprotectedinherited

Return a pointer to the action we are working in.

Definition at line 236 of file Vessel.h.

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

protectedinherited

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

inlineprotectedinherited

Get the value in the ith element of the buffer.

Definition at line 258 of file Vessel.h.

double PLMD::vesselbase::FunctionVessel::getFinalValue ( const unsigned & j )

inlineprotected

Get the nth value in the distribution.

Definition at line 88 of file FunctionVessel.h.

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

inherited

Return the label.

Definition at line 80 of file Vessel.cpp.

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

inherited

Return the name.

Definition at line 76 of file Vessel.cpp.

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

inlineprotectedinherited

Return the value of the neighbor list tolerance.

Definition at line 231 of file Vessel.h.

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

inlinevirtual

Return number of terms.

Implements PLMD::vesselbase::Vessel.

Definition at line 72 of file FunctionVessel.h.

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

inlineprotectedinherited

Return the numerical label.

Definition at line 216 of file Vessel.h.

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

inlineprotectedinherited

Return the value of the tolerance.

Definition at line 226 of file Vessel.h.

void PLMD::vesselbase::FunctionVessel::mergeFinalDerivatives ( const std::vector< double > & df )

protected

This does a combination of the product and chain rules.

Definition at line 60 of file FunctionVessel.cpp.

template<class T >

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

protectedinherited

Parse something from the input.

Definition at line 169 of file Vessel.h.

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

protectedinherited

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
	)

protectedinherited

Parse one keyword as std::vector.

Definition at line 184 of file Vessel.h.

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

inlinevirtualinherited

Do something before the loop.

Reimplemented in PLMD::vesselbase::BridgeVessel.

Definition at line 155 of file Vessel.h.

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

static

Definition at line 28 of file FunctionVessel.cpp.

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

virtual

This does the resizing of the buffer.

Implements PLMD::vesselbase::Vessel.

Definition at line 54 of file FunctionVessel.cpp.

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

inlineprotectedinherited

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
	)

inlineprotectedinherited

Set the value of the ith element in the buffer.

Definition at line 246 of file Vessel.h.

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

protectedinherited

Add the contents of the stash to the buffer.

Definition at line 133 of file Vessel.cpp.

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

inlineprotected

Set the final value.

Definition at line 94 of file FunctionVessel.h.

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

protectedinherited

Store everything that is the buffers.

Definition at line 128 of file Vessel.cpp.

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

inlineinherited

Set all the buffer elements to zero.

Definition at line 241 of file Vessel.h.

Member Data Documentation

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

protectedinherited

A copy of the communicator.

Definition at line 102 of file Vessel.h.

bool PLMD::vesselbase::FunctionVessel::diffweight

protected

Are the derivatives differentiable.

Definition at line 49 of file FunctionVessel.h.

Value* PLMD::vesselbase::FunctionVessel::final_value

private

This is the pointer to the value we are creating.

Definition at line 46 of file FunctionVessel.h.

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

inherited

Reference to the log on which to output details.

Definition at line 135 of file Vessel.h.

unsigned PLMD::vesselbase::FunctionVessel::nderivatives

private

The number of derivatives.

Definition at line 44 of file FunctionVessel.h.

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

vesselbase/FunctionVessel.h
vesselbase/FunctionVessel.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation