#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 ()

std::string	getType () const

std::string	getDescription () const

unsigned int	numberOfBiases () const

unsigned int	numberOfCoeffsSets () const

std::vector< double >	getStepSizes () const

std::vector< double >	getCurrentStepSizes () const

double	getStepSize (const unsigned int coeffs_id=0) const

double	getCurrentStepSize (const unsigned int coeffs_id=0) const

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

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

unsigned int	getIterationCounter () const

double	getIterationCounterDbl () const

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

void	setIterationCounter (const unsigned int)

void	increaseIterationCounter ()

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

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

void	update ()
	Update. More...

unsigned int	getNumberOfDerivatives ()

bool	fixedStepSize () const

bool	dynamicStepSize () const

bool	useHessian () const

bool	diagonalHessian () const

bool	useMultipleWalkers () const

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

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

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

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

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

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

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

bool	isBiasOutputActive () const

unsigned int	getBiasOutputStride () const

void	setBiasOutputStride (unsigned int stride)

void	writeBiasOutputFiles () const

bool	isFesOutputActive () const

unsigned int	getFesOutputStride () const

void	setFesOutputStride (unsigned int stride)

void	writeFesOutputFiles () const

bool	isFesProjOutputActive () const

unsigned int	getFesProjOutputStride () const

void	setFesProjOutputStride (unsigned int stride)

void	writeFesProjOutputFiles () const

bool	isTargetDistOutputActive () const

unsigned int	getTargetDistOutputStride () const

void	setTargetDistOutputStride (unsigned int stride)

void	writeTargetDistOutputFiles () const

bool	isTargetDistProjOutputActive () const

unsigned int	getTargetDistProjOutputStride () const

void	setTargetDistProjOutputStride (unsigned int stride)

void	writeTargetDistProjOutputFiles () const

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

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

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

void	exit (int c=0)
	Exit with error code c. More...

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

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

virtual void	lockRequests ()

virtual void	unlockRequests ()

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

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

void	fflush ()
	Tell to the Action to flush open files. More...

virtual std::string	getDocumentation () const

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

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

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

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

virtual void	clearOptions ()

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

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

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

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

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

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

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

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

int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...

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

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...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual void	checkFieldsAllowed ()

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

Static Public Member Functions
static void	registerKeywords (Keywords &)

static void	useMultipleWalkersKeywords (Keywords &)

static void	useHessianKeywords (Keywords &)

static void	useFixedStepSizeKeywords (Keywords &)

static void	useDynamicStepSizeKeywords (Keywords &)

static void	useMaskKeywords (Keywords &)

static void	useRestartKeywords (Keywords &)

static void	useMonitorAverageGradientKeywords (Keywords &)

static void	useDynamicTargetDistributionKeywords (Keywords &)

static void	useReweightFactorKeywords (Keywords &)

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

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

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

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

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

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

Protected Member Functions
void	turnOnHessian ()

void	turnOffHessian ()

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

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

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

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

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

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

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

double	StepSize (const unsigned int coeffs_id=0) const

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

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

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

void	turnOffCoeffsOutputFiles ()

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

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

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

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

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

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

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

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

Private Member Functions
void	updateOutputComponents ()

void	writeOutputFiles (const unsigned int coeffs_id=0)

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

void	setAllCoeffsSetIterationCounters ()

Private Attributes
const std::string	description_

const std::string	type_

std::vector< double >	stepsizes_

std::vector< double >	current_stepsizes

bool	fixed_stepsize_

unsigned int	iter_counter

bool	use_hessian_

bool	diagonal_hessian_

bool	hessian_covariance_from_averages_

bool	monitor_instantaneous_gradient_

bool	use_mwalkers_mpi_

bool	mwalkers_mpi_single_files_

std::vector< bool >	dynamic_targetdists_

unsigned int	ustride_targetdist_

unsigned int	ustride_reweightfactor_

std::string	coeffssetid_prefix_

unsigned int	coeffs_wstride_

std::vector< OFile * >	coeffsOFiles_

std::string	coeffs_output_fmt_

unsigned int	gradient_wstride_

std::vector< OFile * >	gradientOFiles_

std::string	gradient_output_fmt_

unsigned int	hessian_wstride_

std::vector< OFile * >	hessianOFiles_

std::string	hessian_output_fmt_

unsigned int	targetdist_averages_wstride_

std::vector< OFile * >	targetdist_averagesOFiles_

std::string	targetdist_averages_output_fmt_

unsigned int	nbiases_

std::vector< VesBias * >	bias_pntrs_

unsigned int	ncoeffssets_

std::vector< CoeffsVector * >	coeffs_pntrs_

std::vector< CoeffsVector * >	aux_coeffs_pntrs_

std::vector< CoeffsVector * >	gradient_pntrs_

std::vector< CoeffsVector * >	aver_gradient_pntrs_

std::vector< CoeffsMatrix * >	hessian_pntrs_

std::vector< CoeffsVector * >	coeffs_mask_pntrs_

std::vector< CoeffsVector * >	targetdist_averages_pntrs_

bool	identical_coeffs_shape_

bool	bias_output_active_

unsigned int	bias_output_stride_

bool	fes_output_active_

unsigned int	fes_output_stride_

bool	fesproj_output_active_

unsigned int	fesproj_output_stride_

bool	targetdist_output_active_

unsigned int	targetdist_output_stride_

bool	targetdist_proj_output_active_

unsigned int	targetdist_proj_output_stride_

bool	isFirstStep

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 )

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.

◆ 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::ves::Optimizer::apply ( )

inlinevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ 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 ( )

inlinevirtual

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

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap.

◆ checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

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

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

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

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ 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, and PLMD::ves::Opt_Dummy.

◆ 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.

◆ diagonalHessian()

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

inline

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ 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

◆ 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.

◆ getCurrentStepSize()

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

inline

◆ getCurrentStepSizes()

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

inline

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ getDescription()

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

inline

◆ getDocumentation()

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

virtualinherited

◆ 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

◆ 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

◆ 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.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

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

inlinevirtual

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

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

inlineinherited

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

◆ getOutputQuantity() [2/2]

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

inlineinherited

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

◆ 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.

◆ 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.

◆ 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

◆ 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::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ActionAtomistic, PLMD::ActionWithArguments, PLMD::mapping::Mapping, and PLMD::vesselbase::ActionWithAveraging.

◆ 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.

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.

◆ parseFilenames() [1/2]

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

inlineprotected

◆ parseFilenames() [2/2]

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

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::multicolvar::MultiColvarBase, PLMD::function::FuncPathMSD, PLMD::generic::DumpMassCharge, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::generic::Read, PLMD::bias::ReweightTemperature, PLMD::gridtools::ConvertToFES, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

◆ readAtomsFromPDB()

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

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

RunFinalJobs This method is called once at the very end of the calculation.

The set of all Actions in run for the final time in forward order.

Reimplemented in PLMD::analysis::Analysis, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::GridPrintingBase.

◆ 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 ( )

inherited

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

◆ 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

◆ setupOFiles()

void PLMD::ves::Optimizer::setupOFiles	(	std::vector< std::string > &	fnames,
		std::vector< 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::analysis::Histogram, PLMD::isdb::MetainferenceBase, PLMD::eds::EDS, PLMD::multicolvar::MultiColvarBase, PLMD::generic::Read, PLMD::adjmat::ClusterDiameter, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterSize, PLMD::mapping::Mapping, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::adjmat::ClusterAnalysisBase, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, and PLMD::gridtools::ActionWithIntegral.

◆ turnOnHessian()

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

protected

◆ unlockRequests()

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

◆ update()

void PLMD::ves::Optimizer::update ( )

virtual

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

◆ 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

◆ 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

◆ aux_coeffs_pntrs_

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

private

◆ aver_gradient_pntrs_

std::vector<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<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<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

◆ description_

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

private

◆ diagonal_hessian_

bool PLMD::ves::Optimizer::diagonal_hessian_

private

◆ 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

◆ fixed_stepsize_

bool PLMD::ves::Optimizer::fixed_stepsize_

private

◆ 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<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<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

◆ 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

◆ nbiases_

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

private

◆ ncoeffssets_

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

private

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ stepsizes_

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

private

◆ 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<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

◆ type_

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

private

◆ 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

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()

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ Coeffs()

◆ CoeffsMask()

◆ coeffsUpdate()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ diagonalHessian()

◆ doNotCalculateDerivatives()

◆ dynamicStepSize()

◆ enableHessian()

◆ error()

◆ exists()

◆ exit()

◆ fclose()

◆ fflush()

◆ fixedStepSize()

◆ fopen()

◆ getAuxCoeffsPntrs()

◆ getBiasOutputStride()

◆ getBiasPntrs()

◆ getCoeffsMaskPntrs()

◆ getCoeffsPntrs()

◆ getComponentsList()

◆ getComponentsVector()

◆ getCPT()

◆ getCurrentStepSize()

◆ getCurrentStepSizes()

◆ getDependencies()

◆ getDescription()

◆ getDocumentation()

◆ getExchangeStep()

◆ getFesOutputStride()

◆ getFesProjOutputStride()

◆ getGradientPntrs()

◆ getHessianPntrs()

◆ getIterationCounter()

◆ getIterationCounterDbl()

◆ getIterationCounterStr()

◆ getKeyword()

◆ getLabel()