Base class for all the input Actions. More...

#include <Action.h>

Inheritance diagram for PLMD::Action:

[legend]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

	Action (const ActionOptions &)
	Standard constructor from ActionOptions. More...

virtual	~Action ()
	Destructor. More...

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

virtual void	unlockRequests ()

virtual void	calculate ()=0
	Calculate an Action. More...

virtual void	apply ()=0
	Apply an Action. More...

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

virtual void	update ()
	Update. More...

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

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

virtual std::string	getDocumentation () const

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

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

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

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

virtual void	clearOptions ()

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

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

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

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

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

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

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

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

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

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

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

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

Static Public Member Functions
static void	registerKeywords (Keywords &keys)
	Register all the relevant keywords for the action. More...

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

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

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

Private Member Functions
	Action (const Action &a)
	Copy constructor is disabled (private and unimplemented) More...

Action &	operator= (const Action &a)
	Assignment operator is disabled (private and unimplemented) More...

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

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...

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

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

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

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

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

bool	restart

bool	doCheckPoint

int	replica_index

Detailed Description

Base class for all the input Actions.

The input Actions are more or less corresponding to the directives in the plumed.dat file and are applied in order at each time-step.

Member Typedef Documentation

◆ Dependencies

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

Constructor & Destructor Documentation

◆ Action() [1/2]

PLMD::Action::Action ( const ActionOptions & ao )

explicit

Standard constructor from ActionOptions.

◆ ~Action()

PLMD::Action::~Action ( )

virtual

Destructor.

◆ Action() [2/2]

PLMD::Action::Action ( const Action & a )

explicitprivate

Copy constructor is disabled (private and unimplemented)

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtual

Set action to active.

◆ addDependency()

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

Specify that this Action depends on another one.

◆ apply()

virtual void PLMD::Action::apply ( )

pure virtual

Apply an Action.

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

Implemented in PLMD::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::multicolvar::MultiColvarBase, PLMD::ves::BasisFunctions, PLMD::generic::FitToTemplate, PLMD::ves::TargetDistribution, PLMD::generic::WrapAround, PLMD::ves::VesBias, PLMD::generic::Include, PLMD::generic::DumpAtoms, PLMD::generic::Group, PLMD::generic::EffectiveEnergyDrift, PLMD::analysis::Analysis, PLMD::generic::WholeMolecules, PLMD::multicolvar::MultiColvarDensity, PLMD::adjmat::Sprint, PLMD::generic::DumpMassCharge, PLMD::analysis::Average, PLMD::mapping::Mapping, PLMD::generic::ResetCell, PLMD::multicolvar::DistanceFromContour, PLMD::generic::UpdateIf, PLMD::ves::OutputFesBias, PLMD::generic::Print, PLMD::ves::OutputBasisFunctions, PLMD::ves::OutputTargetDistribution, PLMD::adjmat::OutputCluster, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::manyrestraints::ManyRestraintsBase, PLMD::generic::DumpProjections, PLMD::generic::Debug, PLMD::adjmat::DumpGraph, PLMD::Colvar, PLMD::adjmat::ClusteringBase, PLMD::bias::Bias, PLMD::generic::Time, PLMD::function::Function, PLMD::ActionWithVirtualAtom, PLMD::gridtools::ActionWithInputGrid, PLMD::bias::ReweightBase, PLMD::gridtools::ActionWithIntegral, PLMD::ActionSetup, and PLMD::gridtools::GridPrintingBase.

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtual

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.

◆ calculate()

virtual void PLMD::Action::calculate ( )

pure virtual

Calculate an Action.

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

Implemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::function::Matheval, PLMD::function::FuncSumHills, PLMD::isdb::EMMI, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::eds::EDS, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::generic::FitToTemplate, PLMD::bias::MaxEnt, PLMD::multicolvar::MultiColvarBase, PLMD::generic::WrapAround, PLMD::isdb::Rescale, PLMD::generic::Include, PLMD::function::FuncPathMSD, PLMD::generic::DumpAtoms, PLMD::colvar::Dimer, PLMD::bias::ExtendedLagrangian, PLMD::generic::Group, PLMD::colvar::ContactMap, PLMD::colvar::Distance, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::analysis::Analysis, PLMD::isdb::SAXS, PLMD::generic::WholeMolecules, PLMD::colvar::DRMSD, PLMD::function::Target, PLMD::isdb::JCoupling, PLMD::generic::DumpMassCharge, PLMD::adjmat::Sprint, PLMD::bias::External, PLMD::colvar::Torsion, PLMD::analysis::Average, PLMD::colvar::EEFSolv, PLMD::generic::ResetCell, PLMD::mapping::AdaptivePath, PLMD::colvar::Gyration, PLMD::multicolvar::CenterOfMultiColvar, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::isdb::FretEfficiency, PLMD::multicolvar::DistanceFromContour, PLMD::ves::OutputFesBias, PLMD::colvar::PathMSDBase, PLMD::generic::UpdateIf, PLMD::function::Combine, PLMD::isdb::PRE, PLMD::ves::OutputBasisFunctions, PLMD::generic::Print, PLMD::function::LocalEnsemble, PLMD::ves::OutputTargetDistribution, PLMD::adjmat::OutputCluster, PLMD::vatom::Center, PLMD::vatom::FixedAtom, PLMD::bias::BiasValue, PLMD::generic::Read, PLMD::isdb::NOE, PLMD::generic::RandomExchanges, PLMD::colvar::Puckering, PLMD::function::Piecewise, PLMD::multicolvar::DumpMultiColvar, PLMD::adjmat::ClusterDistribution, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::bias::LWalls, PLMD::isdb::Select, PLMD::vatom::COM, PLMD::bias::UWalls, PLMD::colvar::Position, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::colvar::Constant, PLMD::bias::Restraint, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::adjmat::ClusterProperties, PLMD::function::Ensemble, PLMD::colvar::Energy, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::function::Stats, PLMD::colvar::Dipole, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::Debug, PLMD::colvar::Template, PLMD::generic::DumpProjections, PLMD::manyrestraints::ManyRestraintsBase, PLMD::vatom::Ghost, PLMD::colvar::Cell, PLMD::adjmat::DumpGraph, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::generic::Time, PLMD::adjmat::ClusteringBase, PLMD::gridtools::ActionWithGrid, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::PCARMSD, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, and PLMD::mapping::PathBase.

◆ calculateFromPDB()

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

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()

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

virtual

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::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::multicolvar::MultiColvarBase, PLMD::ActionAtomistic, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithInputVessel.

◆ checkNeedsGradients()

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

inlinevirtual

Check if the action needs gradient.

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

◆ checkNumericalDerivatives()

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

inlinevirtual

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )

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

Check if action should be updated.

◆ cite()

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

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

Clear the dependence list for this Action.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtual

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtual

Set action to inactive.

◆ error()

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

Crash calculation and print documentation.

◆ exit()

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

Exit with error code c.

◆ fclose()

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

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

◆ fflush()

void PLMD::Action::fflush ( )

Tell to the Action to flush open files.

◆ fopen()

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

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)

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

Return true if we are doing at a checkpoint step.

◆ getDependencies()

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

inline

Return dependencies.

◆ getDocumentation()

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

virtual

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

Check if we are on an exchange step.

◆ getKeyword()

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

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

◆ getLabel()

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

inline

Returns the label.

◆ getName()

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

inline

Returns the name.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inline

Return true if we are doing a restart.

◆ getStep()

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

Return the present timestep.

◆ getTime()

double PLMD::Action::getTime ( ) const

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

Return the timestep.

◆ isActive()

bool PLMD::Action::isActive ( ) const

inline

Check if action is active.

◆ isOptionOn()

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

inline

Check if an option is on.

◆ lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtual

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ operator=()

Action& PLMD::Action::operator= ( const Action & a )

private

Assignment operator is disabled (private and unimplemented)

◆ parse()

template<class T >

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

Parse one keyword as generic type.

◆ parseFlag()

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

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T >

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

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
	)

Parse a vector with a number.

◆ parseVector()

template<class T >

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

Parse one keyword as std::vector.

◆ prepare()

void PLMD::Action::prepare ( )

virtual

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::multicolvar::MultiColvarBase, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::generic::Read, PLMD::bias::ReweightTemperature, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

◆ readAtomsFromPDB()

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

inlinevirtual

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::Action::registerKeywords ( Keywords & keys )

static

Register all the relevant keywords for the action.

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtual

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.

Reimplemented in PLMD::analysis::Analysis, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::GridPrintingBase.

◆ setOption()

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

virtual

◆ unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtual

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ update()

virtual void PLMD::Action::update ( )

inlinevirtual

Update.

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

Reimplemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::eds::EDS, PLMD::ves::TargetDistribution, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::isdb::SAXS, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::mapping::AdaptivePath, PLMD::generic::Print, PLMD::ves::OutputFesBias, PLMD::isdb::PRE, PLMD::adjmat::OutputCluster, PLMD::generic::Read, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::vesselbase::ActionWithAveraging, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, and PLMD::gridtools::GridPrintingBase.

◆ warning()

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

Issue a warning.

Member Data Documentation

◆ active

bool PLMD::Action::active

private

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after

private

Actions on which this Action depends.

◆ comm

Communicator& PLMD::Action::comm

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

private

◆ files

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

◆ keywords

const Keywords& PLMD::Action::keywords

◆ label

std::string PLMD::Action::label

private

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

◆ line

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

private

Directive line.

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

◆ log

Log& PLMD::Action::log

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

◆ name

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

private

Name of the directive in the plumed.dat file.

◆ options

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

private

Option that you might have enabled.

◆ plumed

PlumedMain& PLMD::Action::plumed

Reference to main plumed object.

◆ replica_index

int PLMD::Action::replica_index

private

◆ restart

bool PLMD::Action::restart

private

◆ update_from

double PLMD::Action::update_from

private

Update only after this time.

◆ update_until

double PLMD::Action::update_until

private

Update only until this time.

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

core/Action.h
core/Action.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ Action() [1/2]

◆ ~Action()

◆ Action() [2/2]

Member Function Documentation

◆ activate()

◆ addDependency()

◆ apply()

◆ beforeUpdate()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearOptions()

◆ deactivate()

◆ error()

◆ exit()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getCPT()

◆ getDependencies()

◆ getDocumentation()

◆ getExchangeStep()

◆ getKeyword()

◆ getLabel()

◆ getName()

◆ getRestart()

◆ getStep()

◆ getTime()

◆ getTimeStep()

◆ isActive()

◆ isOptionOn()

◆ lockRequests()

◆ operator=()

◆ parse()

◆ parseFlag()

◆ parseNumbered()

◆ parseNumberedVector()

◆ parseVector()

◆ prepare()

◆ readAtomsFromPDB()

◆ registerKeywords()

◆ runFinalJobs()

◆ setOption()

◆ unlockRequests()

◆ update()

◆ warning()

Member Data Documentation

◆ active

◆ after

◆ comm

◆ doCheckPoint

◆ files

◆ keywords

◆ label

◆ line

◆ log

◆ multi_sim_comm

◆ name

◆ options

◆ plumed

◆ replica_index

◆ restart

◆ update_from

◆ update_until