Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__m_e_m_e_t_i_c__s_a_m_p_l_i_n_g.html"> "MAZE_MEMETIC_SAMPLING More...

#include "maze/Memetic.h"

Inheritance diagram for PLMD::maze::Memetic:

[legend]

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

Public Member Functions
	Memetic (const ActionOptions &ao)
	PLMD constructor. More...

	~Memetic ()
	Destructor required for deriving classes. More...

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

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

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

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

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

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

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

void	applyForces ()

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

void	calculate ()
	Calculate the optimal direction of pulling. More...

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

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

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

Vector	center_of_mass () const
	Calculate the center of mass. More...

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

virtual void	checkFieldsAllowed ()

bool	checkIsEnergy ()

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

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

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

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

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

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

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

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

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

virtual void	clearOptions ()

void	clearOutputForces ()

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

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

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

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

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

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

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

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

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

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

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

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

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

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

unsigned int	get_capacity () const
	Setters and getters. More...

double	get_cauchy_mean () const

double	get_cauchy_spread () const

unsigned int	get_coding_len () const

std::string	get_label () const
	Getters and setters. More...

double	get_local_search_rate () const

std::string	get_local_search_type () const

double	get_mating_rate () const

double	get_mutation_rate () const

unsigned int	get_n_global_iterations () const

unsigned int	get_n_iterations () const

unsigned int	get_n_local_iterations () const

unsigned int	get_n_threads_openmp () const

double	get_nl_cutofff () const

unsigned int	get_nl_stride () const

Vector	get_opt () const

double	get_opt_value () const

unsigned int	get_optimizer_stride () const

unsigned int	get_rank_openmp () const

double	get_sampling_radius () const

unsigned int	get_stride_openmp () const

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

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

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

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

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

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

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

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

virtual std::string	getDocumentation () const

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

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

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

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

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

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

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

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

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

unsigned	getNumberOfDerivatives () override

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

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

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

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

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

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

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

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

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

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

bool	is_local_search_on () const

bool	is_pbc_on () const

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

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

void	local_search_off ()

void	local_search_on ()

void	lockRequests () override

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

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

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

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

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

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

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

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

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

void	optimize () override
	Each class deriving from Optimizer needs to override this function. More...

virtual double	pairing (double distance) const
	The pairing function needs to be overridden by a specific optimizer. More...

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

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

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

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

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

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

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

void	pbc_off ()

void	pbc_on ()

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

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

void	prepare ()
	Prepare the neighbor list. More...

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

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

virtual void	retrieveAtoms ()

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

double	sampling_radius ()
	Calculate sampling radius as the minimal distance between two groups in neighbors list. More...

double	score ()
	Score a ligand-protein configuration. More...

void	set_capacity (unsigned int)

void	set_cauchy_mean (double)

void	set_cauchy_spread (double)

void	set_coding_len (unsigned int)

void	set_label (const std::string &)

void	set_local_search_rate (double)

void	set_local_search_type (const std::string &)

void	set_mating_rate (double)

void	set_mutation_rate (double)

void	set_n_global_iterations (unsigned int)

void	set_n_iterations (unsigned int)

void	set_n_local_iterations (unsigned int)

void	set_n_threads_openmp (unsigned int)

void	set_nl_cutoff (double)

void	set_nl_stride (unsigned int)

void	set_opt (Vector)

void	set_opt_value (double)

void	set_optimizer_stride (unsigned int)

void	set_rank_openmp (unsigned int)

void	set_sampling_radius (double)

void	set_stride_openmp (unsigned int)

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

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

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

void	start_step_0 ()

void	start_step_stride ()

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

void	unlockRequests () override

virtual void	update ()
	Update. More...

void	update_nl ()
	Load new positions of atoms in the neighbor list. More...

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

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

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

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

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

static void	registerKeywords (Keywords &keys)
	Registers PLMD keywords. More...

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

Public Attributes
Communicator &	comm

std::set< FILE * >	files

const Keywords &	keywords

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

Communicator &	multi_sim_comm

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

Value *	value_action_
	Loss value. More...

Value *	value_sampling_radius_
	Sampling radiues value. More...

Value *	value_x_
	Biased cv. More...

Value *	value_y_

Value *	value_z_

Protected Member Functions
void	adaptive_random_search (Member &m, const std::vector< double > &params={1.0, 1.e-5, 2.0, 2.0, 3.0, 3.0})
	Solis-Wets random walk. More...

void	annealing (Member &m, const std::vector< double > &params={300.0, 0.95})
	Local annealing. More...

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

const Tensor &	getBoxDerivatives () const

const double &	getForce () const

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

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

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

void	local_search (std::vector< Member > &members)
	Apply local search to members. More...

void	luus_jaakola (Member &m, const std::vector< double > &params)
	Luus–Jaakola heuristics. More...

void	random_restart_hill_climbing (Member &m, const std::vector< double > &params={10})
	Random-restart hill climbing. More...

void	requestAtoms (const std::vector< AtomNumber > &a)

void	setAtomsDerivatives (int, const Vector &)

void	setAtomsDerivatives (Value *, int, const Vector &)

void	setBoxDerivatives (const Tensor &)

void	setBoxDerivatives (Value *, const Tensor &)

void	setBoxDerivativesNoPbc ()
	Set box derivatives automatically. More...

void	setBoxDerivativesNoPbc (Value *)

void	setExtraCV (const std::string &name)

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

Vector	solve ()
	Return an optimal biasing direction. More...

void	stochastic_hill_climbing (Member &m, const std::vector< double > &params={})
	Local searches to improve global solutions. More...

Protected Attributes
bool	adaptation_
	If a local search is performed. More...

Atoms &	atoms

double	bound_
	Bound. More...

unsigned int	capacity_
	Size of population. More...

double	cauchy_mean_alpha_
	Mean and spread of cauchy sampler. More...

double	cauchy_mean_beta_

unsigned int	coding_len_
	Length of coding. More...

bool	first_step_
	Start either at time = 0 or time = optimizer stride. More...

bool	isEnergy

bool	isExtraCV

std::string	label_
	Optimizer label. More...

bool	local_search_on_
	If local search is employed in sampling. More...

double	local_search_rate_
	Rate of local mutation. More...

std::string	local_search_type_
	Type of local search, stochastic_hill_climbing or adaptive_random_search. More...

double	mating_rate_
	Probability of mating. More...

Member	member_best_

std::vector< Member >	members_
	Population. More...

double	mutation_rate_
	Probability of mutation. More...

unsigned int	n_global_iterations_
	Number of global search iterations, doomsday. More...

unsigned int	n_iter_
	Number of global iterations. More...

unsigned int	n_local_iterations_
	Number of local search iterations. More...

unsigned int	n_threads_

NeighborList *	neighbor_list_
	Neighbor list of ligand-protein atom pairs. More...

double	nl_cutoff_
	Neighbor list cut-off. More...

int	nl_stride_
	Neighbor list stride. More...

Vector	opt_
	Biasing direction. More...

double	opt_value_
	Current loss function value. More...

unsigned int	optimizer_stride_
	Optimizer stride. More...

bool	pbc_
	Periodic boundary conditions. More...

unsigned int	rank_
	OpenMP. More...

double	sampling_r_
	Sampling radius. More...

double	score_best_

double	score_worst_
	Scores. More...

unsigned int	stride_

Private Member Functions
Vector	create_coding ()
	Encode a ligand conformation. More...

void	crossover (Member &m1, Member &m2)
	Mate two members. More...

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

void	initialize_members ()
	Create a set of translations relative to the ligand, each translation encodes a probable biasing direction. More...

void	mating (std::vector< Member > &members)
	Perform mating in the population. More...

void	mutation (Member &m)
	Mutate a member. More...

void	mutation (std::vector< Member > &members)
	Mutate the population. More...

bool	out_of_bounds (double v)
	Check if the vector length is out of bounds. More...

void	print_status () const
	Print a status. More...

double	score_mean ()
	Calculate the mean score. More...

double	score_member (const Vector &v)
	Score a single member. More...

void	score_members ()
	Score each translation by the loss function. More...

void	selection_roulette ()
	Select a new population using the roulette selection. More...

void	sort_members ()
	Sort the population using heaps, required for finding a minimum of the loss function. More...

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

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

std::vector< double >	charges

bool	chargesWereSet

bool	doCheckPoint

bool	donotforce

bool	donotretrieve

double	energy

std::string	extraCV

bool	first_time_

double	forceOnEnergy

double	forceOnExtraCV

std::vector< Vector >	forces

std::vector< AtomNumber >	indexes

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	lockRequestAtoms

Loss *	loss_
	Pointer to the loss function. More...

std::vector< double >	masses

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

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...

Pbc &	pbc =*pbc_fwd

ForwardDecl< Pbc >	pbc_fwd

std::vector< Vector >	positions

int	replica_index

bool	restart

bool	serial_

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

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

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

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

bool	validate_list_

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

std::vector< Loss * >	vec_loss_

Tensor	virial

Detailed Description

Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__m_e_m_e_t_i_c__s_a_m_p_l_i_n_g.html"> "MAZE_MEMETIC_SAMPLING

Memetic algorithms for the optimization of the loss function.

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ Memetic()

PLMD::maze::Memetic::Memetic ( const ActionOptions & ao )

explicit

PLMD constructor.

Parameters

[in] ao PLMD::ActionOptions&.

◆ ~Memetic()

PLMD::maze::Memetic::~Memetic ( )

Destructor required for deriving classes.

Member Function Documentation

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ adaptive_random_search()

void PLMD::maze::Memetic::adaptive_random_search	(	Member &	m,
		const std::vector< double > &	params = `{1.0, 1.e-5, 2.0, 2.0, 3.0, 3.0}`
	)

protected

Solis-Wets random walk.

Adaptive random search algorithm was designed to address the limitations of the fixed step size. The strategy for adaptive random search is to continually approximate the optimal step size required to reach the global optimum in the search space. This is achieved by trialling and adopting smaller or larger step sizes only if they result in an improvement in the search performance.

Very large step sizes are trialled with a much lower frequency. This strategy of preferring large moves is intended to allow the technique to escape local optima. Smaller step sizes are adopted if no improvement is made for an extended period.

Parameters

[in,out]	m	Member.
[in]	params

◆ 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.

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )

inlineinherited

Allow calls to modifyGlobalForce()

◆ annealing()

void PLMD::maze::Memetic::annealing	(	Member &	m,
		const std::vector< double > &	params = `{300.0, 0.95}`
	)

protected

Local annealing.

Parameters

[in,out]	m	Member.
[in]	params	T, alpha.

◆ apply()

void PLMD::Colvar::apply ( )

overrideprotectedvirtualinherited

Apply an Action.

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

Implements PLMD::Action.

◆ applyForces()

void PLMD::ActionAtomistic::applyForces ( )

inherited

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

This is a special method that is called just before the update() method. It can be used by actions that want to do something irrespectively of the fact that update() is active or not. In other words, this is always called, even when action is not active.

Reimplemented in PLMD::generic::UpdateIf.

◆ calculate()

void PLMD::maze::Optimizer::calculate ( )

virtualinherited

Calculate the optimal direction of pulling.

Implements PLMD::Action.

◆ calculateAtomicNumericalDerivatives()

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

inherited

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

◆ calculateFromPDB()

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

inherited

Calculate the action given a pdb file as input.

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

◆ calculateNumericalDerivatives()

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

overridevirtualinherited

N.B.

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

Reimplemented from PLMD::Action.

Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvarBase, PLMD::mapping::Mapping, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, and PLMD::mapping::PCAVars.

◆ center_of_mass()

Vector PLMD::maze::Optimizer::center_of_mass ( ) const

inherited

Calculate the center of mass.

Returns: center of mass

◆ changeBox()

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

inherited

Change the box shape.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

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

◆ checkIsEnergy()

bool PLMD::Colvar::checkIsEnergy ( )

inlineinherited

◆ checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

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

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

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

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )

inherited

◆ componentIsNotPeriodic()

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

inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

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

staticinherited

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

◆ copyOutput() [1/2]

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

inherited

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

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

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

inherited

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

Use getPntrToComponent instead.

◆ create_coding()

Vector PLMD::maze::Memetic::create_coding ( )

private

Encode a ligand conformation.

◆ crossover()

void PLMD::maze::Memetic::crossover	(	Member &	m1,
		Member &	m2
	)

private

Mate two members.

Parameters

[in,out]	m1	1st member.
[in,out]	m2	2nd member.

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ doNotForce()

void PLMD::ActionAtomistic::doNotForce ( )

inlineinherited

Skip atom forces - use with care.

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

◆ doNotRetrieve()

void PLMD::ActionAtomistic::doNotRetrieve ( )

inlineinherited

Skip atom retrieval - use with care.

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

◆ error()

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

inherited

Crash calculation and print documentation.

◆ exists()

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

inherited

Check if a value with a particular name is present.

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

◆ exit()

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

inherited

Exit with error code c.

◆ fclose()

int PLMD::Action::fclose ( FILE * fp )

inherited

Closes a file opened with Action::fclose().

◆ fflush()

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

◆ fopen()

FILE * PLMD::Action::fopen	(	const char *	path,
		const char *	mode
	)

inherited

Opens a file.

This is similar to plain fopen, but with some extra functionality.

When opened for writing, processors other than the one with rank 0 just open /dev/null
PlumedMain::fopen is used, so that other tricks may appear (see PlumedMain::fopen)

◆ get_capacity()

unsigned int PLMD::maze::Memetic::get_capacity ( ) const

inline

Setters and getters.

◆ get_cauchy_mean()

double PLMD::maze::Memetic::get_cauchy_mean ( ) const

inline

◆ get_cauchy_spread()

double PLMD::maze::Memetic::get_cauchy_spread ( ) const

inline

◆ get_coding_len()

unsigned int PLMD::maze::Memetic::get_coding_len ( ) const

inline

◆ get_label()

std::string PLMD::maze::Optimizer::get_label ( ) const

inlineinherited

Getters and setters.

◆ get_local_search_rate()

double PLMD::maze::Memetic::get_local_search_rate ( ) const

inline

◆ get_local_search_type()

std::string PLMD::maze::Memetic::get_local_search_type ( ) const

inline

◆ get_mating_rate()

double PLMD::maze::Memetic::get_mating_rate ( ) const

inline

◆ get_mutation_rate()

double PLMD::maze::Memetic::get_mutation_rate ( ) const

inline

◆ get_n_global_iterations()

unsigned int PLMD::maze::Memetic::get_n_global_iterations ( ) const

inline

◆ get_n_iterations()

unsigned int PLMD::maze::Optimizer::get_n_iterations ( ) const

inlineinherited

◆ get_n_local_iterations()

unsigned int PLMD::maze::Memetic::get_n_local_iterations ( ) const

inline

◆ get_n_threads_openmp()

unsigned int PLMD::maze::Optimizer::get_n_threads_openmp ( ) const

inlineinherited

◆ get_nl_cutofff()

double PLMD::maze::Optimizer::get_nl_cutofff ( ) const

inlineinherited

◆ get_nl_stride()

unsigned int PLMD::maze::Optimizer::get_nl_stride ( ) const

inlineinherited

◆ get_opt()

Vector PLMD::maze::Optimizer::get_opt ( ) const

inlineinherited

◆ get_opt_value()

double PLMD::maze::Optimizer::get_opt_value ( ) const

inlineinherited

◆ get_optimizer_stride()

unsigned int PLMD::maze::Optimizer::get_optimizer_stride ( ) const

inlineinherited

◆ get_rank_openmp()

unsigned int PLMD::maze::Optimizer::get_rank_openmp ( ) const

inlineinherited

◆ get_sampling_radius()

double PLMD::maze::Optimizer::get_sampling_radius ( ) const

inlineinherited

◆ get_stride_openmp()

unsigned int PLMD::maze::Optimizer::get_stride_openmp ( ) const

inlineinherited

◆ getAbsoluteIndex()

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

inlineinherited

Get the absolute index of an atom.

◆ getAbsoluteIndexes()

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

inlinevirtualinherited

Get the vector of absolute indexes.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ getBox()

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

inlineinherited

Get box shape.

◆ getBoxDerivatives()

const Tensor& PLMD::Colvar::getBoxDerivatives ( ) const

protectedinherited

◆ getCharge()

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

inlineinherited

Get charge of i-th atom.

◆ getComponent()

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

privateinherited

Return the index for the component named name.

◆ getComponentsList()

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

inherited

get a string that contains all the available components

◆ getComponentsVector()

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

inherited

get a vector that contains the label for all the components

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ getDocumentation()

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

virtualinherited

◆ getEnergy()

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

inlineinherited

Get energy.

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getForce()

const double& PLMD::Colvar::getForce ( ) const

protectedinherited

◆ getGlobalPosition()

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

inlineinherited

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

With direct access to the global atom array.

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

◆ getKeyword()

std::string PLMD::Action::getKeyword ( const std::string & key )

inherited

Just read one of the keywords and return the whole thing as a string.

◆ getLabel()

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

inlineinherited

Returns the label.

◆ getMass()

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

inlineinherited

Get mass of i-th atom.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

unsigned PLMD::Colvar::getNumberOfDerivatives ( )

inlineoverridevirtualinherited

Implements PLMD::ActionWithValue.

◆ getOutputQuantity() [1/2]

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

inlineinherited

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

◆ getOutputQuantity() [2/2]

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

inlineinherited

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

◆ getPbc()

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

inlineinherited

Get reference to Pbc.

◆ getPntrToComponent() [1/2]

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

protectedinherited

Return a pointer to the value by name.

◆ getPntrToComponent() [2/2]

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

protectedinherited

Return a pointer to the component by index.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

◆ getPosition()

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

inlineinherited

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

◆ getPositions()

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

inlineinherited

Get the array of all positions.

◆ 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.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getTotAtoms()

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inlineinherited

Get total number of atoms, including virtual ones.

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

◆ getUnique()

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

inlineinherited

◆ getUniqueLocal()

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

inlineinherited

◆ initialize_members()

void PLMD::maze::Memetic::initialize_members ( )

private

Create a set of translations relative to the ligand, each translation encodes a probable biasing direction.

◆ interpretAtomList()

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

inherited

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

◆ is_local_search_on()

bool PLMD::maze::Memetic::is_local_search_on ( ) const

inline

◆ is_pbc_on()

bool PLMD::maze::Optimizer::is_pbc_on ( ) const

inlineinherited

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isOptionOn()

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

inlineinherited

Check if an option is on.

◆ local_search()

void PLMD::maze::Memetic::local_search ( std::vector< Member > & members )

protected

Apply local search to members.

Parameters

[in,out] members Population.

◆ local_search_off()

void PLMD::maze::Memetic::local_search_off ( )

inline

◆ local_search_on()

void PLMD::maze::Memetic::local_search_on ( )

inline

◆ lockRequests()

void PLMD::ActionAtomistic::lockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

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

◆ luus_jaakola()

void PLMD::maze::Memetic::luus_jaakola	(	Member &	m,
		const std::vector< double > &	params
	)

protected

Luus–Jaakola heuristics.

Parameters

[in,out]	m	Member.
[in]	params	Bounds.

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )

inherited

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

◆ mating()

void PLMD::maze::Memetic::mating ( std::vector< Member > & members )

private

Perform mating in the population.

Parameters

[in,out] members Population.

◆ modifyForceOnEnergy()

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

◆ modifyForceOnExtraCV()

double & PLMD::ActionAtomistic::modifyForceOnExtraCV ( )

inlineinherited

Get a reference to force on extraCV.

◆ modifyForces()

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

inlineinherited

Get a reference to forces array.

◆ modifyGlobalForce()

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

inlineinherited

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

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

◆ modifyGlobalPbc()

Pbc & PLMD::ActionAtomistic::modifyGlobalPbc ( )

inlineinherited

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

◆ modifyGlobalPosition()

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

inlineinherited

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

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

◆ modifyGlobalVirial()

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inlineinherited

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

◆ modifyVirial()

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

◆ mutation() [1/2]

void PLMD::maze::Memetic::mutation ( Member & m )

private

Mutate a member.

Parameters

[in,out] m Member.

◆ mutation() [2/2]

void PLMD::maze::Memetic::mutation ( std::vector< Member > & members )

private

Mutate the population.

Parameters

[in,out] members Population.

◆ 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.

◆ optimize()

void PLMD::maze::Memetic::optimize ( )

overridevirtual

Each class deriving from Optimizer needs to override this function.

Implements PLMD::maze::Optimizer.

◆ out_of_bounds()

bool PLMD::maze::Memetic::out_of_bounds ( double v )

private

Check if the vector length is out of bounds.

Parameters

[in] v Vector length.

◆ pairing()

double PLMD::maze::Optimizer::pairing ( double distance ) const

virtualinherited

The pairing function needs to be overridden by a specific optimizer.

Parameters

[in] distance distance between a pair of atoms

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ parseAtomList() [1/2]

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

inherited

Parse an list of atom with a numbred keyword.

◆ parseAtomList() [2/2]

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

inherited

Parse a list of atoms without a numbered keyword.

◆ parseFlag()

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

inherited

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T >

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

inherited

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

template<class T >

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

inherited

Parse a vector with a number.

◆ parseVector()

template<class T >

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

inherited

Parse one keyword as std::vector.

◆ pbc_off()

void PLMD::maze::Optimizer::pbc_off ( )

inlineinherited

◆ pbc_on()

void PLMD::maze::Optimizer::pbc_on ( )

inlineinherited

◆ pbcApply()

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

inherited

Applies PBCs to a seriens of positions or distances.

◆ pbcDistance()

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

inherited

Compute the pbc distance between two positions.

◆ prepare()

void PLMD::maze::Optimizer::prepare ( )

virtualinherited

Prepare the neighbor list.

Reimplemented from PLMD::Action.

◆ print_status()

void PLMD::maze::Memetic::print_status ( ) const

private

Print a status.

◆ random_restart_hill_climbing()

void PLMD::maze::Memetic::random_restart_hill_climbing	(	Member &	m,
		const std::vector< double > &	params = `{10}`
	)

protected

Random-restart hill climbing.

The algorithm can be restarted and repeated a number of times after it converges to provide an improved result.

Parameters

[in,out]	m	Member.
[in]	params	Number of restarts.

◆ readAtomsFromPDB()

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

overridevirtualinherited

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

Reimplemented from PLMD::Action.

◆ registerKeywords()

void PLMD::maze::Memetic::registerKeywords ( Keywords & keys )

static

Registers PLMD keywords.

Register MAZE_MEMETIC_SAMPLING.

Parameters

[in] keys Keywords.

◆ requestAtoms() [1/2]

void PLMD::Colvar::requestAtoms ( const std::vector< AtomNumber > & a )

protectedinherited

◆ requestAtoms() [2/2]

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

inherited

Request an array of atoms.

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

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( )

virtualinherited

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ runFinalJobs()

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

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

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

Reimplemented in PLMD::vesselbase::ActionWithAveraging, PLMD::analysis::AnalysisBase, PLMD::gridtools::ConvertToFES, PLMD::analysis::ReadDissimilarityMatrix, and PLMD::gridtools::GridPrintingBase.

◆ sampling_radius()

double PLMD::maze::Optimizer::sampling_radius ( )

inherited

Calculate sampling radius as the minimal distance between two groups in neighbors list.

Returns: minimal distance of ligand-protein atom pairs

◆ score()

double PLMD::maze::Optimizer::score ( )

inherited

Score a ligand-protein configuration.

Returns: score

◆ score_mean()

double PLMD::maze::Memetic::score_mean ( )

private

Calculate the mean score.

◆ score_member()

double PLMD::maze::Memetic::score_member ( const Vector & v )

private

Score a single member.

Parameters

[in] v Member's translation.

◆ score_members()

void PLMD::maze::Memetic::score_members ( )

private

Score each translation by the loss function.

◆ selection_roulette()

void PLMD::maze::Memetic::selection_roulette ( )

private

Select a new population using the roulette selection.

◆ set_capacity()

void PLMD::maze::Memetic::set_capacity ( unsigned int capacity )

inline

◆ set_cauchy_mean()

void PLMD::maze::Memetic::set_cauchy_mean ( double cauchy_mean_alpha )

inline

◆ set_cauchy_spread()

void PLMD::maze::Memetic::set_cauchy_spread ( double cauchy_mean_beta )

inline

◆ set_coding_len()

void PLMD::maze::Memetic::set_coding_len ( unsigned int coding_len )

inline

◆ set_label()

void PLMD::maze::Optimizer::set_label ( const std::string & label )

inlineinherited

◆ set_local_search_rate()

void PLMD::maze::Memetic::set_local_search_rate ( double local_search_rate )

inline

◆ set_local_search_type()

void PLMD::maze::Memetic::set_local_search_type ( const std::string & local_search_type )

inline

◆ set_mating_rate()

void PLMD::maze::Memetic::set_mating_rate ( double mating_rate )

inline

◆ set_mutation_rate()

void PLMD::maze::Memetic::set_mutation_rate ( double mutation_rate )

inline

◆ set_n_global_iterations()

void PLMD::maze::Memetic::set_n_global_iterations ( unsigned int n_global_iterations )

inline

◆ set_n_iterations()

void PLMD::maze::Optimizer::set_n_iterations ( unsigned int n_iter )

inlineinherited

◆ set_n_local_iterations()

void PLMD::maze::Memetic::set_n_local_iterations ( unsigned int n_local_iterations )

inline

◆ set_n_threads_openmp()

void PLMD::maze::Optimizer::set_n_threads_openmp ( unsigned int n_threads )

inlineinherited

◆ set_nl_cutoff()

void PLMD::maze::Optimizer::set_nl_cutoff ( double nl_cutoff )

inlineinherited

◆ set_nl_stride()

void PLMD::maze::Optimizer::set_nl_stride ( unsigned int nl_stride )

inlineinherited

◆ set_opt()

void PLMD::maze::Optimizer::set_opt ( Vector opt )

inlineinherited

◆ set_opt_value()

void PLMD::maze::Optimizer::set_opt_value ( double opt_value )

inlineinherited

◆ set_optimizer_stride()

void PLMD::maze::Optimizer::set_optimizer_stride ( unsigned int optimizer_stride )

inlineinherited

◆ set_rank_openmp()

void PLMD::maze::Optimizer::set_rank_openmp ( unsigned int rank )

inlineinherited

◆ set_sampling_radius()

void PLMD::maze::Optimizer::set_sampling_radius ( double sampling_r )

inlineinherited

◆ set_stride_openmp()

void PLMD::maze::Optimizer::set_stride_openmp ( unsigned int stride )

inlineinherited

◆ setAtomsDerivatives() [1/2]

void PLMD::Colvar::setAtomsDerivatives	(	int	i,
		const Vector &	d
	)

inlineprotectedinherited

◆ setAtomsDerivatives() [2/2]

void PLMD::Colvar::setAtomsDerivatives	(	Value *	v,
		int	i,
		const Vector &	d
	)

inlineprotectedinherited

◆ setBoxDerivatives() [1/2]

void PLMD::Colvar::setBoxDerivatives ( const Tensor & d )

inlineprotectedinherited

◆ setBoxDerivatives() [2/2]

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

inlineprotectedinherited

◆ setBoxDerivativesNoPbc() [1/2]

void PLMD::Colvar::setBoxDerivativesNoPbc ( )

inlineprotectedinherited

Set box derivatives automatically.

It should be called after the setAtomsDerivatives has been used for all single atoms.

Warning: It only works for collective variable NOT using PBCs!

◆ setBoxDerivativesNoPbc() [2/2]

void PLMD::Colvar::setBoxDerivativesNoPbc ( Value * v )

protectedinherited

◆ setExtraCV()

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

inlineprotectedinherited

◆ setForcesOnAtoms()

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

inherited

Add the forces to the atoms.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

◆ 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.

◆ 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.

◆ solve()

Vector PLMD::maze::Memetic::solve ( )

protected

Return an optimal biasing direction.

◆ sort_members()

void PLMD::maze::Memetic::sort_members ( )

private

Sort the population using heaps, required for finding a minimum of the loss function.

◆ start_step_0()

void PLMD::maze::Optimizer::start_step_0 ( )

inlineinherited

◆ start_step_stride()

void PLMD::maze::Optimizer::start_step_stride ( )

inlineinherited

◆ stochastic_hill_climbing()

void PLMD::maze::Memetic::stochastic_hill_climbing	(	Member &	m,
		const std::vector< double > &	params = `{}`
	)

protected

Local searches to improve global solutions.

Stochastic hill climbing.

Neighbors with better or equal cost should be accepted, allowing the technique to navigate across plateaus in the response surface.

Parameters

[in,out]	m	Member.
[in]	params	None.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

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

◆ unlockRequests()

void PLMD::ActionAtomistic::unlockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

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

◆ update()

virtual void PLMD::Action::update ( )

inlinevirtualinherited

Update.

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

Reimplemented in PLMD::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::ves::TargetDistribution, PLMD::ves::VesDeltaF, PLMD::opes::OPESexpanded, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::multicolvar::VolumeTetrapore, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::mapping::AdaptivePath, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::analysis::AnalysisBase, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::vesselbase::ActionWithAveraging, PLMD::adjmat::OutputCluster, PLMD::isdb::PRE, PLMD::multicolvar::DumpMultiColvar, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::analysis::ReadDissimilarityMatrix, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::adjmat::DumpGraph, PLMD::analysis::ReadAnalysisFrames, PLMD::gridtools::GridPrintingBase, PLMD::logmfd::LogMFD, PLMD::eds::EDS, and PLMD::fisst::FISST.

◆ update_nl()

void PLMD::maze::Optimizer::update_nl ( )

inherited

Load new positions of atoms in the neighbor list.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( )

inherited

updates local unique atoms

◆ useCustomisableComponents()

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

staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ warning()

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

inherited

Issue a warning.

Member Data Documentation

◆ active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

◆ adaptation_

bool PLMD::maze::Memetic::adaptation_

protected

If a local search is performed.

◆ after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

◆ bound_

double PLMD::maze::Memetic::bound_

protected

Bound.

◆ capacity_

unsigned int PLMD::maze::Memetic::capacity_

protected

Size of population.

◆ cauchy_mean_alpha_

double PLMD::maze::Memetic::cauchy_mean_alpha_

protected

Mean and spread of cauchy sampler.

◆ cauchy_mean_beta_

double PLMD::maze::Memetic::cauchy_mean_beta_

protected

◆ charges

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

privateinherited

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet

privateinherited

◆ coding_len_

unsigned int PLMD::maze::Memetic::coding_len_

protected

Length of coding.

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ donotforce

bool PLMD::ActionAtomistic::donotforce

privateinherited

◆ donotretrieve

bool PLMD::ActionAtomistic::donotretrieve

privateinherited

◆ energy

double PLMD::ActionAtomistic::energy

privateinherited

◆ extraCV

std::string PLMD::ActionAtomistic::extraCV

privateinherited

◆ files

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

inherited

◆ first_step_

bool PLMD::maze::Optimizer::first_step_

protectedinherited

Start either at time = 0 or time = optimizer stride.

◆ first_time_

bool PLMD::maze::Optimizer::first_time_

privateinherited

◆ forceOnEnergy

double PLMD::ActionAtomistic::forceOnEnergy

privateinherited

◆ forceOnExtraCV

double PLMD::ActionAtomistic::forceOnExtraCV

privateinherited

◆ forces

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

privateinherited

◆ indexes

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

privateinherited

◆ isEnergy

bool PLMD::Colvar::isEnergy

protectedinherited

◆ isExtraCV

bool PLMD::Colvar::isExtraCV

protectedinherited

◆ 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.

◆ label_

std::string PLMD::maze::Optimizer::label_

protectedinherited

Optimizer label.

◆ 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.

◆ local_search_on_

bool PLMD::maze::Memetic::local_search_on_

protected

If local search is employed in sampling.

◆ local_search_rate_

double PLMD::maze::Memetic::local_search_rate_

protected

Rate of local mutation.

◆ local_search_type_

std::string PLMD::maze::Memetic::local_search_type_

protected

Type of local search, stochastic_hill_climbing or adaptive_random_search.

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ loss_

Loss* PLMD::maze::Optimizer::loss_

privateinherited

Pointer to the loss function.

◆ masses

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

privateinherited

◆ mating_rate_

double PLMD::maze::Memetic::mating_rate_

protected

Probability of mating.

◆ member_best_

Member PLMD::maze::Memetic::member_best_

protected

◆ members_

std::vector<Member> PLMD::maze::Memetic::members_

protected

Population.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ mutation_rate_

double PLMD::maze::Memetic::mutation_rate_

protected

Probability of mutation.

◆ n_global_iterations_

unsigned int PLMD::maze::Memetic::n_global_iterations_

protected

Number of global search iterations, doomsday.

◆ n_iter_

unsigned int PLMD::maze::Optimizer::n_iter_

protectedinherited

Number of global iterations.

◆ n_local_iterations_

unsigned int PLMD::maze::Memetic::n_local_iterations_

protected

Number of local search iterations.

◆ n_threads_

unsigned int PLMD::maze::Optimizer::n_threads_

protectedinherited

◆ name

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

privateinherited

Name of the directive in the plumed.dat file.

◆ neighbor_list_

NeighborList* PLMD::maze::Optimizer::neighbor_list_

protectedinherited

Neighbor list of ligand-protein atom pairs.

◆ nl_cutoff_

double PLMD::maze::Optimizer::nl_cutoff_

protectedinherited

Neighbor list cut-off.

◆ nl_stride_

int PLMD::maze::Optimizer::nl_stride_

protectedinherited

Neighbor list stride.

◆ 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.

◆ opt_

Vector PLMD::maze::Optimizer::opt_

protectedinherited

Biasing direction.

◆ opt_value_

double PLMD::maze::Optimizer::opt_value_

protectedinherited

Current loss function value.

◆ optimizer_stride_

unsigned int PLMD::maze::Optimizer::optimizer_stride_

protectedinherited

Optimizer stride.

◆ options

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

privateinherited

Option that you might have enabled.

◆ pbc

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

privateinherited

◆ pbc_

bool PLMD::maze::Optimizer::pbc_

protectedinherited

Periodic boundary conditions.

◆ pbc_fwd

ForwardDecl<Pbc> PLMD::ActionAtomistic::pbc_fwd

privateinherited

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ positions

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

privateinherited

◆ rank_

unsigned int PLMD::maze::Optimizer::rank_

protectedinherited

OpenMP.

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ sampling_r_

double PLMD::maze::Optimizer::sampling_r_

protectedinherited

Sampling radius.

◆ score_best_

double PLMD::maze::Memetic::score_best_

protected

◆ score_worst_

double PLMD::maze::Memetic::score_worst_

protected

Scores.

◆ serial_

bool PLMD::maze::Optimizer::serial_

privateinherited

◆ stride_

unsigned int PLMD::maze::Optimizer::stride_

protectedinherited

◆ unique

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

privateinherited

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

◆ unique_local

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

privateinherited

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

◆ update_from

double PLMD::Action::update_from

privateinherited

Update only after this time.

◆ update_until

double PLMD::Action::update_until

privateinherited

Update only until this time.

◆ validate_list_

bool PLMD::maze::Optimizer::validate_list_

privateinherited

◆ value_action_

Value* PLMD::maze::Optimizer::value_action_

inherited

Loss value.

◆ value_sampling_radius_

Value* PLMD::maze::Optimizer::value_sampling_radius_

inherited

Sampling radiues value.

◆ value_x_

Value* PLMD::maze::Optimizer::value_x_

inherited

Biased cv.

◆ value_y_

Value* PLMD::maze::Optimizer::value_y_

inherited

◆ value_z_

Value* PLMD::maze::Optimizer::value_z_

inherited

◆ values

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

privateinherited

An array containing the values for this action.

◆ vec_loss_

std::vector<Loss*> PLMD::maze::Optimizer::vec_loss_

privateinherited

◆ virial

Tensor PLMD::ActionAtomistic::virial

privateinherited

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

maze/Memetic.h
maze/Memetic.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ Memetic()

◆ ~Memetic()

Member Function Documentation

◆ activate()

◆ adaptive_random_search()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addValue()

◆ addValueWithDerivatives()

◆ allowToAccessGlobalForces()

◆ annealing()

◆ apply()

◆ applyForces()

◆ beforeUpdate()

◆ calculate()

◆ calculateAtomicNumericalDerivatives()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ center_of_mass()

◆ changeBox()

◆ checkFieldsAllowed()

◆ checkIsEnergy()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ clearOutputForces()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ create_coding()

◆ crossover()

◆ deactivate()

◆ doNotCalculateDerivatives()

◆ doNotForce()

◆ doNotRetrieve()

◆ error()

◆ exists()

◆ exit()

◆ fclose()

◆ fflush()

◆ fopen()

◆ get_capacity()

◆ get_cauchy_mean()

◆ get_cauchy_spread()

◆ get_coding_len()

◆ get_label()

◆ get_local_search_rate()

◆ get_local_search_type()

◆ get_mating_rate()

◆ get_mutation_rate()

◆ get_n_global_iterations()

◆ get_n_iterations()

◆ get_n_local_iterations()

◆ get_n_threads_openmp()

◆ get_nl_cutofff()

◆ get_nl_stride()

◆ get_opt()

◆ get_opt_value()