#include <StoreColvarVessel.h>

Inheritance diagram for PLMD::multicolvar::StoreColvarVessel:

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

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

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

virtual void	local_resizing ()=0
	This makes sure things further down the chain are resized. More...

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

void	finish ()
	Makes sure the dynamic lists are gathered. More...

virtual void	performCalculationUsingAllValues ()=0
	Do the calculation. 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 std::string	description ()=0
	Return a description of the vessel contents. More...

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

virtual bool	applyForce (std::vector< double > &forces)=0
	Retrieve the forces on the quantities in the vessel. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

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

Protected Member Functions
unsigned	getNumberOfStoredColvars () const
	Get the number of stored colvar values. More...

double	getValue (const unsigned &) const
	Get the ith value in the vessel. More...

double	getWeight (const unsigned &) const
	Get the weight of the ith quantity in the vessel. More...

void	addDerivatives (const unsigned &ival, double &pref, Value *value_out)
	Add the derivatives from the value. More...

void	addWeightDerivatives (const unsigned &ival, double &pref, Value *value_out)
	Add the derivatives from the weight of the 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...

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

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

Protected Attributes
bool	diffweight
	Are the weights differentiable. More...

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

Private Attributes
unsigned	bufsize

std::vector< unsigned >	start

MultiColvarBase *	mycolv

std::vector< DynamicList < unsigned > >	active_atoms

Detailed Description

Definition at line 36 of file StoreColvarVessel.h.

Constructor & Destructor Documentation

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

Constructor.

Definition at line 36 of file StoreColvarVessel.cpp.

Member Function Documentation

void PLMD::multicolvar::StoreColvarVessel::addDerivatives	(	const unsigned &	ival,
		double &	pref,
		Value *	value_out
	)

protected

Add the derivatives from the value.

Definition at line 103 of file StoreColvarVessel.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.

void PLMD::multicolvar::StoreColvarVessel::addWeightDerivatives	(	const unsigned &	ival,
		double &	pref,
		Value *	value_out
	)

protected

Add the derivatives from the weight of the value.

Definition at line 117 of file StoreColvarVessel.cpp.

virtual bool PLMD::vesselbase::Vessel::applyForce ( std::vector< double > & forces )

pure virtualinherited

Retrieve the forces on the quantities in the vessel.

Implemented in PLMD::vesselbase::FunctionVessel, PLMD::vesselbase::BridgeVessel, PLMD::multicolvar::StoreCentralAtomsVessel, PLMD::vesselbase::ShortcutVessel, and PLMD::multicolvar::Moments.

bool PLMD::multicolvar::StoreColvarVessel::calculate ( )

virtual

This makes sure all values are stored.

Implements PLMD::vesselbase::Vessel.

Definition at line 62 of file StoreColvarVessel.cpp.

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

inherited

Check that readin was fine.

Definition at line 111 of file Vessel.cpp.

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

pure virtualinherited

Return a description of the vessel contents.

Implemented in PLMD::vesselbase::FunctionVessel, PLMD::vesselbase::BridgeVessel, PLMD::multicolvar::StoreCentralAtomsVessel, PLMD::multicolvar::Moments, and PLMD::vesselbase::ShortcutVessel.

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

protectedinherited

Report an error.

Definition at line 122 of file Vessel.cpp.

void PLMD::multicolvar::StoreColvarVessel::finish ( )

virtual

Makes sure the dynamic lists are gathered.

Implements PLMD::vesselbase::Vessel.

Definition at line 98 of file StoreColvarVessel.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::StoreColvarVessel::getNumberOfStoredColvars ( ) const

inlineprotected

Get the number of stored colvar values.

Definition at line 86 of file StoreColvarVessel.h.

unsigned PLMD::multicolvar::StoreColvarVessel::getNumberOfTerms ( )

inlinevirtual

Return the number of terms.

Implements PLMD::vesselbase::Vessel.

Definition at line 60 of file StoreColvarVessel.h.

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

inlineprotectedinherited

Return the numerical label.

Definition at line 216 of file Vessel.h.

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

inlineprotectedinherited

Return the value of the tolerance.

Definition at line 226 of file Vessel.h.

double PLMD::multicolvar::StoreColvarVessel::getValue ( const unsigned & ival ) const

inlineprotected

Get the ith value in the vessel.

Definition at line 74 of file StoreColvarVessel.h.

double PLMD::multicolvar::StoreColvarVessel::getWeight ( const unsigned & ival ) const

inlineprotected

Get the weight of the ith quantity in the vessel.

Definition at line 80 of file StoreColvarVessel.h.

virtual void PLMD::multicolvar::StoreColvarVessel::local_resizing ( )

pure virtual

This makes sure things further down the chain are resized.

Implemented in PLMD::multicolvar::Moments.

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::multicolvar::StoreColvarVessel::performCalculationUsingAllValues ( )

pure virtual

Do the calculation.

Implemented in PLMD::multicolvar::Moments.

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::multicolvar::StoreColvarVessel::registerKeywords ( Keywords & keys )

static

Definition at line 31 of file StoreColvarVessel.cpp.

void PLMD::multicolvar::StoreColvarVessel::resize ( )

virtual

This does the resizing of the buffer.

Implements PLMD::vesselbase::Vessel.

Definition at line 46 of file StoreColvarVessel.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::StoreColvarVessel::active_atoms

private

Definition at line 41 of file StoreColvarVessel.h.

unsigned PLMD::multicolvar::StoreColvarVessel::bufsize

private

Definition at line 38 of file StoreColvarVessel.h.

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

protectedinherited

A copy of the communicator.

Definition at line 102 of file Vessel.h.

bool PLMD::multicolvar::StoreColvarVessel::diffweight

protected

Are the weights differentiable.

Definition at line 44 of file StoreColvarVessel.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::StoreColvarVessel::mycolv

private

Definition at line 40 of file StoreColvarVessel.h.

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

private

Definition at line 39 of file StoreColvarVessel.h.

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

multicolvar/StoreColvarVessel.h
multicolvar/StoreColvarVessel.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