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 &)

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

unsigned	getStoreIndex (const unsigned &) const
	Get the index to store a particular index inside. More...

virtual void	recalculateStoredQuantity (const unsigned &myelm, MultiValue &myvals)
	Recalculate one of the base quantities. More...

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

void	addActionThatUses (ActionWithVessel *actionThatUses)
	Add an action that uses this data. More...

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

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

void	retrieveValueWithIndex (const unsigned &myelem, const bool &normed, std::vector< double > &values) const

double	retrieveWeightWithIndex (const unsigned &myelem) const

virtual 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 ()
	Return a description of the vessel contents. 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 void	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)
	Final step in gathering data. More...

bool	storedValueIsActive (const unsigned &iatom) const
	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...

unsigned	getNumberOfDataUsers () const
	Get the number of data users. More...

ActionWithVessel *	getDataUser (const unsigned &)
	Get one of the ith data user. More...

void	resizeTemporyMultiValues (const unsigned &nvals)
	Set the number of tempory multivalues we need. More...

MultiValue &	getTemporyMultiValue (const unsigned &ind)
	Return a tempory multi value - we do this so as to avoid vector resizing. 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
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...

std::vector< ActionWithVessel * >	userActions
	The actions that are going to use the stored data. More...

unsigned	tmp_index
	We create a vector of tempory MultiValues here so as to avoid lots of vector resizing. More...

std::vector< MultiValue >	my_tmp_vals

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

◆ StoreDataVessel()

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

explicit

Member Function Documentation

◆ activateIndices()

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

inlinevirtual

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

◆ addActionThatUses()

void PLMD::vesselbase::StoreDataVessel::addActionThatUses ( ActionWithVessel * actionThatUses )

Add an action that uses this data.

◆ applyForce()

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.

◆ calculate()

void 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.

◆ checkRead()

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

inherited

Check that readin was fine.

◆ completeSetup()

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.

◆ description()

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

inlinevirtual

Return a description of the vessel contents.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::vesselbase::Moments.

◆ error()

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

protectedinherited

Report an error.

◆ finish()

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

virtual

Final step in gathering data.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::vesselbase::Moments.

◆ getAction()

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

inlineprotectedinherited

Return a pointer to the action we are working in.

◆ getAllInput()

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

protectedinherited

This returns the whole input line (it is used for less_than/more_than/between)

◆ getDataUser()

ActionWithVessel * PLMD::vesselbase::StoreDataVessel::getDataUser ( const unsigned & idata )

inline

Get one of the ith data user.

◆ getLabel()

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

inherited

Return the label.

◆ getLocalDerivative()

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

protected

Get the ibuf'th local derivative value.

◆ getName()

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

inherited

Return the name.

◆ getNLTolerance()

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

inlineprotectedinherited

Return the value of the neighbor list tolerance.

◆ getNumberOfComponents()

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

inline

Return the number of components in the vector.

◆ getNumberOfDataUsers()

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

inline

Get the number of data users.

◆ getNumberOfDerivatives()

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

Get the number of derivatives for the ith value.

◆ getNumberOfDerivativeSpacesPerComponent()

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

inlineprotected

Return value of nspace.

◆ getNumberOfStoredValues()

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

inlinevirtual

Get the number of values that have been stored.

◆ getNumericalLabel()

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

inlineprotectedinherited

Return the numerical label.

◆ getSizeOfDerivativeList()

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

inline

Get the size of the derivative list.

◆ getStoreIndex()

unsigned PLMD::vesselbase::StoreDataVessel::getStoreIndex ( const unsigned & ind ) const

inline

Get the index to store a particular index inside.

◆ getTemporyMultiValue()

MultiValue & PLMD::vesselbase::StoreDataVessel::getTemporyMultiValue ( const unsigned & ind )

Return a tempory multi value - we do this so as to avoid vector resizing.

◆ getTolerance()

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

inlineprotectedinherited

Return the value of the tolerance.

◆ parse()

template<class T >

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

protectedinherited

Parse something from the input.

◆ parseFlag()

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

protectedinherited

Parse one keyword as boolean flag.

◆ parseVector()

template<class T >

void PLMD::vesselbase::Vessel::parseVector	(	const std::string &	key,
		std::vector< T > &	t
	)

protectedinherited

Parse one keyword as std::vector.

◆ prepare()

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

inlinevirtualinherited

Do something before the loop.

Reimplemented in PLMD::vesselbase::BridgeVessel, and PLMD::mapping::SpathVessel.

◆ recalculateStoredQuantity()

void PLMD::vesselbase::StoreDataVessel::recalculateStoredQuantity	(	const unsigned &	myelm,
		MultiValue &	myvals
	)

inlinevirtual

Recalculate one of the base quantities.

Reimplemented in PLMD::adjmat::AdjacencyMatrixVessel.

◆ registerKeywords()

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

static

◆ resize()

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

virtual

Do all resizing of data.

Implements PLMD::vesselbase::Vessel.

Reimplemented in PLMD::vesselbase::Moments.

◆ resizeBuffer()

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

inlineprotectedinherited

Set the size of the data buffer.

◆ resizeTemporyMultiValues()

void PLMD::vesselbase::StoreDataVessel::resizeTemporyMultiValues ( const unsigned & nvals )

Set the number of tempory multivalues we need.

◆ retrieveDerivatives()

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

virtual

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

Reimplemented in PLMD::adjmat::AdjacencyMatrixVessel.

◆ retrieveSequentialValue()

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

Get the values of all the components in the vector.

◆ retrieveValueWithIndex()

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

◆ retrieveWeightWithIndex()

double PLMD::vesselbase::StoreDataVessel::retrieveWeightWithIndex ( const unsigned & myelem ) const

◆ setActiveValsAndDerivatives()

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

Set the active values.

◆ setBufferStart()

void PLMD::vesselbase::Vessel::setBufferStart ( unsigned & start )

inlinevirtualinherited

Set the start of the buffer.

Reimplemented in PLMD::vesselbase::BridgeVessel.

◆ setHardCutoffOnWeight()

void PLMD::vesselbase::StoreDataVessel::setHardCutoffOnWeight ( const double & mytol )

Set a hard cutoff on the weight of an element.

◆ setLocalDerivative()

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

protected

Set the ibuf'th local derivative value.

◆ storeDerivatives()

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.

◆ storedValueIsActive()

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

inline

Is a particular stored value active at the present time.

◆ storeValues()

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

protected

Retrieve the values from the underlying ActionWithVessel.

◆ transformDerivatives()

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.

◆ transformName()

std::string PLMD::vesselbase::Vessel::transformName ( const std::string & name )

staticinherited

Convert the name to the label of the component.

◆ usingLowMem()

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

inlineprotected

Are we using low mem option.

◆ weightHasDerivatives()

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

inlineprotected

Is the weight differentiable.

Friends And Related Function Documentation

◆ Moments

friend class Moments

friend

Member Data Documentation

◆ active_der

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

private

The currently active values.

The active derivative elements

◆ bufstart

unsigned PLMD::vesselbase::Vessel::bufstart

protectedinherited

The start of this Vessel's buffer in buffer in the underlying ActionWithVessel.

◆ comm

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

protectedinherited

A copy of the communicator.

◆ hasderiv

bool PLMD::vesselbase::StoreDataVessel::hasderiv

private

Do the quantities being stored in here need derivatives.

◆ local_buffer

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

private

The buffer.

◆ log

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

inherited

Reference to the log on which to output details.

◆ max_lowmem_stash

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.

◆ my_tmp_vals

std::vector<MultiValue> PLMD::vesselbase::StoreDataVessel::my_tmp_vals

private

◆ nspace

unsigned PLMD::vesselbase::StoreDataVessel::nspace

private

The amount of data per vector element.

◆ tmp_index

unsigned PLMD::vesselbase::StoreDataVessel::tmp_index

private

We create a vector of tempory MultiValues here so as to avoid lots of vector resizing.

◆ userActions

std::vector<ActionWithVessel*> PLMD::vesselbase::StoreDataVessel::userActions

private

The actions that are going to use the stored data.

◆ vecsize

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

Friends

Detailed Description

Constructor & Destructor Documentation

◆ StoreDataVessel()

Member Function Documentation

◆ activateIndices()

◆ addActionThatUses()

◆ applyForce()

◆ calculate()

◆ checkRead()

◆ completeSetup()

◆ description()

◆ error()

◆ finish()

◆ getAction()

◆ getAllInput()

◆ getDataUser()

◆ getLabel()

◆ getLocalDerivative()

◆ getName()

◆ getNLTolerance()

◆ getNumberOfComponents()

◆ getNumberOfDataUsers()

◆ getNumberOfDerivatives()

◆ getNumberOfDerivativeSpacesPerComponent()

◆ getNumberOfStoredValues()

◆ getNumericalLabel()

◆ getSizeOfDerivativeList()

◆ getStoreIndex()

◆ getTemporyMultiValue()

◆ getTolerance()

◆ parse()

◆ parseFlag()

◆ parseVector()

◆ prepare()

◆ recalculateStoredQuantity()

◆ registerKeywords()

◆ resize()

◆ resizeBuffer()

◆ resizeTemporyMultiValues()

◆ retrieveDerivatives()

◆ retrieveSequentialValue()

◆ retrieveValueWithIndex()

◆ retrieveWeightWithIndex()

◆ setActiveValsAndDerivatives()

◆ setBufferStart()

◆ setHardCutoffOnWeight()

◆ setLocalDerivative()

◆ storeDerivatives()

◆ storedValueIsActive()

◆ storeValues()

◆ transformDerivatives()

◆ transformName()

◆ usingLowMem()

◆ weightHasDerivatives()

Friends And Related Function Documentation

◆ Moments

Member Data Documentation

◆ active_der

◆ bufstart

◆ comm

◆ hasderiv

◆ local_buffer

◆ log

◆ max_lowmem_stash

◆ my_tmp_vals

◆ nspace

◆ tmp_index

◆ userActions

◆ vecsize