#include <TargetDistribution.h>

Inheritance diagram for PLMD::ves::TargetDistribution:

[legend]

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

Public Member Functions
	TargetDistribution (const ActionOptions &)

	~TargetDistribution ()

bool	isStatic () const

bool	isDynamic () const

bool	forcedNormalization () const

bool	isTargetDistGridShiftedToZero () const

bool	biasGridNeeded () const

bool	biasWithoutCutoffGridNeeded () const

bool	fesGridNeeded () const

void	allowBiasCutoff ()

void	doNotAllowBiasCutoff ()

bool	isBiasCutoffAllowed () const

bool	biasCutoffActive () const

void	setDimension (const unsigned int dimension)

unsigned	getDimension () const

virtual void	linkVesBias (VesBias *)

virtual void	linkAction (Action *)

virtual void	linkBiasGrid (Grid *)

virtual void	linkBiasWithoutCutoffGrid (Grid *)

virtual void	linkFesGrid (Grid *)

void	setupBiasCutoff ()

Grid *	getTargetDistGridPntr () const

Grid *	getLogTargetDistGridPntr () const

void	clearLogTargetDistGrid ()

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

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

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

void	updateTargetDist ()

void	readInRestartTargetDistGrid (const std::string &)

void	update ()
	Update. More...

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

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

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

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

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

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

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

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

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

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

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

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

template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

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

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

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

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

virtual void	unlockRequests ()

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

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

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

virtual std::string	getDocumentation () const

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

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

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

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

virtual void	clearOptions ()

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

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

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

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

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

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

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

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

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

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

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

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

Static Public Member Functions
static void	registerKeywords (Keywords &)

static double	integrateGrid (const Grid *)

static double	normalizeGrid (Grid *)

static Grid	getMarginalDistributionGrid (Grid *, const std::vector< std::string > &)

Public Attributes
PlumedMain &	plumed
	Reference to main plumed object. More...

Log &	log
	Reference to the log stream. More...

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

Protected Member Functions
void	setStatic ()

void	setDynamic ()

void	setForcedNormalization ()

void	unsetForcedNormalization ()

void	setBiasGridNeeded ()

void	setBiasWithoutCutoffGridNeeded ()

void	setFesGridNeeded ()

VesBias *	getPntrToVesBias () const

Action *	getPntrToAction () const

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

void	normalizeTargetDistGrid ()

Grid &	targetDistGrid () const

Grid &	logTargetDistGrid () const

Grid *	getBiasGridPntr () const

Grid *	getBiasWithoutCutoffGridPntr () const

Grid *	getFesGridPntr () const

double	getBeta () const

void	applyTargetDistModiferToGrid (TargetDistModifer *modifer_pntr)

void	setMinimumOfTargetDistGridToZero ()

void	updateLogTargetDistGrid ()

virtual void	updateGrid ()

Private Types
enum	TargetDistType { static_targetdist, dynamic_targetdist }

Private Member Functions
void	calculateStaticDistributionGrid ()

void	updateBiasCutoffForTargetDistGrid ()

void	checkNanAndInf ()

Private Attributes
enum PLMD::ves::TargetDistribution::TargetDistType	type_

bool	force_normalization_

bool	check_normalization_

bool	check_nonnegative_

bool	check_nan_inf_

bool	shift_targetdist_to_zero_

unsigned int	dimension_

std::vector< Value * >	grid_args_

Grid *	targetdist_grid_pntr_

Grid *	log_targetdist_grid_pntr_

std::vector< TargetDistModifer * >	targetdist_modifer_pntrs_

Action *	action_pntr_

VesBias *	vesbias_pntr_

bool	needs_bias_grid_

bool	needs_bias_withoutcutoff_grid_

bool	needs_fes_grid_

Grid *	bias_grid_pntr_

Grid *	bias_withoutcutoff_grid_pntr_

Grid *	fes_grid_pntr_

bool	static_grid_calculated

bool	allow_bias_cutoff_

bool	bias_cutoff_active_

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::multicolvar::MultiColvarBase, PLMD::ActionAtomistic, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, 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_GeneralizedNormal, PLMD::ves::TD_GeneralizedExtremeValue, PLMD::ves::TD_VonMises, PLMD::ves::TD_WellTempered, PLMD::ves::TD_Grid, 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::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ 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::isdb::EMMI, PLMD::multicolvar::MultiColvarBase, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::generic::Read, PLMD::bias::ReweightTemperature, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, 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::analysis::Analysis, PLMD::gridtools::ConvertToFES, 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_Custom, PLMD::ves::TD_LinearCombination, PLMD::ves::TD_ProductCombination, 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::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ 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()