#include <Optimizer.h>

Inheritance diagram for PLMD::ves::Optimizer:

[legend]

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

Public Member Functions
	Optimizer (const ActionOptions &ao)

	~Optimizer ()

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

void	addComponent (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with a name like label.name. More...

virtual void	addComponentWithDerivatives (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
	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	addValue (const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with the name label. More...

virtual void	addValueWithDerivatives (const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with the name label that has derivatives. More...

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

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

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

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

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

virtual bool	calculateOnUpdate ()
	This is used to check if we run calculate during the update step. More...

virtual ActionAtomistic *	castToActionAtomistic () noexcept

virtual ActionForInterface *	castToActionForInterface () noexcept

virtual ActionShortcut *	castToActionShortcut () noexcept

virtual ActionToGetData *	castToActionToGetData () noexcept

virtual ActionToPutData *	castToActionToPutData () noexcept

virtual ActionWithArguments *	castToActionWithArguments () noexcept

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

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

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

virtual DomainDecomposition *	castToDomainDecomposition () noexcept

virtual PbcAction *	castToPbcAction () noexcept

virtual void	checkFieldsAllowed ()

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

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

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

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

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

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

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

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

virtual void	clearDerivatives (const bool &force=false)
	Clear the derivatives of values wrt parameters. More...

virtual void	clearInputForces (const bool &force=false)
	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...

bool	diagonalHessian () const

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

bool	dynamicStepSize () const

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...

bool	fixedStepSize () const

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

std::vector< CoeffsVector * >	getAuxCoeffsPntrs () const

unsigned int	getBiasOutputStride () const

std::vector< VesBias * >	getBiasPntrs () const

std::vector< CoeffsVector * >	getCoeffsMaskPntrs () const

std::vector< CoeffsVector * >	getCoeffsPntrs () const

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...

double	getCurrentStepSize (const unsigned int coeffs_id=0) const

std::vector< double >	getCurrentStepSizes () const

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

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

std::string	getDescription () const

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

unsigned int	getFesOutputStride () const

unsigned int	getFesProjOutputStride () const

std::vector< CoeffsVector * >	getGradientPntrs () const

std::vector< CoeffsMatrix * >	getHessianPntrs () const

unsigned int	getIterationCounter () const

double	getIterationCounterDbl () const

std::string	getIterationCounterStr (const int offset=0) const

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

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

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

virtual void	getMatrixColumnTitles (std::vector< std::string > &argnames) const
	Get the titles to use for the columns of the matrix. More...

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

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

unsigned int	getNumberOfDerivatives () override

virtual std::string	getOutputComponentDescription (const std::string &cname, const Keywords &keys) const
	Get the description of this component. 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...

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

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

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

double	getStepSize (const unsigned int coeffs_id=0) const

std::vector< double >	getStepSizes () const

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

std::vector< CoeffsVector * >	getTargetDistAveragesPntrs () const

unsigned int	getTargetDistOutputStride () const

unsigned int	getTargetDistProjOutputStride () const

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

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

std::string	getType () const

void	increaseIterationCounter ()

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

bool	isBiasOutputActive () const

bool	isFesOutputActive () const

bool	isFesProjOutputActive () const

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

bool	isTargetDistOutputActive () const

bool	isTargetDistProjOutputActive () const

virtual void	lockRequests ()

unsigned int	numberOfBiases () const

unsigned int	numberOfCoeffsSets () const

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

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

void	setBiasOutputStride (unsigned int stride)

void	setFesOutputStride (unsigned int stride)

void	setFesProjOutputStride (unsigned int stride)

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

void	setIterationCounter (const unsigned int)

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	setStepSize (const double, const unsigned int coeffs_id=0)

void	setStepSizes (const std::vector< double > &)

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

void	setTargetDistOutputStride (unsigned int stride)

void	setTargetDistProjOutputStride (unsigned int stride)

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

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

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

virtual void	unlockRequests ()

void	update () override
	Update. More...

bool	useHessian () const

bool	useMultipleWalkers () const

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

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

void	writeBiasOutputFiles () const

void	writeFesOutputFiles () const

void	writeFesProjOutputFiles () const

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

void	writeTargetDistOutputFiles () const

void	writeTargetDistProjOutputFiles () const

Static Public Member Functions
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 &)

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

static void	useDynamicStepSizeKeywords (Keywords &)

static void	useDynamicTargetDistributionKeywords (Keywords &)

static void	useFixedStepSizeKeywords (Keywords &)

static void	useHessianKeywords (Keywords &)

static void	useMaskKeywords (Keywords &)

static void	useMonitorAverageGradientKeywords (Keywords &)

static void	useMultipleWalkersKeywords (Keywords &)

static void	useRestartKeywords (Keywords &)

static void	useReweightFactorKeywords (Keywords &)

Public Attributes
Communicator &	comm

std::set< FILE * >	files

const Keywords &	keywords

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

Communicator &	multi_sim_comm

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

Protected Member Functions
void	addCoeffsSetIDsToFilenames (std::vector< std::string > &, std::string &)

CoeffsVector &	AuxCoeffs (const unsigned int coeffs_id=0) const

bool	checkForForces ()
	Accumulate the forces from the Values. More...

CoeffsVector &	Coeffs (const unsigned int coeffs_id=0) const

CoeffsVector &	CoeffsMask (const unsigned int coeffs_id=0) const

virtual void	coeffsUpdate (const unsigned int coeffs_id=0)=0

std::vector< CoeffsMatrix * >	enableHessian (VesBias *, const bool diagonal_hessian=false)

const Value *	getConstPntrToComponent (int i) const
	Get a const pointer to the ith component. More...

const std::vector< double > &	getForcesToApply () const
	Get the forces to apply. More...

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

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

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

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

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

CoeffsVector &	Gradient (const unsigned int coeffs_id=0) const

CoeffsMatrix &	Hessian (const unsigned int coeffs_id=0) const

void	parseFilenames (const std::string &, std::vector< std::string > &)

void	parseFilenames (const std::string &, std::vector< std::string > &, const std::string &)

template<class T >
bool	parseMultipleValues (const std::string &, std::vector< T > &)

template<class T >
bool	parseMultipleValues (const std::string &, std::vector< T > &, const T &)

void	setCurrentStepSize (const double, const unsigned int i=0)

void	setCurrentStepSizes (const std::vector< double > &)

void	setupOFiles (std::vector< std::string > &, std::vector< std::unique_ptr< OFile >> &, const bool multi_sim_single_files=false)

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

double	StepSize (const unsigned int coeffs_id=0) const

CoeffsVector &	TargetDistAverages (const unsigned int coeffs_id=0) const

void	turnOffCoeffsOutputFiles ()

void	turnOffHessian ()

void	turnOnHessian ()

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

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

void	readCoeffsFromFiles (const std::vector< std::string > &, const bool)

void	setAllCoeffsSetIterationCounters ()

void	updateOutputComponents ()

void	writeOutputFiles (const unsigned int coeffs_id=0)

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

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

std::vector< std::unique_ptr< CoeffsVector > >	aux_coeffs_pntrs_

std::vector< std::unique_ptr< CoeffsVector > >	aver_gradient_pntrs_

bool	bias_output_active_

unsigned int	bias_output_stride_

std::vector< VesBias * >	bias_pntrs_

std::vector< std::unique_ptr< CoeffsVector > >	coeffs_mask_pntrs_

std::string	coeffs_output_fmt_

std::vector< CoeffsVector * >	coeffs_pntrs_

unsigned int	coeffs_wstride_

std::vector< std::unique_ptr< OFile > >	coeffsOFiles_

std::string	coeffssetid_prefix_

std::vector< double >	current_stepsizes

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

const std::string	description_

bool	diagonal_hessian_

bool	doCheckPoint

std::vector< bool >	dynamic_targetdists_

bool	fes_output_active_

unsigned int	fes_output_stride_

bool	fesproj_output_active_

unsigned int	fesproj_output_stride_

bool	firststep
	This finishes setup on first step to check if actions are calculated during update. More...

bool	fixed_stepsize_

std::vector< double >	forcesForApply
	A vector that is used to hold the forces that we will apply on the input quantities. More...

std::string	gradient_output_fmt_

std::vector< CoeffsVector * >	gradient_pntrs_

unsigned int	gradient_wstride_

std::vector< std::unique_ptr< OFile > >	gradientOFiles_

bool	hessian_covariance_from_averages_

std::string	hessian_output_fmt_

std::vector< CoeffsMatrix * >	hessian_pntrs_

unsigned int	hessian_wstride_

std::vector< std::unique_ptr< OFile > >	hessianOFiles_

bool	identical_coeffs_shape_

bool	isFirstStep

unsigned int	iter_counter

std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...

std::vector< std::string >	line
	Directive line. More...

bool	monitor_instantaneous_gradient_

bool	mwalkers_mpi_single_files_

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

unsigned int	nbiases_

unsigned int	ncoeffssets_

bool	never_activate

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

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

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

int	replica_index

bool	restart

std::vector< double >	stepsizes_

int	stride

std::string	targetdist_averages_output_fmt_

std::vector< CoeffsVector * >	targetdist_averages_pntrs_

unsigned int	targetdist_averages_wstride_

std::vector< std::unique_ptr< OFile > >	targetdist_averagesOFiles_

bool	targetdist_output_active_

unsigned int	targetdist_output_stride_

bool	targetdist_proj_output_active_

unsigned int	targetdist_proj_output_stride_

double	timestep
	Save the timestep here. More...

const std::string	type_

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

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

bool	use_hessian_

bool	use_mwalkers_mpi_

unsigned int	ustride_reweightfactor_

unsigned int	ustride_targetdist_

std::vector< unsigned >	valsToForce

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

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ Optimizer()

PLMD::ves::Optimizer::Optimizer ( const ActionOptions & ao )

explicit

◆ ~Optimizer()

PLMD::ves::Optimizer::~Optimizer ( )

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addCoeffsSetIDsToFilenames()

void PLMD::ves::Optimizer::addCoeffsSetIDsToFilenames	(	std::vector< std::string > &	fnames,
		std::string &	coeffssetid_prefix
	)

protected

◆ addComponent()

void PLMD::ActionWithValue::addComponent	(	const std::string &	name,
		const std::vector< unsigned > &	shape = `std::vector<unsigned>()`
	)

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives	(	const std::string &	name,
		const std::vector< unsigned > &	shape = `std::vector<unsigned>()`
	)

virtualinherited

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

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addValue()

void PLMD::ActionWithValue::addValue ( const std::vector< unsigned > & shape = std::vector<unsigned>() )

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( const std::vector< unsigned > & shape = std::vector<unsigned>() )

virtualinherited

Add a value with the name label that has derivatives.

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

◆ apply()

void PLMD::ves::Optimizer::apply ( )

inlineoverridevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ AuxCoeffs()

CoeffsVector & PLMD::ves::Optimizer::AuxCoeffs ( const unsigned int coeffs_id = 0 ) const

inlineprotected

◆ 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.

◆ calculate()

void PLMD::ves::Optimizer::calculate ( )

inlineoverridevirtual

Calculate an Action.

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

Implements PLMD::Action.

◆ calculateFromPDB()

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

inherited

Calculate the action given a pdb file as input.

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

◆ calculateNumericalDerivatives()

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

virtualinherited

Perform calculation using numerical derivatives N.B.

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

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

◆ calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )

virtualinherited

This is used to check if we run calculate during the update step.

Reimplemented in PLMD::generic::Accumulate, and PLMD::generic::Collect.

◆ castToActionAtomistic()

virtual ActionAtomistic* PLMD::Action::castToActionAtomistic ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionAtomistic.

◆ castToActionForInterface()

virtual ActionForInterface* PLMD::Action::castToActionForInterface ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

◆ castToActionShortcut()

virtual ActionShortcut* PLMD::Action::castToActionShortcut ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

◆ castToActionToGetData()

virtual ActionToGetData* PLMD::Action::castToActionToGetData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

◆ castToActionToPutData()

virtual ActionToPutData* PLMD::Action::castToActionToPutData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

◆ castToActionWithArguments()

virtual ActionWithArguments* PLMD::Action::castToActionWithArguments ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

◆ castToActionWithValue() [1/2]

virtual ActionWithValue* PLMD::Action::castToActionWithValue ( )

inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ castToActionWithValue() [2/2]

ActionWithValue* PLMD::ActionWithValue::castToActionWithValue ( )

inlinefinalvirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented from PLMD::Action.

◆ castToActionWithVirtualAtom()

virtual ActionWithVirtualAtom* PLMD::Action::castToActionWithVirtualAtom ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

◆ castToDomainDecomposition()

virtual DomainDecomposition* PLMD::Action::castToDomainDecomposition ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

◆ castToPbcAction()

virtual PbcAction* PLMD::Action::castToPbcAction ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

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

◆ checkForDependency()

bool PLMD::Action::checkForDependency ( Action * action )

inherited

Check that this action does not depend on the action in the argument.

◆ checkForForces()

bool PLMD::ActionWithValue::checkForForces ( )

protectedinherited

Accumulate the forces from the Values.

◆ checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

Reimplemented in PLMD::bias::MetaD, PLMD::bias::PBMetaD, and PLMD::generic::DumpProjections.

◆ checkNumericalDerivatives() [1/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

This checks if Action::line is empty. It must be called after a final Action has been initialized

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

std::string PLMD::Action::cite ( const std::string & s )

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( const bool & force = false )

virtualinherited

Clear the derivatives of values wrt parameters.

Reimplemented in PLMD::ActionWithVector, PLMD::ActionForInterface, PLMD::generic::Constant, and PLMD::mapping::PathDisplacements.

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( const bool & force = false )

virtualinherited

Clear the forces on the values.

Reimplemented in PLMD::ActionWithVector.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ Coeffs()

CoeffsVector & PLMD::ves::Optimizer::Coeffs ( const unsigned int coeffs_id = 0 ) const

inlineprotected

◆ CoeffsMask()

CoeffsVector & PLMD::ves::Optimizer::CoeffsMask ( const unsigned int coeffs_id = 0 ) const

inlineprotected

◆ coeffsUpdate()

virtual void PLMD::ves::Optimizer::coeffsUpdate ( const unsigned int coeffs_id = 0 )

protectedpure virtual

Implemented in PLMD::ves::Opt_BachAveragedSGD, PLMD::ves::Opt_Dummy, PLMD::ves::Opt_Adam, and PLMD::ves::Opt_RobbinsMonroSGD.

◆ 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.

◆ 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.

◆ diagonalHessian()

bool PLMD::ves::Optimizer::diagonalHessian ( ) const

inline

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

◆ dynamicStepSize()

bool PLMD::ves::Optimizer::dynamicStepSize ( ) const

inline

◆ enableHessian()

std::vector< CoeffsMatrix * > PLMD::ves::Optimizer::enableHessian	(	VesBias *	bias_pntr_in,
		const bool	diagonal_hessian = `false`
	)

protected

◆ 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.

◆ 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.

◆ fixedStepSize()

bool PLMD::ves::Optimizer::fixedStepSize ( ) const

inline

◆ 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)

◆ getAuxCoeffsPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getAuxCoeffsPntrs ( ) const

inline

◆ getBiasOutputStride()

unsigned int PLMD::ves::Optimizer::getBiasOutputStride ( ) const

inline

◆ getBiasPntrs()

std::vector<VesBias*> PLMD::ves::Optimizer::getBiasPntrs ( ) const

inline

◆ getCoeffsMaskPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getCoeffsMaskPntrs ( ) const

inline

◆ getCoeffsPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getCoeffsPntrs ( ) const

inline

◆ getComponent()

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

privateinherited

Return the index for the component named name.

◆ getComponentsList()

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

inherited

get a string that contains all the available components

◆ getComponentsVector()

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

inherited

get a vector that contains the label for all the components

◆ getConstPntrToComponent()

const Value * PLMD::ActionWithValue::getConstPntrToComponent ( int i ) const

protectedinherited

Get a const pointer to the ith component.

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getCurrentStepSize()

double PLMD::ves::Optimizer::getCurrentStepSize ( const unsigned int coeffs_id = 0 ) const

inline

◆ getCurrentStepSizes()

std::vector< double > PLMD::ves::Optimizer::getCurrentStepSizes ( ) const

inline

◆ getDefaultString()

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

inlineinherited

Get the defaults.

◆ getDependencies()

const Dependencies& PLMD::Action::getDependencies ( ) const

inlineinherited

Return dependencies.

◆ getDescription()

std::string PLMD::ves::Optimizer::getDescription ( ) const

inline

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getFesOutputStride()

unsigned int PLMD::ves::Optimizer::getFesOutputStride ( ) const

inline

◆ getFesProjOutputStride()

unsigned int PLMD::ves::Optimizer::getFesProjOutputStride ( ) const

inline

◆ getForcesToApply()

const std::vector< double > & PLMD::ActionWithValue::getForcesToApply ( ) const

inlineprotectedinherited

Get the forces to apply.

◆ getGradientPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getGradientPntrs ( ) const

inline

◆ getHessianPntrs()

std::vector<CoeffsMatrix*> PLMD::ves::Optimizer::getHessianPntrs ( ) const

inline

◆ getIterationCounter()

unsigned int PLMD::ves::Optimizer::getIterationCounter ( ) const

inline

◆ getIterationCounterDbl()

double PLMD::ves::Optimizer::getIterationCounterDbl ( ) const

inline

◆ getIterationCounterStr()

std::string PLMD::ves::Optimizer::getIterationCounterStr ( const int offset = 0 ) const

◆ getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const

protectedinherited

Get the value of Boltzmann's constant.

◆ getkBT()

double PLMD::Action::getkBT ( )

inherited

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

◆ 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.

◆ getMatrixColumnTitles()

void PLMD::ActionWithValue::getMatrixColumnTitles ( std::vector< std::string > & argnames ) const

virtualinherited

Get the titles to use for the columns of the matrix.

Reimplemented in PLMD::valtools::VStack, and PLMD::valtools::SelectWithMask.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned int PLMD::ves::Optimizer::getNumberOfDerivatives ( )

inlineoverridevirtual

Implements PLMD::ActionWithValue.

◆ getOutputComponentDescription()

std::string PLMD::ActionWithValue::getOutputComponentDescription	(	const std::string &	cname,
		const Keywords &	keys
	)		const

virtualinherited

Get the description of this component.

Reimplemented in PLMD::generic::Read, PLMD::colvar::PropertyMap, PLMD::function::LocalEnsemble, PLMD::function::Ensemble, PLMD::function::FunctionOfVector< T >, PLMD::opes::ExpansionCVs, PLMD::function::FunctionOfScalar< T >, PLMD::colvar::ColvarFake, PLMD::matrixtools::MatrixTimesVector, PLMD::symfunc::ThreeBodyGFunctions, and PLMD::contour::FindContour.

◆ getOutputQuantity() [1/2]

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

inlineinherited

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

◆ getOutputQuantity() [2/2]

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

inlineinherited

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

◆ getPntrToComponent() [1/2]

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

protectedinherited

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

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

protectedinherited

Return a pointer to the component by index.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

inlineprotectedinherited

Get a pointer to the default value.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getStep()

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

inherited

Return the present timestep.

◆ getStepSize()

double PLMD::ves::Optimizer::getStepSize ( const unsigned int coeffs_id = 0 ) const

inline

◆ getStepSizes()

std::vector< double > PLMD::ves::Optimizer::getStepSizes ( ) const

inline

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

◆ getTargetDistAveragesPntrs()

std::vector<CoeffsVector*> PLMD::ves::Optimizer::getTargetDistAveragesPntrs ( ) const

inline

◆ getTargetDistOutputStride()

unsigned int PLMD::ves::Optimizer::getTargetDistOutputStride ( ) const

inline

◆ getTargetDistProjOutputStride()

unsigned int PLMD::ves::Optimizer::getTargetDistProjOutputStride ( ) const

inline

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getType()

std::string PLMD::ves::Optimizer::getType ( ) const

inline

◆ getUnits()

const Units & PLMD::Action::getUnits ( ) const

protectedinherited

Get the units that we are operating in.

◆ Gradient()

CoeffsVector & PLMD::ves::Optimizer::Gradient ( const unsigned int coeffs_id = 0 ) const

inlineprotected

◆ Hessian()

CoeffsMatrix & PLMD::ves::Optimizer::Hessian ( const unsigned int coeffs_id = 0 ) const

inlineprotected

◆ increaseIterationCounter()

void PLMD::ves::Optimizer::increaseIterationCounter ( )

inline

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isBiasOutputActive()

bool PLMD::ves::Optimizer::isBiasOutputActive ( ) const

inline

◆ isFesOutputActive()

bool PLMD::ves::Optimizer::isFesOutputActive ( ) const

inline

◆ isFesProjOutputActive()

bool PLMD::ves::Optimizer::isFesProjOutputActive ( ) const

inline

◆ isOptionOn()

bool PLMD::Action::isOptionOn ( const std::string & s ) const

inlineinherited

Check if an option is on.

◆ isTargetDistOutputActive()

bool PLMD::ves::Optimizer::isTargetDistOutputActive ( ) const

inline

◆ isTargetDistProjOutputActive()

bool PLMD::ves::Optimizer::isTargetDistProjOutputActive ( ) const

inline

◆ lockRequests()

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

◆ 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.

◆ numberOfBiases()

unsigned int PLMD::ves::Optimizer::numberOfBiases ( ) const

inline

◆ numberOfCoeffsSets()

unsigned int PLMD::ves::Optimizer::numberOfCoeffsSets ( ) const

inline

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ parseFilenames() [1/2]

void PLMD::ves::Optimizer::parseFilenames	(	const std::string &	keyword,
		std::vector< std::string > &	fnames
	)

inlineprotected

◆ parseFilenames() [2/2]

void PLMD::ves::Optimizer::parseFilenames	(	const std::string &	keyword,
		std::vector< std::string > &	fnames,
		const std::string &	default_fname
	)

inlineprotected

◆ parseFlag()

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

inherited

Parse one keyword as boolean flag.

◆ parseMultipleValues() [1/2]

template<class T >

bool PLMD::ves::Optimizer::parseMultipleValues	(	const std::string &	keyword,
		std::vector< T > &	values
	)

protected

◆ parseMultipleValues() [2/2]

template<class T >

bool PLMD::ves::Optimizer::parseMultipleValues	(	const std::string &	keyword,
		std::vector< T > &	values,
		const T &	default_value
	)

protected

◆ 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::ActionWithVector, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::GenericMolInfo, PLMD::dimred::ArrangePoints, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::adjmat::AdjacencyMatrixBase, PLMD::matrixtools::MatrixTimesMatrix, PLMD::valtools::SelectWithMask, PLMD::dimred::ProjectPoints, PLMD::generic::CreateMask, PLMD::matrixtools::DiagonalizeMatrix, PLMD::matrixtools::MatrixTimesVector, PLMD::matrixtools::OuterProduct, PLMD::valtools::VStack, PLMD::landmarks::FarthestPointSampling, PLMD::colvar::CoordinationBase, PLMD::matrixtools::TransposeMatrix, PLMD::matrixtools::Voronoi, PLMD::function::FuncPathGeneral, PLMD::maze::Optimizer, and PLMD::s2cm::S2ContactModel.

◆ 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.

◆ readCoeffsFromFiles()

void PLMD::ves::Optimizer::readCoeffsFromFiles	(	const std::vector< std::string > &	fnames,
		const bool	read_aux_coeffs
	)

private

◆ registerKeywords()

void PLMD::ves::Optimizer::registerKeywords ( Keywords & keys )

static

◆ resetStoredTimestep()

void PLMD::Action::resetStoredTimestep ( )

inherited

Set the timestep that is stored in the action to the correct value.

◆ 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.

◆ setAllCoeffsSetIterationCounters()

void PLMD::ves::Optimizer::setAllCoeffsSetIterationCounters ( )

private

◆ setBiasOutputStride()

void PLMD::ves::Optimizer::setBiasOutputStride ( unsigned int stride )

inline

◆ setCurrentStepSize()

void PLMD::ves::Optimizer::setCurrentStepSize	(	const double	current_stepsize_in,
		const unsigned int	i = `0`
	)

inlineprotected

◆ setCurrentStepSizes()

void PLMD::ves::Optimizer::setCurrentStepSizes ( const std::vector< double > & current_stepsizes_in )

inlineprotected

◆ setFesOutputStride()

void PLMD::ves::Optimizer::setFesOutputStride ( unsigned int stride )

inline

◆ setFesProjOutputStride()

void PLMD::ves::Optimizer::setFesProjOutputStride ( unsigned int stride )

inline

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

virtualinherited

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

Reimplemented in PLMD::ActionForInterface.

◆ setIterationCounter()

void PLMD::ves::Optimizer::setIterationCounter ( const unsigned int iter_counter_in )

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

◆ setPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

◆ setStepSize()

void PLMD::ves::Optimizer::setStepSize	(	const double	stepsize_in,
		const unsigned int	coeffs_id = `0`
	)

inline

◆ setStepSizes()

void PLMD::ves::Optimizer::setStepSizes ( const std::vector< double > & stepsizes_in )

inline

◆ setStride()

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

inherited

Set the value of the stride.

◆ setTargetDistOutputStride()

void PLMD::ves::Optimizer::setTargetDistOutputStride ( unsigned int stride )

inline

◆ setTargetDistProjOutputStride()

void PLMD::ves::Optimizer::setTargetDistProjOutputStride ( unsigned int stride )

inline

◆ setupConstantValues()

void PLMD::Action::setupConstantValues ( const bool & have_atoms )

inherited

This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.

◆ setupOFiles()

void PLMD::ves::Optimizer::setupOFiles	(	std::vector< std::string > &	fnames,
		std::vector< std::unique_ptr< OFile >> &	OFiles,
		const bool	multi_sim_single_files = `false`
	)

protected

◆ 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.

◆ StepSize()

double PLMD::ves::Optimizer::StepSize ( const unsigned int coeffs_id = 0 ) const

inlineprotected

◆ TargetDistAverages()

CoeffsVector& PLMD::ves::Optimizer::TargetDistAverages ( const unsigned int coeffs_id = 0 ) const

protected

◆ turnOffCoeffsOutputFiles()

void PLMD::ves::Optimizer::turnOffCoeffsOutputFiles ( )

protected

◆ turnOffHessian()

void PLMD::ves::Optimizer::turnOffHessian ( )

protected

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::Read, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::function::FunctionOfScalar< T >, PLMD::adjmat::Neighbors, PLMD::eds::EDS, and PLMD::fisst::FISST.

◆ turnOnHessian()

void PLMD::ves::Optimizer::turnOnHessian ( )

protected

◆ unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

◆ update()

void PLMD::ves::Optimizer::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.

◆ updateOutputComponents()

void PLMD::ves::Optimizer::updateOutputComponents ( )

private

◆ useCustomisableComponents()

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

staticinherited

The components in the action will depend on the user.

◆ useDynamicStepSizeKeywords()

void PLMD::ves::Optimizer::useDynamicStepSizeKeywords ( Keywords & keys )

static

◆ useDynamicTargetDistributionKeywords()

void PLMD::ves::Optimizer::useDynamicTargetDistributionKeywords ( Keywords & keys )

static

◆ useFixedStepSizeKeywords()

void PLMD::ves::Optimizer::useFixedStepSizeKeywords ( Keywords & keys )

static

◆ useHessian()

bool PLMD::ves::Optimizer::useHessian ( ) const

inline

◆ useHessianKeywords()

void PLMD::ves::Optimizer::useHessianKeywords ( Keywords & keys )

static

◆ useMaskKeywords()

void PLMD::ves::Optimizer::useMaskKeywords ( Keywords & keys )

static

◆ useMonitorAverageGradientKeywords()

void PLMD::ves::Optimizer::useMonitorAverageGradientKeywords ( Keywords & keys )

static

◆ useMultipleWalkers()

bool PLMD::ves::Optimizer::useMultipleWalkers ( ) const

inline

◆ useMultipleWalkersKeywords()

void PLMD::ves::Optimizer::useMultipleWalkersKeywords ( Keywords & keys )

static

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ useRestartKeywords()

void PLMD::ves::Optimizer::useRestartKeywords ( Keywords & keys )

static

◆ useReweightFactorKeywords()

void PLMD::ves::Optimizer::useReweightFactorKeywords ( Keywords & keys )

static

◆ usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const

protectedinherited

Are we using natural units.

◆ warning()

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

inherited

Issue a warning.

◆ writeBiasOutputFiles()

void PLMD::ves::Optimizer::writeBiasOutputFiles ( ) const

◆ writeFesOutputFiles()

void PLMD::ves::Optimizer::writeFesOutputFiles ( ) const

◆ writeFesProjOutputFiles()

void PLMD::ves::Optimizer::writeFesProjOutputFiles ( ) const

◆ writeInGraph()

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

virtualinherited

Get the info on what to calculate.

Reimplemented in PLMD::generic::Print, PLMD::adjmat::ContactMatrix, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfMatrix< T >, PLMD::generic::PrintNDX, PLMD::function::FunctionOfScalar< T >, and PLMD::gridtools::FunctionOfGrid< T >.

◆ writeOutputFiles()

void PLMD::ves::Optimizer::writeOutputFiles ( const unsigned int coeffs_id = 0 )

private

◆ writeTargetDistOutputFiles()

void PLMD::ves::Optimizer::writeTargetDistOutputFiles ( ) const

◆ writeTargetDistProjOutputFiles()

void PLMD::ves::Optimizer::writeTargetDistProjOutputFiles ( ) const

Member Data Documentation

◆ active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

◆ aux_coeffs_pntrs_

std::vector<std::unique_ptr<CoeffsVector> > PLMD::ves::Optimizer::aux_coeffs_pntrs_

private

◆ aver_gradient_pntrs_

std::vector<std::unique_ptr<CoeffsVector> > PLMD::ves::Optimizer::aver_gradient_pntrs_

private

◆ bias_output_active_

bool PLMD::ves::Optimizer::bias_output_active_

private

◆ bias_output_stride_

unsigned int PLMD::ves::Optimizer::bias_output_stride_

private

◆ bias_pntrs_

std::vector<VesBias*> PLMD::ves::Optimizer::bias_pntrs_

private

◆ coeffs_mask_pntrs_

std::vector<std::unique_ptr<CoeffsVector> > PLMD::ves::Optimizer::coeffs_mask_pntrs_

private

◆ coeffs_output_fmt_

std::string PLMD::ves::Optimizer::coeffs_output_fmt_

private

◆ coeffs_pntrs_

std::vector<CoeffsVector*> PLMD::ves::Optimizer::coeffs_pntrs_

private

◆ coeffs_wstride_

unsigned int PLMD::ves::Optimizer::coeffs_wstride_

private

◆ coeffsOFiles_

std::vector<std::unique_ptr<OFile> > PLMD::ves::Optimizer::coeffsOFiles_

private

◆ coeffssetid_prefix_

std::string PLMD::ves::Optimizer::coeffssetid_prefix_

private

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ current_stepsizes

std::vector<double> PLMD::ves::Optimizer::current_stepsizes

private

◆ defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

◆ description_

const std::string PLMD::ves::Optimizer::description_

private

◆ diagonal_hessian_

bool PLMD::ves::Optimizer::diagonal_hessian_

private

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ dynamic_targetdists_

std::vector<bool> PLMD::ves::Optimizer::dynamic_targetdists_

private

◆ fes_output_active_

bool PLMD::ves::Optimizer::fes_output_active_

private

◆ fes_output_stride_

unsigned int PLMD::ves::Optimizer::fes_output_stride_

private

◆ fesproj_output_active_

bool PLMD::ves::Optimizer::fesproj_output_active_

private

◆ fesproj_output_stride_

unsigned int PLMD::ves::Optimizer::fesproj_output_stride_

private

◆ files

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

inherited

◆ firststep

bool PLMD::ActionWithValue::firststep

privateinherited

This finishes setup on first step to check if actions are calculated during update.

◆ fixed_stepsize_

bool PLMD::ves::Optimizer::fixed_stepsize_

private

◆ forcesForApply

std::vector<double> PLMD::ActionWithValue::forcesForApply

privateinherited

A vector that is used to hold the forces that we will apply on the input quantities.

◆ gradient_output_fmt_

std::string PLMD::ves::Optimizer::gradient_output_fmt_

private

◆ gradient_pntrs_

std::vector<CoeffsVector*> PLMD::ves::Optimizer::gradient_pntrs_

private

◆ gradient_wstride_

unsigned int PLMD::ves::Optimizer::gradient_wstride_

private

◆ gradientOFiles_

std::vector<std::unique_ptr<OFile> > PLMD::ves::Optimizer::gradientOFiles_

private

◆ hessian_covariance_from_averages_

bool PLMD::ves::Optimizer::hessian_covariance_from_averages_

private

◆ hessian_output_fmt_

std::string PLMD::ves::Optimizer::hessian_output_fmt_

private

◆ hessian_pntrs_

std::vector<CoeffsMatrix*> PLMD::ves::Optimizer::hessian_pntrs_

private

◆ hessian_wstride_

unsigned int PLMD::ves::Optimizer::hessian_wstride_

private

◆ hessianOFiles_

std::vector<std::unique_ptr<OFile> > PLMD::ves::Optimizer::hessianOFiles_

private

◆ identical_coeffs_shape_

bool PLMD::ves::Optimizer::identical_coeffs_shape_

private

◆ isFirstStep

bool PLMD::ves::Optimizer::isFirstStep

private

◆ iter_counter

unsigned int PLMD::ves::Optimizer::iter_counter

private

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ label

std::string PLMD::Action::label

privateinherited

Label of the Action, as set with LABEL= in the plumed.dat file.

◆ line

std::vector<std::string> PLMD::Action::line

privateinherited

Directive line.

This line is progressively erased during Action construction so as to check if all the present keywords are correct.

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ monitor_instantaneous_gradient_

bool PLMD::ves::Optimizer::monitor_instantaneous_gradient_

private

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ mwalkers_mpi_single_files_

bool PLMD::ves::Optimizer::mwalkers_mpi_single_files_

private

◆ name

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

privateinherited

Name of the directive in the plumed.dat file.

◆ nbiases_

unsigned int PLMD::ves::Optimizer::nbiases_

private

◆ ncoeffssets_

unsigned int PLMD::ves::Optimizer::ncoeffssets_

private

◆ never_activate

bool PLMD::Action::never_activate

privateinherited

◆ noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

◆ numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives

privateinherited

Are we using numerical derivatives to differentiate.

◆ options

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

privateinherited

Option that you might have enabled.

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ stepsizes_

std::vector<double> PLMD::ves::Optimizer::stepsizes_

private

◆ stride

int PLMD::ActionPilot::stride

privateinherited

◆ targetdist_averages_output_fmt_

std::string PLMD::ves::Optimizer::targetdist_averages_output_fmt_

private

◆ targetdist_averages_pntrs_

std::vector<CoeffsVector*> PLMD::ves::Optimizer::targetdist_averages_pntrs_

private

◆ targetdist_averages_wstride_

unsigned int PLMD::ves::Optimizer::targetdist_averages_wstride_

private

◆ targetdist_averagesOFiles_

std::vector<std::unique_ptr<OFile> > PLMD::ves::Optimizer::targetdist_averagesOFiles_

private

◆ targetdist_output_active_

bool PLMD::ves::Optimizer::targetdist_output_active_

private

◆ targetdist_output_stride_

unsigned int PLMD::ves::Optimizer::targetdist_output_stride_

private

◆ targetdist_proj_output_active_

bool PLMD::ves::Optimizer::targetdist_proj_output_active_

private

◆ targetdist_proj_output_stride_

unsigned int PLMD::ves::Optimizer::targetdist_proj_output_stride_

private

◆ timestep

double PLMD::Action::timestep

privateinherited

Save the timestep here.

◆ type_

const std::string PLMD::ves::Optimizer::type_

private

◆ update_from

double PLMD::Action::update_from

privateinherited

Update only after this time.

◆ update_until

double PLMD::Action::update_until

privateinherited

Update only until this time.

◆ use_hessian_

bool PLMD::ves::Optimizer::use_hessian_

private

◆ use_mwalkers_mpi_

bool PLMD::ves::Optimizer::use_mwalkers_mpi_

private

◆ ustride_reweightfactor_

unsigned int PLMD::ves::Optimizer::ustride_reweightfactor_

private

◆ ustride_targetdist_

unsigned int PLMD::ves::Optimizer::ustride_targetdist_

private

◆ valsToForce

std::vector<unsigned> PLMD::ActionWithValue::valsToForce

privateinherited

◆ values

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

privateinherited

An array containing the values for this action.

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

ves/Optimizer.h
ves/Optimizer.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ Optimizer()

◆ ~Optimizer()

Member Function Documentation

◆ activate()

◆ addCoeffsSetIDsToFilenames()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ AuxCoeffs()

◆ beforeUpdate()

◆ calculate()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ calculateOnUpdate()

◆ castToActionAtomistic()

◆ castToActionForInterface()

◆ castToActionShortcut()

◆ castToActionToGetData()

◆ castToActionToPutData()

◆ castToActionWithArguments()

◆ castToActionWithValue() [1/2]

◆ castToActionWithValue() [2/2]

◆ castToActionWithVirtualAtom()

◆ castToDomainDecomposition()

◆ castToPbcAction()

◆ checkFieldsAllowed()

◆ checkForDependency()

◆ checkForForces()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ Coeffs()

◆ CoeffsMask()

◆ coeffsUpdate()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ diagonalHessian()

◆ doNotCalculateDerivatives()

◆ dynamicStepSize()

◆ enableHessian()

◆ error()

◆ exists()

◆ exit()

◆ fclose()

◆ fflush()

◆ fixedStepSize()

◆ fopen()

◆ getAuxCoeffsPntrs()

◆ getBiasOutputStride()

◆ getBiasPntrs()

◆ getCoeffsMaskPntrs()

◆ getCoeffsPntrs()

◆ getComponent()

◆ getComponentsList()

◆ getComponentsVector()

◆ getConstPntrToComponent()

◆ getCPT()