Provides the keyword METAD More...

Inheritance diagram for PLMD::bias::MetaD:

[legend]

Classes
struct	Gaussian

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

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

Public Member Functions
	MetaD (const ActionOptions &)

	~MetaD ()

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

void	update ()
	Update. More...

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

void	apply ()
	Apply an Action. More...

unsigned	getNumberOfDerivatives ()

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

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

bool	checkUpdate () const
	Check if action should be updated. More...

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

void	clearDependencies ()
	Clear the dependence list for this Action. More...

long int	getStep () const
	Return the present timestep. More...

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

double	getTimeStep () const
	Return the timestep. More...

bool	getRestart () const
	Return true if we are doing a restart. More...

bool	getCPT () const
	Return true if we are doing at a checkpoint step. More...

std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string. More...

template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. More...

template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...

template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...

template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

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

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

void	exit (int c=0)
	Exit with error code c. More...

void	checkRead ()
	Check if Action was properly read. More...

virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

virtual void	lockRequests ()

void	lockRequests ()

virtual void	unlockRequests ()

void	unlockRequests ()

virtual void	beforeUpdate ()
	Before 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...

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

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

virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Calculate the 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...

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

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

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

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

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

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

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

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...

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

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...

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

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

virtual void	clearDerivatives ()
	Clear the derivatives of values wrt parameters. More...

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

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

virtual void	checkFieldsAllowed ()

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

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

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

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

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

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

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

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

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

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

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

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

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

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

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	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...

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

Public Attributes
PlumedMain &	plumed
	Reference to main plumed object. More...

Log &	log
	Reference to the log stream. More...

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

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

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

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

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

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

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

Private Member Functions
void	readGaussians (IFile *)

bool	readChunkOfGaussians (IFile *ifile, unsigned n)

void	writeGaussian (const Gaussian &, OFile &)

void	addGaussian (const Gaussian &)

double	getHeight (const vector< double > &)

double	getBiasAndDerivatives (const vector< double > &, double *der=NULL)

double	evaluateGaussian (const vector< double > &, const Gaussian &, double *der=NULL)

void	finiteDifferenceGaussian (const vector< double > &, const Gaussian &)

double	getGaussianNormalization (const Gaussian &)

vector< unsigned >	getGaussianSupport (const Gaussian &)

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

void	computeReweightingFactor ()

Private Attributes
vector< double >	sigma0_

vector< double >	sigma0min_

vector< double >	sigma0max_

vector< Gaussian >	hills_

OFile	hillsOfile_

OFile	gridfile_

Grid *	BiasGrid_

bool	storeOldGrids_

int	wgridstride_

bool	grid_

double	height0_

double	biasf_

double	dampfactor_

std::string	targetfilename_

Grid *	TargetGrid_

double	kbt_

int	stride_

bool	welltemp_

double *	dp_

int	adaptive_

FlexibleBin *	flexbin

int	mw_n_

string	mw_dir_

int	mw_id_

int	mw_rstride_

bool	walkers_mpi

unsigned	mpi_nw_

bool	acceleration

double	acc

vector< IFile * >	ifiles

vector< string >	ifilesnames

double	uppI_

double	lowI_

bool	doInt_

bool	isFirstStep

double	reweight_factor

vector< unsigned >	rewf_grid_

unsigned	rewf_ustride_

double	work_

long int	last_step_warn_grid

string	fmt

Detailed Description

Provides the keyword METAD

Member Typedef Documentation

◆ Dependencies

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

inherited

◆ files_iterator

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

inherited

Constructor & Destructor Documentation

◆ MetaD()

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

explicit

◆ ~MetaD()

PLMD::bias::MetaD::~MetaD ( )

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 ( )

virtualinherited

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 ( )

virtual

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

virtualinherited

Calculate the numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::Action.

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

◆ calculateNumericalDerivatives() [2/2]

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::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithInputVessel.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap.

◆ checkNeedsGradients()

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

inlinevirtual

Check if the action needs gradient.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [1/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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.

◆ 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 vector< double > &	cv,
		const Gaussian &	hill,
		double *	der = `NULL`
	)

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 ( 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.

◆ finiteDifferenceGaussian()

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

private

◆ 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

inlineinherited

Returns an array of pointers to the arguments.

◆ getBiasAndDerivatives()

double PLMD::bias::MetaD::getBiasAndDerivatives	(	const vector< double > &	cv,
		double *	der = `NULL`
	)

private

◆ 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.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ getDocumentation()

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

virtualinherited

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getGaussianNormalization()

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

private

◆ getGaussianSupport()

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

private

◆ getHeight()

double PLMD::bias::MetaD::getHeight ( const 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 ( )

inlinevirtualinherited

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

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

inlineinherited

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

◆ getOutputQuantity() [2/2]

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)

◆ getPntrToArgument()

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

inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

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

protectedinherited

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

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

protectedinherited

Return a pointer to the value by name.

◆ 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 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.

◆ 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]

void PLMD::ActionWithArguments::lockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

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

◆ lockRequests() [2/2]

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

◆ 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.

◆ 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]

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

inherited

Parse a list of arguments.

◆ parseArgumentList() [2/2]

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

inherited

Parse a numbered 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::multicolvar::MultiColvarBase, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Read, PLMD::generic::Print, PLMD::bias::ReweightTemperature, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

◆ readAtomsFromPDB()

virtual void PLMD::Action::readAtomsFromPDB ( const PDB & )

inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

◆ readChunkOfGaussians()

bool PLMD::bias::MetaD::readChunkOfGaussians	(	IFile *	ifile,
		unsigned	n
	)

private

◆ readGaussians()

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

private

◆ registerKeywords()

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

static

◆ requestArguments()

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

inherited

Setup the dependencies.

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

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

◆ scanOneHill()

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

private

takes a pointer to the file and a template 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.

◆ 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.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::adjmat::ClusterDiameter, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterSize, PLMD::mapping::Mapping, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ClusterAnalysisBase, and PLMD::adjmat::ClusteringBase.

◆ unlockRequests() [1/2]

void PLMD::ActionWithArguments::unlockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

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

◆ unlockRequests() [2/2]

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

◆ update()

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

virtual

Update.

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

Reimplemented from PLMD::Action.

◆ 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

◆ acceleration

bool PLMD::bias::MetaD::acceleration

private

◆ adaptive_

int PLMD::bias::MetaD::adaptive_

private

◆ biasf_

double PLMD::bias::MetaD::biasf_

private

◆ BiasGrid_

Grid* PLMD::bias::MetaD::BiasGrid_

private

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ dampfactor_

double PLMD::bias::MetaD::dampfactor_

private

◆ doInt_

bool PLMD::bias::MetaD::doInt_

private

◆ dp_

double* PLMD::bias::MetaD::dp_

private

◆ files

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

inherited

◆ flexbin

FlexibleBin* PLMD::bias::MetaD::flexbin

private

◆ fmt

string PLMD::bias::MetaD::fmt

private

◆ grid_

bool PLMD::bias::MetaD::grid_

private

◆ gridfile_

OFile PLMD::bias::MetaD::gridfile_

private

◆ height0_

double PLMD::bias::MetaD::height0_

private

◆ hills_

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

private

◆ hillsOfile_

OFile PLMD::bias::MetaD::hillsOfile_

private

◆ ifiles

vector<IFile*> PLMD::bias::MetaD::ifiles

private

◆ ifilesnames

vector<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

◆ last_step_warn_grid

long int PLMD::bias::MetaD::last_step_warn_grid

private

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ lowI_

double PLMD::bias::MetaD::lowI_

private

◆ mpi_nw_

unsigned PLMD::bias::MetaD::mpi_nw_

private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ mw_dir_

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

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ reweight_factor

double PLMD::bias::MetaD::reweight_factor

private

◆ rewf_grid_

vector<unsigned> PLMD::bias::MetaD::rewf_grid_

private

◆ rewf_ustride_

unsigned PLMD::bias::MetaD::rewf_ustride_

private

◆ sigma0_

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

private

◆ sigma0max_

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

private

◆ sigma0min_

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

private

◆ storeOldGrids_

bool PLMD::bias::MetaD::storeOldGrids_

private

◆ stride_

int PLMD::bias::MetaD::stride_

private

◆ targetfilename_

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

private

◆ TargetGrid_

Grid* PLMD::bias::MetaD::TargetGrid_

private

◆ uppI_

double PLMD::bias::MetaD::uppI_

private

◆ 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

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

◆ files_iterator

Constructor & Destructor Documentation

◆ MetaD()

◆ ~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()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ finiteDifferenceGaussian()

◆ fopen()

◆ getArgument()

◆ getArguments()

◆ getBiasAndDerivatives()

◆ getComponentsList()

◆ getComponentsVector()

◆ getCPT()

◆ getDependencies()

◆ getDocumentation()

◆ getExchangeStep()

◆ getGaussianNormalization()

◆ getGaussianSupport()

◆ getHeight()

◆ getKeyword()

◆ getLabel()

◆ getName()

◆ getNumberOfArguments()

◆ getNumberOfComponents()

◆ getNumberOfDerivatives()

◆ getOutputQuantity() [1/2]

◆ getOutputQuantity() [2/2]