class for LogMFD parameters, variables and subroutines. More...

Inheritance diagram for PLMD::logmfd::LogMFD:

[legend]

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

Public Member Functions
	LogMFD (const ActionOptions &)
	constructor of LogMFD class More...

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...

double	calcClog ()
	calculate coefficient for flattening. More...

double	calcEkin ()
	calculate kinetic energy of fictitious variables. More...

double	calcFlog ()
	calculate free energy of fictitious variables. More...

void	calcMeanForce ()
	calculate mean force for fictitious variables. More...

void	calculate ()
	calculate forces for fictitious variables at every MD steps. 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 ()

virtual bool	checkNeedsGradients () const
	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...

const Dependencies &	getDependencies () const
	Return dependencies. More...

virtual std::string	getDocumentation () const

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 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 ()
	update fictitious variables. More...

void	updateNVE ()
	update fictitious variables by NVE mechanics. More...

void	updateNVT ()
	update fictitious variables by NVT mechanics. More...

void	updateVS ()
	update fictitious variables by VS mechanics. 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
int	getComponent (const std::string &name) const
	Return the index for the component named name. More...

double	sgn (double x)

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

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

double	alpha
	input parameter, alpha parameter for LogMFD. More...

std::vector< Value * >	arguments

double	delta_t
	input parameter, one time step of MFD when fictitious dynamical variables are evolved. More...

bool	doCheckPoint

std::vector< double >	ffict
	current force of each fictitous dynamical variable. More...

std::vector< double >	fict
	current values of each fictitous dynamical variable. More...

std::vector< double >	fict_ave
	averaged values of each collective variable. More...

std::vector< double >	fict_max
	input parameter, maximum of each fictitous dynamical variable. More...

std::vector< double >	fict_min
	input parameter, minimum of each fictitous dynamical variable. More...

std::vector< Value * >	fictValue
	pointers to fictitious dynamical variables More...

bool	firsttime
	flag that indicates first MFD step or not. More...

double	flog
	current free energy More...

double	gamma
	input parameter, gamma parameter for LogMFD. More...

double	hlog
	value invariant More...

int	interval
	input parameter, period of MD steps when fictitious dynamical variables are evolved. More...

std::vector< double >	kappa
	input parameter, strength of the harmonic restraining potential. More...

double	kbt
	k_B*temperature More...

std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...

std::vector< std::string >	line
	Directive line. More...

bool	lockRequestArguments

double	meta
	mass of eta variable of thermostat. More...

std::vector< double >	mfict
	mass of each fictitous dynamical variable. More...

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

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

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...

double	phivs
	potential used in VS method More...

int	replica_index

bool	restart

int	stride

int	TAMD
	input parameter, perform TAMD instead of LogMFD. More...

string	thermostat
	input parameter, type of thermostat for canonical dyanamics. More...

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

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

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...

double	veta
	current velocity of eta variable of thermostat. More...

std::vector< double >	vfict
	current velocity of each fictitous dynamical variable. More...

std::vector< Value * >	vfictValue
	pointers to velocity of fictitious dynamical variables More...

double	weight
	current weight of this replica. More...

double	work
	current works done by fictitious dynamical variables in this replica. More...

double	xeta
	current eta variable of thermostat. More...

Detailed Description

class for LogMFD parameters, variables and subroutines.

Provides the keyword LOGMFD

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ LogMFD()

PLMD::logmfd::LogMFD::LogMFD ( const ActionOptions & ao )

explicit

constructor of LogMFD class

This constructor initializes all parameters and variables, reads input file and set value of parameters and initial value of variables, and writes messages as Plumed log.

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)

◆ 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.

◆ calcClog()

double PLMD::logmfd::LogMFD::calcClog ( )

calculate coefficient for flattening.

Return values

flattering coefficient.

This function returns 1.0 for TAMD, flattening coefficient for LogMFD.

◆ calcEkin()

double PLMD::logmfd::LogMFD::calcEkin ( )

calculate kinetic energy of fictitious variables.

Return values

kinetic energy.

This function calculates sum of kinetic energy of all fictitious variables.

◆ calcFlog()

double PLMD::logmfd::LogMFD::calcFlog ( )

calculate free energy of fictitious variables.

Return values

free energy.

This function calculates free energy by using invariant of canonical mechanics.

◆ calcMeanForce()

void PLMD::logmfd::LogMFD::calcMeanForce ( )

calculate mean force for fictitious variables.

This function calculates mean forces by averaging forces accumulated during one MFD step, update work variables done by fictitious variables by one MFD step, calculate weight variable of this replica for LogPD.

◆ calculate()

void PLMD::logmfd::LogMFD::calculate ( )

virtual

calculate forces for fictitious variables at every MD steps.

This function calculates initial values of fictitious variables and write header messages to LogMFD log files at the first MFD step, calculates restraining fources comes from difference between the fictitious variable and collective variable at every MD steps.

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()

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() [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.

◆ 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.

◆ 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.

◆ 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.

◆ 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.

◆ 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 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]

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.

◆ 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]

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.

◆ registerKeywords()

static void PLMD::logmfd::LogMFD::registerKeywords ( Keywords & keys )

static

◆ 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.

◆ 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.

◆ sgn()

double PLMD::logmfd::LogMFD::sgn ( double x )

inlineprivate

◆ 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::logmfd::LogMFD::update ( )

virtual

update fictitious variables.

This function manages evolution of fictitious variables. This function calculates mean force, updates fictitious variables by one MFD step, bounces back variables, updates free energy, and record logs.

Reimplemented from PLMD::Action.

◆ updateNVE()

void PLMD::logmfd::LogMFD::updateNVE ( )

update fictitious variables by NVE mechanics.

This function updates ficitious variables by one NVE-MFD step using mean forces and flattening coefficient and free energy.

◆ updateNVT()

void PLMD::logmfd::LogMFD::updateNVT ( )

update fictitious variables by NVT mechanics.

This function updates ficitious variables by one NVT-MFD step using mean forces and flattening coefficient and free energy.

◆ updateVS()

void PLMD::logmfd::LogMFD::updateVS ( )

update fictitious variables by VS mechanics.

This function updates ficitious variables by one VS-MFD step using mean forces and flattening coefficient and free energy.

◆ 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.

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.

◆ alpha

double PLMD::logmfd::LogMFD::alpha

private

input parameter, alpha parameter for LogMFD.

◆ arguments

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

privateinherited

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ delta_t

double PLMD::logmfd::LogMFD::delta_t

private

input parameter, one time step of MFD when fictitious dynamical variables are evolved.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ ffict

std::vector<double> PLMD::logmfd::LogMFD::ffict

private

current force of each fictitous dynamical variable.

◆ fict

std::vector<double> PLMD::logmfd::LogMFD::fict

private

current values of each fictitous dynamical variable.

◆ fict_ave

std::vector<double> PLMD::logmfd::LogMFD::fict_ave

private

averaged values of each collective variable.

◆ fict_max

std::vector<double> PLMD::logmfd::LogMFD::fict_max

private

input parameter, maximum of each fictitous dynamical variable.

◆ fict_min

std::vector<double> PLMD::logmfd::LogMFD::fict_min

private

input parameter, minimum of each fictitous dynamical variable.

◆ fictValue

std::vector<Value*> PLMD::logmfd::LogMFD::fictValue

private

pointers to fictitious dynamical variables

◆ files

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

inherited

◆ firsttime

bool PLMD::logmfd::LogMFD::firsttime

private

flag that indicates first MFD step or not.

◆ flog

double PLMD::logmfd::LogMFD::flog

private

current free energy

◆ gamma

double PLMD::logmfd::LogMFD::gamma

private

input parameter, gamma parameter for LogMFD.

◆ hlog

double PLMD::logmfd::LogMFD::hlog

private

value invariant

◆ interval

int PLMD::logmfd::LogMFD::interval

private

input parameter, period of MD steps when fictitious dynamical variables are evolved.

◆ kappa

std::vector<double> PLMD::logmfd::LogMFD::kappa

private

input parameter, strength of the harmonic restraining potential.

◆ kbt

double PLMD::logmfd::LogMFD::kbt

private

k_B*temperature

◆ 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.

◆ meta

double PLMD::logmfd::LogMFD::meta

private

mass of eta variable of thermostat.

◆ mfict

std::vector<double> PLMD::logmfd::LogMFD::mfict

private

mass of each fictitous dynamical variable.

◆ 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.

◆ noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

◆ 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

◆ phivs

double PLMD::logmfd::LogMFD::phivs

private

potential used in VS method

◆ 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

◆ stride

int PLMD::ActionPilot::stride

privateinherited

◆ TAMD

int PLMD::logmfd::LogMFD::TAMD

private

input parameter, perform TAMD instead of LogMFD.

◆ thermostat

string PLMD::logmfd::LogMFD::thermostat

private

input parameter, type of thermostat for canonical dyanamics.

◆ 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.

◆ 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.

◆ veta

double PLMD::logmfd::LogMFD::veta

private

current velocity of eta variable of thermostat.

◆ vfict

std::vector<double> PLMD::logmfd::LogMFD::vfict

private

current velocity of each fictitous dynamical variable.

◆ vfictValue

std::vector<Value*> PLMD::logmfd::LogMFD::vfictValue

private

pointers to velocity of fictitious dynamical variables

◆ weight

double PLMD::logmfd::LogMFD::weight

private

current weight of this replica.

◆ work

double PLMD::logmfd::LogMFD::work

private

current works done by fictitious dynamical variables in this replica.

◆ xeta

double PLMD::logmfd::LogMFD::xeta

private

current eta variable of thermostat.

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

logmfd/LogMFD.cpp

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

Constructor & Destructor Documentation

◆ LogMFD()

Member Function Documentation

◆ activate()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ calcClog()

◆ calcEkin()

◆ calcFlog()

◆ calcMeanForce()

◆ 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()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ difference()

◆ doNotCalculateDerivatives()

◆ error()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getArgument()

◆ getArguments()

◆ getComponent()

◆ getComponentsList()

◆ getComponentsVector()

◆ getCPT()

◆ getDependencies()

◆ getDocumentation()

◆ getExchangeStep()

◆ getKeyword()

◆ getLabel()

◆ getName()

◆ getNumberOfArguments()

◆ getNumberOfComponents()

◆ getNumberOfDerivatives()

◆ getOutputQuantity() [1/2]

◆ getOutputQuantity() [2/2]

◆ getPntrToArgument()

◆ getPntrToComponent() [1/2]

◆ getPntrToComponent() [2/2]

◆ getPntrToValue()

◆ getProjection()

◆ getRestart()