#include <AdjacencyMatrixVessel.h>

Inheritance diagram for PLMD::adjmat::AdjacencyMatrixVessel:

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

AdjacencyMatrixBase *	getMatrixAction ()
	Get the underlying adjacency matrix action object. More...

bool	matrixElementIsActive (const unsigned &ielem, const unsigned &jelem) const
	Is an element of the matrix currently active. More...

unsigned	getStoreIndexFromMatrixIndices (const unsigned &ielem, const unsigned &jelem) const
	Get the index that a particular element is stored in from the matrix indices. More...

void	retrieveMatrix (DynamicList< unsigned > &myactive_elements, Matrix< double > &mymatrix)
	Get the adjacency matrix. More...

void	retrieveAdjacencyLists (std::vector< unsigned > &nneigh, Matrix< unsigned > &adj_list)
	Get the neighbour list based on the adjacency matrix. More...

void	retrieveEdgeList (unsigned &nedge, std::vector< std::pair< unsigned, unsigned > > &edge_list)
	Retrieve the list of edges in the adjacency matrix/graph. More...

void	retrieveDerivatives (const unsigned &myelem, const bool &normed, MultiValue &myvals)
	Retrieve the derivatives of the matrix element - this is overwritten as if we have derivatives wrt a weight... More...

void	getMatrixIndices (const unsigned &code, unsigned &i, unsigned &j) const

void	recalculateStoredQuantity (const unsigned &myelm, MultiValue &myvals)
	Recalculate a stored quantity. More...

bool	undirectedGraph () const
	Can we think of the matrix as an undirected graph. More...

bool	isSymmetric () const
	Is the matrix symmetric. More...

unsigned	getNumberOfRows () const
	Get the number of rows. More...

unsigned	getNumberOfColumns () const
	Get the number of columns. More...

bool	nodesAreConnected (const unsigned &iatom, const unsigned &jatom) const
	Are these two nodes connected. More...

double	getCutoffForConnection () const
	Get the cutoff that we are using for connections. More...

Vector	getNodePosition (const unsigned &taskIndex) const

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...

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	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
AdjacencyMatrixBase *	function
	Pointer to underlying action. More...

bool	symmetric
	Is the matrix symmetric and are we calculating hbonds. More...

bool	hbonds

Friends
class	AdjacencyMatrixBase

class	ActionWithInputMatrix

Constructor & Destructor Documentation

◆ AdjacencyMatrixVessel()

PLMD::adjmat::AdjacencyMatrixVessel::AdjacencyMatrixVessel ( const vesselbase::VesselOptions & da )

explicit

Constructor.

Member Function Documentation

◆ activateIndices()

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

inlinevirtualinherited

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

◆ addActionThatUses()

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

inherited

Add an action that uses this data.

◆ applyForce()

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.

◆ calculate()

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

virtualinherited

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 &
	)

protectedinherited

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

◆ description()

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

inlinevirtualinherited

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 )

virtualinherited

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)

◆ getCutoffForConnection()

double PLMD::adjmat::AdjacencyMatrixVessel::getCutoffForConnection ( ) const

Get the cutoff that we are using for connections.

◆ getDataUser()

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

inlineinherited

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 )

protectedinherited

Get the ibuf'th local derivative value.

◆ getMatrixAction()

AdjacencyMatrixBase * PLMD::adjmat::AdjacencyMatrixVessel::getMatrixAction ( )

Get the underlying adjacency matrix action object.

◆ getMatrixIndices()

void PLMD::adjmat::AdjacencyMatrixVessel::getMatrixIndices	(	const unsigned &	code,
		unsigned &	i,
		unsigned &	j
	)		const

◆ 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.

◆ getNodePosition()

Vector PLMD::adjmat::AdjacencyMatrixVessel::getNodePosition ( const unsigned & taskIndex ) const

◆ getNumberOfColumns()

unsigned PLMD::adjmat::AdjacencyMatrixVessel::getNumberOfColumns ( ) const

Get the number of columns.

◆ getNumberOfComponents()

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

inlineinherited

Return the number of components in the vector.

◆ getNumberOfDataUsers()

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

inlineinherited

Get the number of data users.

◆ getNumberOfDerivatives()

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

inherited

Get the number of derivatives for the ith value.

◆ getNumberOfDerivativeSpacesPerComponent()

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

inlineprotectedinherited

Return value of nspace.

◆ getNumberOfRows()

unsigned PLMD::adjmat::AdjacencyMatrixVessel::getNumberOfRows ( ) const

Get the number of rows.

◆ getNumberOfStoredValues()

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

inlinevirtualinherited

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

inlineinherited

Get the size of the derivative list.

◆ getStoreIndex()

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

inlineinherited

Get the index to store a particular index inside.

◆ getStoreIndexFromMatrixIndices()

unsigned PLMD::adjmat::AdjacencyMatrixVessel::getStoreIndexFromMatrixIndices	(	const unsigned &	ielem,
		const unsigned &	jelem
	)		const

Get the index that a particular element is stored in from the matrix indices.

◆ getTemporyMultiValue()

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

inherited

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.

◆ isSymmetric()

bool PLMD::adjmat::AdjacencyMatrixVessel::isSymmetric ( ) const

Is the matrix symmetric.

◆ matrixElementIsActive()

bool PLMD::adjmat::AdjacencyMatrixVessel::matrixElementIsActive	(	const unsigned &	ielem,
		const unsigned &	jelem
	)		const

Is an element of the matrix currently active.

◆ nodesAreConnected()

bool PLMD::adjmat::AdjacencyMatrixVessel::nodesAreConnected	(	const unsigned &	iatom,
		const unsigned &	jatom
	)		const

Are these two nodes connected.

◆ 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::adjmat::AdjacencyMatrixVessel::recalculateStoredQuantity	(	const unsigned &	myelm,
		MultiValue &	myvals
	)

virtual

Recalculate a stored quantity.

Reimplemented from PLMD::vesselbase::StoreDataVessel.

◆ registerKeywords()

void PLMD::adjmat::AdjacencyMatrixVessel::registerKeywords ( Keywords & keys )

static

◆ resize()

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

virtualinherited

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 )

inherited

Set the number of tempory multivalues we need.

◆ retrieveAdjacencyLists()

void PLMD::adjmat::AdjacencyMatrixVessel::retrieveAdjacencyLists	(	std::vector< unsigned > &	nneigh,
		Matrix< unsigned > &	adj_list
	)

Get the neighbour list based on the adjacency matrix.

◆ retrieveDerivatives()

void PLMD::adjmat::AdjacencyMatrixVessel::retrieveDerivatives	(	const unsigned &	myelem,
		const bool &	normed,
		MultiValue &	myvals
	)

virtual

Retrieve the derivatives of the matrix element - this is overwritten as if we have derivatives wrt a weight...

Reimplemented from PLMD::vesselbase::StoreDataVessel.

◆ retrieveEdgeList()

void PLMD::adjmat::AdjacencyMatrixVessel::retrieveEdgeList	(	unsigned &	nedge,
		std::vector< std::pair< unsigned, unsigned > > &	edge_list
	)

Retrieve the list of edges in the adjacency matrix/graph.

◆ retrieveMatrix()

void PLMD::adjmat::AdjacencyMatrixVessel::retrieveMatrix	(	DynamicList< unsigned > &	myactive_elements,
		Matrix< double > &	mymatrix
	)

Get the adjacency matrix.

◆ retrieveSequentialValue()

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

inherited

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

inherited

◆ retrieveWeightWithIndex()

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

inherited

◆ setActiveValsAndDerivatives()

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

inherited

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 )

inherited

Set a hard cutoff on the weight of an element.

◆ setLocalDerivative()

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

protectedinherited

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

protectedinherited

This stores the data we get from the calculation.

◆ storedValueIsActive()

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

inlineinherited

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

protectedinherited

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.

◆ undirectedGraph()

bool PLMD::adjmat::AdjacencyMatrixVessel::undirectedGraph ( ) const

Can we think of the matrix as an undirected graph.

◆ usingLowMem()

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

inlineprotectedinherited

Are we using low mem option.

◆ weightHasDerivatives()

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

inlineprotectedinherited

Is the weight differentiable.

Friends And Related Function Documentation

◆ ActionWithInputMatrix

friend class ActionWithInputMatrix

friend

◆ AdjacencyMatrixBase

friend class AdjacencyMatrixBase

friend

Member Data Documentation

◆ 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.

◆ function

AdjacencyMatrixBase* PLMD::adjmat::AdjacencyMatrixVessel::function

private

Pointer to underlying action.

◆ hbonds

bool PLMD::adjmat::AdjacencyMatrixVessel::hbonds

private

◆ log

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

inherited

Reference to the log on which to output details.

◆ symmetric

bool PLMD::adjmat::AdjacencyMatrixVessel::symmetric

private

Is the matrix symmetric and are we calculating hbonds.

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

adjmat/AdjacencyMatrixVessel.h
adjmat/AdjacencyMatrixVessel.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Constructor & Destructor Documentation

◆ AdjacencyMatrixVessel()

Member Function Documentation

◆ activateIndices()

◆ addActionThatUses()

◆ applyForce()

◆ calculate()

◆ checkRead()

◆ completeSetup()

◆ description()

◆ error()

◆ finish()

◆ getAction()

◆ getAllInput()

◆ getCutoffForConnection()

◆ getDataUser()

◆ getLabel()

◆ getLocalDerivative()

◆ getMatrixAction()

◆ getMatrixIndices()

◆ getName()

◆ getNLTolerance()

◆ getNodePosition()

◆ getNumberOfColumns()

◆ getNumberOfComponents()

◆ getNumberOfDataUsers()

◆ getNumberOfDerivatives()

◆ getNumberOfDerivativeSpacesPerComponent()

◆ getNumberOfRows()

◆ getNumberOfStoredValues()

◆ getNumericalLabel()

◆ getSizeOfDerivativeList()

◆ getStoreIndex()

◆ getStoreIndexFromMatrixIndices()

◆ getTemporyMultiValue()

◆ getTolerance()

◆ isSymmetric()

◆ matrixElementIsActive()

◆ nodesAreConnected()

◆ parse()

◆ parseFlag()

◆ parseVector()

◆ prepare()

◆ recalculateStoredQuantity()

◆ registerKeywords()

◆ resize()

◆ resizeBuffer()

◆ resizeTemporyMultiValues()

◆ retrieveAdjacencyLists()

◆ retrieveDerivatives()

◆ retrieveEdgeList()

◆ retrieveMatrix()

◆ retrieveSequentialValue()

◆ retrieveValueWithIndex()

◆ retrieveWeightWithIndex()

◆ setActiveValsAndDerivatives()

◆ setBufferStart()

◆ setHardCutoffOnWeight()

◆ setLocalDerivative()

◆ storeDerivatives()

◆ storedValueIsActive()

◆ storeValues()

◆ transformDerivatives()

◆ transformName()

◆ undirectedGraph()

◆ usingLowMem()

◆ weightHasDerivatives()

Friends And Related Function Documentation

◆ ActionWithInputMatrix

◆ AdjacencyMatrixBase

Member Data Documentation

◆ bufstart

◆ comm