Provides the keyword EXTENDED_LAGRANGIAN More...

Inheritance diagram for PLMD::bias::ExtendedLagrangian:

[legend]

Public Types
typedef std::vector< Action * >	Dependencies

Public Member Functions
	ExtendedLagrangian (const ActionOptions &)

virtual void	activate ()
	Set action to active. More...

void	addComponent (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with a name like label.name. More...

virtual void	addComponentWithDerivatives (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with a name like label.name that has derivatives. More...

void	addDependency (Action *)
	Specify that this Action depends on another one. More...

void	addForcesOnArguments (const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c)
	Add forces to arguments (used in apply) More...

void	addValue (const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with the name label. More...

virtual void	addValueWithDerivatives (const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with the name label that has derivatives. More...

void	apply () override
	Apply an Action. More...

virtual void	beforeUpdate ()
	Before Update. More...

double	bringBackInPbc (int i, double d1) const
	Takes one value and brings it back into the pbc of argument i. More...

void	calculate () override
	Calculate an Action. More...

virtual bool	calculateConstantValues (const bool &have_atoms)
	Used to calculate constant values in startup. More...

void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...

virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Perform calculation using numerical derivatives N.B. More...

void	calculateNumericalDerivatives (ActionWithValue *a=NULL) override
	Calculate the numerical derivatives N.B. More...

virtual bool	calculateOnUpdate ()
	This is used to check if we run calculate during the update step. More...

virtual ActionAtomistic *	castToActionAtomistic () noexcept

virtual ActionForInterface *	castToActionForInterface () noexcept

virtual ActionShortcut *	castToActionShortcut () noexcept

virtual ActionToGetData *	castToActionToGetData () noexcept

virtual ActionToPutData *	castToActionToPutData () noexcept

virtual ActionWithArguments *	castToActionWithArguments () noexcept

ActionWithArguments *	castToActionWithArguments () noexcept final

virtual ActionWithValue *	castToActionWithValue () noexcept
	Specialized casts, to make PlumedMain run faster. More...

ActionWithValue *	castToActionWithValue () noexcept final
	Specialized casts, to make PlumedMain run faster. More...

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

virtual DomainDecomposition *	castToDomainDecomposition () noexcept

virtual PbcAction *	castToPbcAction () noexcept

virtual void	checkFieldsAllowed ()

bool	checkForDependency (Action *)
	Check that this action does not depend on the action in the argument. More...

virtual bool	checkNeedsGradients () const
	Check if the action needs gradient. More...

virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed. More...

bool	checkNumericalDerivatives () const override
	Check if numerical derivatives should be used. More...

void	checkRead ()
	Check if Action was properly read. More...

bool	checkUpdate () const
	Check if action should be updated. More...

std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. More...

void	clearDependencies ()
	Clear the dependence list for this Action. More...

virtual void	clearDerivatives (const bool &force=false)
	Clear the derivatives of values wrt parameters. More...

virtual void	clearInputForces (const bool &force=false)
	Clear the forces on the values. More...

virtual void	clearOptions ()

void	componentIsNotPeriodic (const std::string &name)
	Set your value component to have no periodicity. More...

void	componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

Value *	copyOutput (const std::string &name) const
	Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...

Value *	copyOutput (const unsigned &n) const
	Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...

virtual void	deactivate ()
	Set action to inactive. More...

double	difference (int, double, double) const
	Takes the difference taking into account pbc for arg i. More...

virtual bool	doNotCalculateDerivatives () const
	Are we not calculating derivatives. More...

void	error (const std::string &msg) const
	Crash calculation and print documentation. More...

bool	exists (const std::string &name) const
	Check if a value with a particular name is present. More...

void	exit (int c=0)
	Exit with error code c. More...

int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...

void	fflush ()
	Tell to the Action to flush open files. More...

FILE *	fopen (const char path, const char mode)
	Opens a file. More...

double	getArgument (const unsigned n) const
	Returns the value of an argument. More...

virtual const std::vector< Value * > &	getArguments () const
	Returns an array of pointers to the arguments. More...

std::string	getComponentsList () const
	get a string that contains all the available components More...

std::vector< std::string >	getComponentsVector () const
	get a vector that contains the label for all the components More...

bool	getCPT () const
	Return true if we are doing at a checkpoint step. More...

std::string	getDefaultString () const
	Get the defaults. More...

const Dependencies &	getDependencies () const
	Return dependencies. More...

bool	getExchangeStep () const
	Check if we are on an exchange step. More...

double	getkBT ()
	Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. More...

std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string. More...

const std::string &	getLabel () const
	Returns the label. More...

virtual void	getMatrixColumnTitles (std::vector< std::string > &argnames) const
	Get the titles to use for the columns of the matrix. More...

const std::string &	getName () const
	Returns the name. More...

virtual unsigned	getNumberOfArguments () const
	Returns the number of arguments. More...

int	getNumberOfComponents () const
	Returns the number of values defined. More...

unsigned	getNumberOfDerivatives () override

virtual std::string	getOutputComponentDescription (const std::string &cname, const Keywords &keys) const
	Get the description of this component. More...

double	getOutputQuantity (const std::string &name) const
	Get the value with a specific name (N.B. if there is no such value this returns zero) More...

double	getOutputQuantity (const unsigned j) const
	Get the value of one of the components of the PLMD::Action. More...

Value *	getPntrToArgument (const unsigned n) const
	Return a pointer to specific argument. More...

double	getProjection (unsigned i, unsigned j) const
	Get the scalar product between the gradients of two variables. More...

bool	getRestart () const
	Return true if we are doing a restart. More...

long long int	getStep () const
	Return the present timestep. More...

int	getStride () const
	Get the stride. More...

double	getTime () const
	Return the present time. More...

double	getTimeStep () const
	Return the timestep. More...

bool	isActive () const
	Check if action is active. More...

bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...

virtual void	lockRequests ()

void	lockRequests () override

virtual bool	onStep () const
	Check if the action is active on this step. More...

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

bool	parseArgumentList (const std::string &key, int i, std::vector< Value * > &args)
	Parse a numbered list of arguments. More...

void	parseArgumentList (const std::string &key, std::vector< Value * > &args)
	Parse a list of arguments. More...

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

template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...

template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...

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

virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

virtual void	readAtomsFromPDB (const PDB &)
	This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...

void	requestArguments (const std::vector< Value * > &arg)
	Setup the dependencies. More...

void	requestExtraDependencies (const std::vector< Value * > &extra)

void	resetStoredTimestep ()
	Set the timestep that is stored in the action to the correct value. More...

virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...

void	setGradients (Value *myval, unsigned &start) const
	Get the gradient for this action. More...

virtual void	setGradientsIfNeeded ()
	Calculate the gradients and store them for all the values (need for projections) More...

void	setNotPeriodic ()
	Set your default value to have no periodicity. More...

virtual void	setOption (const std::string &s)

void	setPeriodic (const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

void	setStride (const int &n)
	Set the value of the stride. More...

void	setupConstantValues (const bool &have_atoms)
	This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...

void	setValue (Value *, double)
	Set the value. More...

virtual void	turnOnDerivatives ()
	Activate the calculation of derivatives. More...

virtual void	unlockRequests ()

void	unlockRequests () override

void	update () override
	Update. More...

void	useNumericalDerivatives ()
	This forces the class to use numerical derivatives. More...

void	warning (const std::string &msg)
	Issue a warning. More...

virtual std::string	writeInGraph () const
	Get the info on what to calculate. More...

Static Public Member Functions
static void	interpretArgumentList (const std::vector< std::string > &c, const ActionSet &as, Action action, std::vector< Value > &arg)
	Convert a list of argument names into a list of pointers to the values. More...

static void	noAnalyticalDerivatives (Keywords &keys)
	Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...

static void	registerKeywords (Keywords &keys)

static void	useCustomisableComponents (Keywords &keys)
	The components in the action will depend on the user. More...

Public Attributes
Communicator &	comm

std::set< FILE * >	files

const Keywords &	keywords

Log &	log
	Reference to the log stream. More...

Communicator &	multi_sim_comm

PlumedMain &	plumed
	Reference to main plumed object. More...

Protected Member Functions
bool	checkForForces ()
	Accumulate the forces from the Values. More...

void	expandArgKeywordInPDB (const PDB &pdb)
	This changes the arg keyword in the pdb file. More...

const Value *	getConstPntrToComponent (int i) const
	Get a const pointer to the ith component. More...

const std::vector< double > &	getForcesToApply () const
	Get the forces to apply. More...

double	getKBoltzmann () const
	Get the value of Boltzmann's constant. More...

Value *	getPntrToComponent (const std::string &name)
	Return a pointer to the value by name. More...

Value *	getPntrToComponent (int i)
	Return a pointer to the component by index. More...

Value *	getPntrToValue ()
	Get a pointer to the default value. More...

const Units &	getUnits () const
	Get the units that we are operating in. More...

void	setBias (double bias)
	set the value of the bias More...

void	setOutputForce (int i, double f)
	set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f More...

void	setValue (const double &d)
	Set the default value (the one without name) More...

bool	usingNaturalUnits () const
	Are we using natural units. More...

Private Member Functions
int	getComponent (const std::string &name) const
	Return the index for the component named name. More...

Private Attributes
bool	active
	Switch to activate Action on this step. More...

Dependencies	after
	Actions on which this Action depends. More...

std::vector< Value * >	arguments

std::string	defaults
	The set of default arguments that we are using. More...

bool	doCheckPoint

std::vector< double >	f

std::vector< double >	ffict

std::vector< double >	fict

std::vector< Value * >	fictValue

bool	firststep
	This finishes setup on first step to check if actions are calculated during update. More...

bool	firsttime

std::vector< double >	forces

std::vector< double >	forcesForApply
	A vector that is used to hold the forces that we will apply on the input quantities. More...

std::vector< double >	friction

std::vector< double >	kappa

double	kbt

std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...

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

bool	lockRequestArguments

const std::string	name
	Name of the directive in the plumed.dat file. More...

bool	never_activate

bool	noderiv
	Are we skipping the calculation of the derivatives. More...

bool	numericalDerivatives
	Are we using numerical derivatives to differentiate. More...

std::set< std::string >	options
	Option that you might have enabled. More...

std::vector< double >	outputForces
	the vector of the forces More...

Random	rand

int	replica_index

bool	restart

int	stride

std::vector< double >	tau

double	timestep
	Save the timestep here. More...

double	update_from
	Update only after this time. More...

double	update_until
	Update only until this time. More...

std::vector< unsigned >	valsToForce

Value *	valueBias
	the pointer to the bias component More...

std::vector< std::unique_ptr< Value > >	values
	An array containing the values for this action. More...

std::vector< double >	vfict

std::vector< double >	vfict_laststep

std::vector< Value * >	vfictValue

Detailed Description

Provides the keyword EXTENDED_LAGRANGIAN

Member Typedef Documentation

◆ Dependencies

typedef std::vector<Action*> PLMD::Action::Dependencies

inherited

Constructor & Destructor Documentation

◆ ExtendedLagrangian()

PLMD::bias::ExtendedLagrangian::ExtendedLagrangian ( const ActionOptions & ao )

explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addComponent()

void PLMD::ActionWithValue::addComponent	(	const std::string &	name,
		const std::vector< unsigned > &	shape = `std::vector<unsigned>()`
	)

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives	(	const std::string &	name,
		const std::vector< unsigned > &	shape = `std::vector<unsigned>()`
	)

virtualinherited

Add a value with a name like label.name that has derivatives.

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ addDependency()

void PLMD::Action::addDependency ( Action * action )

inherited

Specify that this Action depends on another one.

◆ addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments	(	const unsigned &	argstart,
		const std::vector< double > &	forces,
		unsigned &	ind,
		const std::string &	c
	)

inherited

Add forces to arguments (used in apply)

◆ addValue()

void PLMD::ActionWithValue::addValue ( const std::vector< unsigned > & shape = std::vector<unsigned>() )

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( const std::vector< unsigned > & shape = std::vector<unsigned>() )

virtualinherited

Add a value with the name label that has derivatives.

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ apply()

void PLMD::bias::Bias::apply ( )

overridevirtualinherited

Apply an Action.

This method is called one time per step. The set of all Actions is applied in backward order.

Implements PLMD::Action.

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

This is a special method that is called just before the update() method. It can be used by actions that want to do something irrespectively of the fact that update() is active or not. In other words, this is always called, even when action is not active.

Reimplemented in PLMD::generic::UpdateIf.

◆ bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc	(	int	i,
		double	d1
	)		const

inlineinherited

Takes one value and brings it back into the pbc of argument i.

◆ calculate()

void PLMD::bias::ExtendedLagrangian::calculate ( )

overridevirtual

Calculate an Action.

This method is called one or more times per step. The set of all Actions is calculated in forward order.

Implements PLMD::Action.

◆ calculateConstantValues()

bool PLMD::ActionWithArguments::calculateConstantValues ( const bool & have_atoms )

virtualinherited

Used to calculate constant values in startup.

Reimplemented in PLMD::generic::Accumulate, and PLMD::generic::Collect.

◆ calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB & pdb )

inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

◆ calculateNumericalDerivatives() [1/2]

void PLMD::Action::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtualinherited

Perform calculation using numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing.

Reimplemented in PLMD::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.

◆ calculateNumericalDerivatives() [2/2]

void PLMD::ActionWithArguments::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

overridevirtualinherited

Calculate the numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::Action.

Reimplemented in PLMD::ActionWithVector, PLMD::generic::DumpAtoms, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, and PLMD::isdb::MetainferenceBase.

◆ calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )

virtualinherited

This is used to check if we run calculate during the update step.

Reimplemented in PLMD::generic::Accumulate, and PLMD::generic::Collect.

◆ castToActionAtomistic()

virtual ActionAtomistic* PLMD::Action::castToActionAtomistic ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionAtomistic.

◆ castToActionForInterface()

virtual ActionForInterface* PLMD::Action::castToActionForInterface ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

◆ castToActionShortcut()

virtual ActionShortcut* PLMD::Action::castToActionShortcut ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

◆ castToActionToGetData()

virtual ActionToGetData* PLMD::Action::castToActionToGetData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

◆ castToActionToPutData()

virtual ActionToPutData* PLMD::Action::castToActionToPutData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

◆ castToActionWithArguments() [1/2]

virtual ActionWithArguments* PLMD::Action::castToActionWithArguments ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

◆ castToActionWithArguments() [2/2]

ActionWithArguments* PLMD::ActionWithArguments::castToActionWithArguments ( )

inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

◆ castToActionWithValue() [1/2]

virtual ActionWithValue* PLMD::Action::castToActionWithValue ( )

inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ castToActionWithValue() [2/2]

ActionWithValue* PLMD::ActionWithValue::castToActionWithValue ( )

inlinefinalvirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented from PLMD::Action.

◆ castToActionWithVirtualAtom()

virtual ActionWithVirtualAtom* PLMD::Action::castToActionWithVirtualAtom ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

◆ castToDomainDecomposition()

virtual DomainDecomposition* PLMD::Action::castToDomainDecomposition ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

◆ castToPbcAction()

virtual PbcAction* PLMD::Action::castToPbcAction ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap, and PLMD::piv::PIV.

◆ checkForDependency()

bool PLMD::Action::checkForDependency ( Action * action )

inherited

Check that this action does not depend on the action in the argument.

◆ checkForForces()

bool PLMD::ActionWithValue::checkForForces ( )

protectedinherited

Accumulate the forces from the Values.

◆ checkNeedsGradients()

virtual bool PLMD::Action::checkNeedsGradients ( ) const

inlinevirtualinherited

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.

◆ checkNumericalDerivatives() [1/2]

virtual bool PLMD::Action::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

std::string PLMD::Action::cite ( const std::string & s )

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( const bool & force = false )

virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::ActionWithVector, PLMD::ActionForInterface, PLMD::generic::Constant, and PLMD::mapping::PathDisplacements.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( const bool & force = false )

virtualinherited

Clear the forces on the values.

Reimplemented in PLMD::ActionWithVector.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ componentIsNotPeriodic()

void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string & name )

inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

void PLMD::ActionWithValue::componentIsPeriodic	(	const std::string &	name,
		const std::string &	min,
		const std::string &	max
	)

inherited

Set the value to be periodic with a particular domain.

◆ copyOutput() [1/2]

Value * PLMD::ActionWithValue::copyOutput ( const std::string & name ) const

inherited

Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

Value * PLMD::ActionWithValue::copyOutput ( const unsigned & n ) const

inherited

Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ difference()

double PLMD::ActionWithArguments::difference	(	int	i,
		double	d1,
		double	d2
	)		const

inlineinherited

Takes the difference taking into account pbc for arg i.

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

◆ error()

void PLMD::Action::error ( const std::string & msg ) const

inherited

Crash calculation and print documentation.

◆ exists()

bool PLMD::ActionWithValue::exists ( const std::string & name ) const

inherited

Check if a value with a particular name is present.

This is only used in PLMD::ActionWithArguments. You should not use it when manipulating components.

◆ exit()

void PLMD::Action::exit ( int c = 0 )

inherited

Exit with error code c.

◆ expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( const PDB & pdb )

protectedinherited

This changes the arg keyword in the pdb file.

◆ fclose()

int PLMD::Action::fclose ( FILE * fp )

inherited

Closes a file opened with Action::fclose().

◆ fflush()

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

◆ fopen()

FILE * PLMD::Action::fopen	(	const char *	path,
		const char *	mode
	)

inherited

Opens a file.

This is similar to plain fopen, but with some extra functionality.

When opened for writing, processors other than the one with rank 0 just open /dev/null
PlumedMain::fopen is used, so that other tricks may appear (see PlumedMain::fopen)

◆ getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned n ) const

inlineinherited

Returns the value of an argument.

◆ getArguments()

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const

inlinevirtualinherited

Returns an array of pointers to the arguments.

◆ getComponent()

int PLMD::ActionWithValue::getComponent ( const std::string & name ) const

privateinherited

Return the index for the component named name.

◆ getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const

inherited

get a string that contains all the available components

◆ getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const

inherited

get a vector that contains the label for all the components

◆ getConstPntrToComponent()

const Value * PLMD::ActionWithValue::getConstPntrToComponent ( int i ) const

protectedinherited

Get a const pointer to the ith component.

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getDefaultString()

std::string PLMD::Action::getDefaultString ( ) const

inlineinherited

Get the defaults.

◆ getDependencies()

const Dependencies& PLMD::Action::getDependencies ( ) const

inlineinherited

Return dependencies.

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getForcesToApply()

const std::vector< double > & PLMD::ActionWithValue::getForcesToApply ( ) const

inlineprotectedinherited

Get the forces to apply.

◆ getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const

protectedinherited

Get the value of Boltzmann's constant.

◆ getkBT()

double PLMD::Action::getkBT ( )

inherited

Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code.

◆ getKeyword()

std::string PLMD::Action::getKeyword ( const std::string & key )

inherited

Just read one of the keywords and return the whole thing as a string.

◆ getLabel()

const std::string & PLMD::Action::getLabel ( ) const

inlineinherited

Returns the label.

◆ getMatrixColumnTitles()

void PLMD::ActionWithValue::getMatrixColumnTitles ( std::vector< std::string > & argnames ) const

virtualinherited

Get the titles to use for the columns of the matrix.

Reimplemented in PLMD::valtools::VStack, and PLMD::valtools::SelectWithMask.

◆ getName()

const std::string & PLMD::Action::getName ( ) const

inlineinherited

Returns the name.

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inlinevirtualinherited

Returns the number of arguments.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::bias::Bias::getNumberOfDerivatives ( )

inlineoverridevirtualinherited

Implements PLMD::ActionWithValue.

◆ getOutputComponentDescription()

std::string PLMD::ActionWithValue::getOutputComponentDescription	(	const std::string &	cname,
		const Keywords &	keys
	)		const

virtualinherited

Get the description of this component.

Reimplemented in PLMD::generic::Read, PLMD::colvar::PropertyMap, PLMD::function::LocalEnsemble, PLMD::function::Ensemble, PLMD::function::FunctionOfVector< T >, PLMD::opes::ExpansionCVs, PLMD::function::FunctionOfScalar< T >, PLMD::colvar::ColvarFake, PLMD::matrixtools::MatrixTimesVector, PLMD::symfunc::ThreeBodyGFunctions, and PLMD::contour::FindContour.

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string & name ) const

inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getOutputQuantity() [2/2]

double PLMD::ActionWithValue::getOutputQuantity ( const unsigned j ) const

inlineinherited

Get the value of one of the components of the PLMD::Action.

◆ getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned n ) const

inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( const std::string & name )

protectedinherited

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( int i )

protectedinherited

Return a pointer to the component by index.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

inlineprotectedinherited

Get a pointer to the default value.

◆ getProjection()

double PLMD::ActionWithArguments::getProjection	(	unsigned	i,
		unsigned	j
	)		const

inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getStep()

long long int PLMD::Action::getStep ( ) const

inherited

Return the present timestep.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getUnits()

const Units & PLMD::Action::getUnits ( ) const

protectedinherited

Get the units that we are operating in.

◆ interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList	(	const std::vector< std::string > &	c,
		const ActionSet &	as,
		Action *	action,
		std::vector< Value * > &	arg
	)

staticinherited

Convert a list of argument names into a list of pointers to the values.

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isOptionOn()

bool PLMD::Action::isOptionOn ( const std::string & s ) const

inlineinherited

Check if an option is on.

◆ lockRequests() [1/2]

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, and PLMD::contour::DistanceFromContourBase.

◆ lockRequests() [2/2]

void PLMD::ActionWithArguments::lockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, and PLMD::generic::PrintNDX.

◆ noAnalyticalDerivatives()

void PLMD::ActionWithValue::noAnalyticalDerivatives ( Keywords & keys )

staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

bool PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		int	i,
		std::vector< Value * > &	args
	)

inherited

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

void PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		std::vector< Value * > &	args
	)

inherited

Parse a list of arguments.

◆ parseFlag()

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

inherited

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T >

bool PLMD::Action::parseNumbered	(	const std::string &	key,
		const int	no,
		T &	t
	)

inherited

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

template<class T >

bool PLMD::Action::parseNumberedVector	(	const std::string &	key,
		const int	no,
		std::vector< T > &	t
	)

inherited

Parse a vector with a number.

◆ parseVector()

template<class T >

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

inherited

Parse one keyword as std::vector.

◆ prepare()

void PLMD::Action::prepare ( )

virtualinherited

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented in PLMD::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::ActionWithVector, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::dimred::ArrangePoints, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::adjmat::AdjacencyMatrixBase, PLMD::matrixtools::MatrixTimesMatrix, PLMD::valtools::SelectWithMask, PLMD::dimred::ProjectPoints, PLMD::generic::CreateMask, PLMD::matrixtools::DiagonalizeMatrix, PLMD::matrixtools::MatrixTimesVector, PLMD::matrixtools::OuterProduct, PLMD::valtools::VStack, PLMD::landmarks::FarthestPointSampling, PLMD::colvar::CoordinationBase, PLMD::matrixtools::TransposeMatrix, PLMD::matrixtools::Voronoi, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

◆ readAtomsFromPDB()

virtual void PLMD::Action::readAtomsFromPDB ( const PDB & )

inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

◆ registerKeywords()

void PLMD::bias::ExtendedLagrangian::registerKeywords ( Keywords & keys )

static

◆ requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value * > & arg )

inherited

Setup the dependencies.

◆ requestExtraDependencies()

void PLMD::ActionWithArguments::requestExtraDependencies ( const std::vector< Value * > & extra )

inherited

◆ resetStoredTimestep()

void PLMD::Action::resetStoredTimestep ( )

inherited

Set the timestep that is stored in the action to the correct value.

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

◆ setBias()

void PLMD::bias::Bias::setBias ( double bias )

inlineprotectedinherited

set the value of the bias

◆ setGradients()

void PLMD::ActionWithArguments::setGradients	(	Value *	myval,
		unsigned &	start
	)		const

inherited

Get the gradient for this action.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

virtualinherited

Calculate the gradients and store them for all the values (need for projections)

Reimplemented in PLMD::ActionForInterface.

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

◆ setOption()

void PLMD::Action::setOption ( const std::string & s )

virtualinherited

◆ setOutputForce()

void PLMD::bias::Bias::setOutputForce	(	int	i,
		double	f
	)

inlineprotectedinherited

set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f

◆ setPeriodic()

void PLMD::ActionWithValue::setPeriodic	(	const std::string &	min,
		const std::string &	max
	)

inherited

Set the value to be periodic with a particular domain.

◆ setStride()

void PLMD::ActionPilot::setStride ( const int & n )

inherited

Set the value of the stride.

◆ setupConstantValues()

void PLMD::Action::setupConstantValues ( const bool & have_atoms )

inherited

This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.

◆ setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double & d )

inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

void PLMD::ActionWithValue::setValue	(	Value *	,
		double
	)

inherited

Set the value.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::Read, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::function::FunctionOfScalar< T >, PLMD::adjmat::Neighbors, PLMD::eds::EDS, and PLMD::fisst::FISST.

◆ unlockRequests() [1/2]

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, and PLMD::contour::DistanceFromContourBase.

◆ unlockRequests() [2/2]

void PLMD::ActionWithArguments::unlockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, and PLMD::generic::PrintNDX.

◆ update()

void PLMD::bias::ExtendedLagrangian::update ( )

overridevirtual

Update.

This method is called one time per step. The set of all Actions is updated in forward order.

Reimplemented from PLMD::Action.

◆ useCustomisableComponents()

void PLMD::ActionWithValue::useCustomisableComponents ( Keywords & keys )

staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const

protectedinherited

Are we using natural units.

◆ warning()

void PLMD::Action::warning ( const std::string & msg )

inherited

Issue a warning.

◆ writeInGraph()

std::string PLMD::Action::writeInGraph ( ) const

virtualinherited

Get the info on what to calculate.

Reimplemented in PLMD::generic::Print, PLMD::adjmat::ContactMatrix, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::generic::PrintNDX, PLMD::function::FunctionOfScalar< T >, and PLMD::gridtools::FunctionOfGrid< T >.

Member Data Documentation

◆ active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

◆ arguments

std::vector<Value*> PLMD::ActionWithArguments::arguments

privateinherited

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ f

std::vector<double> PLMD::bias::Bias::f

privateinherited

◆ ffict

std::vector<double> PLMD::bias::ExtendedLagrangian::ffict

private

◆ fict

std::vector<double> PLMD::bias::ExtendedLagrangian::fict

private

◆ fictValue

std::vector<Value*> PLMD::bias::ExtendedLagrangian::fictValue

private

◆ files

std::set<FILE*> PLMD::Action::files

inherited

◆ firststep

bool PLMD::ActionWithValue::firststep

privateinherited

This finishes setup on first step to check if actions are calculated during update.

◆ firsttime

bool PLMD::bias::ExtendedLagrangian::firsttime

private

◆ forces

std::vector<double> PLMD::bias::Bias::forces

privateinherited

◆ forcesForApply

std::vector<double> PLMD::ActionWithValue::forcesForApply

privateinherited

A vector that is used to hold the forces that we will apply on the input quantities.

◆ friction

std::vector<double> PLMD::bias::ExtendedLagrangian::friction

private

◆ kappa

std::vector<double> PLMD::bias::ExtendedLagrangian::kappa

private

◆ kbt

double PLMD::bias::ExtendedLagrangian::kbt

private

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ label

std::string PLMD::Action::label

privateinherited

Label of the Action, as set with LABEL= in the plumed.dat file.

◆ line

std::vector<std::string> PLMD::Action::line

privateinherited

Directive line.

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

◆ lockRequestArguments

bool PLMD::ActionWithArguments::lockRequestArguments

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ name

const std::string PLMD::Action::name

privateinherited

Name of the directive in the plumed.dat file.

◆ never_activate

bool PLMD::Action::never_activate

privateinherited

◆ noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

◆ numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives

privateinherited

Are we using numerical derivatives to differentiate.

◆ options

std::set<std::string> PLMD::Action::options

privateinherited

Option that you might have enabled.

◆ outputForces

std::vector<double> PLMD::bias::Bias::outputForces

privateinherited

the vector of the forces

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ rand

Random PLMD::bias::ExtendedLagrangian::rand

private

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ stride

int PLMD::ActionPilot::stride

privateinherited

◆ tau

std::vector<double> PLMD::bias::ExtendedLagrangian::tau

private

◆ timestep

double PLMD::Action::timestep

privateinherited

Save the timestep here.

◆ update_from

double PLMD::Action::update_from

privateinherited

Update only after this time.

◆ update_until

double PLMD::Action::update_until

privateinherited

Update only until this time.

◆ valsToForce

std::vector<unsigned> PLMD::ActionWithValue::valsToForce

privateinherited

◆ valueBias

Value* PLMD::bias::Bias::valueBias

privateinherited

the pointer to the bias component

◆ values

std::vector<std::unique_ptr<Value> > PLMD::ActionWithValue::values

privateinherited

An array containing the values for this action.

◆ vfict

std::vector<double> PLMD::bias::ExtendedLagrangian::vfict

private

◆ vfict_laststep

std::vector<double> PLMD::bias::ExtendedLagrangian::vfict_laststep

private

◆ vfictValue

std::vector<Value*> PLMD::bias::ExtendedLagrangian::vfictValue

private

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

bias/ExtendedLagrangian.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ ExtendedLagrangian()

Member Function Documentation

◆ activate()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ calculate()

◆ calculateConstantValues()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives() [1/2]

◆ calculateNumericalDerivatives() [2/2]

◆ calculateOnUpdate()

◆ castToActionAtomistic()

◆ castToActionForInterface()

◆ castToActionShortcut()

◆ castToActionToGetData()

◆ castToActionToPutData()

◆ castToActionWithArguments() [1/2]

◆ castToActionWithArguments() [2/2]

◆ castToActionWithValue() [1/2]

◆ castToActionWithValue() [2/2]

◆ castToActionWithVirtualAtom()

◆ castToDomainDecomposition()

◆ castToPbcAction()

◆ checkFieldsAllowed()

◆ checkForDependency()

◆ checkForForces()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ difference()

◆ doNotCalculateDerivatives()

◆ error()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getArgument()

◆ getArguments()

◆ getComponent()

◆ getComponentsList()

◆ getComponentsVector()

◆ getConstPntrToComponent()

◆ getCPT()

◆ getDefaultString()

◆ getDependencies()

◆ getExchangeStep()

◆ getForcesToApply()

◆ getKBoltzmann()