#include <StoreVectorsVessel.h>

Inheritance diagram for PLMD::crystallization::StoreVectorsVessel:

Public Member Functions
	StoreVectorsVessel (const vesselbase::VesselOptions &)
	Constructor. More...

void	usedInFunction (const bool &)
	This turns on the full use of this action for storage. More...

bool	calculate ()
	This makes sure vectors are normalized (they are already stored) More...

void	recompute (const unsigned &, const unsigned &)
	This reperforms a calculation. More...

std::string	description ()
	This does nothing. More...

void	getVector (const unsigned &, std::vector< double > &)
	Get the orientation of the ith vector. More...

void	chainRuleForComponent (const unsigned &, const unsigned &, const unsigned &jout, const unsigned &, const double &, multicolvar::MultiColvarFunction *)
	Chain rule for component. More...

void	chainRuleForVector (const unsigned &, const unsigned &, const unsigned &, const std::vector< double > &, multicolvar::MultiColvarFunction *)
	Chain rule for whole vector. 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...

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

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

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

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 Member Functions
void	normalizeVector (const int &)

Private Attributes
bool	store_director
	We want to store the director rather than the value. More...

unsigned	ncomponents

std::vector< double >	myfvec

VectorMultiColvar *	vecs

Friends
class	VectorMultiColvar

Constructor & Destructor Documentation

PLMD::crystallization::StoreVectorsVessel::StoreVectorsVessel ( const vesselbase::VesselOptions & da )

Constructor.

Member Function Documentation

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

inlinevirtualinherited

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 > & )

inlinevirtualinherited

Forces on vectors should always be applied elsewhere.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::vesselbase::Moments.

bool PLMD::crystallization::StoreVectorsVessel::calculate ( )

virtual

This makes sure vectors are normalized (they are already stored)

Implements PLMD::vesselbase::Vessel.

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

protectedinherited

This is the proper chain rule for vectors.

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

protectedinherited

Chain rule the vector and output derivatives to a value.

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

inherited

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

void PLMD::crystallization::StoreVectorsVessel::chainRuleForComponent	(	const unsigned &	icolv,
		const unsigned &	jin,
		const unsigned &	jout,
		const unsigned &	base_cv_no,
		const double &	weight,
		multicolvar::MultiColvarFunction *	funcout
	)

Chain rule for component.

void PLMD::crystallization::StoreVectorsVessel::chainRuleForVector	(	const unsigned &	icolv,
		const unsigned &	jout,
		const unsigned &	base_cv_no,
		const std::vector< double > &	df,
		multicolvar::MultiColvarFunction *	funcout
	)

Chain rule for whole vector.

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

inherited

Check that readin was fine.

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

protectedinherited

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

std::string PLMD::crystallization::StoreVectorsVessel::description ( )

inlinevirtual

This does nothing.

Implements PLMD::vesselbase::Vessel.

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

protectedinherited

Report an error.

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

virtualinherited

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 & )

inlinevirtualinherited

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
	)

inlineinherited

Get a component of the stored vector.

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

inlineinherited

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
	)

virtualinherited

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 )

inlineprotectedinherited

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

inlineinherited

Return the number of components in the vector.

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

inlineinherited

Get the number of derivatives for the ith value.

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

inlineprotectedinherited

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
	)

inlineinherited

Get one of the stored indexes.

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

inlineprotectedinherited

Return the value of the tolerance.

void PLMD::crystallization::StoreVectorsVessel::getVector	(	const unsigned &	imol,
		std::vector< double > &	vec
	)

inline

Get the orientation of the ith vector.

void PLMD::crystallization::StoreVectorsVessel::normalizeVector ( const int & jstore )

private

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 )

inlinevirtualinherited

This reperforms the task in the underlying action.

Reimplemented in PLMD::multicolvar::StoreCentralAtomsVessel.

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

virtualinherited

Clear certain data before start of main loop.

Reimplemented from PLMD::vesselbase::Vessel.

void PLMD::crystallization::StoreVectorsVessel::recompute	(	const unsigned &	ivec,
		const unsigned &	jstore
	)

virtual

This reperforms a calculation.

Reimplemented from PLMD::vesselbase::StoreDataVessel.

void PLMD::crystallization::StoreVectorsVessel::registerKeywords ( Keywords & keys )

static

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

virtualinherited

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
	)

inlineprotectedinherited

Set a component of one of the vectors.

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

inlineprotectedinherited

Set the ibuf'th local derivative value.

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

protectedinherited

Set the Task that needs redoing.

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

inherited

This stores the data we get from the calculation.

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

inherited

This stores the data we get from the calculation.

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

protectedinherited

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.

void PLMD::crystallization::StoreVectorsVessel::usedInFunction ( const bool & store )

This turns on the full use of this action for storage.

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

inlineprotectedinherited

Are we using low mem option.

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

inlineprotectedinherited

Is the weight differentiable.

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

inlineinherited

Set all the buffer elements to zero.

Friends And Related Function Documentation

friend class VectorMultiColvar

friend

Member Data Documentation

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

protectedinherited

A copy of the communicator.

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

inherited

Reference to the log on which to output details.

std::vector<double> PLMD::crystallization::StoreVectorsVessel::myfvec

private

unsigned PLMD::crystallization::StoreVectorsVessel::ncomponents

private

bool PLMD::crystallization::StoreVectorsVessel::store_director

private

We want to store the director rather than the value.

VectorMultiColvar* PLMD::crystallization::StoreVectorsVessel::vecs

private

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

crystallization/StoreVectorsVessel.h
crystallization/StoreVectorsVessel.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation