#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 () override
	Apply an Action. More...

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

bool	biasCutoffActive () const

bool	biasGridNeeded () const

bool	biasWithoutCutoffGridNeeded () const

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...

virtual ActionAtomistic *	castToActionAtomistic () noexcept

virtual ActionForInterface *	castToActionForInterface () noexcept

virtual ActionShortcut *	castToActionShortcut () noexcept

virtual ActionToGetData *	castToActionToGetData () noexcept

virtual ActionToPutData *	castToActionToPutData () noexcept

virtual ActionWithArguments *	castToActionWithArguments () noexcept

virtual ActionWithValue *	castToActionWithValue () noexcept
	Specialized casts, to make PlumedMain run faster. More...

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

virtual DomainDecomposition *	castToDomainDecomposition () noexcept

virtual PbcAction *	castToPbcAction () noexcept

bool	checkForDependency (Action *)
	Check that this action does not depend on the action in the argument. 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...

std::string	getDefaultString () const
	Get the defaults. More...

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

unsigned	getDimension () const

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

double	getkBT ()
	Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. 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 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 &)

void	resetStoredTimestep ()
	Set the timestep that is stored in the action to the correct value. More...

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	setupConstantValues (const bool &have_atoms)
	This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...

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 () override
	Update. More...

void	updateTargetDist ()

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

virtual std::string	writeInGraph () const
	Get the info on what to calculate. 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

double	getKBoltzmann () const
	Get the value of Boltzmann's constant. More...

Action *	getPntrToAction () const

VesBias *	getPntrToVesBias () const

const Units &	getUnits () const
	Get the units that we are operating in. More...

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 ()

bool	usingNaturalUnits () const
	Are we using natural units. More...

Private Types
enum	TargetDistType { static_targetdist, dynamic_targetdist }

Private Member Functions
void	calculateStaticDistributionGrid ()

void	checkNanAndInf ()

void	updateBiasCutoffForTargetDistGrid ()

Private Attributes
Action *	action_pntr_

bool	active
	Switch to activate Action on this step. More...

Dependencies	after
	Actions on which this Action depends. More...

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_

std::string	defaults
	The set of default arguments that we are using. More...

unsigned int	dimension_

bool	doCheckPoint

Grid *	fes_grid_pntr_

bool	force_normalization_

std::vector< Value * >	grid_args_

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...

std::unique_ptr< Grid >	log_targetdist_grid_pntr_

const std::string	name
	Name of the directive in the plumed.dat file. More...

bool	needs_bias_grid_

bool	needs_bias_withoutcutoff_grid_

bool	needs_fes_grid_

bool	never_activate

std::set< std::string >	options
	Option that you might have enabled. More...

int	replica_index

bool	restart

bool	shift_targetdist_to_zero_

bool	static_grid_calculated

std::unique_ptr< Grid >	targetdist_grid_pntr_

std::vector< std::unique_ptr< TargetDistModifer > >	targetdist_modifer_pntrs_

double	timestep
	Save the timestep here. More...

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

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

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 ( )

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.

◆ 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 ( )

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::ActionWithVector, PLMD::ActionAtomistic, PLMD::generic::DumpAtoms, PLMD::ActionWithArguments, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::contour::DistanceFromContourBase.

◆ calculateStaticDistributionGrid()

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

private