#include <ActionWithArguments.h>

Inheritance diagram for PLMD::ActionWithArguments:

[legend]

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

Public Member Functions
	ActionWithArguments (const ActionOptions &)

virtual	~ActionWithArguments ()

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

virtual void	apply ()=0
	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...

virtual void	calculate ()=0
	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...

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

virtual ActionAtomistic *	castToActionAtomistic () noexcept

virtual ActionForInterface *	castToActionForInterface () noexcept

virtual ActionShortcut *	castToActionShortcut () noexcept

virtual ActionToGetData *	castToActionToGetData () noexcept

virtual ActionToPutData *	castToActionToPutData () noexcept

ActionWithArguments *	castToActionWithArguments () noexcept final

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

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

virtual DomainDecomposition *	castToDomainDecomposition () noexcept

virtual PbcAction *	castToPbcAction () noexcept

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...

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	clearOptions ()

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...

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

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...

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

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

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...

void	lockRequests () override

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	setOption (const std::string &s)

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	unlockRequests () override

virtual void	update ()
	Update. 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	registerKeywords (Keywords &keys)
	Registers the list of keywords. 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
void	expandArgKeywordInPDB (const PDB &pdb)
	This changes the arg keyword in the pdb file. More...

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

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

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

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

int	replica_index

bool	restart

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...

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ ActionWithArguments()

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

explicit

◆ ~ActionWithArguments()

virtual PLMD::ActionWithArguments::~ActionWithArguments ( )

inlinevirtual

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.

◆ addForcesOnArguments()

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

Add forces to arguments (used in apply)

◆ 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::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::FitToTemplate, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::generic::DumpAtoms, PLMD::metatensor::MetatensorPlumedAction, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::WholeMolecules, PLMD::generic::ResetCell, PLMD::ves::OutputFesBias, PLMD::generic::Read, PLMD::DomainDecomposition, PLMD::clusters::ClusterDistribution, PLMD::generic::UpdateIf, PLMD::generic::DumpMassCharge, PLMD::wham::Wham, PLMD::generic::Print, PLMD::ves::OutputBasisFunctions, PLMD::ves::OutputTargetDistribution, PLMD::ActionToPutData, PLMD::generic::RandomExchanges, PLMD::colvar::Energy, PLMD::generic::Committor, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::GenericMolInfo, PLMD::generic::Constant, PLMD::dimred::ArrangePoints, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::DumpPDB, PLMD::generic::DumpProjections, PLMD::clusters::ClusterWeights, PLMD::generic::Debug, PLMD::bias::Bias, PLMD::valtools::SelectWithMask, PLMD::ActionShortcut, PLMD::Colvar, PLMD::dimred::ProjectPoints, PLMD::generic::PrintNDX, PLMD::vatom::ArgsToVatom, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::gridtools::FunctionOfGrid< T >, PLMD::clusters::ClusteringBase, PLMD::generic::DumpVector, PLMD::colvar::RMSDVector, PLMD::generic::CreateMask, PLMD::matrixtools::InvertMatrix, PLMD::opes::ExpansionCVs, PLMD::contour::DumpContour, PLMD::valtools::Flatten, PLMD::function::Function, PLMD::generic::Time, PLMD::matrixtools::TransposeMatrix, PLMD::bias::ReweightBase, PLMD::landmarks::FarthestPointSampling, PLMD::matrixtools::MatrixOperationBase, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::Group, PLMD::ActionWithVector, PLMD::ActionWithVirtualAtom, PLMD::mapping::PathReparameterization, PLMD::contour::DistanceFromContourBase, PLMD::mapping::PathDisplacements, PLMD::valtools::Concatenate, PLMD::ActionToGetData, and PLMD::generic::GatherReplicas.

◆ 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

inline

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

◆ 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::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::EMMI, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::function::FuncPathMSD, PLMD::generic::FitToTemplate, PLMD::function::FuncSumHills, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::vatom::Center, PLMD::colvar::Distance, PLMD::metatensor::MetatensorPlumedAction, PLMD::colvar::Dimer, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::colvar::Torsion, PLMD::bias::MovingRestraint, PLMD::bias::External, PLMD::colvar::ContactMap, PLMD::generic::WholeMolecules, PLMD::colvar::ERMSD, PLMD::colvar::Angle, PLMD::crystdistrib::Quaternion, PLMD::isdb::Shadow, PLMD::colvar::Position, PLMD::generic::ResetCell, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::colvar::EEFSolv, PLMD::generic::Read, PLMD::sizeshape::position_linear_proj, PLMD::colvar::Dipole, PLMD::vatom::FixedAtom, PLMD::colvar::PathMSDBase, PLMD::colvar::SelectMassCharge, PLMD::ActionWithMatrix, PLMD::bias::ABMD, PLMD::clusters::ClusterDistribution, PLMD::generic::DumpMassCharge, PLMD::wham::Wham, PLMD::colvar::Gyration, PLMD::isdb::FretEfficiency, PLMD::ves::OutputBasisFunctions, PLMD::generic::UpdateIf, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::generic::Print, PLMD::ves::OutputTargetDistribution, PLMD::isdb::PRE, PLMD::membranefusion::memFusionP, PLMD::sizeshape::position_maha_dist, PLMD::fourier::FourierTransform, PLMD::membranefusion::fusionPoreNucleationP, PLMD::function::LocalEnsemble, PLMD::membranefusion::fusionPoreExpansionP, PLMD::generic::RandomExchanges, PLMD::bias::BiasValue, PLMD::contour::DistanceFromContour, PLMD::isdb::NOE, PLMD::maze::Loss, PLMD::bias::Restraint, PLMD::colvar::DihedralCorrelation, PLMD::colvar::Puckering, PLMD::colvar::Plane, PLMD::ActionForInterface, PLMD::generic::Committor, PLMD::vatom::Ghost, PLMD::function::FunctionOfVector< T >, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::function::Ensemble, PLMD::GenericMolInfo, PLMD::generic::Constant, PLMD::function::Stats, PLMD::dimred::ArrangePoints, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::DumpPDB, PLMD::generic::Debug, PLMD::gridtools::FindGridOptimum, PLMD::clusters::ClusterWeights, PLMD::generic::DumpProjections, PLMD::dimred::ProjectPoints, PLMD::valtools::SelectWithMask, PLMD::colvar::Template, PLMD::ActionShortcut, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::vatom::ArgsToVatom, PLMD::generic::DumpVector, PLMD::colvar::Cell, PLMD::opes::ExpansionCVs, PLMD::matrixtools::DiagonalizeMatrix, PLMD::valtools::Concatenate, PLMD::clusters::ClusteringBase, PLMD::generic::CreateMask, PLMD::colvar::RMSDVector, PLMD::contour::DumpContour, PLMD::function::FunctionOfScalar< T >, PLMD::matrixtools::InvertMatrix, PLMD::colvar::MultiColvarTemplate< T >, PLMD::colvar::Volume, PLMD::generic::PrintNDX, PLMD::generic::Time, PLMD::valtools::Flatten, PLMD::colvar::ColvarFake, PLMD::landmarks::FarthestPointSampling, PLMD::matrixtools::TransposeMatrix, PLMD::mapping::GeometricPath, PLMD::symfunc::ThreeBodyGFunctions, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::refdist::MatrixProductDiagonal, PLMD::colvar::PCARMSD, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::colvar::RMSD, PLMD::gridtools::ActionWithGrid, PLMD::Group, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::piv::PIV, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, PLMD::fisst::FISST, PLMD::isdb::Rescale, PLMD::maze::OptimizerBias, PLMD::funnel::Funnel, PLMD::function::FuncPathGeneral, PLMD::funnel::FUNNEL_PS, PLMD::function::annfunc::ANN, PLMD::isdb::Caliber, PLMD::maze::Optimizer, PLMD::s2cm::S2ContactModel, PLMD::colvar::ProjectionOnAxis, PLMD::isdb::Select, PLMD::mapping::PathReparameterization, PLMD::volumes::ActionVolume, PLMD::mapping::PathDisplacements, PLMD::ActionToGetData, PLMD::generic::GatherReplicas, and PLMD::contour::DistanceFromSphericalContour.

◆ calculateConstantValues()

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

virtual

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()

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

overridevirtual

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.

◆ 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()

ActionWithArguments* PLMD::ActionWithArguments::castToActionWithArguments ( )

inlinefinalvirtualnoexcept

Reimplemented from PLMD::Action.

◆ castToActionWithValue()

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

inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ 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.

◆ checkForDependency()

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

inherited

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

◆ 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.

◆ difference()

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

inline

Takes the difference taking into account pbc for arg i.

◆ 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.

◆ expandArgKeywordInPDB()

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

protected

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

inline

Returns the value of an argument.

◆ getArguments()

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

inlinevirtual

Returns an array of pointers to the arguments.

◆ 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.

◆ 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.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inlinevirtual

Returns the number of arguments.

◆ getPntrToArgument()

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

inline

Return a pointer to specific argument.

◆ getProjection()

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

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.

◆ 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
	)

static

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()

void PLMD::ActionWithArguments::lockRequests ( )

inlineoverridevirtual

Reimplemented from PLMD::Action.

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

◆ 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
	)

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

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

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::ActionWithArguments::registerKeywords ( Keywords & keys )

static

Registers the list of keywords.

◆ requestArguments()

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

Setup the dependencies.

◆ requestExtraDependencies()

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

◆ 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.

◆ setGradients()

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

Get the gradient for this action.

◆ setOption()

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

virtualinherited

◆ 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.

◆ unlockRequests()

void PLMD::ActionWithArguments::unlockRequests ( )

inlineoverridevirtual

Reimplemented from PLMD::Action.

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

◆ 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::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::volumes::VolumeTetrapore, PLMD::volumes::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpPDB, PLMD::generic::DumpProjections, PLMD::generic::PrintNDX, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::generic::DumpVector, PLMD::contour::DumpContour, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::mapping::PathReparameterization, and PLMD::mapping::PathDisplacements.

◆ 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

private

◆ 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

◆ files

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

inherited

◆ 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

private

◆ 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

◆ options

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

privateinherited

Option that you might have enabled.

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ 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.

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

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ ActionWithArguments()

◆ ~ActionWithArguments()

Member Function Documentation

◆ activate()

◆ addDependency()

◆ addForcesOnArguments()

◆ apply()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ calculate()

◆ calculateConstantValues()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ castToActionAtomistic()

◆ castToActionForInterface()

◆ castToActionShortcut()

◆ castToActionToGetData()

◆ castToActionToPutData()

◆ castToActionWithArguments()

◆ castToActionWithValue()

◆ castToActionWithVirtualAtom()

◆ castToDomainDecomposition()

◆ castToPbcAction()

◆ checkForDependency()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearOptions()

◆ deactivate()

◆ difference()

◆ error()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getArgument()

◆ getArguments()

◆ getCPT()

◆ getDefaultString()

◆ getDependencies()

◆ getExchangeStep()

◆ getKBoltzmann()

◆ getkBT()

◆ getKeyword()

◆ getLabel()

◆ getName()

◆ getNumberOfArguments()

◆ getPntrToArgument()

◆ getProjection()

◆ getRestart()

◆ getStep()

◆ getTime()

◆ getTimeStep()

◆ getUnits()

◆ interpretArgumentList()

◆ isActive()

◆ isOptionOn()

◆ lockRequests()

◆ parse()

◆ parseArgumentList() [1/2]

◆ parseArgumentList() [2/2]

◆ parseFlag()

◆ parseNumbered()

◆ parseNumberedVector()

◆ parseVector()

◆ prepare()

◆ readAtomsFromPDB()