This is used to create PLMD::Action objects that are run with some set frequency. More...

#include <ActionPilot.h>

Inheritance diagram for PLMD::ActionPilot:

[legend]

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

Public Member Functions
	ActionPilot (const ActionOptions &)

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

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

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

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...

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)
	Create the keywords for actionPilot. 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 Attributes
int	stride

Detailed Description

This is used to create PLMD::Action objects that are run with some set frequency.

Any PLMD::Action that does not inherit from PLMD::Action is only run when some other Action requires the output from it in order to run. This class is used in PLMD::Bias Action which drives the execution of other Action's. Action's of this kind are executed with a fixed stride which is specified on the directive line with a STRIDE= keyword

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ ActionPilot()

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

explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ apply()

virtual void PLMD::Action::apply ( )

pure virtualinherited

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 ( )

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.

◆ calculate()

virtual void PLMD::Action::calculate ( )

pure virtualinherited

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 )

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()

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::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

inlinevirtualinherited

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ 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.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ error()

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

inherited

Crash calculation and print documentation.

◆ exit()

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

inherited

Exit with error code c.

◆ 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)

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ getDocumentation()

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

virtualinherited

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ 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.

◆ getName()

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

inlineinherited

Returns the name.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getStep()

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

inherited

Return the present timestep.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

Get the stride.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ 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()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtual

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ 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::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 & )

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::ActionPilot::registerKeywords ( Keywords & keys )

static

Create the keywords for actionPilot.

◆ 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.

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

◆ setOption()

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

virtualinherited

◆ setStride()

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

Set the value of the stride.

◆ unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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 ( )

inlinevirtualinherited

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 )

inherited

Issue a warning.

Member Data Documentation

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ files

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

inherited

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ stride

int PLMD::ActionPilot::stride

private

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

core/ActionPilot.h
core/ActionPilot.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ ActionPilot()

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()

◆ getStride()

◆ getTime()

◆ getTimeStep()

◆ isActive()

◆ isOptionOn()

◆ lockRequests()

◆ onStep()

◆ parse()

◆ parseFlag()

◆ parseNumbered()

◆ parseNumberedVector()

◆ parseVector()

◆ prepare()

◆ readAtomsFromPDB()

◆ registerKeywords()

◆ runFinalJobs()

◆ setOption()

◆ setStride()

◆ unlockRequests()

◆ update()

◆ warning()

Member Data Documentation

◆ comm

◆ files

◆ keywords

◆ log

◆ multi_sim_comm

◆ plumed

◆ stride