This is used to create PLMD::Action objects that take the output from some other Action as input. More...

#include <ActionWithArguments.h>

Inheritance diagram for PLMD::ActionWithArguments:

[legend]

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

typedef std::set< FILE * >::iterator	files_iterator

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

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

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

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

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

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

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

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

void	addForcesOnArguments (const std::vector< double > &forces)
	Add forces to arguments (used in apply) More...

	ActionWithArguments (const ActionOptions &)

virtual	~ActionWithArguments ()

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

void	lockRequests ()

void	unlockRequests ()

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

void	interpretArgumentList (const std::vector< std::string > &c, std::vector< Value * > &arg)
	Convert a list of argument names into a list of pointers to the values. 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...

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

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

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)
	Registers the list of keywords. 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

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

Private Attributes
std::vector< Value * >	arguments

bool	lockRequestArguments

Detailed Description

This is used to create PLMD::Action objects that take the output from some other Action as input.

This is used in PLMD::Function and PLMD::Bias PLMD::Action objects that inherit from PLMD::ActionWithArguments take values and components calculated in other PLMD::Action objects and use this information to calculate some new function. If you have only one list of arguments you should use the reserved keyword ARG when you use parseArgumentList.

Member Typedef Documentation

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

inherited

typedef std::set<FILE*>::iterator PLMD::Action::files_iterator

inherited

Constructor & Destructor Documentation

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

explicit

virtual PLMD::ActionWithArguments::~ActionWithArguments ( )

inlinevirtual

Member Function Documentation

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

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

inherited

Specify that this Action depends on another one.

void PLMD::ActionWithArguments::addForcesOnArguments ( const std::vector< double > & forces )

Add forces to arguments (used in 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::mapping::PCAVars, PLMD::generic::WrapAround, PLMD::analysis::Analysis, PLMD::generic::Group, PLMD::generic::DumpAtoms, PLMD::generic::EffectiveEnergyDrift, PLMD::multicolvar::MultiColvarBase, PLMD::generic::WholeMolecules, PLMD::generic::DumpMassCharge, PLMD::generic::FitToTemplate, PLMD::multicolvar::Sprint, PLMD::mapping::Mapping, PLMD::IMD, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvarDensity, PLMD::generic::Print, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::generic::Include, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::manyrestraints::ManyRestraintsBase, PLMD::generic::Debug, PLMD::Colvar, PLMD::generic::Time, PLMD::bias::Bias, PLMD::generic::DumpProjections, PLMD::function::Function, PLMD::ActionWithVirtualAtom, and PLMD::ActionSetup.

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

inline

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

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::bias::MetaD, PLMD::bias::PBMetaD, PLMD::function::FuncSumHills, PLMD::mapping::PCAVars, PLMD::function::Matheval, PLMD::generic::WrapAround, PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::RDC, PLMD::bias::ExtendedLagrangian, PLMD::generic::Group, PLMD::colvar::Distance, PLMD::generic::DumpAtoms, PLMD::bias::MovingRestraint, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::WholeMolecules, PLMD::bias::External, PLMD::generic::DumpMassCharge, PLMD::generic::FitToTemplate, PLMD::colvar::Gyration, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::colvar::ContactMap, PLMD::colvar::DRMSD, PLMD::function::Combine, PLMD::bias::BiasValue, PLMD::colvar::NOE, PLMD::IMD, PLMD::vatom::Center, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::RandomExchanges, PLMD::multicolvar::MultiColvarFunction, PLMD::function::Piecewise, PLMD::colvar::PathMSDBase, PLMD::colvar::Position, PLMD::multicolvar::DumpMultiColvar, PLMD::colvar::Torsion, PLMD::multicolvar::MultiColvarDensity, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::vatom::COM, PLMD::generic::Include, PLMD::generic::Print, PLMD::bias::Restraint, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::colvar::Energy, PLMD::multicolvar::MultiColvar, PLMD::function::Sort, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::generic::DumpDerivatives, PLMD::colvar::Constant, PLMD::generic::DumpForces, PLMD::function::Ensemble, PLMD::generic::Debug, PLMD::colvar::Dipole, PLMD::colvar::Puckering, PLMD::manyrestraints::ManyRestraintsBase, PLMD::vatom::Ghost, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::function::Target, PLMD::colvar::Template, PLMD::generic::Time, PLMD::generic::DumpProjections, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::PCARMSD, PLMD::colvar::CoordinationBase, PLMD::ActionSetup, and PLMD::mapping::PathBase.

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

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

virtual

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::mapping::PCAVars, PLMD::analysis::Analysis, and PLMD::mapping::Mapping.

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

inlinevirtualinherited

Check if the action needs gradient.

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

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

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

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

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

inherited

Cite a paper see PlumedMain::cite.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

void PLMD::Action::clearOptions ( )

virtualinherited

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

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

inline

Takes the difference taking into account pbc for arg i.

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

inherited

Crash calculation and print documentation.

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

inherited

Exit with error code c.

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

protected

This changes the arg keyword in the pdb file.

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

inherited

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

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

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)

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

inline

Returns the value of an argument.

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

inline

Returns an array of pointers to the arguments.

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

inlineinherited

Return dependencies.

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

virtualinherited

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

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

inlineinherited

Returns the label.

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

inlineinherited

Returns the name.

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inline

Returns the number of arguments.

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

inline

Return a pointer to specific argument.

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

Get the scalar product between the gradients of two variables.

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

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

inherited

Return the present timestep.

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

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

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

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

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

inlineinherited

Check if an option is on.

void PLMD::ActionWithArguments::lockRequests ( )

inlinevirtual

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::PCAVars, and PLMD::mapping::Mapping.

template<class T >

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

inherited

Parse one keyword as generic type.

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

Parse a list of arguments.

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

inherited

Parse one keyword as boolean flag.

template<class T >

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

inherited

Parse one numbered keyword as generic type.

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.

template<class T >

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

inherited

Parse one keyword as std::vector.

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::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

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.

void PLMD::ActionWithArguments::registerKeywords ( Keywords & keys )

static

Registers the list of keywords.

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

Setup the dependencies.

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.

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

virtualinherited

void PLMD::ActionWithArguments::unlockRequests ( )

inlinevirtual

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::PCAVars, and PLMD::mapping::Mapping.

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::bias::MetaD, PLMD::bias::PBMetaD, PLMD::analysis::Analysis, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::DumpAtoms, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvarDensity, PLMD::generic::Print, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::multicolvar::VolumeTetrapore, and PLMD::generic::DumpProjections.

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

inherited

Issue a warning.

Member Data Documentation

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

private

Communicator& PLMD::Action::comm

inherited

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

inherited

const Keywords& PLMD::Action::keywords

inherited

bool PLMD::ActionWithArguments::lockRequestArguments

private

Log& PLMD::Action::log

inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm

inherited

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

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

core/ActionWithArguments.h
core/ActionWithArguments.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation