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. More...

#include <MetainferenceBase.h>

Inheritance diagram for PLMD::isdb::MetainferenceBase:

[legend]

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

Public Member Functions
	MetainferenceBase (const ActionOptions &)

	~MetainferenceBase ()

void	Initialise (const unsigned input)

void	Selector ()

unsigned	getNarg ()

void	setNarg (const unsigned input)

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

void	setParameter (const double input)

void	setCalcData (const unsigned index, const double datum)

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

bool	getDoScore ()

unsigned	getWstride ()

double	getScore ()

void	setScore (const double score)

void	setDerivatives ()

double	getMetaDer (const unsigned index)

void	writeStatus ()

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

unsigned	getNumberOfDerivatives ()

void	lockRequests ()

void	unlockRequests ()

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

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

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	requestAtoms (const std::vector< AtomNumber > &a)
	Request an array of atoms. More...

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

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

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

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

Vector &	modifyGlobalForce (AtomNumber)
	Get modifiable force 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...

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

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

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

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

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

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

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

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

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

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

Vector	pbcDistance (const Vector &, const Vector &) const
	Compute the pbc distance between two positions. More...

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

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

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

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

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

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

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

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

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

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

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

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

void	clearOutputForces ()

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

virtual void	retrieveAtoms ()

void	applyForces ()

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

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

void	readAtomsFromPDB (const PDB &pdb)
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. 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	calculate ()=0
	Calculate an Action. More...

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

virtual void	update ()
	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...

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...

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...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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...

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

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...

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

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

virtual void	clearDerivatives ()
	Clear the derivatives of values wrt parameters. More...

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

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

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

virtual void	checkFieldsAllowed ()

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

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	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...

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

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

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

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

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

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

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)

void	setMetaDer (const unsigned index, const double der)

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

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

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

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

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

double	getCalcData (const unsigned index)

void	get_weights (double &fact, double &var_fact)

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

void	get_sigma_mean (const double fact, const double var_fact, const std::vector< double > &mean)

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

Private Attributes
std::vector< double >	forces

std::vector< double >	forcesToApply

bool	doscore_

unsigned	write_stride_

unsigned	narg

std::vector< double >	parameters

std::vector< double >	metader_

std::vector< double >	calc_data_

unsigned	noise_type_

unsigned	gen_likelihood_

bool	doscale_

unsigned	scale_prior_

double	scale_

double	scale_mu_

double	scale_min_

double	scale_max_

double	Dscale_

unsigned	offset_prior_

bool	dooffset_

double	offset_

double	offset_mu_

double	offset_min_

double	offset_max_

double	Doffset_

std::vector< double >	sigma_

std::vector< double >	sigma_min_

std::vector< double >	sigma_max_

std::vector< double >	Dsigma_

std::vector< double >	sigma_mean2_

std::vector< double >	ftilde_

double	Dftilde_

double	kbt_

std::vector< Random >	random

unsigned	MCsteps_

unsigned	MCstride_

long unsigned	MCaccept_

long unsigned	MCacceptScale_

long unsigned	MCacceptFT_

long unsigned	MCtrial_

unsigned	MCchunksize_

Value *	valueScore

Value *	valueScale

Value *	valueOffset

Value *	valueAccept

Value *	valueAcceptScale

Value *	valueAcceptFT

std::vector< Value * >	valueSigma

std::vector< Value * >	valueSigmaMean

std::vector< Value * >	valueFtilde

std::string	status_file_name_

OFile	sfile_

bool	firstTime

std::vector< bool >	firstTimeW

bool	master

bool	do_reweight_

unsigned	do_optsigmamean_

unsigned	nrep_

unsigned	replica_

unsigned	nsel_

std::string	selector_

unsigned	iselect

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

unsigned	optsigmamean_stride_

double	decay_w_

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

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 ( )

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.

◆ 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::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::function::Matheval, PLMD::function::FuncSumHills, PLMD::isdb::EMMI, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::eds::EDS, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::generic::FitToTemplate, PLMD::bias::MaxEnt, PLMD::multicolvar::MultiColvarBase, PLMD::generic::WrapAround, PLMD::isdb::Rescale, PLMD::generic::Include, PLMD::function::FuncPathMSD, PLMD::generic::DumpAtoms, PLMD::colvar::Dimer, PLMD::bias::ExtendedLagrangian, PLMD::generic::Group, PLMD::colvar::ContactMap, PLMD::colvar::Distance, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::analysis::Analysis, PLMD::isdb::SAXS, PLMD::generic::WholeMolecules, PLMD::colvar::DRMSD, PLMD::function::Target, PLMD::isdb::JCoupling, PLMD::generic::DumpMassCharge, PLMD::adjmat::Sprint, PLMD::bias::External, PLMD::colvar::Torsion, PLMD::analysis::Average, PLMD::colvar::EEFSolv, PLMD::generic::ResetCell, PLMD::mapping::AdaptivePath, PLMD::colvar::Gyration, PLMD::multicolvar::CenterOfMultiColvar, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::isdb::FretEfficiency, PLMD::multicolvar::DistanceFromContour, PLMD::ves::OutputFesBias, PLMD::colvar::PathMSDBase, PLMD::generic::UpdateIf, PLMD::function::Combine, PLMD::isdb::PRE, PLMD::ves::OutputBasisFunctions, PLMD::generic::Print, PLMD::function::LocalEnsemble, PLMD::ves::OutputTargetDistribution, PLMD::adjmat::OutputCluster, PLMD::vatom::Center, PLMD::vatom::FixedAtom, PLMD::bias::BiasValue, PLMD::generic::Read, PLMD::isdb::NOE, PLMD::generic::RandomExchanges, PLMD::colvar::Puckering, PLMD::function::Piecewise, PLMD::multicolvar::DumpMultiColvar, PLMD::adjmat::ClusterDistribution, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::bias::LWalls, PLMD::isdb::Select, PLMD::vatom::COM, PLMD::bias::UWalls, PLMD::colvar::Position, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::colvar::Constant, PLMD::bias::Restraint, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::adjmat::ClusterProperties, PLMD::function::Ensemble, PLMD::colvar::Energy, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::function::Stats, PLMD::colvar::Dipole, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::generic::Debug, PLMD::colvar::Template, PLMD::generic::DumpProjections, PLMD::manyrestraints::ManyRestraintsBase, PLMD::vatom::Ghost, PLMD::colvar::Cell, PLMD::adjmat::DumpGraph, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::generic::Time, PLMD::adjmat::ClusteringBase, PLMD::gridtools::ActionWithGrid, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::PCARMSD, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, and PLMD::mapping::PathBase.

◆ 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 )

inlinevirtual

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.

◆ 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]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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.

◆ 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.

◆ doMonteCarlo()

void 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 ( 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	fact,
		const double	var_fact,
		const std::vector< double > &	mean
	)

private

◆ get_weights()

void PLMD::isdb::MetainferenceBase::get_weights	(	double &	fact,
		double &	var_fact
	)

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

inlineinherited

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.

◆ 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()

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

private

◆ getEnergyForceGJE()

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

private

◆ getEnergyForceMIGEN()

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

private

◆ getEnergyForceSP()

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

private

◆ getEnergyForceSPE()

double 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.

◆ 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 ( )

inlinevirtual

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

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

inlineinherited

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

◆ getOutputQuantity() [2/2]

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)

◆ 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 ( int i )

protectedinherited

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

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

protectedinherited

Return a pointer to the value by name.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

◆ getPosition() [1/2]

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

inlineinherited

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

◆ getPosition() [2/2]

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

inlineinherited

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

With direct access to the global atom array

◆ 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 modifyPosition or getPosition(AtomNumber)

◆ 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 ( )

inlinevirtual

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.

◆ 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.

◆ modifyGlobalVirial()

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inlineinherited

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

◆ modifyPosition()

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

inlineinherited

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

Should be used by action that need to modify the stored atomic coordinates

◆ modifyVirial()

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

◆ 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]

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

inherited

Parse a list of arguments.

◆ parseArgumentList() [2/2]

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

inherited

Parse a numbered list of arguments.

◆ parseAtomList() [1/2]

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

inherited

Parse a list of atoms without a numbered keyword.

◆ parseAtomList() [2/2]

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.

◆ 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::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()

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

virtualinherited

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	fact,
		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 )

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

◆ 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::analysis::Analysis, PLMD::gridtools::ConvertToFES, 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 unsigned	index,
		const double	datum
	)

inline

◆ setCalcData() [2/2]

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

inline

◆ setDerivatives()

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

inline

◆ 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 ( )

inlinevirtual

Activate the calculation of derivatives.

Reimplemented from PLMD::ActionWithValue.

◆ unlockRequests()

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

inlinevirtual

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::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::eds::EDS, PLMD::ves::TargetDistribution, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::isdb::SAXS, PLMD::generic::DumpMassCharge, PLMD::isdb::JCoupling, PLMD::mapping::AdaptivePath, PLMD::generic::Print, PLMD::ves::OutputFesBias, PLMD::isdb::PRE, PLMD::adjmat::OutputCluster, PLMD::generic::Read, PLMD::isdb::NOE, PLMD::multicolvar::DumpMultiColvar, PLMD::vesselbase::ActionWithAveraging, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, and PLMD::gridtools::GridPrintingBase.

◆ 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

◆ 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

◆ 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

◆ Doffset_

double PLMD::isdb::MetainferenceBase::Doffset_

private

◆ dooffset_

bool PLMD::isdb::MetainferenceBase::dooffset_

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

◆ files

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

inherited

◆ firstTime

bool PLMD::isdb::MetainferenceBase::firstTime

private

◆ firstTimeW

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

private

◆ 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

◆ iselect

unsigned PLMD::isdb::MetainferenceBase::iselect

private

◆ kbt_

double PLMD::isdb::MetainferenceBase::kbt_

private

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ 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

◆ MCstride_

unsigned PLMD::isdb::MetainferenceBase::MCstride_

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

◆ narg

unsigned PLMD::isdb::MetainferenceBase::narg

private

◆ noise_type_

unsigned PLMD::isdb::MetainferenceBase::noise_type_

private

◆ nrep_

unsigned PLMD::isdb::MetainferenceBase::nrep_

private

◆ nsel_

unsigned PLMD::isdb::MetainferenceBase::nsel_

private

◆ 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

◆ optsigmamean_stride_

unsigned PLMD::isdb::MetainferenceBase::optsigmamean_stride_

private

◆ parameters

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

private

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ random

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

private

◆ replica_

unsigned PLMD::isdb::MetainferenceBase::replica_

private

◆ 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_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

◆ status_file_name_

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

private

◆ 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

◆ 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

◆ 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()

◆ doMonteCarlo()

◆ doNotCalculateDerivatives()

◆ doNotForce()

◆ doNotRetrieve()

◆ error()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ fopen()

◆ get_sigma_mean()

◆ get_weights()

◆ getAbsoluteIndex()

◆ getAbsoluteIndexes()

◆ getArgument()

◆ getArguments()

◆ getBox()

◆ getCalcData()

◆ getCharge()

◆ getComponentsList()

◆ getComponentsVector()

◆ getCPT()

◆ getDependencies()