Provides the keyword METAINFERENCE More...

Inheritance diagram for PLMD::isdb::Metainference:

[legend]

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

Public Member Functions
	Metainference (const ActionOptions &)

	~Metainference ()

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

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...

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

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

void	calculateNumericalDerivatives (ActionWithValue *a=NULL) override
	Calculate the numerical derivatives N.B. More...

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

virtual void	checkFieldsAllowed ()

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

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

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

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

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

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

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

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

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

virtual void	clearOptions ()

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	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...

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...

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

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

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

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

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

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

unsigned	getNumberOfDerivatives () override

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...

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

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

int	getStride () const
	Get the stride. More...

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

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

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

virtual void	lockRequests ()

virtual bool	onStep () const
	Check if the action is active on this step. More...

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

template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...

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

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

virtual void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

virtual void	readAtomsFromPDB (const PDB &)
	This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...

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

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

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

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

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

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

void	setStride (const int &n)
	Set the value of the stride. More...

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

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

void	unlockRequests () override

virtual void	unlockRequests ()

void	update () override
	Update. More...

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

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

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

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

void	setBias (double bias)
	set the value of the bias More...

void	setOutputForce (int i, double f)
	set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f More...

void	setupOutputForces ()
	setup the OutputForce vector - this is needed if the bias does not use a normal ARG keyword More...

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

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 vector< double > &mean)

double	doMonteCarlo (const vector< double > &mean)

void	get_sigma_mean (const unsigned iselect, const double fact, const double var_fact, const vector< double > &mean)

void	get_weights (const unsigned iselect, double &fact, double &var_fact)

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

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

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

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

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

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

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

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

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

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

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

void	writeStatus ()

Private Attributes
vector< vector< double > >	average_weights_

unsigned	average_weights_stride_

double	Dftilde_

unsigned	do_optsigmamean_

bool	do_reweight_

double	Doffset_

bool	dooffset_

bool	doregres_zero_

bool	doscale_

double	Dscale_

vector< double >	Dsigma_

bool	firstTime

vector< bool >	firstTimeW

vector< double >	ftilde_

unsigned	gen_likelihood_

double	kbt_

bool	master

long unsigned	MCaccept_

long unsigned	MCacceptFT_

long unsigned	MCacceptScale_

unsigned	MCchunksize_

unsigned	MCsteps_

long unsigned	MCtrial_

unsigned	narg

unsigned	noise_type_

int	nregres_zero_

unsigned	nrep_

double	offset_

double	offset_max_

double	offset_min_

double	offset_mu_

unsigned	offset_prior_

unsigned	optsigmamean_stride_

vector< double >	parameters

vector< Random >	random

unsigned	replica_

double	scale_

double	scale_max_

double	scale_min_

double	scale_mu_

unsigned	scale_prior_

string	selector_

OFile	sfile_

vector< double >	sigma_

vector< double >	sigma_max_

vector< double >	sigma_mean2_

vector< vector< vector< double > > >	sigma_mean2_last_

vector< double >	sigma_min_

Value *	valueAccept

Value *	valueAcceptFT

Value *	valueAcceptScale

vector< Value * >	valueFtilde

Value *	valueOffset

Value *	valueScale

vector< Value * >	valueSigma

vector< Value * >	valueSigmaMean

unsigned	write_stride_

Detailed Description

Provides the keyword METAINFERENCE

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

◆ Metainference()

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

explicit

◆ ~Metainference()

PLMD::isdb::Metainference::~Metainference ( )

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.

◆ apply()

void PLMD::bias::Bias::apply ( )

overridevirtualinherited

Apply an Action.

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

Implements PLMD::Action.

Reimplemented in PLMD::ves::VesBias.

◆ 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()

void PLMD::isdb::Metainference::calculate ( )

overridevirtual

Calculate an Action.

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

Implements PLMD::Action.

◆ calculateFromPDB()

void PLMD::Action::calculateFromPDB ( const PDB & pdb )

inherited

Calculate the action given a pdb file as input.

This is used to initialize things like distance from a point in CV map space given a pdb as an input file

◆ calculateNumericalDerivatives() [1/2]

void PLMD::ActionWithArguments::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

overridevirtualinherited

Calculate the numerical derivatives 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::Action.

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::vesselbase::ActionWithAveraging, and PLMD::mapping::Mapping.

◆ calculateNumericalDerivatives() [2/2]

void PLMD::Action::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtualinherited

Perform calculation using numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing.

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::multicolvar::MultiColvarBase, PLMD::analysis::AnalysisBase, PLMD::vesselbase::ActionWithAveraging, PLMD::mapping::Mapping, PLMD::multicolvar::DumpMultiColvar, PLMD::ActionWithArguments, PLMD::multicolvar::BridgedMultiColvarFunction, and PLMD::vesselbase::ActionWithInputVessel.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::piv::PIV, and 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

inlineoverridevirtualinherited

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

◆ 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::Metainference::do_regression_zero ( const vector< double > & mean )

private

◆ doMonteCarlo()

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

private

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ 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::Metainference::get_sigma_mean	(	const unsigned	iselect,
		const double	fact,
		const double	var_fact,
		const vector< double > &	mean
	)

private

◆ get_weights()

void PLMD::isdb::Metainference::get_weights	(	const unsigned	iselect,
		double &	fact,
		double &	var_fact
	)

private

◆ 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.

◆ 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

◆ getEnergyForceGJ()

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

private

◆ getEnergyForceGJE()

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

private

◆ getEnergyForceMIGEN()

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

private

◆ getEnergyForceSP()

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

private

◆ getEnergyForceSPE()

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

private

◆ getEnergyGJ()

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

private

◆ getEnergyGJE()

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

private

◆ getEnergyMIGEN()

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

private

◆ getEnergySP()

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

private

◆ getEnergySPE()

double PLMD::isdb::Metainference::getEnergySPE	(	const vector< double > &	mean,
		const 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.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inlinevirtualinherited

Returns the number of arguments.

Reimplemented in PLMD::vesselbase::ActionWithAveraging.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::bias::Bias::getNumberOfDerivatives ( )

inlineoverridevirtualinherited

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)

◆ 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.

◆ 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.

◆ getStep()

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

inherited

Return the present timestep.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ 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.

◆ 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() [1/2]

void PLMD::ActionWithArguments::lockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ lockRequests() [2/2]

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::mapping::Mapping, PLMD::vesselbase::ActionWithAveraging, PLMD::ActionWithArguments, and PLMD::analysis::AnalysisBase.

◆ 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.

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ 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.

◆ parseFlag()

void PLMD::Action::parseFlag	(	const std::string &	key,
		bool &	t
	)

inherited

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T >

bool PLMD::Action::parseNumbered	(	const std::string &	key,
		const int	no,
		T &	t
	)

inherited

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

template<class T >

bool PLMD::Action::parseNumberedVector	(	const std::string &	key,
		const int	no,
		std::vector< T > &	t
	)

inherited

Parse a vector with a number.

◆ parseVector()

template<class T >

void PLMD::Action::parseVector	(	const std::string &	key,
		std::vector< T > &	t
	)

inherited

Parse one keyword as std::vector.

◆ prepare()

void PLMD::Action::prepare ( )

virtualinherited

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented in PLMD::isdb::EMMI, PLMD::function::FuncPathMSD, PLMD::generic::Plumed, PLMD::multicolvar::MultiColvarBase, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::maze::Optimizer, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::gridtools::ConvertToFES, PLMD::SetupMolInfo, PLMD::colvar::Energy, PLMD::colvar::ExtraCV, and PLMD::colvar::CoordinationBase.

◆ readAtomsFromPDB()

virtual void PLMD::Action::readAtomsFromPDB ( const PDB & )

inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

◆ registerKeywords()

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

static

◆ replica_averaging()

void PLMD::isdb::Metainference::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.

◆ 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.

◆ setBias()

void PLMD::bias::Bias::setBias ( double bias )

inlineprotectedinherited

set the value of the bias

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

◆ setOption()

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

virtualinherited

◆ setOutputForce()

void PLMD::bias::Bias::setOutputForce	(	int	i,
		double	f
	)

inlineprotectedinherited

set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f

◆ setPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

◆ setStride()

void PLMD::ActionPilot::setStride ( const int & n )

inherited

Set the value of the stride.

◆ setupOutputForces()

void PLMD::bias::Bias::setupOutputForces ( )

protectedinherited

setup the OutputForce vector - this is needed if the bias does not use a normal ARG keyword

◆ 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::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::eds::EDS, PLMD::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ClusterAnalysisBase, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, and PLMD::gridtools::ActionWithIntegral.

◆ unlockRequests() [1/2]

void PLMD::ActionWithArguments::unlockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ unlockRequests() [2/2]

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::mapping::Mapping, PLMD::vesselbase::ActionWithAveraging, PLMD::ActionWithArguments, and PLMD::analysis::AnalysisBase.

◆ update()

void PLMD::isdb::Metainference::update ( )

overridevirtual

Update.

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

Reimplemented from PLMD::Action.

◆ 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::Metainference::writeStatus ( )

private

Member Data Documentation

◆ average_weights_

vector< vector <double> > PLMD::isdb::Metainference::average_weights_

private

◆ average_weights_stride_

unsigned PLMD::isdb::Metainference::average_weights_stride_

private

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ Dftilde_

double PLMD::isdb::Metainference::Dftilde_

private

◆ do_optsigmamean_

unsigned PLMD::isdb::Metainference::do_optsigmamean_

private

◆ do_reweight_

bool PLMD::isdb::Metainference::do_reweight_

private

◆ Doffset_

double PLMD::isdb::Metainference::Doffset_

private

◆ dooffset_

bool PLMD::isdb::Metainference::dooffset_

private

◆ doregres_zero_

bool PLMD::isdb::Metainference::doregres_zero_

private

◆ doscale_

bool PLMD::isdb::Metainference::doscale_

private

◆ Dscale_

double PLMD::isdb::Metainference::Dscale_

private

◆ Dsigma_

vector<double> PLMD::isdb::Metainference::Dsigma_

private

◆ files

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

inherited

◆ firstTime

bool PLMD::isdb::Metainference::firstTime

private

◆ firstTimeW

vector<bool> PLMD::isdb::Metainference::firstTimeW

private

◆ ftilde_

vector<double> PLMD::isdb::Metainference::ftilde_

private

◆ gen_likelihood_

unsigned PLMD::isdb::Metainference::gen_likelihood_

private

◆ kbt_

double PLMD::isdb::Metainference::kbt_

private

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ master

bool PLMD::isdb::Metainference::master

private

◆ MCaccept_

long unsigned PLMD::isdb::Metainference::MCaccept_

private

◆ MCacceptFT_

long unsigned PLMD::isdb::Metainference::MCacceptFT_

private

◆ MCacceptScale_

long unsigned PLMD::isdb::Metainference::MCacceptScale_

private

◆ MCchunksize_

unsigned PLMD::isdb::Metainference::MCchunksize_

private

◆ MCsteps_

unsigned PLMD::isdb::Metainference::MCsteps_

private

◆ MCtrial_

long unsigned PLMD::isdb::Metainference::MCtrial_

private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ narg

unsigned PLMD::isdb::Metainference::narg

private

◆ noise_type_

unsigned PLMD::isdb::Metainference::noise_type_

private

◆ nregres_zero_

int PLMD::isdb::Metainference::nregres_zero_

private

◆ nrep_

unsigned PLMD::isdb::Metainference::nrep_

private

◆ offset_

double PLMD::isdb::Metainference::offset_

private

◆ offset_max_

double PLMD::isdb::Metainference::offset_max_

private

◆ offset_min_

double PLMD::isdb::Metainference::offset_min_

private

◆ offset_mu_

double PLMD::isdb::Metainference::offset_mu_

private

◆ offset_prior_

unsigned PLMD::isdb::Metainference::offset_prior_

private

◆ optsigmamean_stride_

unsigned PLMD::isdb::Metainference::optsigmamean_stride_

private

◆ parameters

vector<double> PLMD::isdb::Metainference::parameters

private

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ random

vector<Random> PLMD::isdb::Metainference::random

private

◆ replica_

unsigned PLMD::isdb::Metainference::replica_

private

◆ scale_

double PLMD::isdb::Metainference::scale_

private

◆ scale_max_

double PLMD::isdb::Metainference::scale_max_

private

◆ scale_min_

double PLMD::isdb::Metainference::scale_min_

private

◆ scale_mu_

double PLMD::isdb::Metainference::scale_mu_

private

◆ scale_prior_

unsigned PLMD::isdb::Metainference::scale_prior_

private

◆ selector_

string PLMD::isdb::Metainference::selector_

private

◆ sfile_

OFile PLMD::isdb::Metainference::sfile_

private

◆ sigma_

vector<double> PLMD::isdb::Metainference::sigma_

private

◆ sigma_max_

vector<double> PLMD::isdb::Metainference::sigma_max_

private

◆ sigma_mean2_

vector<double> PLMD::isdb::Metainference::sigma_mean2_

private

◆ sigma_mean2_last_

vector< vector < vector <double> > > PLMD::isdb::Metainference::sigma_mean2_last_

private

◆ sigma_min_

vector<double> PLMD::isdb::Metainference::sigma_min_

private

◆ valueAccept

Value* PLMD::isdb::Metainference::valueAccept

private

◆ valueAcceptFT

Value* PLMD::isdb::Metainference::valueAcceptFT

private

◆ valueAcceptScale

Value* PLMD::isdb::Metainference::valueAcceptScale

private

◆ valueFtilde

vector<Value*> PLMD::isdb::Metainference::valueFtilde

private

◆ valueOffset

Value* PLMD::isdb::Metainference::valueOffset

private

◆ valueScale

Value* PLMD::isdb::Metainference::valueScale

private

◆ valueSigma

vector<Value*> PLMD::isdb::Metainference::valueSigma

private

◆ valueSigmaMean

vector<Value*> PLMD::isdb::Metainference::valueSigmaMean

private

◆ write_stride_

unsigned PLMD::isdb::Metainference::write_stride_

private

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

isdb/Metainference.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

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

◆ Metainference()

◆ ~Metainference()

Member Function Documentation

◆ activate()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives() [1/2]

◆ calculateNumericalDerivatives() [2/2]

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ difference()

◆ do_regression_zero()

◆ doMonteCarlo()

◆ doNotCalculateDerivatives()

◆ error()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ fopen()

◆ get_sigma_mean()

◆ get_weights()

◆ getArgument()

◆ getArguments()

◆ getComponentsList()

◆ getComponentsVector()

◆ getCPT()

◆ getDependencies()

◆ getDocumentation()

◆ getEnergyForceGJ()

◆ getEnergyForceGJE()

◆ getEnergyForceMIGEN()

◆ getEnergyForceSP()

◆ getEnergyForceSPE()

◆ getEnergyGJ()

◆ getEnergyGJE()

◆ getEnergyMIGEN()

◆ getEnergySP()

◆ getEnergySPE()