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

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

void	prepare ()
	Clear certain data before start of main loop. More...

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

unsigned	getStoredIndex (const unsigned &, const unsigned &)
	Get one of the stored indexes. More...

double	getComponent (const unsigned &, const unsigned &)
	Get a component of the stored vector. More...

virtual void	recompute (const unsigned &, const unsigned &)
	Recalculate a vector - used in lowmem mode. More...

virtual void	performTask (const unsigned &)
	This reperforms the task in the underlying action. More...

virtual void	finishTask (const unsigned &)
	This reperforms the task. More...

void	chainRule (const unsigned &, const std::vector< double > &)
	Chain rule and store output in local array called final_derivatives with vectors this does chain rule for dot products. More...

double	getFinalDerivative (const unsigned &ider) const
	Get the ider'th final derivative value. More...

bool	calculate ()
	This stores the data when not using lowmem. More...

void	storeDerivativesLowMem (const unsigned &)
	This stores the data we get from the calculation. More...

void	storeDerivativesHighMem (const unsigned &)
	This stores the data we get from the calculation. More...

virtual void	finish ()
	Final step in gathering data. More...

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

virtual void	getIndexList (const unsigned &, const unsigned &, const unsigned &, std::vector< unsigned > &)
	Get the list of indices that we are storing data for. 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...

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...

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 &)
	Retrieve the values from the underlying ActionWithVessel. More...

void	setTaskToRecompute (const unsigned &ivec)
	Set the Task that needs redoing. More...

void	setComponent (const unsigned &, const unsigned &, const double &)
	Set a component of one of the vectors. More...

double	chainRule (const unsigned &, const unsigned &, const std::vector< double > &)
	This is the proper chain rule for vectors. More...

void	chainRule (const unsigned &, const std::vector< double > &, Value *)
	Chain rule the vector and output derivatives to a value. 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 ()
	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...

Protected Attributes
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	data_start
	The start point for the data we are storing in this particular object. 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 active derivative elements. More...

std::vector< double >	fvec
	This is a tempory vector that is used to store data. More...

std::vector< double >	local_derivatives
	The local derivatives. More...

std::vector< double >	final_derivatives
	The final derivatives. More...

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 )

Member Function Documentation

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

inlinevirtual

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

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

inlineinherited

Add something to the ith element in the buffer.

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 ( )

virtual

This stores the data when not using lowmem.

Implements PLMD::vesselbase::Vessel.

double PLMD::vesselbase::StoreDataVessel::chainRule	(	const unsigned &	ival,
		const unsigned &	ider,
		const std::vector< double > &	df
	)

protected

This is the proper chain rule for vectors.

void PLMD::vesselbase::StoreDataVessel::chainRule	(	const unsigned &	ival,
		const std::vector< double > &	df,
		Value *	val
	)

protected

Chain rule the vector and output derivatives to a value.

void PLMD::vesselbase::StoreDataVessel::chainRule	(	const unsigned &	ival,
		const std::vector< double > &	df
	)

Chain rule and store output in local array called final_derivatives with vectors this does chain rule for dot products.

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

inherited

Check that readin was fine.

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

protected

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

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

pure virtualinherited

Return a description of the vessel contents.

Implemented in PLMD::vesselbase::FunctionVessel, PLMD::vesselbase::BridgeVessel, PLMD::crystallization::StoreVectorsVessel, PLMD::multicolvar::AdjacencyMatrixVessel, PLMD::multicolvar::StoreCentralAtomsVessel, PLMD::vesselbase::Moments, PLMD::multicolvar::StoreColvarVessel, PLMD::vesselbase::ShortcutVessel, and PLMD::vesselbase::StoreValueVessel.

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

protectedinherited

Report an error.

void PLMD::vesselbase::StoreDataVessel::finish ( )

virtual

Final step in gathering data.

Implements PLMD::vesselbase::Vessel.

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

virtual void PLMD::vesselbase::StoreDataVessel::finishTask ( const unsigned & )

inlinevirtual

This reperforms the task.

Reimplemented in PLMD::multicolvar::StoreCentralAtomsVessel.

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

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)

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

inlineprotectedinherited

Get the value in the ith element of the buffer.

double PLMD::vesselbase::StoreDataVessel::getComponent	(	const unsigned &	ival,
		const unsigned &	jcomp
	)

inline

Get a component of the stored vector.

double PLMD::vesselbase::StoreDataVessel::getFinalDerivative ( const unsigned & ider ) const

inline

Get the ider'th final derivative value.

void PLMD::vesselbase::StoreDataVessel::getIndexList	(	const unsigned &	ntotal,
		const unsigned &	jstore,
		const unsigned &	maxder,
		std::vector< unsigned > &	indices
	)

virtual

Get the list of indices that we are storing data for.

Reimplemented in PLMD::multicolvar::StoreCentralAtomsVessel.

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

inherited

Return the label.

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

inlineprotected

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 & ival )

inline

Get the number of derivatives for the ith value.

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

inlineprotected

Return value of nspace.

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

inlineprotectedinherited

Return the numerical label.

unsigned PLMD::vesselbase::StoreDataVessel::getStoredIndex	(	const unsigned &	ival,
		const unsigned &	jindex
	)

inline

Get one of the stored indexes.

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::vesselbase::StoreDataVessel::performTask ( const unsigned & ivec )

inlinevirtual

This reperforms the task in the underlying action.

Reimplemented in PLMD::multicolvar::StoreCentralAtomsVessel.

void PLMD::vesselbase::StoreDataVessel::prepare ( )

virtual

Clear certain data before start of main loop.

Reimplemented from PLMD::vesselbase::Vessel.

void PLMD::vesselbase::StoreDataVessel::recompute	(	const unsigned &	ivec,
		const unsigned &	jstore
	)

virtual

Recalculate a vector - used in lowmem mode.

Reimplemented in PLMD::crystallization::StoreVectorsVessel, and PLMD::multicolvar::AdjacencyMatrixVessel.

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

inlineprotectedinherited

Set the value of the ith element in the buffer.

void PLMD::vesselbase::StoreDataVessel::setComponent	(	const unsigned &	ival,
		const unsigned &	jcomp,
		const double &	val
	)

inlineprotected

Set a component of one of the vectors.

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

inlineprotected

Set the ibuf'th local derivative value.

void PLMD::vesselbase::StoreDataVessel::setTaskToRecompute ( const unsigned & ivec )

protected

Set the Task that needs redoing.

void PLMD::vesselbase::StoreDataVessel::storeDerivativesHighMem ( const unsigned & myelem )

This stores the data we get from the calculation.

void PLMD::vesselbase::StoreDataVessel::storeDerivativesLowMem ( const unsigned & jstore )

This stores the data we get from the calculation.

void PLMD::vesselbase::StoreDataVessel::storeValues ( const unsigned & myelem )

protected

Retrieve the values from the underlying ActionWithVessel.

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::weightHasDerivatives ( )

inlineprotected

Is the weight differentiable.

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

inlineinherited

Set all the buffer elements to zero.

Member Data Documentation

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

private

The active derivative elements.

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

protectedinherited

A copy of the communicator.

unsigned PLMD::vesselbase::StoreDataVessel::data_start

private

The start point for the data we are storing in this particular object.

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

private

The final derivatives.

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

private

This is a tempory vector that is used to store data.

bool PLMD::vesselbase::StoreDataVessel::hasderiv

private

Do the quantities being stored in here need derivatives.

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

private

The local derivatives.

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.

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

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation