#include <TargetDistribution.h>

Inheritance diagram for PLMD::ves::TargetDistribution:

[legend]

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

Public Member Functions
	TargetDistribution (const ActionOptions &)

	~TargetDistribution ()

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

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

void	allowBiasCutoff ()

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

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

bool	biasCutoffActive () const

bool	biasGridNeeded () const

bool	biasWithoutCutoffGridNeeded () const

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...

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...

void	clearLogTargetDistGrid ()

virtual void	clearOptions ()

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

void	doNotAllowBiasCutoff ()

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...

bool	fesGridNeeded () const

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

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

bool	forcedNormalization () const

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

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

unsigned	getDimension () 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...

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

Grid *	getLogTargetDistGridPntr () const

Grid	getMarginal (const std::vector< std::string > &)

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

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

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

Grid *	getTargetDistGridPntr () const

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

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

virtual double	getValue (const std::vector< double > &) const =0

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

bool	isBiasCutoffAllowed () const

bool	isDynamic () const

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

bool	isStatic () const

bool	isTargetDistGridShiftedToZero () const

virtual void	linkAction (Action *)

virtual void	linkBiasGrid (Grid *)

virtual void	linkBiasWithoutCutoffGrid (Grid *)

virtual void	linkFesGrid (Grid *)

virtual void	linkVesBias (VesBias *)

virtual void	lockRequests ()

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...

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	readInRestartTargetDistGrid (const std::string &)

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

void	setDimension (const unsigned int dimension)

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

void	setupBiasCutoff ()

void	setupGrids (const std::vector< Value *> &, const std::vector< std::string > &, const std::vector< std::string > &, const std::vector< unsigned int > &)

virtual void	unlockRequests ()

void	update ()
	Update. More...

void	updateTargetDist ()

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

Static Public Member Functions
static Grid	getMarginalDistributionGrid (Grid *, const std::vector< std::string > &)

static double	integrateGrid (const Grid *)

static double	normalizeGrid (Grid *)

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	applyTargetDistModiferToGrid (TargetDistModifer *modifer_pntr)

double	getBeta () const

Grid *	getBiasGridPntr () const

Grid *	getBiasWithoutCutoffGridPntr () const

Grid *	getFesGridPntr () const

Action *	getPntrToAction () const

VesBias *	getPntrToVesBias () const

Grid &	logTargetDistGrid () const

void	normalizeTargetDistGrid ()

void	setBiasGridNeeded ()

void	setBiasWithoutCutoffGridNeeded ()

void	setDynamic ()

void	setFesGridNeeded ()

void	setForcedNormalization ()

void	setMinimumOfTargetDistGridToZero ()

void	setStatic ()

virtual void	setupAdditionalGrids (const std::vector< Value *> &, const std::vector< std::string > &, const std::vector< std::string > &, const std::vector< unsigned int > &)

Grid &	targetDistGrid () const

void	unsetForcedNormalization ()

virtual void	updateGrid ()

void	updateLogTargetDistGrid ()

Private Types
enum	TargetDistType { static_targetdist, dynamic_targetdist }

Private Member Functions
void	calculateStaticDistributionGrid ()

void	checkNanAndInf ()

void	updateBiasCutoffForTargetDistGrid ()

Private Attributes
Action *	action_pntr_

bool	allow_bias_cutoff_

bool	bias_cutoff_active_

Grid *	bias_grid_pntr_

Grid *	bias_withoutcutoff_grid_pntr_

bool	check_nan_inf_

bool	check_nonnegative_

bool	check_normalization_

unsigned int	dimension_

Grid *	fes_grid_pntr_

bool	force_normalization_

std::vector< Value * >	grid_args_

Grid *	log_targetdist_grid_pntr_

bool	needs_bias_grid_

bool	needs_bias_withoutcutoff_grid_

bool	needs_fes_grid_

bool	shift_targetdist_to_zero_

bool	static_grid_calculated

Grid *	targetdist_grid_pntr_

std::vector< TargetDistModifer * >	targetdist_modifer_pntrs_

enum PLMD::ves::TargetDistribution::TargetDistType	type_

VesBias *	vesbias_pntr_

Member Typedef Documentation

◆ Dependencies

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

inherited

Member Enumeration Documentation

◆ TargetDistType

enum PLMD::ves::TargetDistribution::TargetDistType

private

Enumerator
static_targetdist
dynamic_targetdist

Constructor & Destructor Documentation

◆ TargetDistribution()

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

explicit

◆ ~TargetDistribution()

PLMD::ves::TargetDistribution::~TargetDistribution ( )

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.

◆ allowBiasCutoff()

void PLMD::ves::TargetDistribution::allowBiasCutoff ( )

inline

◆ apply()

void PLMD::ves::TargetDistribution::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.

◆ applyTargetDistModiferToGrid()

void PLMD::ves::TargetDistribution::applyTargetDistModiferToGrid ( TargetDistModifer * modifer_pntr )

protected

◆ 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::TargetDistribution::biasCutoffActive ( ) const

inline

◆ biasGridNeeded()

bool PLMD::ves::TargetDistribution::biasGridNeeded ( ) const

inline

◆ biasWithoutCutoffGridNeeded()

bool PLMD::ves::TargetDistribution::biasWithoutCutoffGridNeeded ( ) const

inline

◆ calculate()

void PLMD::ves::TargetDistribution::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.

◆ calculateStaticDistributionGrid()

void PLMD::ves::TargetDistribution::calculateStaticDistributionGrid ( )

private

◆ checkNanAndInf()

void PLMD::ves::TargetDistribution::checkNanAndInf ( )

private

◆ 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.

◆ clearLogTargetDistGrid()

void PLMD::ves::TargetDistribution::clearLogTargetDistGrid ( )

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ doNotAllowBiasCutoff()

void PLMD::ves::TargetDistribution::doNotAllowBiasCutoff ( )

inline

◆ 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().

◆ fesGridNeeded()

bool PLMD::ves::TargetDistribution::fesGridNeeded ( ) const

inline

◆ 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)

◆ forcedNormalization()

bool PLMD::ves::TargetDistribution::forcedNormalization ( ) const

inline

◆ getBeta()

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

protected

◆ getBiasGridPntr()

Grid* PLMD::ves::TargetDistribution::getBiasGridPntr ( ) const

inlineprotected

◆ getBiasWithoutCutoffGridPntr()

Grid* PLMD::ves::TargetDistribution::getBiasWithoutCutoffGridPntr ( ) const

inlineprotected

◆ 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.

◆ getDimension()

unsigned PLMD::ves::TargetDistribution::getDimension ( ) 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.

◆ getFesGridPntr()

Grid* PLMD::ves::TargetDistribution::getFesGridPntr ( ) const

inlineprotected

◆ 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.

◆ getLogTargetDistGridPntr()

Grid* PLMD::ves::TargetDistribution::getLogTargetDistGridPntr ( ) const

inline

◆ getMarginal()

Grid PLMD::ves::TargetDistribution::getMarginal ( const std::vector< std::string > & args )

◆ getMarginalDistributionGrid()

Grid PLMD::ves::TargetDistribution::getMarginalDistributionGrid	(	Grid *	grid_pntr,
		const std::vector< std::string > &	args
	)

static

◆ getName()

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

inlineinherited

Returns the name.

◆ getPntrToAction()

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

inlineprotected

◆ getPntrToVesBias()

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

inlineprotected

◆ 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.

◆ getTargetDistGridPntr()

Grid* PLMD::ves::TargetDistribution::getTargetDistGridPntr ( ) const

inline

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getValue()

virtual double PLMD::ves::TargetDistribution::getValue ( const std::vector< double > & ) const

pure virtual

Implemented in PLMD::ves::TD_Uniform, PLMD::ves::TD_Gaussian, PLMD::ves::TD_Custom, PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, PLMD::ves::TD_ExponentiallyModifiedGaussian, PLMD::ves::TD_Grid, PLMD::ves::TD_GeneralizedNormal, PLMD::ves::TD_GeneralizedExtremeValue, PLMD::ves::TD_VonMises, PLMD::ves::TD_WellTempered, PLMD::ves::TD_ProductDistribution, PLMD::ves::TD_Chi, PLMD::ves::TD_ChiSquared, and PLMD::ves::TD_Exponential.

◆ integrateGrid()

double PLMD::ves::TargetDistribution::integrateGrid ( const Grid * grid_pntr )

static

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isBiasCutoffAllowed()

bool PLMD::ves::TargetDistribution::isBiasCutoffAllowed ( ) const

inline

◆ isDynamic()

bool PLMD::ves::TargetDistribution::isDynamic ( ) const

inline

◆ isOptionOn()

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

inlineinherited

Check if an option is on.

◆ isStatic()

bool PLMD::ves::TargetDistribution::isStatic ( ) const

inline

◆ isTargetDistGridShiftedToZero()

bool PLMD::ves::TargetDistribution::isTargetDistGridShiftedToZero ( ) const

inline

◆ linkAction()

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

virtual

Reimplemented in PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, and PLMD::ves::TD_ProductDistribution.

◆ linkBiasGrid()

void PLMD::ves::TargetDistribution::linkBiasGrid ( Grid * bias_grid_pntr_in )

virtual

Reimplemented in PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, and PLMD::ves::TD_ProductDistribution.

◆ linkBiasWithoutCutoffGrid()

void PLMD::ves::TargetDistribution::linkBiasWithoutCutoffGrid ( Grid * bias_withoutcutoff_grid_pntr_in )

virtual

Reimplemented in PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, and PLMD::ves::TD_ProductDistribution.

◆ linkFesGrid()

void PLMD::ves::TargetDistribution::linkFesGrid ( Grid * fes_grid_pntr_in )

virtual

Reimplemented in PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, and PLMD::ves::TD_ProductDistribution.

◆ linkVesBias()

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

virtual

Reimplemented in PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, and PLMD::ves::TD_ProductDistribution.

◆ 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.

◆ logTargetDistGrid()

Grid& PLMD::ves::TargetDistribution::logTargetDistGrid ( ) const

inlineprotected

◆ normalizeGrid()

double PLMD::ves::TargetDistribution::normalizeGrid ( Grid * grid_pntr )

static

◆ normalizeTargetDistGrid()

void PLMD::ves::TargetDistribution::normalizeTargetDistGrid ( )

inlineprotected

◆ 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::function::FuncPathMSD, PLMD::isdb::EMMI, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::bias::ReweightTemperature, PLMD::colvar::Energy, PLMD::gridtools::ConvertToFES, 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.

◆ readInRestartTargetDistGrid()

void PLMD::ves::TargetDistribution::readInRestartTargetDistGrid ( const std::string & grid_fname )

◆ registerKeywords()

void PLMD::ves::TargetDistribution::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.

◆ setBiasGridNeeded()

void PLMD::ves::TargetDistribution::setBiasGridNeeded ( )

inlineprotected

◆ setBiasWithoutCutoffGridNeeded()

void PLMD::ves::TargetDistribution::setBiasWithoutCutoffGridNeeded ( )

inlineprotected

◆ setDimension()

void PLMD::ves::TargetDistribution::setDimension ( const unsigned int dimension )

◆ setDynamic()

void PLMD::ves::TargetDistribution::setDynamic ( )

inlineprotected

◆ setFesGridNeeded()

void PLMD::ves::TargetDistribution::setFesGridNeeded ( )

inlineprotected

◆ setForcedNormalization()

void PLMD::ves::TargetDistribution::setForcedNormalization ( )

inlineprotected

◆ setMinimumOfTargetDistGridToZero()

void PLMD::ves::TargetDistribution::setMinimumOfTargetDistGridToZero ( )

protected

◆ setOption()

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

virtualinherited

◆ setStatic()

void PLMD::ves::TargetDistribution::setStatic ( )

inlineprotected

◆ setupAdditionalGrids()

virtual void PLMD::ves::TargetDistribution::setupAdditionalGrids	(	const std::vector< Value *> &	,
		const std::vector< std::string > &	,
		const std::vector< std::string > &	,
		const std::vector< unsigned int > &
	)

inlineprotectedvirtual

Reimplemented in PLMD::ves::TD_Uniform, PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, PLMD::ves::TD_Custom, and PLMD::ves::TD_ProductDistribution.

◆ setupBiasCutoff()

void PLMD::ves::TargetDistribution::setupBiasCutoff ( )

◆ setupGrids()

void PLMD::ves::TargetDistribution::setupGrids	(	const std::vector< Value *> &	arguments,
		const std::vector< std::string > &	min,
		const std::vector< std::string > &	max,
		const std::vector< unsigned int > &	nbins
	)

◆ targetDistGrid()

Grid& PLMD::ves::TargetDistribution::targetDistGrid ( ) const

inlineprotected

◆ 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.

◆ unsetForcedNormalization()

void PLMD::ves::TargetDistribution::unsetForcedNormalization ( )

inlineprotected

◆ update()

void PLMD::ves::TargetDistribution::update ( )

inlinevirtual

Update.

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

Reimplemented from PLMD::Action.

◆ updateBiasCutoffForTargetDistGrid()

void PLMD::ves::TargetDistribution::updateBiasCutoffForTargetDistGrid ( )

private

◆ updateGrid()

virtual void PLMD::ves::TargetDistribution::updateGrid ( )

inlineprotectedvirtual

Reimplemented in PLMD::ves::TD_Custom, PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, PLMD::ves::TD_WellTempered, and PLMD::ves::TD_ProductDistribution.

◆ updateLogTargetDistGrid()

void PLMD::ves::TargetDistribution::updateLogTargetDistGrid ( )

protected

◆ updateTargetDist()

void PLMD::ves::TargetDistribution::updateTargetDist ( )

◆ warning()

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

inherited

Issue a warning.

Member Data Documentation

◆ action_pntr_

Action* PLMD::ves::TargetDistribution::action_pntr_

private

◆ allow_bias_cutoff_

bool PLMD::ves::TargetDistribution::allow_bias_cutoff_

private

◆ bias_cutoff_active_

bool PLMD::ves::TargetDistribution::bias_cutoff_active_

private

◆ bias_grid_pntr_

Grid* PLMD::ves::TargetDistribution::bias_grid_pntr_

private

◆ bias_withoutcutoff_grid_pntr_

Grid* PLMD::ves::TargetDistribution::bias_withoutcutoff_grid_pntr_

private

◆ check_nan_inf_

bool PLMD::ves::TargetDistribution::check_nan_inf_

private

◆ check_nonnegative_

bool PLMD::ves::TargetDistribution::check_nonnegative_

private

◆ check_normalization_

bool PLMD::ves::TargetDistribution::check_normalization_

private

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ dimension_

unsigned int PLMD::ves::TargetDistribution::dimension_

private

◆ fes_grid_pntr_

Grid* PLMD::ves::TargetDistribution::fes_grid_pntr_

private

◆ files

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

inherited

◆ force_normalization_

bool PLMD::ves::TargetDistribution::force_normalization_

private

◆ grid_args_

std::vector<Value*> PLMD::ves::TargetDistribution::grid_args_

private

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ log_targetdist_grid_pntr_

Grid* PLMD::ves::TargetDistribution::log_targetdist_grid_pntr_

private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ needs_bias_grid_

bool PLMD::ves::TargetDistribution::needs_bias_grid_

private

◆ needs_bias_withoutcutoff_grid_

bool PLMD::ves::TargetDistribution::needs_bias_withoutcutoff_grid_

private

◆ needs_fes_grid_

bool PLMD::ves::TargetDistribution::needs_fes_grid_

private

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ shift_targetdist_to_zero_

bool PLMD::ves::TargetDistribution::shift_targetdist_to_zero_

private

◆ static_grid_calculated

bool PLMD::ves::TargetDistribution::static_grid_calculated

private

◆ targetdist_grid_pntr_

Grid* PLMD::ves::TargetDistribution::targetdist_grid_pntr_

private

◆ targetdist_modifer_pntrs_

std::vector<TargetDistModifer*> PLMD::ves::TargetDistribution::targetdist_modifer_pntrs_

private

◆ type_

enum PLMD::ves::TargetDistribution::TargetDistType PLMD::ves::TargetDistribution::type_

private

◆ vesbias_pntr_

VesBias* PLMD::ves::TargetDistribution::vesbias_pntr_

private

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

ves/TargetDistribution.h
ves/TargetDistribution.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ Dependencies

Member Enumeration Documentation

◆ TargetDistType

Constructor & Destructor Documentation

◆ TargetDistribution()

◆ ~TargetDistribution()

Member Function Documentation

◆ activate()

◆ addDependency()

◆ allowBiasCutoff()

◆ apply()

◆ applyTargetDistModiferToGrid()

◆ beforeUpdate()

◆ biasCutoffActive()

◆ biasGridNeeded()

◆ biasWithoutCutoffGridNeeded()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ calculateStaticDistributionGrid()

◆ checkNanAndInf()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearLogTargetDistGrid()

◆ clearOptions()

◆ deactivate()

◆ doNotAllowBiasCutoff()

◆ error()

◆ exit()

◆ fclose()

◆ fesGridNeeded()

◆ fflush()

◆ fopen()

◆ forcedNormalization()

◆ getBeta()

◆ getBiasGridPntr()

◆ getBiasWithoutCutoffGridPntr()

◆ getCPT()

◆ getDependencies()

◆ getDimension()

◆ getDocumentation()

◆ getExchangeStep()

◆ getFesGridPntr()

◆ getKeyword()

◆ getLabel()

◆ getLogTargetDistGridPntr()

◆ getMarginal()

◆ getMarginalDistributionGrid()

◆ getName()

◆ getPntrToAction()

◆ getPntrToVesBias()

◆ getRestart()

◆ getStep()

◆ getTargetDistGridPntr()

◆ getTime()

◆ getTimeStep()

◆ getValue()

◆ integrateGrid()

◆ isActive()

◆ isBiasCutoffAllowed()

◆ isDynamic()

◆ isOptionOn()

◆ isStatic()

◆ isTargetDistGridShiftedToZero()

◆ linkAction()

◆ linkBiasGrid()

◆ linkBiasWithoutCutoffGrid()