#include <BasisFunctions.h>

Inheritance diagram for PLMD::ves::BasisFunctions:

[legend]

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

Public Member Functions
	BasisFunctions (const ActionOptions &ao)

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

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

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

bool	areOrthogonal () const

bool	arePeriodic () const

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

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

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

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

double	checkIfArgumentInsideInterval (const double, bool &) const

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

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

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

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

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

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

virtual void	clearOptions ()

virtual void	deactivate ()
	Set action to inactive. More...

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

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

int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...

void	fflush ()
	Tell to the Action to flush open files. More...

FILE *	fopen (const char path, const char mode)
	Opens a file. More...

std::vector< std::vector< double > >	getAllInnerProducts () const

std::vector< std::vector< double > >	getAllInnerProducts (const Grid *) const

virtual void	getAllValues (const double, double &, bool &, std::vector< double > &, std::vector< double > &) const =0

std::string	getBasisFunctionLabel (const unsigned int index) const

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

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

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

std::string	getDescription () const

virtual std::string	getDocumentation () const

bool	getExchangeStep () const
	Check if we are on an exchange step. More...

double	getInnerProduct (const unsigned int n, const unsigned int m, const Grid *) const

virtual double	getInnerProductWeight (const double arg) const

virtual std::string	getInnerProductWeightStr () const

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

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

std::string	getKeywordString () const

const std::string &	getLabel () const
	Returns the label. More...

void	getMultipleValue (const std::vector< double > &, std::vector< double > &, std::vector< std::vector< double > > &, std::vector< std::vector< double > > &, const bool numerical_deriv=false) const

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

unsigned int	getNumberOfBasisFunctions () const

unsigned int	getOrder () const

Action *	getPntrToAction () const

VesBias *	getPntrToVesBias () const

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

unsigned int	getSize () const

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

std::vector< double >	getTargetDistributionIntegrals (const TargetDistribution *) const

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

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

std::string	getType () const

std::vector< double >	getUniformIntegrals () const

double	getValue (const double, const unsigned int, double &, bool &) const

bool	hasBeenSet () const

bool	intervalBounded () const

double	intervalDerivf () const

double	intervalMax () const

std::string	intervalMaxStr () const

double	intervalMean () const

double	intervalMin () const

std::string	intervalMinStr () const

double	intervalRange () const

bool	isActive () const
	Check if action is active. More...

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

void	linkAction (Action *)

void	linkVesBias (VesBias *)

virtual void	lockRequests ()

unsigned int	numberOfBasisFunctions () const

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

void	printInfo () const

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...

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

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

double	translateArgument (const double, bool &) const

virtual void	unlockRequests ()

virtual void	update ()
	Update. More...

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

void	writeBasisFunctionsToFile (OFile &, OFile &, const std::string &min_in, const std::string &max_in, unsigned int nbins=1000, const bool ignore_periodicity=false, const std::string &output_fmt="%15.8f", const bool numerical_deriv=false) const

void	writeInnerProductsToFiles (OFile &ofile, const std::string &output_fmt="%15.8f") const

Static Public Member Functions
static void	registerKeywords (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
template<typename T >
void	addKeywordToList (const std::string &, const T)

template<typename T >
void	addKeywordToList (const std::string &, const std::vector< T > &)

void	addKeywordToList (const std::string &, const bool)

double	intrinsicIntervalMax () const

std::string	intrinsicIntervalMaxStr () const

double	intrinsicIntervalMin () const

std::string	intrinsicIntervalMinStr () const

std::vector< double >	numericalTargetDistributionIntegralsFromGrid (const Grid *) const

void	numericalUniformIntegrals ()

void	setAllUniformIntegralsToZero ()

void	setDescription (const std::string &description_in)

void	setInterval (const double, const double)

void	setInterval (const std::string &, const std::string &)

void	setIntervalBounded ()

void	setIntervalNonBounded ()

void	setIntrinsicInterval (const double, const double)

void	setIntrinsicInterval (const std::string &, const std::string &)

void	setLabel (const unsigned int, const std::string &)

void	setLabelPrefix (const std::string &)

void	setLabels (const std::vector< std::string > &)

void	setNonOrthogonal ()

void	setNonPeriodic ()

void	setNumberOfBasisFunctions (const unsigned int)

void	setNumericalIntegrationBins (const unsigned int nbins)

void	setOrder (const unsigned int norder_in)

void	setOrthogonal ()

void	setPeriodic ()

void	setType (const std::string &type_in)

void	setUniformIntegral (const unsigned int, const double)

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

void	setupBF ()

void	setupInterval ()

virtual void	setupLabels ()

virtual void	setupUniformIntegrals ()

Private Member Functions
void	getAllValuesNumericalDerivs (const double, double &, bool &, std::vector< double > &, std::vector< double > &) const

Private Attributes
Action *	action_pntr_

double	argT_derivf_

std::vector< std::string >	bf_keywords_

std::string	bf_label_prefix_

std::vector< std::string >	bf_labels_

std::string	description_

bool	has_been_set

bool	interval_bounded_

double	interval_intrinsic_max_

std::string	interval_intrinsic_max_str_

double	interval_intrinsic_mean_

double	interval_intrinsic_min_

std::string	interval_intrinsic_min_str_

double	interval_intrinsic_range_

double	interval_max_

std::string	interval_max_str_

double	interval_mean_

double	interval_min_

std::string	interval_min_str_

double	interval_range_

unsigned int	nbasis_

unsigned int	nbins_

unsigned int	norder_

bool	numerical_uniform_integrals_

bool	orthogonal_

bool	periodic_

bool	print_debug_info_

std::string	type_

std::vector< double >	uniform_integrals_

VesBias *	vesbias_pntr_

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ BasisFunctions()

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

explicit

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addKeywordToList() [1/3]

template<typename T >

void PLMD::ves::BasisFunctions::addKeywordToList	(	const std::string &	keyword,
		const T	value
	)

protected

◆ addKeywordToList() [2/3]

template<typename T >

void PLMD::ves::BasisFunctions::addKeywordToList	(	const std::string &	keyword,
		const std::vector< T > &	values
	)

protected

◆ addKeywordToList() [3/3]

void PLMD::ves::BasisFunctions::addKeywordToList	(	const std::string &	keyword,
		const bool	value
	)

inlineprotected

◆ apply()

void PLMD::ves::BasisFunctions::apply ( )

inlinevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ areOrthogonal()

bool PLMD::ves::BasisFunctions::areOrthogonal ( ) const

inline

◆ arePeriodic()

bool PLMD::ves::BasisFunctions::arePeriodic ( ) 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.

◆ calculate()

void PLMD::ves::BasisFunctions::calculate ( )

inlinevirtual

Calculate an Action.

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

Implements PLMD::Action.

◆ calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB & pdb )

inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

◆ calculateNumericalDerivatives()

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.

◆ checkIfArgumentInsideInterval()

double PLMD::ves::BasisFunctions::checkIfArgumentInsideInterval	(	const double	arg,
		bool &	inside_interval
	)		const

inline

◆ checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.

◆ checkNumericalDerivatives()

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

std::string PLMD::Action::cite ( const std::string & s )

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ error()

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

inherited

Crash calculation and print documentation.

◆ exit()

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

inherited

Exit with error code c.

◆ 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)

◆ getAllInnerProducts() [1/2]

std::vector< std::vector< double > > PLMD::ves::BasisFunctions::getAllInnerProducts ( ) const

◆ getAllInnerProducts() [2/2]

std::vector< std::vector< double > > PLMD::ves::BasisFunctions::getAllInnerProducts ( const Grid * grid_pntr ) const

◆ getAllValues()

virtual void PLMD::ves::BasisFunctions::getAllValues	(	const double	,
		double &	,
		bool &	,
		std::vector< double > &	,
		std::vector< double > &
	)		const

pure virtual

Implemented in PLMD::ves::BF_Custom, PLMD::ves::BF_Legendre, PLMD::ves::BF_Chebyshev, PLMD::ves::BF_Fourier, PLMD::ves::BF_Cosine, PLMD::ves::BF_Sine, PLMD::ves::BF_Powers, PLMD::ves::BF_Combined, PLMD::ves::BF_CubicBspline, PLMD::ves::BF_Hermite, PLMD::ves::BF_RationalChebyshevFullInf, PLMD::ves::BF_Laguerre, and PLMD::ves::BF_RationalChebyshevSemiInf.

◆ getAllValuesNumericalDerivs()

void PLMD::ves::BasisFunctions::getAllValuesNumericalDerivs	(	const double	arg,
		double &	argT,
		bool &	inside_range,
		std::vector< double > &	values,
		std::vector< double > &	derivs
	)		const

private

◆ getBasisFunctionLabel()

std::string PLMD::ves::BasisFunctions::getBasisFunctionLabel ( const unsigned int index ) const

inline

◆ getBasisFunctionLabels()

std::vector<std::string> PLMD::ves::BasisFunctions::getBasisFunctionLabels ( ) const

inline

◆ 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.

◆ getDescription()

std::string PLMD::ves::BasisFunctions::getDescription ( ) const

inline

◆ getDocumentation()

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

virtualinherited

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getInnerProduct()

double PLMD::ves::BasisFunctions::getInnerProduct	(	const unsigned int	n,
		const unsigned int	m,
		const Grid *	grid_pntr
	)		const

◆ getInnerProductWeight()

virtual double PLMD::ves::BasisFunctions::getInnerProductWeight ( const double arg ) const

inlinevirtual

Reimplemented in PLMD::ves::BF_Chebyshev.

◆ getInnerProductWeightStr()

virtual std::string PLMD::ves::BasisFunctions::getInnerProductWeightStr ( ) const

inlinevirtual

Reimplemented in PLMD::ves::BF_Chebyshev.

◆ 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.

◆ getKeywordList()

std::vector<std::string> PLMD::ves::BasisFunctions::getKeywordList ( ) const

inline

◆ getKeywordString()

std::string PLMD::ves::BasisFunctions::getKeywordString ( ) const

◆ getLabel()

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

inlineinherited

Returns the label.

◆ getMultipleValue()

void PLMD::ves::BasisFunctions::getMultipleValue	(	const std::vector< double > &	args,
		std::vector< double > &	argsT,
		std::vector< std::vector< double > > &	values,
		std::vector< std::vector< double > > &	derivs,
		const bool	numerical_deriv = `false`
	)		const

◆ getName()

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

inlineinherited

Returns the name.

◆ getNumberOfBasisFunctions()

unsigned int PLMD::ves::BasisFunctions::getNumberOfBasisFunctions ( ) const

inline

◆ getOrder()

unsigned int PLMD::ves::BasisFunctions::getOrder ( ) const

inline

◆ getPntrToAction()

Action * PLMD::ves::BasisFunctions::getPntrToAction ( ) const

inline

◆ getPntrToVesBias()

VesBias * PLMD::ves::BasisFunctions::getPntrToVesBias ( ) const

inline

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getSize()

unsigned int PLMD::ves::BasisFunctions::getSize ( ) const

inline

◆ getStep()

long int PLMD::Action::getStep ( ) const

inherited

Return the present timestep.

◆ getTargetDistributionIntegrals()

std::vector< double > PLMD::ves::BasisFunctions::getTargetDistributionIntegrals ( const TargetDistribution * targetdist_pntr ) const

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getType()

std::string PLMD::ves::BasisFunctions::getType ( ) const

inline

◆ getUniformIntegrals()

std::vector<double> PLMD::ves::BasisFunctions::getUniformIntegrals ( ) const

inline

◆ getValue()

double PLMD::ves::BasisFunctions::getValue	(	const double	arg,
		const unsigned int	n,
		double &	argT,
		bool &	inside_range
	)		const

◆ hasBeenSet()

bool PLMD::ves::BasisFunctions::hasBeenSet ( ) const

inline

◆ intervalBounded()

bool PLMD::ves::BasisFunctions::intervalBounded ( ) const

inline

◆ intervalDerivf()

double PLMD::ves::BasisFunctions::intervalDerivf ( ) const

inline

◆ intervalMax()

double PLMD::ves::BasisFunctions::intervalMax ( ) const

inline

◆ intervalMaxStr()

std::string PLMD::ves::BasisFunctions::intervalMaxStr ( ) const

inline

◆ intervalMean()

double PLMD::ves::BasisFunctions::intervalMean ( ) const

inline

◆ intervalMin()

double PLMD::ves::BasisFunctions::intervalMin ( ) const

inline

◆ intervalMinStr()

std::string PLMD::ves::BasisFunctions::intervalMinStr ( ) const

inline

◆ intervalRange()

double PLMD::ves::BasisFunctions::intervalRange ( ) const

inline

◆ intrinsicIntervalMax()

double PLMD::ves::BasisFunctions::intrinsicIntervalMax ( ) const

inlineprotected

◆ intrinsicIntervalMaxStr()

std::string PLMD::ves::BasisFunctions::intrinsicIntervalMaxStr ( ) const

inlineprotected

◆ intrinsicIntervalMin()

double PLMD::ves::BasisFunctions::intrinsicIntervalMin ( ) const

inlineprotected

◆ intrinsicIntervalMinStr()

std::string PLMD::ves::BasisFunctions::intrinsicIntervalMinStr ( ) const

inlineprotected

◆ 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.

◆ linkAction()

void PLMD::ves::BasisFunctions::linkAction ( Action * action_pntr_in )

◆ linkVesBias()

void PLMD::ves::BasisFunctions::linkVesBias ( VesBias * vesbias_pntr_in )

◆ lockRequests()

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.

◆ numberOfBasisFunctions()

unsigned int PLMD::ves::BasisFunctions::numberOfBasisFunctions ( ) const

inline

◆ numericalTargetDistributionIntegralsFromGrid()

std::vector< double > PLMD::ves::BasisFunctions::numericalTargetDistributionIntegralsFromGrid ( const Grid * grid_pntr ) const

protected

◆ numericalUniformIntegrals()

void PLMD::ves::BasisFunctions::numericalUniformIntegrals ( )

protected

◆ parse()

template<class T >

void PLMD::Action::parse	(	const std::string &	key,
		T &	t
	)

inherited

Parse one keyword as generic type.

◆ 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::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.

◆ printInfo()

void PLMD::ves::BasisFunctions::printInfo ( ) const

◆ readAtomsFromPDB()

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

inlinevirtualinherited

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

Reimplemented in PLMD::ActionAtomistic.

◆ registerKeywords()

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

static

◆ 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.

◆ setAllUniformIntegralsToZero()

void PLMD::ves::BasisFunctions::setAllUniformIntegralsToZero ( )

inlineprotected

◆ setDescription()

void PLMD::ves::BasisFunctions::setDescription ( const std::string & description_in )

inlineprotected

◆ setInterval() [1/2]

void PLMD::ves::BasisFunctions::setInterval	(	const double	interval_min_in,
		const double	interval_max_in
	)

protected

◆ setInterval() [2/2]

void PLMD::ves::BasisFunctions::setInterval	(	const std::string &	interval_min_str_in,
		const std::string &	interval_max_str_in
	)

protected

◆ setIntervalBounded()

void PLMD::ves::BasisFunctions::setIntervalBounded ( )

inlineprotected

◆ setIntervalNonBounded()

void PLMD::ves::BasisFunctions::setIntervalNonBounded ( )

inlineprotected

◆ setIntrinsicInterval() [1/2]

void PLMD::ves::BasisFunctions::setIntrinsicInterval	(	const double	interval_intrinsic_min_in,
		const double	interval_intrinsic_max_in
	)

protected

◆ setIntrinsicInterval() [2/2]

void PLMD::ves::BasisFunctions::setIntrinsicInterval	(	const std::string &	interval_intrinsic_min_str_in,
		const std::string &	interval_intrinsic_max_str_in
	)

protected

◆ setLabel()

void PLMD::ves::BasisFunctions::setLabel	(	const unsigned int	index,
		const std::string &	label
	)

inlineprotected

◆ setLabelPrefix()

void PLMD::ves::BasisFunctions::setLabelPrefix ( const std::string & bf_label_prefix_in )

inlineprotected

◆ setLabels()

void PLMD::ves::BasisFunctions::setLabels ( const std::vector< std::string > & bf_labels_in )

inlineprotected

◆ setNonOrthogonal()

void PLMD::ves::BasisFunctions::setNonOrthogonal ( )

inlineprotected

◆ setNonPeriodic()

void PLMD::ves::BasisFunctions::setNonPeriodic ( )

inlineprotected

◆ setNumberOfBasisFunctions()

void PLMD::ves::BasisFunctions::setNumberOfBasisFunctions ( const unsigned int nbasis_in )

inlineprotected

◆ setNumericalIntegrationBins()

void PLMD::ves::BasisFunctions::setNumericalIntegrationBins ( const unsigned int nbins )

inlineprotected

◆ setOption()

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

virtualinherited

◆ setOrder()

void PLMD::ves::BasisFunctions::setOrder ( const unsigned int norder_in )

inlineprotected

◆ setOrthogonal()

void PLMD::ves::BasisFunctions::setOrthogonal ( )

inlineprotected

◆ setPeriodic()

void PLMD::ves::BasisFunctions::setPeriodic ( )

inlineprotected

◆ setType()

void PLMD::ves::BasisFunctions::setType ( const std::string & type_in )

inlineprotected

◆ setUniformIntegral()

void PLMD::ves::BasisFunctions::setUniformIntegral	(	const unsigned	int,
		const double	value
	)

inlineprotected

◆ setUniformIntegrals()

void PLMD::ves::BasisFunctions::setUniformIntegrals ( const std::vector< double > & uniform_integrals_in )

inlineprotected

◆ setupBF()

void PLMD::ves::BasisFunctions::setupBF ( )

protected

◆ setupInterval()

void PLMD::ves::BasisFunctions::setupInterval ( )

protected

◆ setupLabels()

void PLMD::ves::BasisFunctions::setupLabels ( )

protectedvirtual

Reimplemented in PLMD::ves::BF_Fourier, PLMD::ves::BF_Cosine, PLMD::ves::BF_Sine, PLMD::ves::BF_Powers, PLMD::ves::BF_Combined, PLMD::ves::BF_Hermite, and PLMD::ves::BF_Laguerre.

◆ setupUniformIntegrals()

void PLMD::ves::BasisFunctions::setupUniformIntegrals ( )

protectedvirtual

Reimplemented in PLMD::ves::BF_Legendre, PLMD::ves::BF_Chebyshev, PLMD::ves::BF_Fourier, PLMD::ves::BF_Cosine, PLMD::ves::BF_Sine, and PLMD::ves::BF_Combined.

◆ translateArgument()

double PLMD::ves::BasisFunctions::translateArgument	(	const double	arg,
		bool &	inside_interval
	)		const

inline

◆ unlockRequests()

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.

◆ warning()

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

inherited

Issue a warning.

◆ writeBasisFunctionsToFile()

void PLMD::ves::BasisFunctions::writeBasisFunctionsToFile	(	OFile &	ofile_values,
		OFile &	ofile_derivs,
		const std::string &	min_in,
		const std::string &	max_in,
		unsigned int	nbins = `1000`,
		const bool	ignore_periodicity = `false`,
		const std::string &	output_fmt = `"%15.8f"`,
		const bool	numerical_deriv = `false`
	)		const

◆ writeInnerProductsToFiles()

void PLMD::ves::BasisFunctions::writeInnerProductsToFiles	(	OFile &	ofile,
		const std::string &	output_fmt = `"%15.8f"`
	)		const

Member Data Documentation

◆ action_pntr_

Action* PLMD::ves::BasisFunctions::action_pntr_

private

◆ argT_derivf_

double PLMD::ves::BasisFunctions::argT_derivf_

private

◆ bf_keywords_

std::vector<std::string> PLMD::ves::BasisFunctions::bf_keywords_

private

◆ bf_label_prefix_

std::string PLMD::ves::BasisFunctions::bf_label_prefix_

private

◆ bf_labels_

std::vector<std::string> PLMD::ves::BasisFunctions::bf_labels_

private

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ description_

std::string PLMD::ves::BasisFunctions::description_

private

◆ files

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

inherited

◆ has_been_set

bool PLMD::ves::BasisFunctions::has_been_set

private

◆ interval_bounded_

bool PLMD::ves::BasisFunctions::interval_bounded_

private

◆ interval_intrinsic_max_

double PLMD::ves::BasisFunctions::interval_intrinsic_max_

private

◆ interval_intrinsic_max_str_

std::string PLMD::ves::BasisFunctions::interval_intrinsic_max_str_

private

◆ interval_intrinsic_mean_

double PLMD::ves::BasisFunctions::interval_intrinsic_mean_

private

◆ interval_intrinsic_min_

double PLMD::ves::BasisFunctions::interval_intrinsic_min_

private

◆ interval_intrinsic_min_str_

std::string PLMD::ves::BasisFunctions::interval_intrinsic_min_str_

private

◆ interval_intrinsic_range_

double PLMD::ves::BasisFunctions::interval_intrinsic_range_

private

◆ interval_max_

double PLMD::ves::BasisFunctions::interval_max_

private

◆ interval_max_str_

std::string PLMD::ves::BasisFunctions::interval_max_str_

private

◆ interval_mean_

double PLMD::ves::BasisFunctions::interval_mean_

private

◆ interval_min_

double PLMD::ves::BasisFunctions::interval_min_

private

◆ interval_min_str_

std::string PLMD::ves::BasisFunctions::interval_min_str_

private

◆ interval_range_

double PLMD::ves::BasisFunctions::interval_range_

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

◆ nbasis_

unsigned int PLMD::ves::BasisFunctions::nbasis_

private

◆ nbins_

unsigned int PLMD::ves::BasisFunctions::nbins_

private

◆ norder_

unsigned int PLMD::ves::BasisFunctions::norder_

private

◆ numerical_uniform_integrals_

bool PLMD::ves::BasisFunctions::numerical_uniform_integrals_

private

◆ orthogonal_

bool PLMD::ves::BasisFunctions::orthogonal_

private

◆ periodic_

bool PLMD::ves::BasisFunctions::periodic_

private

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ print_debug_info_

bool PLMD::ves::BasisFunctions::print_debug_info_

private

◆ type_

std::string PLMD::ves::BasisFunctions::type_

private

◆ uniform_integrals_

std::vector<double> PLMD::ves::BasisFunctions::uniform_integrals_

private

◆ vesbias_pntr_

VesBias* PLMD::ves::BasisFunctions::vesbias_pntr_

private

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

ves/BasisFunctions.h
ves/BasisFunctions.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ BasisFunctions()

Member Function Documentation

◆ activate()

◆ addDependency()

◆ addKeywordToList() [1/3]

◆ addKeywordToList() [2/3]

◆ addKeywordToList() [3/3]

◆ apply()

◆ areOrthogonal()

◆ arePeriodic()

◆ beforeUpdate()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ checkIfArgumentInsideInterval()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearOptions()

◆ deactivate()

◆ error()

◆ exit()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getAllInnerProducts() [1/2]

◆ getAllInnerProducts() [2/2]

◆ getAllValues()

◆ getAllValuesNumericalDerivs()

◆ getBasisFunctionLabel()

◆ getBasisFunctionLabels()

◆ getCPT()

◆ getDependencies()

◆ getDescription()

◆ getDocumentation()

◆ getExchangeStep()

◆ getInnerProduct()

◆ getInnerProductWeight()

◆ getInnerProductWeightStr()

◆ getKeyword()

◆ getKeywordList()

◆ getKeywordString()

◆ getLabel()

◆ getMultipleValue()

◆ getName()

◆ getNumberOfBasisFunctions()

◆ getOrder()

◆ getPntrToAction()

◆ getPntrToVesBias()

◆ getRestart()

◆ getSize()

◆ getStep()

◆ getTargetDistributionIntegrals()

◆ getTime()

◆ getTimeStep()

◆ getType()

◆ getUniformIntegrals()

◆ getValue()

◆ hasBeenSet()

◆ intervalBounded()

◆ intervalDerivf()

◆ intervalMax()

◆ intervalMaxStr()

◆ intervalMean()

◆ intervalMin()

◆ intervalMinStr()

◆ intervalRange()