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

#include <Action.h>

Inheritance diagram for PLMD::Action:

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

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

Public Member Functions
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...

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	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...

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...

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.

Definition at line 60 of file Action.h.

Member Typedef Documentation

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

Definition at line 75 of file Action.h.

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

Definition at line 140 of file Action.h.

Constructor & Destructor Documentation

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

Standard constructor from ActionOptions.

Definition at line 54 of file Action.cpp.

PLMD::Action::~Action ( )

virtual

Destructor.

Definition at line 77 of file Action.cpp.

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

private

Copy constructor is disabled (private and unimplemented)

Member Function Documentation

void PLMD::Action::activate ( )

virtual

Set action to active.

Definition at line 127 of file Action.cpp.

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

Specify that this Action depends on another one.

Definition at line 123 of file Action.cpp.

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::Analysis, PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarBase, PLMD::generic::WholeMolecules, PLMD::generic::DumpAtoms, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Group, PLMD::IMD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::generic::Print, PLMD::generic::Include, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::Debug, PLMD::Colvar, PLMD::generic::Time, PLMD::manyrestraints::ManyRestraintsBase, PLMD::bias::Bias, PLMD::generic::DumpProjections, PLMD::function::Function, PLMD::ActionWithVirtualAtom, and PLMD::ActionSetup.

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::bias::MetaD, PLMD::function::FuncSumHills, PLMD::analysis::Analysis, PLMD::colvar::Distance, PLMD::bias::MovingRestraint, PLMD::function::FuncPathMSD, PLMD::multicolvar::ActionVolume, PLMD::bias::External, PLMD::generic::WholeMolecules, PLMD::generic::DumpAtoms, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Group, PLMD::bias::BiasValue, PLMD::colvar::DRMSD, PLMD::colvar::Gyration, PLMD::IMD, PLMD::colvar::ContactMap, PLMD::function::Matheval, PLMD::generic::RandomExchanges, PLMD::colvar::PathMSDBase, PLMD::generic::Read, PLMD::function::Piecewise, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::multicolvar::MultiColvar, PLMD::generic::Include, PLMD::generic::Print, PLMD::vatom::Center, PLMD::function::Combine, PLMD::bias::Restraint, PLMD::generic::Flush, PLMD::colvar::Energy, PLMD::function::Sort, PLMD::multicolvar::MultiColvarFunction, PLMD::vatom::Ghost, PLMD::colvar::Constant, PLMD::colvar::Torsion, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::vatom::COM, PLMD::generic::Debug, PLMD::colvar::Dipole, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::colvar::Template, PLMD::generic::Time, PLMD::function::Target, PLMD::generic::DumpProjections, PLMD::colvar::RMSD, PLMD::colvar::CoordinationBase, PLMD::manyrestraints::Sphere, and PLMD::ActionSetup.

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

Definition at line 205 of file Action.cpp.

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::ActionAtomistic, PLMD::multicolvar::ActionVolume, PLMD::ActionWithArguments, and PLMD::multicolvar::MultiColvarFunction.

Definition at line 187 of file Action.cpp.

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

inlinevirtual

Check if the action needs gradient.

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

Definition at line 230 of file Action.h.

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

inlinevirtual

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

Definition at line 227 of file Action.h.

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

Definition at line 161 of file Action.cpp.

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

Cite a paper see PlumedMain::cite.

Definition at line 221 of file Action.cpp.

void PLMD::Action::clearDependencies ( )

Clear the dependence list for this Action.

Definition at line 153 of file Action.cpp.

void PLMD::Action::clearOptions ( )

virtual

Definition at line 147 of file Action.cpp.

void PLMD::Action::deactivate ( )

inlinevirtual

Set action to inactive.

Definition at line 369 of file Action.h.

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

Crash calculation and print documentation.

Definition at line 195 of file Action.cpp.

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

Exit with error code c.

Definition at line 183 of file Action.cpp.

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

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

Definition at line 93 of file Action.cpp.

void PLMD::Action::fflush ( )

Tell to the Action to flush open files.

Definition at line 98 of file Action.cpp.

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)

Definition at line 83 of file Action.cpp.

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

inline

Return dependencies.

Definition at line 224 of file Action.h.

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

virtual

Definition at line 157 of file Action.cpp.

bool PLMD::Action::getExchangeStep ( ) const

Check if we are on an exchange step.

Definition at line 217 of file Action.cpp.

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

inline

Returns the label.

Definition at line 263 of file Action.h.

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

inline

Returns the name.

Definition at line 268 of file Action.h.

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

Return the present timestep.

Definition at line 169 of file Action.cpp.

double PLMD::Action::getTime ( ) const

Return the present time.

Definition at line 173 of file Action.cpp.

double PLMD::Action::getTimeStep ( ) const

Return the timestep.

Definition at line 177 of file Action.cpp.

bool PLMD::Action::isActive ( ) const

inline

Check if action is active.

Definition at line 375 of file Action.h.

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

inline

Check if an option is on.

Definition at line 380 of file Action.h.

virtual void PLMD::Action::lockRequests ( )

inlinevirtual

Reimplemented in PLMD::ActionAtomistic, and PLMD::ActionWithArguments.

Definition at line 172 of file Action.h.

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

private

Assignment operator is disabled (private and unimplemented)

template<class T >

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

Parse one keyword as generic type.

Definition at line 273 of file Action.h.

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

Parse one keyword as boolean flag.

Definition at line 104 of file Action.cpp.

template<class T >

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

Parse one numbered keyword as generic type.

Definition at line 300 of file Action.h.

template<class T >

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

Parse a vector with a number.

Definition at line 352 of file Action.h.

template<class T >

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

Parse one keyword as std::vector.

Definition at line 311 of file Action.h.

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::analysis::Analysis, PLMD::function::FuncPathMSD, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

Definition at line 191 of file Action.cpp.

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.

Definition at line 251 of file Action.h.

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

static

Register all the relevant keywords for the action.

Definition at line 49 of file Action.cpp.

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.

Definition at line 193 of file Action.h.

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

virtual

Definition at line 141 of file Action.cpp.

virtual void PLMD::Action::unlockRequests ( )

inlinevirtual

Reimplemented in PLMD::ActionAtomistic, and PLMD::ActionWithArguments.

Definition at line 173 of file Action.h.

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::bias::MetaD, PLMD::analysis::Analysis, PLMD::generic::DumpAtoms, PLMD::generic::Read, PLMD::generic::Print, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, and PLMD::generic::DumpProjections.

Definition at line 188 of file Action.h.

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

Issue a warning.

Definition at line 201 of file Action.cpp.

Member Data Documentation

bool PLMD::Action::active

private

Switch to activate Action on this step.

Definition at line 82 of file Action.h.

Dependencies PLMD::Action::after

private

Actions on which this Action depends.

Definition at line 79 of file Action.h.

Communicator& PLMD::Action::comm

Definition at line 158 of file Action.h.

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

Definition at line 139 of file Action.h.

const Keywords& PLMD::Action::keywords

Definition at line 161 of file Action.h.

std::string PLMD::Action::label

private

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

Definition at line 67 of file Action.h.

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.

Definition at line 72 of file Action.h.

Log& PLMD::Action::log

Reference to the log stream.

Definition at line 93 of file Action.h.

Communicator& PLMD::Action::multi_sim_comm

Definition at line 159 of file Action.h.

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

private

Name of the directive in the plumed.dat file.

Definition at line 64 of file Action.h.

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

private

Option that you might have enabled.

Definition at line 85 of file Action.h.

PlumedMain& PLMD::Action::plumed

Reference to main plumed object.

Definition at line 90 of file Action.h.

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

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation