Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to store values and derivatives for a set of scalars or vectors that are calculated by a PLMD::vesselbase::ActionWithVessel. More...

#include <StoreDataVessel.h>

Inheritance diagram for PLMD::vesselbase::StoreDataVessel:

[legend]

Public Member Functions
	StoreDataVessel (const VesselOptions &)

unsigned	getNumberOfStoredValues () const
	Get the number of values that have been stored. More...

void	setHardCutoffOnWeight (const double &mytol)
	Set a hard cutoff on the weight of an element. More...

bool	weightCutoffIsOn () const
	Is the hard weight cutoff on. More...

unsigned	getNumberOfComponents () const
	Return the number of components in the vector. More...

void	retrieveValue (const unsigned &myelem, const bool &normed, std::vector< double > &values) const
	Get the values of all the components in the vector. More...

void	retrieveDerivatives (const unsigned &myelem, const bool &normed, MultiValue &myvals)
	Get the derivatives for one of the components in the vector. More...

virtual void	resize ()
	Do all resizing of data. More...

virtual std::string	description ()
	Clear certain data before start of main loop. More...

unsigned	getNumberOfDerivatives (const unsigned &)
	Get the number of derivatives for the ith value. More...

unsigned	getSizeOfDerivativeList () const
	Get the size of the derivative list. More...

virtual bool	calculate (const unsigned &current, MultiValue &myvals, std::vector< double > &buffer, std::vector< unsigned > &der_index) const
	This stores the data when not using lowmem. More...

virtual void	finish (const std::vector< double > &buffer)
	Build index stores. More...

bool	storedValueIsActive (const unsigned &iatom)
	Is a particular stored value active at the present time. More...

void	setActiveValsAndDerivatives (const std::vector< unsigned > &der_index)
	Set the active values. More...

virtual void	activateIndices (ActionWithVessel *)
	Activate indexes (this is used at end of chain rule) More...

virtual bool	applyForce (std::vector< double > &)
	Forces on vectors should always be applied elsewhere. 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
bool	weightHasDerivatives ()
	Is the weight differentiable. More...

bool	usingLowMem ()
	Are we using low mem option. More...

void	completeSetup (const unsigned &, const unsigned &)
	Finish the setup of the storage object by setting how much data has to be stored. More...

unsigned	getNumberOfDerivativeSpacesPerComponent () const
	Return value of nspace. More...

void	storeValues (const unsigned &, MultiValue &, std::vector< double > &) const
	Retrieve the values from the underlying ActionWithVessel. More...

void	storeDerivatives (const unsigned &, MultiValue &myvals, std::vector< double > &, std::vector< unsigned > &) const
	This stores the data we get from the calculation. More...

double	getLocalDerivative (const unsigned &ibuf)
	Get the ibuf'th local derivative value. More...

void	setLocalDerivative (const unsigned &ibuf, const double &val)
	Set the ibuf'th local derivative 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	hard_cut
	Apply a hard cutoff on the weight. More...

double	wtol
	The value of the cutoff on the weight. 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	hasderiv
	Do the quantities being stored in here need derivatives. More...

unsigned	max_lowmem_stash
	What is the maximum number of vectors we are going to have to store when using lowmem option. More...

unsigned	vecsize
	The size of the vector we are computing. More...

unsigned	nspace
	The amount of data per vector element. More...

std::vector< unsigned >	active_der
	The currently active values. More...

std::vector< double >	local_buffer
	The buffer. More...

Friends
class	Moments

Detailed Description

Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to store values and derivatives for a set of scalars or vectors that are calculated by a PLMD::vesselbase::ActionWithVessel.

Functions of these stored quantities can then be calculated in a second step.

Constructor & Destructor Documentation

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

explicit

Member Function Documentation

virtual void PLMD::vesselbase::StoreDataVessel::activateIndices ( ActionWithVessel * )

inlinevirtual

Activate indexes (this is used at end of chain rule)

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

inlinevirtual

Forces on vectors should always be applied elsewhere.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::vesselbase::Moments.

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

virtual

This stores the data when not using lowmem.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::multicolvar::AdjacencyMatrixVessel.

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

inherited

Check that readin was fine.

void PLMD::vesselbase::StoreDataVessel::completeSetup	(	const unsigned &	,
		const unsigned &
	)

protected

Finish the setup of the storage object by setting how much data has to be stored.

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

inlinevirtual

Clear certain data before start of main loop.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::vesselbase::Moments.

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

protectedinherited

Report an error.

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

virtual

Build index stores.

Final step in gathering data

Implements PLMD::vesselbase::Vessel.

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

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)

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

inherited

Return the label.

double PLMD::vesselbase::StoreDataVessel::getLocalDerivative ( const unsigned & ibuf )

protected

Get the ibuf'th local derivative value.

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.

unsigned PLMD::vesselbase::StoreDataVessel::getNumberOfComponents ( ) const

inline

Return the number of components in the vector.

unsigned PLMD::vesselbase::StoreDataVessel::getNumberOfDerivatives ( const unsigned & )

Get the number of derivatives for the ith value.

unsigned PLMD::vesselbase::StoreDataVessel::getNumberOfDerivativeSpacesPerComponent ( ) const

inlineprotected

Return value of nspace.

unsigned PLMD::vesselbase::StoreDataVessel::getNumberOfStoredValues ( ) const

inline

Get the number of values that have been stored.

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

inlineprotectedinherited

Return the numerical label.

unsigned PLMD::vesselbase::StoreDataVessel::getSizeOfDerivativeList ( ) const

inline

Get the size of the derivative list.

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::StoreDataVessel::registerKeywords ( Keywords & keys )

static

void PLMD::vesselbase::StoreDataVessel::resize ( )

virtual

Do all resizing of data.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::vesselbase::Moments.

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

inlineprotectedinherited

Set the size of the data buffer.

void PLMD::vesselbase::StoreDataVessel::retrieveDerivatives	(	const unsigned &	myelem,
		const bool &	normed,
		MultiValue &	myvals
	)

Get the derivatives for one of the components in the vector.

void PLMD::vesselbase::StoreDataVessel::retrieveValue	(	const unsigned &	myelem,
		const bool &	normed,
		std::vector< double > &	values
	)		const

Get the values of all the components in the vector.

void PLMD::vesselbase::StoreDataVessel::setActiveValsAndDerivatives ( const std::vector< unsigned > & der_index )

Set the active values.

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::StoreDataVessel::setHardCutoffOnWeight ( const double & mytol )

Set a hard cutoff on the weight of an element.

void PLMD::vesselbase::StoreDataVessel::setLocalDerivative	(	const unsigned &	ibuf,
		const double &	val
	)

protected

Set the ibuf'th local derivative value.

void PLMD::vesselbase::StoreDataVessel::storeDerivatives	(	const unsigned &	myelem,
		MultiValue &	myvals,
		std::vector< double > &	buffer,
		std::vector< unsigned > &	der_list
	)		const

protected

This stores the data we get from the calculation.

bool PLMD::vesselbase::StoreDataVessel::storedValueIsActive ( const unsigned & iatom )

inline

Is a particular stored value active at the present time.

void PLMD::vesselbase::StoreDataVessel::storeValues	(	const unsigned &	myelem,
		MultiValue &	myvals,
		std::vector< double > &	buffer
	)		const

protected

Retrieve the values from the underlying ActionWithVessel.

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.

bool PLMD::vesselbase::StoreDataVessel::usingLowMem ( )

inlineprotected

Are we using low mem option.

bool PLMD::vesselbase::StoreDataVessel::weightCutoffIsOn ( ) const

Is the hard weight cutoff on.

bool PLMD::vesselbase::StoreDataVessel::weightHasDerivatives ( )

inlineprotected

Is the weight differentiable.

Friends And Related Function Documentation

friend class Moments

friend

Member Data Documentation

std::vector<unsigned> PLMD::vesselbase::StoreDataVessel::active_der

private

The currently active values.

The active derivative elements

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::StoreDataVessel::hard_cut

protected

Apply a hard cutoff on the weight.

bool PLMD::vesselbase::StoreDataVessel::hasderiv

private

Do the quantities being stored in here need derivatives.

std::vector<double> PLMD::vesselbase::StoreDataVessel::local_buffer

private

The buffer.

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

inherited

Reference to the log on which to output details.

unsigned PLMD::vesselbase::StoreDataVessel::max_lowmem_stash

private

What is the maximum number of vectors we are going to have to store when using lowmem option.

unsigned PLMD::vesselbase::StoreDataVessel::nspace

private

The amount of data per vector element.

unsigned PLMD::vesselbase::StoreDataVessel::vecsize

private

The size of the vector we are computing.

double PLMD::vesselbase::StoreDataVessel::wtol

protected

The value of the cutoff on the weight.

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

vesselbase/StoreDataVessel.h
vesselbase/StoreDataVessel.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