Provides the keyword METAD More...

Inheritance diagram for PLMD::bias::MetaD:

[legend]

Classes
struct	Gaussian

struct	TemperingSpecs

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

Public Member Functions
	MetaD (const ActionOptions &)

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

void	addComponent (const std::string &name)
	Add a value with a name like label.name. More...

void	addComponentWithDerivatives (const std::string &name)
	Add a value with a name like label.name that has derivatives. More...

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

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

void	addValue ()
	Add a value with the name label. More...

void	addValueWithDerivatives ()
	Add a value with the name label that has derivatives. More...

void	apply () override
	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...

void	calculate () override
	Calculate an Action. More...

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

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

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

virtual void	checkFieldsAllowed ()

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

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

bool	checkNumericalDerivatives () const override
	Check if numerical derivatives should be used. 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	clearDerivatives ()
	Clear the derivatives of values wrt parameters. More...

void	clearInputForces ()
	Clear the forces on the values. More...

virtual void	clearOptions ()

void	componentIsNotPeriodic (const std::string &name)
	Set your value component to have no periodicity. More...

void	componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

Value *	copyOutput (const std::string &name) const
	Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...

Value *	copyOutput (const unsigned &n) const
	Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...

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...

virtual bool	doNotCalculateDerivatives () const
	Are we not calculating derivatives. More...

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

bool	exists (const std::string &name) const
	Check if a value with a particular name is present. 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...

std::string	getComponentsList () const
	get a string that contains all the available components More...

std::vector< std::string >	getComponentsVector () const
	get a vector that contains the label for all the components 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...

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...

int	getNumberOfComponents () const
	Returns the number of values defined. More...

unsigned	getNumberOfDerivatives () override

double	getOutputQuantity (const std::string &name) const
	Get the value with a specific name (N.B. if there is no such value this returns zero) More...

double	getOutputQuantity (const unsigned j) const
	Get the value of one of the components of the PLMD::Action. More...

Value *	getPntrToArgument (const unsigned n)
	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...

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

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

double	getTimeStep () const
	Return the timestep. 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	isActive () const
	Check if action is active. More...

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

virtual void	lockRequests ()

void	lockRequests () override

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

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)

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

void	setGradientsIfNeeded ()
	Calculate the gradients and store them for all the values (need for projections) More...

void	setNotPeriodic ()
	Set your default value to have no periodicity. More...

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

void	setPeriodic (const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

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

void	setValue (Value *, double)
	Set the value. More...

virtual void	turnOnDerivatives ()
	Activate the calculation of derivatives. More...

virtual void	unlockRequests ()

void	unlockRequests () override

void	update () override
	Update. More...

void	useNumericalDerivatives ()
	This forces the class to use numerical derivatives. More...

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

Static Public Member Functions
static void	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...

static void	noAnalyticalDerivatives (Keywords &keys)
	Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...

static void	registerKeywords (Keywords &keys)

static void	useCustomisableComponents (Keywords &keys)
	The components in the action will depend on the user. 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...

Value *	getPntrToComponent (const std::string &name)
	Return a pointer to the value by name. More...

Value *	getPntrToComponent (int i)
	Return a pointer to the component by index. More...

Value *	getPntrToValue ()
	Get a pointer to the default value. More...

void	setBias (double bias)
	set the value of the bias More...

void	setOutputForce (int i, double f)
	set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f More...

void	setValue (const double &d)
	Set the default value (the one without name) More...

Private Member Functions
void	addGaussian (const Gaussian &)

void	computeReweightingFactor ()

double	evaluateGaussian (const std::vector< double > &, const Gaussian &)

double	evaluateGaussianAndDerivatives (const std::vector< double > &, const Gaussian &, std::vector< double > &, std::vector< double > &)

double	getBias (const std::vector< double > &)

double	getBiasAndDerivatives (const std::vector< double > &, std::vector< double > &)

int	getComponent (const std::string &name) const
	Return the index for the component named name. More...

double	getGaussianNormalization (const Gaussian &)

std::vector< unsigned >	getGaussianSupport (const Gaussian &)

double	getHeight (const std::vector< double > &)

double	getTransitionBarrierBias ()

void	logTemperingSpecs (const TemperingSpecs &t_specs)

void	noStretchWarning ()

void	readGaussians (IFile *)

void	readTemperingSpecs (TemperingSpecs &t_specs)

bool	scanOneHill (IFile *ifile, std::vector< Value > &v, std::vector< double > &center, std::vector< double > &sigma, double &height, bool &multivariate)
	takes a pointer to the file and a template std::string with values v and gives back the next center, sigma and height More...

void	temperHeight (double &height, const TemperingSpecs &t_specs, const double tempering_bias)

void	updateFrequencyAdaptiveStride ()

void	updateNlist ()

void	writeGaussian (const Gaussian &, OFile &)

Static Private Member Functions
static void	registerTemperingKeywords (const std::string &name_stem, const std::string &name, Keywords &keys)

Private Attributes
double	acc_

double	acc_restart_mean_

bool	acceleration_

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

int	adaptive_

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

std::vector< Value * >	arguments

double	biasf_

std::unique_ptr< GridBase >	BiasGrid_

bool	calc_max_bias_

bool	calc_rct_

bool	calc_transition_bias_

bool	calc_work_

int	current_stride_

double	dampfactor_

std::string	defaults
	The set of default arguments that we are using. More...

bool	doCheckPoint

bool	doInt_

int	fa_max_stride_

double	fa_min_acceleration_

int	fa_update_frequency_

std::unique_ptr< FlexibleBin >	flexbin_

bool	flying_

std::string	fmt_

bool	freq_adaptive_

bool	grid_

OFile	gridfile_

double	height0_

std::vector< Gaussian >	hills_

OFile	hillsOfile_

std::vector< std::unique_ptr< IFile > >	ifiles_

std::vector< std::string >	ifilesnames_

bool	isFirstStep_

double	kbt_

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

double	lowI_

double	max_bias_

unsigned	mpi_nw_

std::string	mw_dir_

int	mw_id_

int	mw_n_

int	mw_rstride_

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

bool	nlist_

std::vector< double >	nlist_center_

std::vector< double >	nlist_dev2_

std::vector< Gaussian >	nlist_hills_

std::array< double, 2 >	nlist_param_

unsigned	nlist_steps_

bool	nlist_update_

bool	noderiv
	Are we skipping the calculation of the derivatives. More...

bool	noStretchWarningDone =false

bool	numericalDerivatives
	Are we using numerical derivatives to differentiate. More...

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

std::vector< double >	outputForces
	the vector of the forces More...

unsigned	rct_ustride_

int	replica_index

bool	restart

double	reweight_factor_

std::vector< double >	sigma0_

std::vector< double >	sigma0max_

std::vector< double >	sigma0min_

bool	storeOldGrids_

double	stretchA =1.0

double	stretchB =0.0

int	stride

int	stride_

std::string	targetfilename_

std::unique_ptr< GridBase >	TargetGrid_

double	transition_bias_

std::vector< std::vector< double > >	transitionwells_

struct TemperingSpecs	tt_specs_

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

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

double	uppI_

Value *	valueBias
	the pointer to the bias component More...

std::vector< std::unique_ptr< Value > >	values
	An array containing the values for this action. More...

bool	walkers_mpi_

bool	welltemp_

int	wgridstride_

double	work_

Static Private Attributes
static const size_t	n_tempering_options_ = 1

static const std::string	tempering_names_ [1][2] = {{"TT", "transition tempered"}}

Detailed Description

Provides the keyword METAD

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ MetaD()

PLMD::bias::MetaD::MetaD ( const ActionOptions & ao )

explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string & name )

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string & name )

inherited

Add a value with a name like label.name that has derivatives.

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addForcesOnArguments()

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

inherited

Add forces to arguments (used in apply)

◆ addGaussian()

void PLMD::bias::MetaD::addGaussian ( const Gaussian & hill )

private

◆ addValue()

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

◆ apply()

void PLMD::bias::Bias::apply ( )

overridevirtualinherited

Apply an Action.

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

Implements PLMD::Action.

◆ 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

inlineinherited

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

◆ calculate()

void PLMD::bias::MetaD::calculate ( )

overridevirtual

Calculate an Action.

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

Implements PLMD::Action.

◆ 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() [1/2]

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

◆ calculateNumericalDerivatives() [2/2]

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

overridevirtualinherited

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::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::mapping::PCAVars.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap, and PLMD::piv::PIV.

◆ checkNeedsGradients()

bool PLMD::bias::MetaD::checkNeedsGradients ( ) const

overridevirtual

Check if the action needs gradient.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [1/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ 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.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ componentIsNotPeriodic()

void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string & name )

inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

void PLMD::ActionWithValue::componentIsPeriodic	(	const std::string &	name,
		const std::string &	min,
		const std::string &	max
	)

inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

void PLMD::ActionWithValue::componentsAreNotOptional ( Keywords & keys )

staticinherited

Puts a message into the manual that the components always output.

◆ computeReweightingFactor()

void PLMD::bias::MetaD::computeReweightingFactor ( )

private

◆ copyOutput() [1/2]

Value * PLMD::ActionWithValue::copyOutput ( const std::string & name ) const

inherited

Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

Value * PLMD::ActionWithValue::copyOutput ( const unsigned & n ) const

inherited

Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ difference()

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

inlineinherited

Takes the difference taking into account pbc for arg i.

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ error()

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

inherited

Crash calculation and print documentation.

◆ evaluateGaussian()

double PLMD::bias::MetaD::evaluateGaussian	(	const std::vector< double > &	cv,
		const Gaussian &	hill
	)

private

◆ evaluateGaussianAndDerivatives()

double PLMD::bias::MetaD::evaluateGaussianAndDerivatives	(	const std::vector< double > &	cv,
		const Gaussian &	hill,
		std::vector< double > &	der,
		std::vector< double > &	dp_
	)

private

◆ exists()

bool PLMD::ActionWithValue::exists ( const std::string & name ) const

inherited

Check if a value with a particular name is present.

This is only used in PLMD::ActionWithArguments. You should not use it when manipulating components.

◆ exit()

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

inherited

Exit with error code c.

◆ expandArgKeywordInPDB()

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

protectedinherited

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

inlineinherited

Returns the value of an argument.

◆ getArguments()

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

inlinevirtualinherited

Returns an array of pointers to the arguments.

◆ getBias()

double PLMD::bias::MetaD::getBias ( const std::vector< double > & cv )

private

◆ getBiasAndDerivatives()

double PLMD::bias::MetaD::getBiasAndDerivatives	(	const std::vector< double > &	cv,
		std::vector< double > &	der
	)

private

◆ getComponent()

int PLMD::ActionWithValue::getComponent ( const std::string & name ) const

privateinherited

Return the index for the component named name.

◆ getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const

inherited

get a string that contains all the available components

◆ getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const

inherited

get a vector that contains the label for all the components

◆ 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.

◆ getGaussianNormalization()

double PLMD::bias::MetaD::getGaussianNormalization ( const Gaussian & hill )

private

◆ getGaussianSupport()

std::vector< unsigned > PLMD::bias::MetaD::getGaussianSupport ( const Gaussian & hill )

private

◆ getHeight()

double PLMD::bias::MetaD::getHeight ( const std::vector< double > & cv )

private

◆ 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

inlinevirtualinherited

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::bias::Bias::getNumberOfDerivatives ( )

inlineoverridevirtualinherited

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string & name ) const

inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getOutputQuantity() [2/2]

double PLMD::ActionWithValue::getOutputQuantity ( const unsigned j ) const

inlineinherited

Get the value of one of the components of the PLMD::Action.

◆ getPntrToArgument()

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

inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( const std::string & name )

protectedinherited

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( int i )

protectedinherited

Return a pointer to the component by index.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

◆ getProjection()

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

inherited

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.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getTransitionBarrierBias()

double PLMD::bias::MetaD::getTransitionBarrierBias ( )

private

◆ interpretArgumentList()

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

inherited

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() [1/2]

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

◆ lockRequests() [2/2]

void PLMD::ActionWithArguments::lockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

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

◆ logTemperingSpecs()

void PLMD::bias::MetaD::logTemperingSpecs ( const TemperingSpecs & t_specs )

private

◆ noAnalyticalDerivatives()

void PLMD::ActionWithValue::noAnalyticalDerivatives ( Keywords & keys )

staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

◆ noStretchWarning()

void PLMD::bias::MetaD::noStretchWarning ( )

inlineprivate

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

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.

◆ parseArgumentList() [1/2]

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

inherited

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

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

inherited

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::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::colvar::CoordinationBase, 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.

◆ readGaussians()

void PLMD::bias::MetaD::readGaussians ( IFile * ifile )

private

◆ readTemperingSpecs()

void PLMD::bias::MetaD::readTemperingSpecs ( TemperingSpecs & t_specs )

private

◆ registerKeywords()

void PLMD::bias::MetaD::registerKeywords ( Keywords & keys )

static

◆ registerTemperingKeywords()

void PLMD::bias::MetaD::registerTemperingKeywords	(	const std::string &	name_stem,
		const std::string &	name,
		Keywords &	keys
	)

staticprivate

◆ requestArguments()

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

inherited

Setup the dependencies.

◆ requestExtraDependencies()

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

inherited

◆ 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::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.

◆ scanOneHill()

bool PLMD::bias::MetaD::scanOneHill	(	IFile *	ifile,
		std::vector< Value > &	v,
		std::vector< double > &	center,
		std::vector< double > &	sigma,
		double &	height,
		bool &	multivariate
	)

private

takes a pointer to the file and a template std::string with values v and gives back the next center, sigma and height

◆ setBias()

void PLMD::bias::Bias::setBias ( double bias )

inlineprotectedinherited

set the value of the bias

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

Calculate the gradients and store them for all the values (need for projections)

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

◆ setOption()

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

virtualinherited

◆ setOutputForce()

void PLMD::bias::Bias::setOutputForce	(	int	i,
		double	f
	)

inlineprotectedinherited

set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f

◆ setPeriodic()

void PLMD::ActionWithValue::setPeriodic	(	const std::string &	min,
		const std::string &	max
	)

inherited

Set the value to be periodic with a particular domain.

◆ setStride()

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

inherited

Set the value of the stride.

◆ setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double & d )

inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

void PLMD::ActionWithValue::setValue	(	Value *	,
		double
	)

inherited

Set the value.

◆ temperHeight()

void PLMD::bias::MetaD::temperHeight	(	double &	height,
		const TemperingSpecs &	t_specs,
		const double	tempering_bias
	)

private

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::isdb::EMMI, PLMD::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ClusterAnalysisBase, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, PLMD::gridtools::ActionWithIntegral, PLMD::eds::EDS, and PLMD::fisst::FISST.

◆ unlockRequests() [1/2]

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

◆ unlockRequests() [2/2]

void PLMD::ActionWithArguments::unlockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

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

◆ update()

void PLMD::bias::MetaD::update ( )

overridevirtual

Update.

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

Reimplemented from PLMD::Action.

◆ updateFrequencyAdaptiveStride()

void PLMD::bias::MetaD::updateFrequencyAdaptiveStride ( )

private

◆ updateNlist()

void PLMD::bias::MetaD::updateNlist ( )

private

◆ useCustomisableComponents()

void PLMD::ActionWithValue::useCustomisableComponents ( Keywords & keys )

staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ warning()

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

inherited

Issue a warning.

◆ writeGaussian()

void PLMD::bias::MetaD::writeGaussian	(	const Gaussian &	hill,
		OFile &	file
	)

private

Member Data Documentation

◆ acc_

double PLMD::bias::MetaD::acc_

private

◆ acc_restart_mean_

double PLMD::bias::MetaD::acc_restart_mean_

private

◆ acceleration_

bool PLMD::bias::MetaD::acceleration_

private

◆ active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

◆ adaptive_

int PLMD::bias::MetaD::adaptive_

private

◆ after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

◆ arguments

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

privateinherited

◆ biasf_

double PLMD::bias::MetaD::biasf_

private

◆ BiasGrid_

std::unique_ptr<GridBase> PLMD::bias::MetaD::BiasGrid_

private

◆ calc_max_bias_

bool PLMD::bias::MetaD::calc_max_bias_

private

◆ calc_rct_

bool PLMD::bias::MetaD::calc_rct_

private

◆ calc_transition_bias_

bool PLMD::bias::MetaD::calc_transition_bias_

private

◆ calc_work_

bool PLMD::bias::MetaD::calc_work_

private

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ current_stride_

int PLMD::bias::MetaD::current_stride_

private

◆ dampfactor_

double PLMD::bias::MetaD::dampfactor_

private

◆ defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ doInt_

bool PLMD::bias::MetaD::doInt_

private

◆ fa_max_stride_

int PLMD::bias::MetaD::fa_max_stride_

private

◆ fa_min_acceleration_

double PLMD::bias::MetaD::fa_min_acceleration_

private

◆ fa_update_frequency_

int PLMD::bias::MetaD::fa_update_frequency_

private

◆ files

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

inherited

◆ flexbin_

std::unique_ptr<FlexibleBin> PLMD::bias::MetaD::flexbin_

private

◆ flying_

bool PLMD::bias::MetaD::flying_

private

◆ fmt_

std::string PLMD::bias::MetaD::fmt_

private

◆ freq_adaptive_

bool PLMD::bias::MetaD::freq_adaptive_

private

◆ grid_

bool PLMD::bias::MetaD::grid_

private

◆ gridfile_

OFile PLMD::bias::MetaD::gridfile_

private

◆ height0_

double PLMD::bias::MetaD::height0_

private

◆ hills_

std::vector<Gaussian> PLMD::bias::MetaD::hills_

private

◆ hillsOfile_

OFile PLMD::bias::MetaD::hillsOfile_

private

◆ ifiles_

std::vector<std::unique_ptr<IFile> > PLMD::bias::MetaD::ifiles_

private

◆ ifilesnames_

std::vector<std::string> PLMD::bias::MetaD::ifilesnames_

private

◆ isFirstStep_

bool PLMD::bias::MetaD::isFirstStep_

private

◆ kbt_

double PLMD::bias::MetaD::kbt_

private

◆ 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

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ lowI_

double PLMD::bias::MetaD::lowI_

private

◆ max_bias_

double PLMD::bias::MetaD::max_bias_

private

◆ mpi_nw_

unsigned PLMD::bias::MetaD::mpi_nw_

private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ mw_dir_

std::string PLMD::bias::MetaD::mw_dir_

private

◆ mw_id_

int PLMD::bias::MetaD::mw_id_

private

◆ mw_n_

int PLMD::bias::MetaD::mw_n_

private

◆ mw_rstride_

int PLMD::bias::MetaD::mw_rstride_

private

◆ n_tempering_options_

const size_t PLMD::bias::MetaD::n_tempering_options_ = 1

staticprivate

◆ name

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

privateinherited

Name of the directive in the plumed.dat file.

◆ nlist_

bool PLMD::bias::MetaD::nlist_

private

◆ nlist_center_

std::vector<double> PLMD::bias::MetaD::nlist_center_

private

◆ nlist_dev2_

std::vector<double> PLMD::bias::MetaD::nlist_dev2_

private

◆ nlist_hills_

std::vector<Gaussian> PLMD::bias::MetaD::nlist_hills_

private

◆ nlist_param_

std::array<double,2> PLMD::bias::MetaD::nlist_param_

private

◆ nlist_steps_

unsigned PLMD::bias::MetaD::nlist_steps_

private

◆ nlist_update_

bool PLMD::bias::MetaD::nlist_update_

private

◆ noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

◆ noStretchWarningDone

bool PLMD::bias::MetaD::noStretchWarningDone =false

private

◆ numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives

privateinherited

Are we using numerical derivatives to differentiate.

◆ options

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

privateinherited

Option that you might have enabled.

◆ outputForces

std::vector<double> PLMD::bias::Bias::outputForces

privateinherited

the vector of the forces

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ rct_ustride_

unsigned PLMD::bias::MetaD::rct_ustride_

private

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ reweight_factor_

double PLMD::bias::MetaD::reweight_factor_

private

◆ sigma0_

std::vector<double> PLMD::bias::MetaD::sigma0_

private

◆ sigma0max_

std::vector<double> PLMD::bias::MetaD::sigma0max_

private

◆ sigma0min_

std::vector<double> PLMD::bias::MetaD::sigma0min_

private

◆ storeOldGrids_

bool PLMD::bias::MetaD::storeOldGrids_

private

◆ stretchA

double PLMD::bias::MetaD::stretchA =1.0

private

◆ stretchB

double PLMD::bias::MetaD::stretchB =0.0

private

◆ stride

int PLMD::ActionPilot::stride

privateinherited

◆ stride_

int PLMD::bias::MetaD::stride_

private

◆ targetfilename_

std::string PLMD::bias::MetaD::targetfilename_

private

◆ TargetGrid_

std::unique_ptr<GridBase> PLMD::bias::MetaD::TargetGrid_

private

◆ tempering_names_

const std::string PLMD::bias::MetaD::tempering_names_ = {{"TT", "transition tempered"}}

staticprivate

◆ transition_bias_

double PLMD::bias::MetaD::transition_bias_

private

◆ transitionwells_

std::vector<std::vector<double> > PLMD::bias::MetaD::transitionwells_

private

◆ tt_specs_

struct TemperingSpecs PLMD::bias::MetaD::tt_specs_

private

◆ 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.

◆ uppI_

double PLMD::bias::MetaD::uppI_

private

◆ valueBias

Value* PLMD::bias::Bias::valueBias

privateinherited

the pointer to the bias component

◆ values

std::vector<std::unique_ptr<Value> > PLMD::ActionWithValue::values

privateinherited

An array containing the values for this action.

◆ walkers_mpi_

bool PLMD::bias::MetaD::walkers_mpi_

private

◆ welltemp_

bool PLMD::bias::MetaD::welltemp_

private

◆ wgridstride_

int PLMD::bias::MetaD::wgridstride_

private

◆ work_

double PLMD::bias::MetaD::work_

private

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

bias/MetaD.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ MetaD()

Member Function Documentation

◆ activate()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addGaussian()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives() [1/2]

◆ calculateNumericalDerivatives() [2/2]

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ computeReweightingFactor()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ difference()

◆ doNotCalculateDerivatives()

◆ error()

◆ evaluateGaussian()

◆ evaluateGaussianAndDerivatives()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getArgument()

◆ getArguments()

◆ getBias()

◆ getBiasAndDerivatives()

◆ getComponent()

◆ getComponentsList()

◆ getComponentsVector()

◆ getCPT()

◆ getDefaultString()

◆ getDependencies()

◆ getExchangeStep()

◆ getGaussianNormalization()

◆ getGaussianSupport()

◆ getHeight()

◆ getKeyword()

◆ getLabel()

◆ getName()

◆ getNumberOfArguments()

◆ getNumberOfComponents()

◆ getNumberOfDerivatives()