#include <StoreCentralAtomsVessel.h>

Inheritance diagram for PLMD::multicolvar::StoreCentralAtomsVessel:

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

unsigned	getNumberOfTerms ()
	Return the number of terms. More...

void	resize ()
	This does the resizing of the buffer. More...

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

void	finish ()
	This should mpi gather the active atoms. More...

bool	applyForce (std::vector< double > &)
	This does nothing. More...

bool	calculate ()
	This makes sure all vectors are stored. More...

Vector	getPosition (const unsigned &) const
	Get the orientation of the ith vector. More...

void	addAtomsDerivatives (const unsigned &iatom, const Vector &df, MultiColvarFunction *funcout) const
	Add derivatives to central atom position. More...

void	addAtomsDerivativeOfWeight (const unsigned &iatom, const Vector &df, MultiColvarFunction *funcout) const
	Add derivatives of the weight wrt to the central atom position. More...

void	addDerivativeOfCentralAtomPos (const unsigned &iatom, const Tensor &df, MultiColvarFunction *funcout) const
	Add derivative to the central atom position. 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 void	prepare ()
	Do something before the loop. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)
	Reserve any keywords for this particular vessel. More...

Public Attributes
Log &	log
	Reference to the log on which to output details. More...

Protected Member Functions
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...

void	stashBuffers ()
	Store everything that is the buffers. More...

void	setBufferFromStash ()
	Add the contents of the stash to the buffer. More...

Protected Attributes
Communicator &	comm
	A copy of the communicator. More...

Private Attributes
MultiColvarBase *	mycolv

std::vector< unsigned >	start

unsigned	nspace

std::vector< DynamicList < unsigned > >	active_atoms

Detailed Description

Definition at line 34 of file StoreCentralAtomsVessel.h.

Constructor & Destructor Documentation

PLMD::multicolvar::StoreCentralAtomsVessel::StoreCentralAtomsVessel ( const vesselbase::VesselOptions & da )

Constructor.

Definition at line 33 of file StoreCentralAtomsVessel.cpp.

Member Function Documentation

void PLMD::multicolvar::StoreCentralAtomsVessel::addAtomsDerivativeOfWeight	(	const unsigned &	iatom,
		const Vector &	df,
		MultiColvarFunction *	funcout
	)		const

Add derivatives of the weight wrt to the central atom position.

Definition at line 120 of file StoreCentralAtomsVessel.cpp.

void PLMD::multicolvar::StoreCentralAtomsVessel::addAtomsDerivatives	(	const unsigned &	iatom,
		const Vector &	df,
		MultiColvarFunction *	funcout
	)		const

Add derivatives to central atom position.

Definition at line 103 of file StoreCentralAtomsVessel.cpp.

void PLMD::multicolvar::StoreCentralAtomsVessel::addDerivativeOfCentralAtomPos	(	const unsigned &	iatom,
		const Tensor &	df,
		MultiColvarFunction *	funcout
	)		const

Add derivative to the central atom position.

Definition at line 137 of file StoreCentralAtomsVessel.cpp.

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

inlineinherited

Add something to the ith element in the buffer.

Definition at line 252 of file Vessel.h.

bool PLMD::multicolvar::StoreCentralAtomsVessel::applyForce ( std::vector< double > & )

inlinevirtual

This does nothing.

Implements PLMD::vesselbase::Vessel.

Definition at line 52 of file StoreCentralAtomsVessel.h.

bool PLMD::multicolvar::StoreCentralAtomsVessel::calculate ( )

virtual

This makes sure all vectors are stored.

Implements PLMD::vesselbase::Vessel.

Definition at line 61 of file StoreCentralAtomsVessel.cpp.

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

inherited

Check that readin was fine.

Definition at line 111 of file Vessel.cpp.

std::string PLMD::multicolvar::StoreCentralAtomsVessel::description ( )

inlinevirtual

This does nothing.

Implements PLMD::vesselbase::Vessel.

Definition at line 48 of file StoreCentralAtomsVessel.h.

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

protectedinherited

Report an error.

Definition at line 122 of file Vessel.cpp.

void PLMD::multicolvar::StoreCentralAtomsVessel::finish ( )

virtual

This should mpi gather the active atoms.

Implements PLMD::vesselbase::Vessel.

Definition at line 88 of file StoreCentralAtomsVessel.cpp.

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

inlineprotectedinherited

Return a pointer to the action we are working in.

Definition at line 236 of file Vessel.h.

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

protectedinherited

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

Definition at line 84 of file Vessel.cpp.

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

inlineprotectedinherited

Get the value in the ith element of the buffer.

Definition at line 258 of file Vessel.h.

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

inherited

Return the label.

Definition at line 80 of file Vessel.cpp.

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

inherited

Return the name.

Definition at line 76 of file Vessel.cpp.

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

inlineprotectedinherited

Return the value of the neighbor list tolerance.

Definition at line 231 of file Vessel.h.

unsigned PLMD::multicolvar::StoreCentralAtomsVessel::getNumberOfTerms ( )

inlinevirtual

Return the number of terms.

Implements PLMD::vesselbase::Vessel.

Definition at line 44 of file StoreCentralAtomsVessel.h.

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

inlineprotectedinherited

Return the numerical label.

Definition at line 216 of file Vessel.h.

Vector PLMD::multicolvar::StoreCentralAtomsVessel::getPosition ( const unsigned & ivec ) const

Get the orientation of the ith vector.

Definition at line 92 of file StoreCentralAtomsVessel.cpp.

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

inlineprotectedinherited

Return the value of the tolerance.

Definition at line 226 of file Vessel.h.

template<class T >

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

protectedinherited

Parse something from the input.

Definition at line 169 of file Vessel.h.

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

protectedinherited

Parse one keyword as boolean flag.

Definition at line 93 of file Vessel.cpp.

template<class T >

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

protectedinherited

Parse one keyword as std::vector.

Definition at line 184 of file Vessel.h.

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

inlinevirtualinherited

Do something before the loop.

Reimplemented in PLMD::vesselbase::BridgeVessel.

Definition at line 155 of file Vessel.h.

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

staticinherited

Reserve any keywords for this particular vessel.

Definition at line 53 of file Vessel.cpp.

void PLMD::multicolvar::StoreCentralAtomsVessel::resize ( )

virtual

This does the resizing of the buffer.

Implements PLMD::vesselbase::Vessel.

Definition at line 43 of file StoreCentralAtomsVessel.cpp.

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

inlineprotectedinherited

Set the size of the data buffer.

Definition at line 221 of file Vessel.h.

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

inlineprotectedinherited

Set the value of the ith element in the buffer.

Definition at line 246 of file Vessel.h.

void PLMD::vesselbase::Vessel::setBufferFromStash ( )

protectedinherited

Add the contents of the stash to the buffer.

Definition at line 133 of file Vessel.cpp.

void PLMD::vesselbase::Vessel::stashBuffers ( )

protectedinherited

Store everything that is the buffers.

Definition at line 128 of file Vessel.cpp.

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

inlineinherited

Set all the buffer elements to zero.

Definition at line 241 of file Vessel.h.

Member Data Documentation

std::vector< DynamicList<unsigned> > PLMD::multicolvar::StoreCentralAtomsVessel::active_atoms

private

Definition at line 39 of file StoreCentralAtomsVessel.h.

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

protectedinherited

A copy of the communicator.

Definition at line 102 of file Vessel.h.

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

inherited

Reference to the log on which to output details.

Definition at line 135 of file Vessel.h.

MultiColvarBase* PLMD::multicolvar::StoreCentralAtomsVessel::mycolv

private

Definition at line 36 of file StoreCentralAtomsVessel.h.

unsigned PLMD::multicolvar::StoreCentralAtomsVessel::nspace

private

Definition at line 38 of file StoreCentralAtomsVessel.h.

std::vector<unsigned> PLMD::multicolvar::StoreCentralAtomsVessel::start

private

Definition at line 37 of file StoreCentralAtomsVessel.h.

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

multicolvar/StoreCentralAtomsVessel.h
multicolvar/StoreCentralAtomsVessel.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