#include <StoreDataVessel.h>

Inheritance diagram for PLMD::vesselbase::StoreDataVessel:

[legend]

Public Member Functions
	StoreDataVessel (const VesselOptions &)

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

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

bool	applyForce (std::vector< double > &) override
	Forces on vectors should always be applied elsewhere. More...

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

void	checkRead ()
	Check that readin was fine. More...

std::string	description () override
	Return a description of the vessel contents. More...

void	finish (const std::vector< double > &buffer) override
	Final step in gathering data. More...

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

std::string	getLabel () const
	Return the label. More...

std::string	getName () const
	Return the name. More...

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

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

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

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

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

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

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

unsigned	getTrueIndex (const unsigned &) const
	Get the true index of a quantity from the index it is stored in. More...

virtual void	prepare ()
	Do something before the loop. More...

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

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

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

void	retrieveDerivatives (const unsigned &myelem, const bool &normed, MultiValue &myvals)
	Get the derivatives for one of the 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

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

virtual void	setBufferStart (unsigned &start)
	Set the start of the buffer. More...

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

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

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

void	error (const std::string &errmsg)
	Report an error. More...

ActionWithVessel *	getAction () const
	Return a pointer to the action we are working in. More...

std::string	getAllInput ()
	This returns the whole input line (it is used for less_than/more_than/between) More...

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

double	getNLTolerance () const
	Return the value of the neighbor list tolerance. More...

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

int	getNumericalLabel () const
	Return the numerical label. More...

unsigned	getSizeOfBuffer () const
	Return the size of the buffer. More...

double	getTolerance () const
	Return the value of the tolerance. More...

template<class T >
void	parse (const std::string &key, T &t)
	Parse something from the input. More...

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...

void	resizeBuffer (const unsigned &n)
	Set the size of the data buffer. More...

void	setLocalDerivative (const unsigned &ibuf, const double &val)
	Set the ibuf'th local derivative value. More...

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

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

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

bool	weightHasDerivatives ()
	Is the weight differentiable. More...

Protected Attributes
unsigned	bufstart
	The start of this Vessel's buffer in buffer in the underlying ActionWithVessel. More...

Private Attributes
ActionWithVessel *	action
	The action that this vessel is created within. More...

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

unsigned	bufsize
	The number of elements in this vessel's buffered data. More...

bool	finished_read
	This just checks we have done checkRead. More...

bool	hasderiv
	Do the quantities being stored in here need derivatives. More...

const PLMD::Keywords &	keywords
	The keywords. More...

std::vector< std::string >	line
	Directive line. More...

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

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

std::vector< MultiValue >	my_tmp_vals

std::string	mylabel
	The label for the vessel for referencing. More...

std::string	myname
	The keyword for the vessel in the input file. More...

std::size_t	nspace
	The amount of data per vector element. More...

const int	numlab
	The numerical label for this object. More...

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

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

std::size_t	vecsize
	The size of the vector we are computing. 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

◆ 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()

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

inlineoverridevirtual

Forces on vectors should always be applied elsewhere.

Implements PLMD::vesselbase::Vessel.

◆ calculate()

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

overridevirtual

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()

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

inlineoverridevirtual

Return a description of the vessel contents.

Implements PLMD::vesselbase::Vessel.

◆ 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 )

overridevirtual

Final step in gathering data.

Implements PLMD::vesselbase::Vessel.

◆ 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.

◆ getSizeOfBuffer()

unsigned PLMD::vesselbase::Vessel::getSizeOfBuffer ( ) const

inlineprotectedinherited

Return the size of the buffer.

◆ 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.

◆ getTrueIndex()

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

inline

Get the true index of a quantity from the index it is stored in.

◆ 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
	)

inline

Recalculate one of the base quantities.

◆ registerKeywords()

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

static

◆ resize()

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

overridevirtual

Do all resizing of data.

Implements PLMD::vesselbase::Vessel.

◆ 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
	)

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

◆ 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

◆ action

ActionWithVessel* PLMD::vesselbase::Vessel::action

privateinherited

The action that this vessel is created within.

◆ active_der

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

private

The currently active values.

The active derivative elements

◆ bufsize

unsigned PLMD::vesselbase::Vessel::bufsize

privateinherited

The number of elements in this vessel's buffered data.

◆ bufstart

unsigned PLMD::vesselbase::Vessel::bufstart

protectedinherited

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

◆ finished_read

bool PLMD::vesselbase::Vessel::finished_read

privateinherited

This just checks we have done checkRead.

◆ hasderiv

bool PLMD::vesselbase::StoreDataVessel::hasderiv

private

Do the quantities being stored in here need derivatives.

◆ keywords

const PLMD::Keywords& PLMD::vesselbase::Vessel::keywords

privateinherited

The keywords.

◆ line

std::vector<std::string> PLMD::vesselbase::Vessel::line

privateinherited

Directive line.

This line is progressively erased during vessel construction so as to check if all the present keywords are correct.

◆ local_buffer

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

private

The buffer.

◆ 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

◆ mylabel

std::string PLMD::vesselbase::Vessel::mylabel

privateinherited

The label for the vessel for referencing.

◆ myname

std::string PLMD::vesselbase::Vessel::myname

privateinherited

The keyword for the vessel in the input file.

◆ nspace

std::size_t PLMD::vesselbase::StoreDataVessel::nspace

private

The amount of data per vector element.

◆ numlab

const int PLMD::vesselbase::Vessel::numlab

privateinherited

The numerical label for this object.

◆ 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

std::size_t 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

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()

◆ getSizeOfBuffer()

◆ getSizeOfDerivativeList()

◆ getStoreIndex()

◆ getTemporyMultiValue()

◆ getTolerance()

◆ getTrueIndex()

◆ 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

◆ action

◆ active_der

◆ bufsize

◆ bufstart

◆ finished_read

◆ hasderiv

◆ keywords

◆ line

◆ local_buffer

◆ max_lowmem_stash

◆ my_tmp_vals

◆ mylabel

◆ myname

◆ nspace

◆ numlab