PLMD::ves::BasisFunctions Class Reference

#include <BasisFunctions.h>

Inheritance diagram for PLMD::ves::BasisFunctions:

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 () override
	Apply an Action. More...
bool	arePeriodic () const
virtual void	beforeUpdate ()
	Before Update. More...
void	calculate () override
	Calculate an Action. More...
void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...
virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Perform calculation using numerical derivatives N.B. More...
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...
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...
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

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
void	addKeywordToList (const std::string &, const bool)
template<typename T >
void	addKeywordToList (const std::string &, const std::vector< T > &)
template<typename T >
void	addKeywordToList (const std::string &, const T)
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	setNonPeriodic ()
void	setNumberOfBasisFunctions (const unsigned int)
void	setNumericalIntegrationBins (const unsigned int nbins)
void	setOrder (const unsigned int norder_in)
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_
bool	active
	Switch to activate Action on this step. More...
Dependencies	after
	Actions on which this Action depends. More...
double	argT_derivf_
std::vector< std::string >	bf_keywords_
std::string	bf_label_prefix_
std::vector< std::string >	bf_labels_
std::string	description_
bool	doCheckPoint
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_
std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...
std::vector< std::string >	line
	Directive line. More...
const std::string	name
	Name of the directive in the plumed.dat file. More...
unsigned int	nbasis_
unsigned int	nbins_
unsigned int	norder_
bool	numerical_uniform_integrals_
std::set< std::string >	options
	Option that you might have enabled. More...
bool	periodic_
bool	print_debug_info_
int	replica_index
bool	restart
std::string	type_
std::vector< double >	uniform_integrals_
double	update_from
	Update only after this time. More...
double	update_until
	Update only until this time. More...
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]

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

inlineprotected

addKeywordToList() [2/3]

template<typename T >

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

protected

addKeywordToList() [3/3]

template<typename T >

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

protected

apply()

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

inlineoverridevirtual

Apply an Action.

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

Implements PLMD::Action.

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 ( )

inlineoverridevirtual

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

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)

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, and PLMD::ves::BF_Combined.

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.

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::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, PLMD::colvar::CoordinationBase, PLMD::function::FuncPathGeneral, and PLMD::maze::Optimizer.

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

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

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    )

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, and PLMD::ves::BF_Combined.

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::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::isdb::RDC, PLMD::opes::OPESmetad, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeTetrapore, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::isdb::JCoupling, PLMD::ves::OutputFesBias, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::isdb::PRE, 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, PLMD::gridtools::GridPrintingBase, PLMD::logmfd::LogMFD, PLMD::eds::EDS, and PLMD::fisst::FISST.

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

Member Data Documentation

action_pntr_

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

private

active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

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

doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

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

label

std::string PLMD::Action::label

privateinherited

Label of the Action, as set with LABEL= in the plumed.dat file.

line

std::vector<std::string> PLMD::Action::line

privateinherited

Directive line.

This line is progressively erased during Action construction so as to check if all the present keywords are correct.

log

Log& PLMD::Action::log

inherited

Reference to the log stream.

multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

name

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

privateinherited

Name of the directive in the plumed.dat file.

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

options

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

privateinherited

Option that you might have enabled.

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

replica_index

int PLMD::Action::replica_index

privateinherited

restart

bool PLMD::Action::restart

privateinherited

type_

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

private

uniform_integrals_

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

private

update_from

double PLMD::Action::update_from

privateinherited

Update only after this time.

update_until

double PLMD::Action::update_until

privateinherited

Update only until this time.

vesbias_pntr_

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

private

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

• ves/BasisFunctions.h
• ves/BasisFunctions.cpp