Abstract base class for implementing biases the extents the normal Bias.h class to include functions related to the variational approach. More...

#include <VesBias.h>

Inheritance diagram for PLMD::ves::VesBias:

[legend]

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

Public Member Functions
	VesBias (const ActionOptions &ao)

	~VesBias ()

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 ()
	Apply an Action. More...

void	applyBiasCutoff (double &, std::vector< double > &) const

void	applyBiasCutoff (double &, std::vector< double > &, std::vector< double > &) const

virtual void	beforeUpdate ()
	Before Update. More...

bool	biasCutoffActive () const

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

virtual void	calculate ()=0
	Calculate an Action. More...

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

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

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

virtual double	calculateReweightFactor () const

virtual void	checkFieldsAllowed ()

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

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

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

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

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

std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. More...

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

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

void	clearGradientAndHessian ()

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

virtual void	clearOptions ()

CoeffsVector &	Coeffs (const unsigned int coeffs_id=0) const

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...

bool	computeHessian () const

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...

bool	diagonalHessian () const

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

void	disableBiasFileOutput ()

void	disableDynamicTargetDistFileOutput ()

void	disableDynamicTargetDistribution ()

void	disableFesFileOutput ()

void	disableFesFileProjOutput ()

void	disableHessian ()

void	disableStaticTargetDistFileOutput ()

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

bool	dynamicTargetDistribution () const

void	enableBiasFileOutput ()

void	enableDynamicTargetDistFileOutput ()

void	enableDynamicTargetDistribution ()

void	enableFesFileOutput ()

void	enableFesProjFileOutput ()

void	enableHessian (const bool diagonal_hessian=true)

void	enableIterationNumberInFilenames ()

void	enableMultipleCoeffsSets ()

void	enableStaticTargetDistFileOutput ()

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...

bool	filenamesIncludeIterationNumber () const

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...

double	getBeta () const

double	getBiasCutoffSwitchingFunction (const double, double &) const

double	getBiasCutoffSwitchingFunction (const double) const

double	getBiasCutoffValue () const

std::string	getBiasFileFmt () const

std::string	getBiasOutputFilename () const

size_t	getCoeffsIndex (const std::vector< unsigned int > &indices, const unsigned int coeffs_id=0) const

std::vector< unsigned int >	getCoeffsIndices (const size_t index, const unsigned int coeffs_id=0) const

CoeffsVector *	getCoeffsPntr (const unsigned int coeffs_id=0) const

std::vector< CoeffsVector * >	getCoeffsPntrs () const

std::string	getCoeffsSetFilenameSuffix (const unsigned int coeffs_id) const

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...

double	getCurrentBiasMaxValue () const

std::string	getCurrentBiasOutputFilename (const std::string &suffix="") const

std::string	getCurrentFesOutputFilename (const std::string &suffix="") const

std::string	getCurrentOutputFilename (const std::string &, const std::string &suffix="") const

std::string	getCurrentTargetDistOutputFilename (const std::string &suffix="") const

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	getFesFileFmt () const

std::string	getFesOutputFilename () const

CoeffsVector *	getGradientPntr (const unsigned int coeffs_id=0) const

std::vector< CoeffsVector * >	getGradientPntrs () const

std::vector< unsigned int >	getGridBins () const

std::vector< double >	getGridMax () const

std::vector< double >	getGridMin () const

size_t	getHessianIndex (const size_t index1, const size_t index2, const unsigned int coeffs_id=0) const

CoeffsMatrix *	getHessianPntr (const unsigned int coeffs_id=0) const

std::vector< CoeffsMatrix * >	getHessianPntrs () const

unsigned int	getIterationCounter () const

std::string	getIterationFilenameSuffix () const

double	getKbT () const

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...

unsigned int	getNumberOfArgumentsPerSet () const

unsigned int	getNumberOfArgumentsSets () const

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

unsigned	getNumberOfDerivatives () override

unsigned int	getNumberOfProjectionArguments () const

unsigned int	getNumberOfTargetDistributionPntrs () const

OFile *	getOFile (const std::string &filename, const bool multi_sim_single_file=false, const bool enforce_backup=true)

Optimizer *	getOptimizerPntr () const

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...

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...

std::vector< std::string >	getProjectionArgument (unsigned int i) const

std::vector< std::vector< std::string > >	getProjectionArguments () const

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...

CoeffsVector *	getTargetDistAveragesPntr (const unsigned int coeffs_id=0) const

std::vector< CoeffsVector * >	getTargetDistAveragesPntrs () const

std::string	getTargetDistFileFmt () const

std::string	getTargetDistOutputFilename () const

std::string	getTargetDistRestartFileFmt () const

std::vector< TargetDistribution * >	getTargetDistributionPntrs () const

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

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

unsigned int	getTotalNumberOfArguments () const

CoeffsVector &	Gradient (const unsigned int coeffs_id=0) const

CoeffsMatrix &	Hessian (const unsigned int coeffs_id=0) const

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	isBiasFileOutputActive () const

bool	isDynamicTargetDistFileOutputActive () const

bool	isFesFileOutputActive () const

bool	isFesProjFileOutputActive () const

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

bool	isReweightFactorCalculated () const

bool	isStaticTargetDistFileOutputActive () const

void	linkOptimizer (Optimizer *)

void	lockRequests () override

virtual void	lockRequests ()

size_t	numberOfCoeffs (const unsigned int coeffs_id=0) const

unsigned int	numberOfCoeffsSets () const

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

bool	optimizeCoeffs () const

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

virtual void	resetBiasFileOutput ()

virtual void	resetFesFileOutput ()

virtual void	resetFesProjFileOutput ()

virtual void	resetTargetDistFileOutput ()

virtual void	resetTargetDistProjFileOutput ()

virtual void	restartTargetDistributions ()

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

std::vector< std::vector< double > > &	sampledAverages ()

std::vector< std::vector< double > > &	sampledCrossAverages ()

void	setCurrentBiasMaxValue (const double max_value)

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

void	setGridBins (const std::vector< unsigned int > &)

void	setGridBins (const unsigned int)

void	setGridMax (const std::vector< double > &)

void	setGridMin (const std::vector< double > &)

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	setupBiasCutoff (const double, const double)

virtual void	setupBiasFileOutput ()

virtual void	setupFesFileOutput ()

virtual void	setupFesProjFileOutput ()

virtual void	setupTargetDistFileOutput ()

virtual void	setupTargetDistProjFileOutput ()

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

CoeffsVector &	TargetDistAverages (const unsigned int coeffs_id=0) const

size_t	totalNumberOfCoeffs () const

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

void	unlockRequests () override

virtual void	unlockRequests ()

virtual void	update ()
	Update. More...

void	updateGradientAndHessian (const bool)

void	updateReweightFactor ()

virtual void	updateTargetDistributions ()

bool	useMultipleWalkers () const

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

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

virtual void	writeBiasToFile ()

virtual void	writeFesProjToFile ()

virtual void	writeFesToFile ()

virtual void	writeTargetDistProjToFile ()

virtual void	writeTargetDistToFile ()

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 &)

static void	useArgsSetKeywords (Keywords &)

static void	useBiasCutoffKeywords (Keywords &)

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

static void	useGridBinKeywords (Keywords &)

static void	useGridLimitsKeywords (Keywords &)

static void	useInitialCoeffsKeywords (Keywords &)

static void	useMultipleTargetDistributionKeywords (Keywords &)

static void	useProjectionArgKeywords (Keywords &)

static void	useReweightFactorKeywords (Keywords &)

static void	useTargetDistributionKeywords (Keywords &)

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	addCoeffsSet (const std::vector< std::string > &, const std::vector< unsigned int > &)

void	addCoeffsSet (std::vector< Value > &, std::vector< BasisFunctions > &)

void	addCoeffsSet (CoeffsVector *)

void	addToSampledAverages (const std::vector< double > &, const unsigned int c_id=0)

void	checkThatTemperatureIsGiven ()

void	clearCoeffsPntrsVector ()

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

std::string	getCoeffsSetLabelString (const std::string &, const unsigned int coeffs_id=0) const

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...

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

template<class T >
bool	parseMultipleValues (const std::string &, std::vector< T > &, unsigned int)

template<class T >
bool	parseMultipleValues (const std::string &, std::vector< T > &, unsigned int, const T &)

bool	readCoeffsFromFiles ()

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	setTargetDistAverages (const std::vector< double > &, const unsigned int coeffs_id=0)

void	setTargetDistAverages (const CoeffsVector &, const unsigned int coeffs_id=0)

void	setTargetDistAveragesToZero (const unsigned int coeffs_id=0)

void	setupOutputForces ()
	setup the OutputForce vector - this is needed if the bias does not use a normal ARG keyword More...

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

Private Member Functions
std::vector< double >	computeCovarianceFromAverages (const unsigned int) const

void	initializeCoeffs (CoeffsVector *)

void	multiSimSumAverages (const unsigned int, const double walker_weight=1.0)

Private Attributes
std::vector< unsigned int >	aver_counters

double	bias_current_max_value

bool	bias_cutoff_active_

FermiSwitchingFunction *	bias_cutoff_swfunc_pntr_

double	bias_cutoff_value_

std::string	bias_file_fmt_

std::string	bias_filename_

bool	bias_fileoutput_active_

bool	calc_reweightfactor_

std::vector< std::string >	coeffs_fnames

std::string	coeffs_id_prefix_

std::vector< CoeffsVector * >	coeffs_pntrs_

bool	compute_hessian_

bool	diagonal_hessian_

bool	dynamic_targetdist_

bool	dynamic_targetdist_fileoutput_active_

std::string	fes_file_fmt_

std::string	fes_filename_

bool	fes_fileoutput_active_

bool	fesproj_fileoutput_active_

bool	filenames_have_iteration_number_

std::vector< CoeffsVector * >	gradient_pntrs_

std::vector< unsigned int >	grid_bins_

std::vector< double >	grid_max_

std::vector< double >	grid_min_

std::vector< CoeffsMatrix * >	hessian_pntrs_

double	kbt_

unsigned int	nargs_per_argsset_

unsigned int	nargs_tot_

unsigned int	nargssets_

size_t	ncoeffs_total_

unsigned int	ncoeffssets_

bool	optimize_coeffs_

Optimizer *	optimizer_pntr_

std::vector< std::vector< std::string > >	projection_args_

std::vector< std::vector< double > >	sampled_averages

std::vector< std::vector< double > >	sampled_cross_averages

bool	static_targetdist_fileoutput_active_

std::string	targetdist_averages_filename_

std::vector< CoeffsVector * >	targetdist_averages_pntrs_

std::string	targetdist_file_fmt_

std::string	targetdist_filename_

std::vector< TargetDistribution * >	targetdist_pntrs_

std::string	targetdist_restart_file_fmt_

bool	use_multiple_coeffssets_

Detailed Description

Abstract base class for implementing biases the extents the normal Bias.h class to include functions related to the variational approach.

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ VesBias()

PLMD::ves::VesBias::VesBias ( const ActionOptions & ao )

explicit

◆ ~VesBias()

PLMD::ves::VesBias::~VesBias ( )

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addCoeffsSet() [1/3]

void PLMD::ves::VesBias::addCoeffsSet	(	const std::vector< std::string > &	dimension_labels,
		const std::vector< unsigned int > &	indices_shape
	)

protected

◆ addCoeffsSet() [2/3]

void PLMD::ves::VesBias::addCoeffsSet	(	std::vector< Value *> &	args,
		std::vector< BasisFunctions *> &	basisf
	)

protected

◆ addCoeffsSet() [3/3]

void PLMD::ves::VesBias::addCoeffsSet ( CoeffsVector * coeffs_pntr_in )

protected

◆ 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)

◆ addToSampledAverages()

void PLMD::ves::VesBias::addToSampledAverages	(	const std::vector< double > &	values,
		const unsigned int	c_id = `0`
	)

protected

◆ 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::ves::VesBias::apply ( )

virtual

Apply an Action.

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

Reimplemented from PLMD::bias::Bias.

◆ applyBiasCutoff() [1/2]

void PLMD::ves::VesBias::applyBiasCutoff	(	double &	bias,
		std::vector< double > &	forces
	)		const

inline

◆ applyBiasCutoff() [2/2]

void PLMD::ves::VesBias::applyBiasCutoff	(	double &	bias,
		std::vector< double > &	forces,
		std::vector< double > &	coeffsderivs_values
	)		const

inline

◆ 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.

◆ biasCutoffActive()

bool PLMD::ves::VesBias::biasCutoffActive ( ) const

inline

◆ 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()

virtual void PLMD::Action::calculate ( )

pure virtualinherited

Calculate an Action.

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

Implemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::logmfd::LogMFD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::isdb::EMMI, PLMD::eds::EDS, PLMD::function::FuncPathMSD, PLMD::isdb::RDC, PLMD::piv::PIV, PLMD::function::FuncSumHills, PLMD::generic::FitToTemplate, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::function::Custom, PLMD::multicolvar::MultiColvarBase, PLMD::bias::MaxEnt, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::isdb::Rescale, PLMD::generic::Include, PLMD::ves::VesDeltaF, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::generic::Group, PLMD::colvar::Dimer, PLMD::maze::OptimizerBias, PLMD::vatom::Center, PLMD::bias::ExtendedLagrangian, PLMD::bias::External, PLMD::colvar::DRMSD, PLMD::colvar::ContactMap, PLMD::colvar::Distance, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::generic::WholeMolecules, PLMD::function::Target, PLMD::generic::ResetCell, PLMD::generic::DumpMassCharge, PLMD::mapping::AdaptivePath, PLMD::isdb::JCoupling, PLMD::adjmat::Sprint, PLMD::colvar::Torsion, PLMD::colvar::EEFSolv, PLMD::generic::Read, PLMD::analysis::Average, PLMD::analysis::AnalysisBase, PLMD::isdb::Caliber, PLMD::multicolvar::CenterOfMultiColvar, PLMD::vatom::FixedAtom, PLMD::colvar::Gyration, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::colvar::PathMSDBase, PLMD::isdb::FretEfficiency, PLMD::ves::OutputFesBias, PLMD::generic::UpdateIf, PLMD::maze::Optimizer, PLMD::multicolvar::DistanceFromContour, PLMD::isdb::PRE, PLMD::ves::OutputBasisFunctions, PLMD::function::Combine, PLMD::generic::Print, PLMD::colvar::Position, PLMD::ves::OutputTargetDistribution, PLMD::function::LocalEnsemble, PLMD::adjmat::OutputCluster, PLMD::bias::BiasValue, PLMD::isdb::NOE, PLMD::colvar::Puckering, PLMD::generic::RandomExchanges, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::DumpMultiColvar, PLMD::adjmat::ClusterDistribution, PLMD::function::Piecewise, PLMD::bias::LWalls, PLMD::isdb::Select, PLMD::maze::Loss, PLMD::bias::UWalls, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::colvar::Dipole, PLMD::bias::Restraint, PLMD::colvar::Constant, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::adjmat::ClusterProperties, PLMD::function::Ensemble, PLMD::colvar::Energy, PLMD::function::Stats, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::Debug, PLMD::colvar::Template, PLMD::generic::DumpProjections, PLMD::manyrestraints::ManyRestraintsBase, PLMD::vatom::Ghost, PLMD::colvar::Cell, PLMD::adjmat::DumpGraph, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::colvar::ExtraCV, PLMD::generic::Time, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, PLMD::colvar::MultiRMSD, PLMD::colvar::PCARMSD, PLMD::colvar::RMSD, PLMD::ActionShortcut, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, and PLMD::mapping::PathBase.

◆ 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 )

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

◆ calculateReweightFactor()

double PLMD::ves::VesBias::calculateReweightFactor ( ) const

virtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

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

◆ 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]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

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

◆ checkThatTemperatureIsGiven()

void PLMD::ves::VesBias::checkThatTemperatureIsGiven ( )

protected

◆ 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.

◆ clearCoeffsPntrsVector()

void PLMD::ves::VesBias::clearCoeffsPntrsVector ( )

inlineprotected

◆ 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.

◆ clearGradientAndHessian()

void PLMD::ves::VesBias::clearGradientAndHessian ( )

inline

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ Coeffs()

CoeffsVector& PLMD::ves::VesBias::Coeffs ( const unsigned int coeffs_id = 0 ) const

inline

◆ 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.

◆ computeCovarianceFromAverages()

std::vector< double > PLMD::ves::VesBias::computeCovarianceFromAverages ( const unsigned int c_id ) const

inlineprivate

◆ computeHessian()

bool PLMD::ves::VesBias::computeHessian ( ) const

inline

◆ 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.

◆ diagonalHessian()

bool PLMD::ves::VesBias::diagonalHessian ( ) const

inline

◆ difference()

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

inlineinherited

Takes the difference taking into account pbc for arg i.

◆ disableBiasFileOutput()

void PLMD::ves::VesBias::disableBiasFileOutput ( )

inline

◆ disableDynamicTargetDistFileOutput()

void PLMD::ves::VesBias::disableDynamicTargetDistFileOutput ( )

inline

◆ disableDynamicTargetDistribution()

void PLMD::ves::VesBias::disableDynamicTargetDistribution ( )

inline

◆ disableFesFileOutput()

void PLMD::ves::VesBias::disableFesFileOutput ( )

inline

◆ disableFesFileProjOutput()

void PLMD::ves::VesBias::disableFesFileProjOutput ( )

inline

◆ disableHessian()

void PLMD::ves::VesBias::disableHessian ( )

◆ disableStaticTargetDistFileOutput()

void PLMD::ves::VesBias::disableStaticTargetDistFileOutput ( )

inline

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ dynamicTargetDistribution()

bool PLMD::ves::VesBias::dynamicTargetDistribution ( ) const

inline

◆ enableBiasFileOutput()

void PLMD::ves::VesBias::enableBiasFileOutput ( )

inline

◆ enableDynamicTargetDistFileOutput()

void PLMD::ves::VesBias::enableDynamicTargetDistFileOutput ( )

inline

◆ enableDynamicTargetDistribution()

void PLMD::ves::VesBias::enableDynamicTargetDistribution ( )

inline

◆ enableFesFileOutput()

void PLMD::ves::VesBias::enableFesFileOutput ( )

inline

◆ enableFesProjFileOutput()

void PLMD::ves::VesBias::enableFesProjFileOutput ( )

inline

◆ enableHessian()

void PLMD::ves::VesBias::enableHessian ( const bool diagonal_hessian = true )

◆ enableIterationNumberInFilenames()

void PLMD::ves::VesBias::enableIterationNumberInFilenames ( )

inline

◆ enableMultipleCoeffsSets()

void PLMD::ves::VesBias::enableMultipleCoeffsSets ( )

inline

◆ enableStaticTargetDistFileOutput()

void PLMD::ves::VesBias::enableStaticTargetDistFileOutput ( )

inline

◆ 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 ( 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.

◆ filenamesIncludeIterationNumber()

bool PLMD::ves::VesBias::filenamesIncludeIterationNumber ( ) const

inline

◆ 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.

◆ getBeta()

double PLMD::ves::VesBias::getBeta ( ) const

inline

◆ getBiasCutoffSwitchingFunction() [1/2]

double PLMD::ves::VesBias::getBiasCutoffSwitchingFunction	(	const double	bias,
		double &	deriv_factor
	)		const

◆ getBiasCutoffSwitchingFunction() [2/2]

double PLMD::ves::VesBias::getBiasCutoffSwitchingFunction ( const double bias ) const

inline

◆ getBiasCutoffValue()

double PLMD::ves::VesBias::getBiasCutoffValue ( ) const

inline

◆ getBiasFileFmt()

std::string PLMD::ves::VesBias::getBiasFileFmt ( ) const

inline

◆ getBiasOutputFilename()

std::string PLMD::ves::VesBias::getBiasOutputFilename ( ) const

inline

◆ getCoeffsIndex()

size_t PLMD::ves::VesBias::getCoeffsIndex	(	const std::vector< unsigned int > &	indices,
		const unsigned int	coeffs_id = `0`
	)		const

inline

◆ getCoeffsIndices()

std::vector< unsigned int > PLMD::ves::VesBias::getCoeffsIndices	(	const size_t	index,
		const unsigned int	coeffs_id = `0`
	)		const

inline

◆ getCoeffsPntr()

CoeffsVector* PLMD::ves::VesBias::getCoeffsPntr ( const unsigned int coeffs_id = 0 ) const

inline

◆ getCoeffsPntrs()

std::vector<CoeffsVector*> PLMD::ves::VesBias::getCoeffsPntrs ( ) const

inline

◆ getCoeffsSetFilenameSuffix()

std::string PLMD::ves::VesBias::getCoeffsSetFilenameSuffix ( const unsigned int coeffs_id ) const

◆ getCoeffsSetLabelString()

std::string PLMD::ves::VesBias::getCoeffsSetLabelString	(	const std::string &	type,
		const unsigned int	coeffs_id = `0`
	)		const

protected

◆ 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.

◆ getCurrentBiasMaxValue()

double PLMD::ves::VesBias::getCurrentBiasMaxValue ( ) const

inline

◆ getCurrentBiasOutputFilename()

std::string PLMD::ves::VesBias::getCurrentBiasOutputFilename ( const std::string & suffix = "" ) const

inline

◆ getCurrentFesOutputFilename()

std::string PLMD::ves::VesBias::getCurrentFesOutputFilename ( const std::string & suffix = "" ) const

inline

◆ getCurrentOutputFilename()

std::string PLMD::ves::VesBias::getCurrentOutputFilename	(	const std::string &	base_filename,
		const std::string &	suffix = `""`
	)		const

◆ getCurrentTargetDistOutputFilename()

std::string PLMD::ves::VesBias::getCurrentTargetDistOutputFilename ( const std::string & suffix = "" ) const

◆ 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.

◆ getFesFileFmt()

std::string PLMD::ves::VesBias::getFesFileFmt ( ) const

inline

◆ getFesOutputFilename()

std::string PLMD::ves::VesBias::getFesOutputFilename ( ) const

inline

◆ getGradientPntr()

CoeffsVector* PLMD::ves::VesBias::getGradientPntr ( const unsigned int coeffs_id = 0 ) const

inline

◆ getGradientPntrs()

std::vector<CoeffsVector*> PLMD::ves::VesBias::getGradientPntrs ( ) const

inline

◆ getGridBins()

std::vector<unsigned int> PLMD::ves::VesBias::getGridBins ( ) const

inline

◆ getGridMax()

std::vector<double> PLMD::ves::VesBias::getGridMax ( ) const

inline

◆ getGridMin()

std::vector<double> PLMD::ves::VesBias::getGridMin ( ) const

inline

◆ getHessianIndex()

size_t PLMD::ves::VesBias::getHessianIndex	(	const size_t	index1,
		const size_t	index2,
		const unsigned int	coeffs_id = `0`
	)		const

inline

◆ getHessianPntr()

CoeffsMatrix* PLMD::ves::VesBias::getHessianPntr ( const unsigned int coeffs_id = 0 ) const

inline

◆ getHessianPntrs()

std::vector<CoeffsMatrix*> PLMD::ves::VesBias::getHessianPntrs ( ) const

inline

◆ getIterationCounter()

unsigned int PLMD::ves::VesBias::getIterationCounter ( ) const

◆ getIterationFilenameSuffix()

std::string PLMD::ves::VesBias::getIterationFilenameSuffix ( ) const

◆ getKbT()

double PLMD::ves::VesBias::getKbT ( ) const

inline

◆ 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.

◆ getNumberOfArgumentsPerSet()

unsigned int PLMD::ves::VesBias::getNumberOfArgumentsPerSet ( ) const

inline

◆ getNumberOfArgumentsSets()

unsigned int PLMD::ves::VesBias::getNumberOfArgumentsSets ( ) const

inline

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

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

inlineoverridevirtualinherited

Implements PLMD::ActionWithValue.

◆ getNumberOfProjectionArguments()

unsigned int PLMD::ves::VesBias::getNumberOfProjectionArguments ( ) const

inline

◆ getNumberOfTargetDistributionPntrs()

unsigned int PLMD::ves::VesBias::getNumberOfTargetDistributionPntrs ( ) const

inline

◆ getOFile()

OFile * PLMD::ves::VesBias::getOFile	(	const std::string &	filename,
		const bool	multi_sim_single_file = `false`,
		const bool	enforce_backup = `true`
	)

◆ getOptimizerPntr()

Optimizer* PLMD::ves::VesBias::getOptimizerPntr ( ) const

inline

◆ 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.

◆ getProjectionArgument()

std::vector<std::string> PLMD::ves::VesBias::getProjectionArgument ( unsigned int i ) const

inline

◆ getProjectionArguments()

std::vector< std::vector<std::string> > PLMD::ves::VesBias::getProjectionArguments ( ) const

inline

◆ 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.

◆ getTargetDistAveragesPntr()

CoeffsVector* PLMD::ves::VesBias::getTargetDistAveragesPntr ( const unsigned int coeffs_id = 0 ) const

inline

◆ getTargetDistAveragesPntrs()

std::vector<CoeffsVector*> PLMD::ves::VesBias::getTargetDistAveragesPntrs ( ) const

inline

◆ getTargetDistFileFmt()

std::string PLMD::ves::VesBias::getTargetDistFileFmt ( ) const

inline

◆ getTargetDistOutputFilename()

std::string PLMD::ves::VesBias::getTargetDistOutputFilename ( ) const

inline

◆ getTargetDistRestartFileFmt()

std::string PLMD::ves::VesBias::getTargetDistRestartFileFmt ( ) const

inline

◆ getTargetDistributionPntrs()

std::vector<TargetDistribution*> PLMD::ves::VesBias::getTargetDistributionPntrs ( ) const

inline

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getTotalNumberOfArguments()

unsigned int PLMD::ves::VesBias::getTotalNumberOfArguments ( ) const

inline

◆ Gradient()

CoeffsVector& PLMD::ves::VesBias::Gradient ( const unsigned int coeffs_id = 0 ) const

inline

◆ Hessian()

CoeffsMatrix& PLMD::ves::VesBias::Hessian ( const unsigned int coeffs_id = 0 ) const

inline

◆ initializeCoeffs()

void PLMD::ves::VesBias::initializeCoeffs ( CoeffsVector * coeffs_pntr_in )

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.

◆ isBiasFileOutputActive()

bool PLMD::ves::VesBias::isBiasFileOutputActive ( ) const

inline

◆ isDynamicTargetDistFileOutputActive()

bool PLMD::ves::VesBias::isDynamicTargetDistFileOutputActive ( ) const

inline

◆ isFesFileOutputActive()

bool PLMD::ves::VesBias::isFesFileOutputActive ( ) const

inline

◆ isFesProjFileOutputActive()

bool PLMD::ves::VesBias::isFesProjFileOutputActive ( ) const

inline

◆ isOptionOn()

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

inlineinherited

Check if an option is on.

◆ isReweightFactorCalculated()

bool PLMD::ves::VesBias::isReweightFactorCalculated ( ) const

inline

◆ isStaticTargetDistFileOutputActive()

bool PLMD::ves::VesBias::isStaticTargetDistFileOutputActive ( ) const

inline

◆ linkOptimizer()

void PLMD::ves::VesBias::linkOptimizer ( Optimizer * optimizer_pntr_in )

◆ lockRequests() [1/2]

void PLMD::ActionWithArguments::lockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

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

◆ lockRequests() [2/2]

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

◆ multiSimSumAverages()

void PLMD::ves::VesBias::multiSimSumAverages	(	const unsigned int	c_id,
		const double	walker_weight = `1.0`
	)

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.

◆ numberOfCoeffs()

size_t PLMD::ves::VesBias::numberOfCoeffs ( const unsigned int coeffs_id = 0 ) const

inline

◆ numberOfCoeffsSets()

unsigned int PLMD::ves::VesBias::numberOfCoeffsSets ( ) const

inline

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ optimizeCoeffs()

bool PLMD::ves::VesBias::optimizeCoeffs ( ) const

inline

◆ 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.

◆ parseMultipleValues() [1/2]

template<class T >

bool PLMD::ves::VesBias::parseMultipleValues	(	const std::string &	keyword,
		std::vector< T > &	values,
		unsigned int	nvalues
	)

protected

◆ parseMultipleValues() [2/2]

template<class T >

bool PLMD::ves::VesBias::parseMultipleValues	(	const std::string &	keyword,
		std::vector< T > &	values,
		unsigned int	nvalues,
		const T &	default_value
	)

protected

◆ 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::DumpMassCharge, PLMD::generic::Read, PLMD::maze::Optimizer, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::gridtools::ConvertToFES, PLMD::SetupMolInfo, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, 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.

◆ readCoeffsFromFiles()

bool PLMD::ves::VesBias::readCoeffsFromFiles ( )

protected

◆ registerKeywords()

void PLMD::ves::VesBias::registerKeywords ( Keywords & keys )

static

◆ requestArguments()

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

inherited

Setup the dependencies.

◆ resetBiasFileOutput()

virtual void PLMD::ves::VesBias::resetBiasFileOutput ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ resetFesFileOutput()

virtual void PLMD::ves::VesBias::resetFesFileOutput ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ resetFesProjFileOutput()

virtual void PLMD::ves::VesBias::resetFesProjFileOutput ( )

inlinevirtual

◆ resetTargetDistFileOutput()

virtual void PLMD::ves::VesBias::resetTargetDistFileOutput ( )

inlinevirtual

◆ resetTargetDistProjFileOutput()

virtual void PLMD::ves::VesBias::resetTargetDistProjFileOutput ( )

inlinevirtual

◆ restartTargetDistributions()

virtual void PLMD::ves::VesBias::restartTargetDistributions ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ 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.

◆ sampledAverages()

std::vector<std::vector<double> >& PLMD::ves::VesBias::sampledAverages ( )

inline

◆ sampledCrossAverages()

std::vector<std::vector<double> >& PLMD::ves::VesBias::sampledCrossAverages ( )

inline

◆ setBias()

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

inlineprotectedinherited

set the value of the bias

◆ setCurrentBiasMaxValue()

void PLMD::ves::VesBias::setCurrentBiasMaxValue ( const double max_value )

inline

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

◆ setGridBins() [1/2]

void PLMD::ves::VesBias::setGridBins ( const std::vector< unsigned int > & grid_bins_in )

◆ setGridBins() [2/2]

void PLMD::ves::VesBias::setGridBins ( const unsigned int nbins )

◆ setGridMax()

void PLMD::ves::VesBias::setGridMax ( const std::vector< double > & grid_max_in )

◆ setGridMin()

void PLMD::ves::VesBias::setGridMin ( const std::vector< double > & grid_min_in )

◆ 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.

◆ setTargetDistAverages() [1/2]

void PLMD::ves::VesBias::setTargetDistAverages	(	const std::vector< double > &	coeffderivs_aver_ps,
		const unsigned int	coeffs_id = `0`
	)

protected

◆ setTargetDistAverages() [2/2]

void PLMD::ves::VesBias::setTargetDistAverages	(	const CoeffsVector &	coeffderivs_aver_ps,
		const unsigned int	coeffs_id = `0`
	)

protected

◆ setTargetDistAveragesToZero()

void PLMD::ves::VesBias::setTargetDistAveragesToZero ( const unsigned int coeffs_id = 0 )

protected

◆ setupBiasCutoff()

void PLMD::ves::VesBias::setupBiasCutoff	(	const double	bias_cutoff_value,
		const double	fermi_lambda
	)

◆ setupBiasFileOutput()

virtual void PLMD::ves::VesBias::setupBiasFileOutput ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ setupFesFileOutput()

virtual void PLMD::ves::VesBias::setupFesFileOutput ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ setupFesProjFileOutput()

virtual void PLMD::ves::VesBias::setupFesProjFileOutput ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ setupOutputForces()

void PLMD::bias::Bias::setupOutputForces ( )

protectedinherited

setup the OutputForce vector - this is needed if the bias does not use a normal ARG keyword

◆ setupTargetDistFileOutput()

virtual void PLMD::ves::VesBias::setupTargetDistFileOutput ( )

inlinevirtual

◆ setupTargetDistProjFileOutput()

virtual void PLMD::ves::VesBias::setupTargetDistProjFileOutput ( )

inlinevirtual

◆ 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.

◆ TargetDistAverages()

CoeffsVector& PLMD::ves::VesBias::TargetDistAverages ( const unsigned int coeffs_id = 0 ) const

inline

◆ totalNumberOfCoeffs()

size_t PLMD::ves::VesBias::totalNumberOfCoeffs ( ) const

inline

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::eds::EDS, 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, and PLMD::gridtools::ActionWithIntegral.

◆ unlockRequests() [1/2]

void PLMD::ActionWithArguments::unlockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

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

◆ unlockRequests() [2/2]

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

◆ update()

virtual void PLMD::Action::update ( )

inlinevirtualinherited

Update.

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

Reimplemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::logmfd::LogMFD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::eds::EDS, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::bias::MaxEnt, PLMD::generic::Plumed, PLMD::ves::VesDeltaF, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeTetrapore, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::ves::OutputFesBias, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, and PLMD::gridtools::GridPrintingBase.

◆ updateGradientAndHessian()

void PLMD::ves::VesBias::updateGradientAndHessian ( const bool use_mwalkers_mpi )

◆ updateReweightFactor()

void PLMD::ves::VesBias::updateReweightFactor ( )

◆ updateTargetDistributions()

virtual void PLMD::ves::VesBias::updateTargetDistributions ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ useArgsSetKeywords()

void PLMD::ves::VesBias::useArgsSetKeywords ( Keywords & keys )

static

◆ useBiasCutoffKeywords()

void PLMD::ves::VesBias::useBiasCutoffKeywords ( Keywords & keys )

static

◆ useCustomisableComponents()

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

staticinherited

The components in the action will depend on the user.

◆ useGridBinKeywords()

void PLMD::ves::VesBias::useGridBinKeywords ( Keywords & keys )

static

◆ useGridLimitsKeywords()

void PLMD::ves::VesBias::useGridLimitsKeywords ( Keywords & keys )

static

◆ useInitialCoeffsKeywords()

void PLMD::ves::VesBias::useInitialCoeffsKeywords ( Keywords & keys )

static

◆ useMultipleTargetDistributionKeywords()

void PLMD::ves::VesBias::useMultipleTargetDistributionKeywords ( Keywords & keys )

static

◆ useMultipleWalkers()

bool PLMD::ves::VesBias::useMultipleWalkers ( ) const

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ useProjectionArgKeywords()

void PLMD::ves::VesBias::useProjectionArgKeywords ( Keywords & keys )

static

◆ useReweightFactorKeywords()

void PLMD::ves::VesBias::useReweightFactorKeywords ( Keywords & keys )

static

◆ useTargetDistributionKeywords()

void PLMD::ves::VesBias::useTargetDistributionKeywords ( Keywords & keys )

static

◆ warning()

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

inherited

Issue a warning.

◆ writeBiasToFile()

virtual void PLMD::ves::VesBias::writeBiasToFile ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ writeFesProjToFile()

virtual void PLMD::ves::VesBias::writeFesProjToFile ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ writeFesToFile()

virtual void PLMD::ves::VesBias::writeFesToFile ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ writeTargetDistProjToFile()

virtual void PLMD::ves::VesBias::writeTargetDistProjToFile ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

◆ writeTargetDistToFile()

virtual void PLMD::ves::VesBias::writeTargetDistToFile ( )

inlinevirtual

Reimplemented in PLMD::ves::VesLinearExpansion.

Member Data Documentation

◆ aver_counters

std::vector<unsigned int> PLMD::ves::VesBias::aver_counters

private

◆ bias_current_max_value

double PLMD::ves::VesBias::bias_current_max_value

private

◆ bias_cutoff_active_

bool PLMD::ves::VesBias::bias_cutoff_active_

private

◆ bias_cutoff_swfunc_pntr_

FermiSwitchingFunction* PLMD::ves::VesBias::bias_cutoff_swfunc_pntr_

private

◆ bias_cutoff_value_

double PLMD::ves::VesBias::bias_cutoff_value_

private

◆ bias_file_fmt_

std::string PLMD::ves::VesBias::bias_file_fmt_

private

◆ bias_filename_

std::string PLMD::ves::VesBias::bias_filename_

private

◆ bias_fileoutput_active_

bool PLMD::ves::VesBias::bias_fileoutput_active_

private

◆ calc_reweightfactor_

bool PLMD::ves::VesBias::calc_reweightfactor_

private

◆ coeffs_fnames

std::vector<std::string> PLMD::ves::VesBias::coeffs_fnames

private

◆ coeffs_id_prefix_

std::string PLMD::ves::VesBias::coeffs_id_prefix_

private

◆ coeffs_pntrs_

std::vector<CoeffsVector*> PLMD::ves::VesBias::coeffs_pntrs_

private

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ compute_hessian_

bool PLMD::ves::VesBias::compute_hessian_

private

◆ diagonal_hessian_

bool PLMD::ves::VesBias::diagonal_hessian_

private

◆ dynamic_targetdist_

bool PLMD::ves::VesBias::dynamic_targetdist_

private

◆ dynamic_targetdist_fileoutput_active_

bool PLMD::ves::VesBias::dynamic_targetdist_fileoutput_active_

private

◆ fes_file_fmt_

std::string PLMD::ves::VesBias::fes_file_fmt_

private

◆ fes_filename_

std::string PLMD::ves::VesBias::fes_filename_

private

◆ fes_fileoutput_active_

bool PLMD::ves::VesBias::fes_fileoutput_active_

private

◆ fesproj_fileoutput_active_

bool PLMD::ves::VesBias::fesproj_fileoutput_active_

private

◆ filenames_have_iteration_number_

bool PLMD::ves::VesBias::filenames_have_iteration_number_

private

◆ files

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

inherited

◆ gradient_pntrs_

std::vector<CoeffsVector*> PLMD::ves::VesBias::gradient_pntrs_

private

◆ grid_bins_

std::vector<unsigned int> PLMD::ves::VesBias::grid_bins_

private

◆ grid_max_

std::vector<double> PLMD::ves::VesBias::grid_max_

private

◆ grid_min_

std::vector<double> PLMD::ves::VesBias::grid_min_

private

◆ hessian_pntrs_

std::vector<CoeffsMatrix*> PLMD::ves::VesBias::hessian_pntrs_

private

◆ kbt_

double PLMD::ves::VesBias::kbt_

private

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ nargs_per_argsset_

unsigned int PLMD::ves::VesBias::nargs_per_argsset_

private

◆ nargs_tot_

unsigned int PLMD::ves::VesBias::nargs_tot_

private

◆ nargssets_

unsigned int PLMD::ves::VesBias::nargssets_

private

◆ ncoeffs_total_

size_t PLMD::ves::VesBias::ncoeffs_total_

private

◆ ncoeffssets_

unsigned int PLMD::ves::VesBias::ncoeffssets_

private

◆ optimize_coeffs_

bool PLMD::ves::VesBias::optimize_coeffs_

private

◆ optimizer_pntr_

Optimizer* PLMD::ves::VesBias::optimizer_pntr_

private

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ projection_args_

std::vector< std::vector<std::string> > PLMD::ves::VesBias::projection_args_

private

◆ sampled_averages

std::vector<std::vector<double> > PLMD::ves::VesBias::sampled_averages

private

◆ sampled_cross_averages

std::vector<std::vector<double> > PLMD::ves::VesBias::sampled_cross_averages

private

◆ static_targetdist_fileoutput_active_

bool PLMD::ves::VesBias::static_targetdist_fileoutput_active_

private

◆ targetdist_averages_filename_

std::string PLMD::ves::VesBias::targetdist_averages_filename_

private

◆ targetdist_averages_pntrs_

std::vector<CoeffsVector*> PLMD::ves::VesBias::targetdist_averages_pntrs_

private

◆ targetdist_file_fmt_

std::string PLMD::ves::VesBias::targetdist_file_fmt_

private

◆ targetdist_filename_

std::string PLMD::ves::VesBias::targetdist_filename_

private

◆ targetdist_pntrs_

std::vector<TargetDistribution*> PLMD::ves::VesBias::targetdist_pntrs_

private

◆ targetdist_restart_file_fmt_

std::string PLMD::ves::VesBias::targetdist_restart_file_fmt_

private

◆ use_multiple_coeffssets_

bool PLMD::ves::VesBias::use_multiple_coeffssets_

private

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

ves/VesBias.h
ves/VesBias.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

◆ VesBias()

◆ ~VesBias()

Member Function Documentation

◆ activate()

◆ addCoeffsSet() [1/3]

◆ addCoeffsSet() [2/3]

◆ addCoeffsSet() [3/3]

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addToSampledAverages()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ applyBiasCutoff() [1/2]

◆ applyBiasCutoff() [2/2]

◆ beforeUpdate()

◆ biasCutoffActive()

◆ bringBackInPbc()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives() [1/2]

◆ calculateNumericalDerivatives() [2/2]

◆ calculateReweightFactor()

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkThatTemperatureIsGiven()

◆ checkUpdate()

◆ cite()

◆ clearCoeffsPntrsVector()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearGradientAndHessian()

◆ clearInputForces()

◆ clearOptions()

◆ Coeffs()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ computeCovarianceFromAverages()

◆ computeHessian()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ diagonalHessian()

◆ difference()

◆ disableBiasFileOutput()

◆ disableDynamicTargetDistFileOutput()

◆ disableDynamicTargetDistribution()

◆ disableFesFileOutput()

◆ disableFesFileProjOutput()

◆ disableHessian()

◆ disableStaticTargetDistFileOutput()

◆ doNotCalculateDerivatives()

◆ dynamicTargetDistribution()

◆ enableBiasFileOutput()

◆ enableDynamicTargetDistFileOutput()

◆ enableDynamicTargetDistribution()

◆ enableFesFileOutput()

◆ enableFesProjFileOutput()

◆ enableHessian()

◆ enableIterationNumberInFilenames()

◆ enableMultipleCoeffsSets()

◆ enableStaticTargetDistFileOutput()

◆ error()