#include <MetainferenceBase.h>

Inheritance diagram for PLMD::isdb::MetainferenceBase:

[legend]

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

Public Member Functions
	MetainferenceBase (const ActionOptions &)

	~MetainferenceBase ()

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

void	addComponent (const std::string &name)
	Add a value with a name like label.name. More...

void	addComponentWithDerivatives (const std::string &name)
	Add a value with a name like label.name that has derivatives. More...

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

void	addForcesOnArguments (const std::vector< double > &forces)
	Add forces to arguments (used in apply) More...

void	addValue ()
	Add a value with the name label. More...

void	addValueWithDerivatives ()
	Add a value with the name label that has derivatives. More...

void	allowToAccessGlobalForces ()
	Allow calls to modifyGlobalForce() More...

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

void	applyForces ()

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

double	bringBackInPbc (int i, double d1) const
	Takes one value and brings it back into the pbc of argument i. More...

virtual void	calculate ()=0
	Calculate an Action. More...

void	calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
	Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...

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

void	calculateNumericalDerivatives (ActionWithValue *a) override
	N.B. More...

void	changeBox (const Tensor &newbox)
	Change the box shape. More...

virtual void	checkFieldsAllowed ()

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

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

bool	checkNumericalDerivatives () const override
	Check if numerical derivatives should be used. 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	clearDerivatives ()
	Clear the derivatives of values wrt parameters. More...

void	clearInputForces ()
	Clear the forces on the values. More...

virtual void	clearOptions ()

void	clearOutputForces ()

void	componentIsNotPeriodic (const std::string &name)
	Set your value component to have no periodicity. More...

void	componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

Value *	copyOutput (const std::string &name) const
	Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...

Value *	copyOutput (const unsigned &n) const
	Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...

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

double	difference (int, double, double) const
	Takes the difference taking into account pbc for arg i. More...

virtual bool	doNotCalculateDerivatives () const
	Are we not calculating derivatives. More...

void	doNotForce ()
	Skip atom forces - use with care. More...

void	doNotRetrieve ()
	Skip atom retrieval - use with care. More...

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

bool	exists (const std::string &name) const
	Check if a value with a particular name is present. 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...

AtomNumber	getAbsoluteIndex (int i) const
	Get the absolute index of an atom. More...

virtual const std::vector< AtomNumber > &	getAbsoluteIndexes () const
	Get the vector of absolute indexes. More...

double	getArgument (const unsigned n) const
	Returns the value of an argument. More...

virtual const std::vector< Value * > &	getArguments () const
	Returns an array of pointers to the arguments. More...

const Tensor &	getBox () const
	Get box shape. More...

double	getCharge (int i) const
	Get charge of i-th atom. More...

std::string	getComponentsList () const
	get a string that contains all the available components More...

std::vector< std::string >	getComponentsVector () const
	get a vector that contains the label for all the components More...

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

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

virtual std::string	getDocumentation () const

bool	getDoScore ()

const double &	getEnergy () const
	Get energy. More...

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

const Vector &	getGlobalPosition (AtomNumber) const
	Get position of i-th atom (access by absolute AtomNumber). 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...

double	getMass (int i) const
	Get mass of i-th atom. More...

double	getMetaDer (const unsigned index)

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

unsigned	getNarg ()

virtual unsigned	getNumberOfArguments () const
	Returns the number of arguments. More...

unsigned	getNumberOfAtoms () const
	Get number of available atoms. More...

int	getNumberOfComponents () const
	Returns the number of values defined. More...

unsigned	getNumberOfDerivatives () override

double	getOutputQuantity (const std::string &name) const
	Get the value with a specific name (N.B. if there is no such value this returns zero) More...

double	getOutputQuantity (const unsigned j) const
	Get the value of one of the components of the PLMD::Action. More...

const Pbc &	getPbc () const
	Get reference to Pbc. More...

Value *	getPntrToArgument (const unsigned n)
	Return a pointer to specific argument. More...

const Vector &	getPosition (int) const
	Get position of i-th atom (access by relative index) More...

const std::vector< Vector > &	getPositions () const
	Get the array of all positions. More...

double	getProjection (unsigned i, unsigned j) const
	Get the scalar product between the gradients of two variables. More...

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

double	getScore ()

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

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

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

unsigned	getTotAtoms () const
	Get total number of atoms, including virtual ones. More...

const std::set< AtomNumber > &	getUnique () const

const std::set< AtomNumber > &	getUniqueLocal () const

unsigned	getWstride ()

void	Initialise (const unsigned input)

void	interpretArgumentList (const std::vector< std::string > &c, std::vector< Value * > &arg)
	Convert a list of argument names into a list of pointers to the values. More...

void	interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
	Convert a set of read in strings into an atom list (this is used in parseAtomList) More...

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

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

void	lockRequests () override

void	makeWhole ()
	Make atoms whole, assuming they are in the proper order. More...

double &	modifyForceOnEnergy ()
	Get a reference to force on energy. More...

double &	modifyForceOnExtraCV ()
	Get a reference to force on extraCV. More...

std::vector< Vector > &	modifyForces ()
	Get a reference to forces array. More...

Vector &	modifyGlobalForce (AtomNumber)
	Get modifiable force of i-th atom (access by absolute AtomNumber). More...

Pbc &	modifyGlobalPbc ()
	Get modifiable PBC Should be used by action that need to modify the stored box. More...

Vector &	modifyGlobalPosition (AtomNumber)
	Get modifiable position of i-th atom (access by absolute AtomNumber). More...

Tensor &	modifyGlobalVirial ()
	Get modifiable virial Should be used by action that need to modify the stored virial. More...

Tensor &	modifyVirial ()
	Get a reference to virial array. More...

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

bool	parseArgumentList (const std::string &key, int i, std::vector< Value * > &args)
	Parse a numbered list of arguments. More...

void	parseArgumentList (const std::string &key, std::vector< Value * > &args)
	Parse a list of arguments. More...

void	parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t)
	Parse an list of atom with a numbred keyword. More...

void	parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
	Parse a list of atoms without a numbered keyword. 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...

void	pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
	Applies PBCs to a seriens of positions or distances. More...

Vector	pbcDistance (const Vector &, const Vector &) const
	Compute the pbc distance between two positions. 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	readAtomsFromPDB (const PDB &pdb) override
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...

void	requestArguments (const std::vector< Value * > &arg)
	Setup the dependencies. More...

void	requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
	Request an array of atoms. More...

void	requestExtraDependencies (const std::vector< Value * > &extra)

virtual void	retrieveAtoms ()

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

void	Selector ()

void	setArgDerivatives (Value *v, const double &d)

void	setAtomsDerivatives (Value *v, const unsigned i, const Vector &d)

void	setBoxDerivatives (Value *v, const Tensor &d)

void	setCalcData (const std::vector< double > &data)

void	setCalcData (const unsigned index, const double datum)

void	setDerivatives ()

void	setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned ind=0)
	Add the forces to the atoms. More...

void	setGradientsIfNeeded ()
	Calculate the gradients and store them for all the values (need for projections) More...

void	setNarg (const unsigned input)

void	setNotPeriodic ()
	Set your default value to have no periodicity. More...

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

void	setParameter (const double input)

void	setParameters (const std::vector< double > &input)

void	setPeriodic (const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...

void	setScore (const double score)

void	setValue (Value *, double)
	Set the value. More...

void	turnOnDerivatives () override
	Activate the calculation of derivatives. More...

void	unlockRequests () override

virtual void	update ()
	Update. More...

void	updateUniqueLocal ()
	updates local unique atoms More...

void	useNumericalDerivatives ()
	This forces the class to use numerical derivatives. More...

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

void	writeStatus ()

Static Public Member Functions
static void	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...

static void	noAnalyticalDerivatives (Keywords &keys)
	Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...

static void	registerKeywords (Keywords &keys)

static void	useCustomisableComponents (Keywords &keys)
	The components in the action will depend on the user. More...

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	expandArgKeywordInPDB (const PDB &pdb)
	This changes the arg keyword in the pdb file. More...

Value *	getPntrToComponent (const std::string &name)
	Return a pointer to the value by name. More...

Value *	getPntrToComponent (int i)
	Return a pointer to the component by index. More...

Value *	getPntrToValue ()
	Get a pointer to the default value. More...

void	setExtraCV (const std::string &name)

void	setValue (const double &d)
	Set the default value (the one without name) More...

Protected Attributes
Atoms &	atoms

Private Types
enum	{ GAUSS, MGAUSS, OUTLIERS, MOUTLIERS, GENERIC }

enum	{ LIKE_GAUSS, LIKE_LOGN }

enum	{ SC_GAUSS, SC_FLAT }

Private Member Functions
void	do_regression_zero (const std::vector< double > &mean)

double	doMonteCarlo (const std::vector< double > &mean)

void	get_sigma_mean (const double weight, const double norm, const double neff, const std::vector< double > &mean)

void	get_weights (double &weight, double &norm, double &neff)

double	getCalcData (const unsigned index)

int	getComponent (const std::string &name) const
	Return the index for the component named name. More...

void	getEnergyForceGJ (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)

void	getEnergyForceGJE (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)

void	getEnergyForceMIGEN (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)

void	getEnergyForceSP (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)

void	getEnergyForceSPE (const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b)

double	getEnergyGJ (const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)

double	getEnergyGJE (const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)

double	getEnergyMIGEN (const std::vector< double > &mean, const std::vector< double > &ftilde, const std::vector< double > &sigma, const double scale, const double offset)

double	getEnergySP (const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)

double	getEnergySPE (const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset)

void	moveScaleOffset (const std::vector< double > &mean_, double &old_energy)

void	moveSigmas (const std::vector< double > &mean_, double &old_energy, const unsigned i, const std::vector< unsigned > &indices, bool &breaknow)

void	moveTilde (const std::vector< double > &mean_, double &old_energy)

void	replica_averaging (const double weight, const double norm, std::vector< double > &mean, std::vector< double > &dmean_b)

void	setMetaDer (const unsigned index, const double der)

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

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

std::vector< Value * >	arguments

std::vector< std::vector< double > >	average_weights_

std::vector< double >	calc_data_

std::vector< double >	charges

bool	chargesWereSet

double	decay_w_

double	Dftilde_

unsigned	do_optsigmamean_

bool	do_reweight_

bool	doCheckPoint

double	Doffset_

bool	donotforce

bool	donotretrieve

bool	dooffset_

bool	doregres_zero_

bool	doscale_

bool	doscore_

double	Dscale_

std::vector< double >	Dsigma_

double	energy

std::string	extraCV

bool	firstTime

std::vector< bool >	firstTimeW

double	forceOnEnergy

double	forceOnExtraCV

std::vector< double >	forces

std::vector< double >	forcesToApply

std::vector< double >	ftilde_

unsigned	gen_likelihood_

std::vector< AtomNumber >	indexes

unsigned	iselect

double	kbt_

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...

bool	lockRequestArguments

bool	lockRequestAtoms

std::vector< double >	masses

bool	master

long unsigned	MCaccept_

long unsigned	MCacceptFT_

long unsigned	MCacceptScale_

unsigned	MCchunksize_

unsigned	MCsteps_

long unsigned	MCtrial_

std::vector< double >	metader_

unsigned	N_optimized_step_

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

unsigned	narg

bool	noderiv
	Are we skipping the calculation of the derivatives. More...

unsigned	noise_type_

int	nregres_zero_

unsigned	nrep_

unsigned	nsel_

bool	numericalDerivatives
	Are we using numerical derivatives to differentiate. More...

double	offset_

double	offset_max_

double	offset_min_

double	offset_mu_

unsigned	offset_prior_

unsigned	optimized_step_

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

unsigned	optsigmamean_stride_

std::vector< double >	parameters

Pbc &	pbc =*pbc_fwd

ForwardDecl< Pbc >	pbc_fwd

std::vector< Vector >	positions

std::vector< Random >	random

unsigned	replica_

int	replica_index

bool	restart

double	scale_

double	scale_max_

double	scale_min_

double	scale_mu_

unsigned	scale_prior_

std::string	selector_

OFile	sfile_

std::vector< double >	sigma_

std::vector< double >	sigma_max_

std::vector< double >	sigma_max_est_

std::vector< double >	sigma_mean2_

std::vector< std::vector< std::vector< double > > >	sigma_mean2_last_

std::vector< double >	sigma_min_

bool	sigmamax_opt_done_

std::string	status_file_name_

std::set< AtomNumber >	unique
	unique should be an ordered set since we later create a vector containing the corresponding indexes More...

std::set< AtomNumber >	unique_local
	unique_local should be an ordered set since we later create a vector containing the corresponding indexes More...

double	update_from
	Update only after this time. More...

double	update_until
	Update only until this time. More...

Value *	valueAccept

Value *	valueAcceptFT

Value *	valueAcceptScale

std::vector< Value * >	valueFtilde

Value *	valueOffset

std::vector< std::unique_ptr< Value > >	values
	An array containing the values for this action. More...

Value *	valueScale

Value *	valueScore

std::vector< Value * >	valueSigma

std::vector< Value * >	valueSigmaMean

Tensor	virial

unsigned	write_stride_

Detailed Description

This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action.

Member Typedef Documentation

◆ Dependencies

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

inherited

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

private

Enumerator
GAUSS
MGAUSS
OUTLIERS
MOUTLIERS
GENERIC

◆ anonymous enum

anonymous enum

private

Enumerator
LIKE_GAUSS
LIKE_LOGN

◆ anonymous enum

anonymous enum

private

Enumerator
SC_GAUSS
SC_FLAT

Constructor & Destructor Documentation

◆ MetainferenceBase()

PLMD::isdb::MetainferenceBase::MetainferenceBase ( const ActionOptions & ao )

explicit

◆ ~MetainferenceBase()

PLMD::isdb::MetainferenceBase::~MetainferenceBase ( )

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string & name )

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string & name )

inherited

Add a value with a name like label.name that has derivatives.

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments ( const std::vector< double > & forces )

inherited

Add forces to arguments (used in apply)

◆ addValue()

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )

inlineinherited

Allow calls to modifyGlobalForce()

◆ apply()

void PLMD::isdb::MetainferenceBase::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.

◆ applyForces()

void PLMD::ActionAtomistic::applyForces ( )

inherited

◆ 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.

◆ bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc	(	int	i,
		double	d1
	)		const

inlineinherited

Takes one value and brings it back into the pbc of argument i.

◆ calculate()

virtual void PLMD::Action::calculate ( )

pure virtualinherited

Calculate an Action.

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

Implemented in PLMD::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::EMMI, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::function::FuncPathMSD, PLMD::generic::FitToTemplate, PLMD::function::FuncSumHills, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::function::Custom, PLMD::ves::VesDeltaF, PLMD::opes::OPESexpanded, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::bias::MaxEnt, PLMD::generic::Group, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::vatom::Center, PLMD::colvar::Dimer, PLMD::bias::ExtendedLagrangian, PLMD::colvar::DRMSD, PLMD::bias::External, PLMD::generic::EffectiveEnergyDrift, PLMD::colvar::Distance, PLMD::colvar::ContactMap, PLMD::generic::WholeMolecules, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::mapping::AdaptivePath, PLMD::ves::OutputFesBias, PLMD::function::Target, PLMD::adjmat::Sprint, PLMD::generic::ResetCell, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::colvar::EEFSolv, PLMD::analysis::Average, PLMD::analysis::AnalysisBase, PLMD::colvar::Torsion, PLMD::multicolvar::CenterOfMultiColvar, PLMD::vatom::FixedAtom, PLMD::colvar::PathMSDBase, PLMD::bias::ABMD, PLMD::generic::DumpMassCharge, PLMD::multicolvar::DistanceFromContour, PLMD::isdb::FretEfficiency, PLMD::ves::OutputBasisFunctions, PLMD::colvar::Gyration, PLMD::generic::UpdateIf, PLMD::colvar::Angle, PLMD::generic::Print, PLMD::ves::OutputTargetDistribution, PLMD::function::Combine, PLMD::isdb::PRE, PLMD::adjmat::OutputCluster, PLMD::function::LocalEnsemble, PLMD::colvar::Position, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::adjmat::ClusterDistribution, PLMD::bias::BiasValue, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::maze::Loss, PLMD::colvar::Puckering, PLMD::function::Piecewise, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::adjmat::ClusterProperties, PLMD::colvar::Energy, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::colvar::Dipole, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::bias::Restraint, PLMD::function::Ensemble, PLMD::colvar::Constant, PLMD::GenericMolInfo, PLMD::function::Stats, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::manyrestraints::ManyRestraintsBase, PLMD::colvar::ExtraCV, PLMD::function::Sort, PLMD::generic::Debug, PLMD::generic::DumpProjections, PLMD::vatom::Ghost, PLMD::adjmat::DumpGraph, PLMD::colvar::Template, PLMD::colvar::Cell, PLMD::opes::ExpansionCVs, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, PLMD::colvar::Volume, PLMD::generic::Time, PLMD::colvar::ColvarFake, PLMD::ActionShortcut, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::colvar::MultiRMSD, PLMD::colvar::PCARMSD, PLMD::colvar::RMSD, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, PLMD::mapping::PathBase, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::piv::PIV, PLMD::fisst::FISST, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, PLMD::isdb::Rescale, PLMD::maze::OptimizerBias, PLMD::funnel::Funnel, PLMD::function::FuncPathGeneral, PLMD::funnel::FUNNEL_PS, PLMD::function::annfunc::ANN, PLMD::isdb::Caliber, PLMD::maze::Optimizer, PLMD::colvar::ProjectionOnAxis, PLMD::s2cm::S2ContactModel, and PLMD::isdb::Select.

◆ calculateAtomicNumericalDerivatives()

void PLMD::ActionAtomistic::calculateAtomicNumericalDerivatives	(	ActionWithValue *	a,
		const unsigned &	startnum
	)

inherited

Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic.

◆ 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::isdb::MetainferenceBase::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

inlineoverridevirtual

N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::ActionAtomistic.

◆ changeBox()

void PLMD::ActionAtomistic::changeBox ( const Tensor & newbox )

inherited

Change the box shape.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap, and PLMD::piv::PIV.

◆ 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() [1/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ 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.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::manyrestraints::ManyRestraintsBase.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )

inherited

◆ componentIsNotPeriodic()

void PLMD::ActionWithValue::componentIsNotPeriodic ( const std::string & name )

inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

void PLMD::ActionWithValue::componentIsPeriodic	(	const std::string &	name,
		const std::string &	min,
		const std::string &	max
	)

inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

void PLMD::ActionWithValue::componentsAreNotOptional ( Keywords & keys )

staticinherited

Puts a message into the manual that the components always output.

◆ copyOutput() [1/2]

Value * PLMD::ActionWithValue::copyOutput ( const std::string & name ) const

inherited

Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

Value * PLMD::ActionWithValue::copyOutput ( const unsigned & n ) const

inherited

Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action.

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ difference()

double PLMD::ActionWithArguments::difference	(	int	i,
		double	d1,
		double	d2
	)		const

inlineinherited

Takes the difference taking into account pbc for arg i.

◆ do_regression_zero()

void PLMD::isdb::MetainferenceBase::do_regression_zero ( const std::vector< double > & mean )

private

◆ doMonteCarlo()

double PLMD::isdb::MetainferenceBase::doMonteCarlo ( const std::vector< double > & mean )

private

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ doNotForce()

void PLMD::ActionAtomistic::doNotForce ( )

inlineinherited

Skip atom forces - use with care.

If this function is called during initialization, then forces are not going to be propagated. Can be used for optimization.

◆ doNotRetrieve()

void PLMD::ActionAtomistic::doNotRetrieve ( )

inlineinherited

Skip atom retrieval - use with care.

If this function is called during initialization, then atoms are not going to be retrieved. Can be used for optimization. Notice that calling getPosition(int) in an Action where DoNotRetrieve() was called might lead to undefined behavior.

◆ error()

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

inherited

Crash calculation and print documentation.

◆ exists()

bool PLMD::ActionWithValue::exists ( const std::string & name ) const

inherited

Check if a value with a particular name is present.

This is only used in PLMD::ActionWithArguments. You should not use it when manipulating components.

◆ exit()

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

inherited

Exit with error code c.

◆ expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( const PDB & pdb )

protectedinherited

This changes the arg keyword in the pdb file.

◆ 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)

◆ get_sigma_mean()

void PLMD::isdb::MetainferenceBase::get_sigma_mean	(	const double	weight,
		const double	norm,
		const double	neff,
		const std::vector< double > &	mean
	)

private

◆ get_weights()

void PLMD::isdb::MetainferenceBase::get_weights	(	double &	weight,
		double &	norm,
		double &	neff
	)

private

◆ getAbsoluteIndex()

AtomNumber PLMD::ActionAtomistic::getAbsoluteIndex ( int i ) const

inlineinherited

Get the absolute index of an atom.

◆ getAbsoluteIndexes()

const std::vector< AtomNumber > & PLMD::ActionAtomistic::getAbsoluteIndexes ( ) const

inlinevirtualinherited

Get the vector of absolute indexes.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned n ) const

inlineinherited

Returns the value of an argument.

◆ getArguments()

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const

inlinevirtualinherited

Returns an array of pointers to the arguments.

◆ getBox()

const Tensor & PLMD::ActionAtomistic::getBox ( ) const

inlineinherited

Get box shape.

◆ getCalcData()

double PLMD::isdb::MetainferenceBase::getCalcData ( const unsigned index )

inlineprivate

◆ getCharge()

double PLMD::ActionAtomistic::getCharge ( int i ) const

inlineinherited

Get charge of i-th atom.

◆ getComponent()

int PLMD::ActionWithValue::getComponent ( const std::string & name ) const

privateinherited

Return the index for the component named name.

◆ getComponentsList()

std::string PLMD::ActionWithValue::getComponentsList ( ) const

inherited

get a string that contains all the available components

◆ getComponentsVector()

std::vector< std::string > PLMD::ActionWithValue::getComponentsVector ( ) const

inherited

get a vector that contains the label for all the components

◆ 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.

◆ getDocumentation()

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

virtualinherited

◆ getDoScore()

bool PLMD::isdb::MetainferenceBase::getDoScore ( )

inline

◆ getEnergy()

const double & PLMD::ActionAtomistic::getEnergy ( ) const

inlineinherited

Get energy.

◆ getEnergyForceGJ()

void PLMD::isdb::MetainferenceBase::getEnergyForceGJ	(	const std::vector< double > &	mean,
		const std::vector< double > &	dmean_x,
		const std::vector< double > &	dmean_b
	)

private

◆ getEnergyForceGJE()

void PLMD::isdb::MetainferenceBase::getEnergyForceGJE	(	const std::vector< double > &	mean,
		const std::vector< double > &	dmean_x,
		const std::vector< double > &	dmean_b
	)

private

◆ getEnergyForceMIGEN()

void PLMD::isdb::MetainferenceBase::getEnergyForceMIGEN	(	const std::vector< double > &	mean,
		const std::vector< double > &	dmean_x,
		const std::vector< double > &	dmean_b
	)

private

◆ getEnergyForceSP()

void PLMD::isdb::MetainferenceBase::getEnergyForceSP	(	const std::vector< double > &	mean,
		const std::vector< double > &	dmean_x,
		const std::vector< double > &	dmean_b
	)

private

◆ getEnergyForceSPE()

void PLMD::isdb::MetainferenceBase::getEnergyForceSPE	(	const std::vector< double > &	mean,
		const std::vector< double > &	dmean_x,
		const std::vector< double > &	dmean_b
	)

private

◆ getEnergyGJ()

double PLMD::isdb::MetainferenceBase::getEnergyGJ	(	const std::vector< double > &	mean,
		const std::vector< double > &	sigma,
		const double	scale,
		const double	offset
	)

private

◆ getEnergyGJE()

double PLMD::isdb::MetainferenceBase::getEnergyGJE	(	const std::vector< double > &	mean,
		const std::vector< double > &	sigma,
		const double	scale,
		const double	offset
	)

private

◆ getEnergyMIGEN()

double PLMD::isdb::MetainferenceBase::getEnergyMIGEN	(	const std::vector< double > &	mean,
		const std::vector< double > &	ftilde,
		const std::vector< double > &	sigma,
		const double	scale,
		const double	offset
	)

private

◆ getEnergySP()

double PLMD::isdb::MetainferenceBase::getEnergySP	(	const std::vector< double > &	mean,
		const std::vector< double > &	sigma,
		const double	scale,
		const double	offset
	)

private

◆ getEnergySPE()

double PLMD::isdb::MetainferenceBase::getEnergySPE	(	const std::vector< double > &	mean,
		const std::vector< double > &	sigma,
		const double	scale,
		const double	offset
	)

private

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getGlobalPosition()

const Vector & PLMD::ActionAtomistic::getGlobalPosition ( AtomNumber i ) const

inlineinherited

Get position of i-th atom (access by absolute AtomNumber).

With direct access to the global atom array.

Warning: Should be only used by actions that need to read the shared position array. This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.

◆ 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.

◆ getMass()

double PLMD::ActionAtomistic::getMass ( int i ) const

inlineinherited

Get mass of i-th atom.

◆ getMetaDer()

double PLMD::isdb::MetainferenceBase::getMetaDer ( const unsigned index )

inline

◆ getName()

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

inlineinherited

Returns the name.

◆ getNarg()

unsigned PLMD::isdb::MetainferenceBase::getNarg ( )

inline

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inlinevirtualinherited

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::isdb::MetainferenceBase::getNumberOfDerivatives ( )

inlineoverridevirtual

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

double PLMD::ActionWithValue::getOutputQuantity ( const std::string & name ) const

inlineinherited

Get the value with a specific name (N.B. if there is no such value this returns zero)

◆ getOutputQuantity() [2/2]

double PLMD::ActionWithValue::getOutputQuantity ( const unsigned j ) const

inlineinherited

Get the value of one of the components of the PLMD::Action.

◆ getPbc()

const Pbc & PLMD::ActionAtomistic::getPbc ( ) const

inlineinherited

Get reference to Pbc.

◆ getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned n )

inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( const std::string & name )

protectedinherited

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

Value * PLMD::ActionWithValue::getPntrToComponent ( int i )

protectedinherited

Return a pointer to the component by index.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

◆ getPosition()

const Vector & PLMD::ActionAtomistic::getPosition ( int i ) const

inlineinherited

Get position of i-th atom (access by relative index)

◆ getPositions()

const std::vector< Vector > & PLMD::ActionAtomistic::getPositions ( ) const

inlineinherited

Get the array of all positions.

◆ getProjection()

double PLMD::ActionWithArguments::getProjection	(	unsigned	i,
		unsigned	j
	)		const

inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getScore()

double PLMD::isdb::MetainferenceBase::getScore ( )

◆ getStep()

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

inherited

Return the present timestep.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getTotAtoms()

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inlineinherited

Get total number of atoms, including virtual ones.

Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.

◆ getUnique()

const std::set< AtomNumber > & PLMD::ActionAtomistic::getUnique ( ) const

inlineinherited

◆ getUniqueLocal()

const std::set< AtomNumber > & PLMD::ActionAtomistic::getUniqueLocal ( ) const

inlineinherited

◆ getWstride()

unsigned PLMD::isdb::MetainferenceBase::getWstride ( )

inline

◆ Initialise()

void PLMD::isdb::MetainferenceBase::Initialise ( const unsigned input )

◆ interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList	(	const std::vector< std::string > &	c,
		std::vector< Value * > &	arg
	)

inherited

Convert a list of argument names into a list of pointers to the values.

◆ interpretAtomList()

void PLMD::ActionAtomistic::interpretAtomList	(	std::vector< std::string > &	strings,
		std::vector< AtomNumber > &	t
	)

inherited

Convert a set of read in strings into an atom list (this is used in parseAtomList)

◆ 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.

◆ lockRequests()

void PLMD::isdb::MetainferenceBase::lockRequests ( )

inlineoverridevirtual

Reimplemented from PLMD::ActionAtomistic.

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )

inherited

Make atoms whole, assuming they are in the proper order.

◆ modifyForceOnEnergy()

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

◆ modifyForceOnExtraCV()

double & PLMD::ActionAtomistic::modifyForceOnExtraCV ( )

inlineinherited

Get a reference to force on extraCV.

◆ modifyForces()

std::vector< Vector > & PLMD::ActionAtomistic::modifyForces ( )

inlineinherited

Get a reference to forces array.

◆ modifyGlobalForce()

Vector & PLMD::ActionAtomistic::modifyGlobalForce ( AtomNumber i )

inlineinherited

Get modifiable force of i-th atom (access by absolute AtomNumber).

Warning: Should be used by action that need to modify the stored atomic forces. This should be used with great care since the plumed core does not usually keep all these forces up to date. In particular, if an action require this, one should during constructor call allowToAccessGlobalForces(). Notice that for efficiency reason plumed does not check if this is done!

◆ modifyGlobalPbc()

Pbc & PLMD::ActionAtomistic::modifyGlobalPbc ( )

inlineinherited

Get modifiable PBC Should be used by action that need to modify the stored box.

◆ modifyGlobalPosition()

Vector & PLMD::ActionAtomistic::modifyGlobalPosition ( AtomNumber i )

inlineinherited

Get modifiable position of i-th atom (access by absolute AtomNumber).

Warning: Should be only used by actions that need to modify the shared position array. This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.

◆ modifyGlobalVirial()

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inlineinherited

Get modifiable virial Should be used by action that need to modify the stored virial.

◆ modifyVirial()

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

◆ moveScaleOffset()

void PLMD::isdb::MetainferenceBase::moveScaleOffset	(	const std::vector< double > &	mean_,
		double &	old_energy
	)

private

◆ moveSigmas()

void PLMD::isdb::MetainferenceBase::moveSigmas	(	const std::vector< double > &	mean_,
		double &	old_energy,
		const unsigned	i,
		const std::vector< unsigned > &	indices,
		bool &	breaknow
	)

private

◆ moveTilde()

void PLMD::isdb::MetainferenceBase::moveTilde	(	const std::vector< double > &	mean_,
		double &	old_energy
	)

private

◆ noAnalyticalDerivatives()

void PLMD::ActionWithValue::noAnalyticalDerivatives ( Keywords & keys )

staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

bool PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		int	i,
		std::vector< Value * > &	args
	)

inherited

Parse a numbered list of arguments.

◆ parseArgumentList() [2/2]

void PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		std::vector< Value * > &	args
	)

inherited

Parse a list of arguments.

◆ parseAtomList() [1/2]

void PLMD::ActionAtomistic::parseAtomList	(	const std::string &	key,
		const int	num,
		std::vector< AtomNumber > &	t
	)

inherited

Parse an list of atom with a numbred keyword.

◆ parseAtomList() [2/2]

void PLMD::ActionAtomistic::parseAtomList	(	const std::string &	key,
		std::vector< AtomNumber > &	t
	)

inherited

Parse a list of atoms without a numbered keyword.

◆ 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.

◆ pbcApply()

void PLMD::ActionAtomistic::pbcApply	(	std::vector< Vector > &	dlist,
		unsigned	max_index = `0`
	)		const

inherited

Applies PBCs to a seriens of positions or distances.

◆ pbcDistance()

Vector PLMD::ActionAtomistic::pbcDistance	(	const Vector &	v1,
		const Vector &	v2
	)		const

inherited

Compute the pbc distance between two positions.

◆ 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, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

◆ readAtomsFromPDB()

void PLMD::ActionAtomistic::readAtomsFromPDB ( const PDB & pdb )

overridevirtualinherited

Read in an input file containing atom positions and calculate the action for the atomic configuration therin.

Reimplemented from PLMD::Action.

◆ registerKeywords()

void PLMD::isdb::MetainferenceBase::registerKeywords ( Keywords & keys )

static

◆ replica_averaging()

void PLMD::isdb::MetainferenceBase::replica_averaging	(	const double	weight,
		const double	norm,
		std::vector< double > &	mean,
		std::vector< double > &	dmean_b
	)

private

◆ requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value * > & arg )

inherited

Setup the dependencies.

◆ requestAtoms()

void PLMD::ActionAtomistic::requestAtoms	(	const std::vector< AtomNumber > &	a,
		const bool	clearDep = `true`
	)

inherited

Request an array of atoms.

This method is used to ask for a list of atoms. Atoms should be asked for by number. If this routine is called during the simulation, atoms will be available at the next step MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC LISTS OF ATOMS

◆ requestExtraDependencies()

void PLMD::ActionWithArguments::requestExtraDependencies ( const std::vector< Value * > & extra )

inherited

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( )

virtualinherited

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ 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.

◆ Selector()

void PLMD::isdb::MetainferenceBase::Selector ( )

◆ setArgDerivatives()

void PLMD::isdb::MetainferenceBase::setArgDerivatives	(	Value *	v,
		const double &	d
	)

inline

◆ setAtomsDerivatives()

void PLMD::isdb::MetainferenceBase::setAtomsDerivatives	(	Value *	v,
		const unsigned	i,
		const Vector &	d
	)

inline

◆ setBoxDerivatives()

void PLMD::isdb::MetainferenceBase::setBoxDerivatives	(	Value *	v,
		const Tensor &	d
	)

inline

◆ setCalcData() [1/2]

void PLMD::isdb::MetainferenceBase::setCalcData ( const std::vector< double > & data )

inline

◆ setCalcData() [2/2]

void PLMD::isdb::MetainferenceBase::setCalcData	(	const unsigned	index,
		const double	datum
	)

inline

◆ setDerivatives()

void PLMD::isdb::MetainferenceBase::setDerivatives ( )

inline

◆ setExtraCV()

void PLMD::ActionAtomistic::setExtraCV ( const std::string & name )

inlineprotectedinherited

◆ setForcesOnAtoms()

void PLMD::ActionAtomistic::setForcesOnAtoms	(	const std::vector< double > &	forcesToApply,
		unsigned	ind = `0`
	)

inherited

Add the forces to the atoms.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

Calculate the gradients and store them for all the values (need for projections)

◆ setMetaDer()

void PLMD::isdb::MetainferenceBase::setMetaDer	(	const unsigned	index,
		const double	der
	)

inlineprivate

◆ setNarg()

void PLMD::isdb::MetainferenceBase::setNarg ( const unsigned input )

inline

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

◆ setOption()

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

virtualinherited

◆ setParameter()

void PLMD::isdb::MetainferenceBase::setParameter ( const double input )

inline

◆ setParameters()

void PLMD::isdb::MetainferenceBase::setParameters ( const std::vector< double > & input )

inline

◆ setPeriodic()

void PLMD::ActionWithValue::setPeriodic	(	const std::string &	min,
		const std::string &	max
	)

inherited

Set the value to be periodic with a particular domain.

◆ setScore()

void PLMD::isdb::MetainferenceBase::setScore ( const double score )

inline

◆ setValue() [1/2]

void PLMD::ActionWithValue::setValue ( const double & d )

inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

void PLMD::ActionWithValue::setValue	(	Value *	,
		double
	)

inherited

Set the value.

◆ turnOnDerivatives()

void PLMD::isdb::MetainferenceBase::turnOnDerivatives ( )

inlineoverridevirtual

Activate the calculation of derivatives.

Reimplemented from PLMD::ActionWithValue.

◆ unlockRequests()

void PLMD::isdb::MetainferenceBase::unlockRequests ( )

inlineoverridevirtual

Reimplemented from PLMD::ActionAtomistic.

◆ 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::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::opes::OPESexpanded, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::PRE, PLMD::multicolvar::DumpMultiColvar, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpDerivatives, 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.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( )

inherited

updates local unique atoms

◆ useCustomisableComponents()

void PLMD::ActionWithValue::useCustomisableComponents ( Keywords & keys )

staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ warning()

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

inherited

Issue a warning.

◆ writeStatus()

void PLMD::isdb::MetainferenceBase::writeStatus ( )

Member Data Documentation

◆ 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.

◆ arguments

std::vector<Value*> PLMD::ActionWithArguments::arguments

privateinherited

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

◆ average_weights_

std::vector< std::vector <double> > PLMD::isdb::MetainferenceBase::average_weights_

private

◆ calc_data_

std::vector<double> PLMD::isdb::MetainferenceBase::calc_data_

private

◆ charges

std::vector<double> PLMD::ActionAtomistic::charges

privateinherited

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet

privateinherited

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ decay_w_

double PLMD::isdb::MetainferenceBase::decay_w_

private

◆ Dftilde_

double PLMD::isdb::MetainferenceBase::Dftilde_

private

◆ do_optsigmamean_

unsigned PLMD::isdb::MetainferenceBase::do_optsigmamean_

private

◆ do_reweight_

bool PLMD::isdb::MetainferenceBase::do_reweight_

private

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ Doffset_

double PLMD::isdb::MetainferenceBase::Doffset_

private

◆ donotforce

bool PLMD::ActionAtomistic::donotforce

privateinherited

◆ donotretrieve

bool PLMD::ActionAtomistic::donotretrieve

privateinherited

◆ dooffset_

bool PLMD::isdb::MetainferenceBase::dooffset_

private

◆ doregres_zero_

bool PLMD::isdb::MetainferenceBase::doregres_zero_

private

◆ doscale_

bool PLMD::isdb::MetainferenceBase::doscale_

private

◆ doscore_

bool PLMD::isdb::MetainferenceBase::doscore_

private

◆ Dscale_

double PLMD::isdb::MetainferenceBase::Dscale_

private

◆ Dsigma_

std::vector<double> PLMD::isdb::MetainferenceBase::Dsigma_

private

◆ energy

double PLMD::ActionAtomistic::energy

privateinherited

◆ extraCV

std::string PLMD::ActionAtomistic::extraCV

privateinherited

◆ files

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

inherited

◆ firstTime

bool PLMD::isdb::MetainferenceBase::firstTime

private

◆ firstTimeW

std::vector<bool> PLMD::isdb::MetainferenceBase::firstTimeW

private

◆ forceOnEnergy

double PLMD::ActionAtomistic::forceOnEnergy

privateinherited

◆ forceOnExtraCV

double PLMD::ActionAtomistic::forceOnExtraCV

privateinherited

◆ forces

std::vector<double> PLMD::isdb::MetainferenceBase::forces

private

◆ forcesToApply

std::vector<double> PLMD::isdb::MetainferenceBase::forcesToApply

private

◆ ftilde_

std::vector<double> PLMD::isdb::MetainferenceBase::ftilde_

private

◆ gen_likelihood_

unsigned PLMD::isdb::MetainferenceBase::gen_likelihood_

private

◆ indexes

std::vector<AtomNumber> PLMD::ActionAtomistic::indexes

privateinherited

◆ iselect

unsigned PLMD::isdb::MetainferenceBase::iselect

private

◆ kbt_

double PLMD::isdb::MetainferenceBase::kbt_

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.

◆ lockRequestArguments

bool PLMD::ActionWithArguments::lockRequestArguments

privateinherited

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ masses

std::vector<double> PLMD::ActionAtomistic::masses

privateinherited

◆ master

bool PLMD::isdb::MetainferenceBase::master

private

◆ MCaccept_

long unsigned PLMD::isdb::MetainferenceBase::MCaccept_

private

◆ MCacceptFT_

long unsigned PLMD::isdb::MetainferenceBase::MCacceptFT_

private

◆ MCacceptScale_

long unsigned PLMD::isdb::MetainferenceBase::MCacceptScale_

private

◆ MCchunksize_

unsigned PLMD::isdb::MetainferenceBase::MCchunksize_

private

◆ MCsteps_

unsigned PLMD::isdb::MetainferenceBase::MCsteps_

private

◆ MCtrial_

long unsigned PLMD::isdb::MetainferenceBase::MCtrial_

private

◆ metader_

std::vector<double> PLMD::isdb::MetainferenceBase::metader_

private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ N_optimized_step_

unsigned PLMD::isdb::MetainferenceBase::N_optimized_step_

private

◆ name

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

privateinherited

Name of the directive in the plumed.dat file.

◆ narg

unsigned PLMD::isdb::MetainferenceBase::narg

private

◆ noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

◆ noise_type_

unsigned PLMD::isdb::MetainferenceBase::noise_type_

private

◆ nregres_zero_

int PLMD::isdb::MetainferenceBase::nregres_zero_

private

◆ nrep_

unsigned PLMD::isdb::MetainferenceBase::nrep_

private

◆ nsel_

unsigned PLMD::isdb::MetainferenceBase::nsel_

private

◆ numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives

privateinherited

Are we using numerical derivatives to differentiate.

◆ offset_

double PLMD::isdb::MetainferenceBase::offset_

private

◆ offset_max_

double PLMD::isdb::MetainferenceBase::offset_max_

private

◆ offset_min_

double PLMD::isdb::MetainferenceBase::offset_min_

private

◆ offset_mu_

double PLMD::isdb::MetainferenceBase::offset_mu_

private

◆ offset_prior_

unsigned PLMD::isdb::MetainferenceBase::offset_prior_

private

◆ optimized_step_

unsigned PLMD::isdb::MetainferenceBase::optimized_step_

private

◆ options

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

privateinherited

Option that you might have enabled.

◆ optsigmamean_stride_

unsigned PLMD::isdb::MetainferenceBase::optsigmamean_stride_

private

◆ parameters

std::vector<double> PLMD::isdb::MetainferenceBase::parameters

private

◆ pbc

Pbc& PLMD::ActionAtomistic::pbc =*pbc_fwd

privateinherited

◆ pbc_fwd

ForwardDecl<Pbc> PLMD::ActionAtomistic::pbc_fwd

privateinherited

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ positions

std::vector<Vector> PLMD::ActionAtomistic::positions

privateinherited

◆ random

std::vector<Random> PLMD::isdb::MetainferenceBase::random

private

◆ replica_

unsigned PLMD::isdb::MetainferenceBase::replica_

private

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ scale_

double PLMD::isdb::MetainferenceBase::scale_

private

◆ scale_max_

double PLMD::isdb::MetainferenceBase::scale_max_

private

◆ scale_min_

double PLMD::isdb::MetainferenceBase::scale_min_

private

◆ scale_mu_

double PLMD::isdb::MetainferenceBase::scale_mu_

private

◆ scale_prior_

unsigned PLMD::isdb::MetainferenceBase::scale_prior_

private

◆ selector_

std::string PLMD::isdb::MetainferenceBase::selector_

private

◆ sfile_

OFile PLMD::isdb::MetainferenceBase::sfile_

private

◆ sigma_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_

private

◆ sigma_max_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_max_

private

◆ sigma_max_est_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_max_est_

private

◆ sigma_mean2_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_mean2_

private

◆ sigma_mean2_last_

std::vector< std::vector < std::vector <double> > > PLMD::isdb::MetainferenceBase::sigma_mean2_last_

private

◆ sigma_min_

std::vector<double> PLMD::isdb::MetainferenceBase::sigma_min_

private

◆ sigmamax_opt_done_

bool PLMD::isdb::MetainferenceBase::sigmamax_opt_done_

private

◆ status_file_name_

std::string PLMD::isdb::MetainferenceBase::status_file_name_

private

◆ unique

std::set<AtomNumber> PLMD::ActionAtomistic::unique

privateinherited

unique should be an ordered set since we later create a vector containing the corresponding indexes

◆ unique_local

std::set<AtomNumber> PLMD::ActionAtomistic::unique_local

privateinherited

unique_local should be an ordered set since we later create a vector containing the corresponding indexes

◆ 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.

◆ valueAccept

Value* PLMD::isdb::MetainferenceBase::valueAccept

private

◆ valueAcceptFT

Value* PLMD::isdb::MetainferenceBase::valueAcceptFT

private

◆ valueAcceptScale

Value* PLMD::isdb::MetainferenceBase::valueAcceptScale

private

◆ valueFtilde

std::vector<Value*> PLMD::isdb::MetainferenceBase::valueFtilde

private

◆ valueOffset

Value* PLMD::isdb::MetainferenceBase::valueOffset

private

◆ values

std::vector<std::unique_ptr<Value> > PLMD::ActionWithValue::values

privateinherited

An array containing the values for this action.

◆ valueScale

Value* PLMD::isdb::MetainferenceBase::valueScale

private

◆ valueScore

Value* PLMD::isdb::MetainferenceBase::valueScore

private

◆ valueSigma

std::vector<Value*> PLMD::isdb::MetainferenceBase::valueSigma

private

◆ valueSigmaMean

std::vector<Value*> PLMD::isdb::MetainferenceBase::valueSigmaMean

private

◆ virial

Tensor PLMD::ActionAtomistic::virial

privateinherited

◆ write_stride_

unsigned PLMD::isdb::MetainferenceBase::write_stride_

private

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

isdb/MetainferenceBase.h
isdb/MetainferenceBase.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Member Enumeration Documentation

◆ anonymous enum

◆ anonymous enum

◆ anonymous enum

Constructor & Destructor Documentation

◆ MetainferenceBase()

◆ ~MetainferenceBase()

Member Function Documentation

◆ activate()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addValue()

◆ addValueWithDerivatives()

◆ allowToAccessGlobalForces()

◆ apply()

◆ applyForces()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ calculate()

◆ calculateAtomicNumericalDerivatives()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ changeBox()

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ clearOutputForces()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ difference()

◆ do_regression_zero()

◆ doMonteCarlo()

◆ doNotCalculateDerivatives()

◆ doNotForce()

◆ doNotRetrieve()

◆ error()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ fopen()

◆ get_sigma_mean()

◆ get_weights()

◆ getAbsoluteIndex()

◆ getAbsoluteIndexes()

◆ getArgument()

◆ getArguments()

◆ getBox()

◆ getCalcData()

◆ getCharge()

◆ getComponent()

◆ getComponentsList()

◆ getComponentsVector()