Base class for implementing optimizers for ligand unbinding. More...

#include "maze/Optimizer.h"

Inheritance diagram for PLMD::maze::Optimizer:

[legend]

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

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

	~Optimizer ()
	Destructor. More...

virtual bool	actionHasForces ()

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

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

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

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

void	addForce (const std::pair< std::size_t, std::size_t > &a, const Vector &f)
	Add force to an atom. More...

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

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

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...

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

ActionAtomistic *	castToActionAtomistic () noexcept final

virtual ActionForInterface *	castToActionForInterface () noexcept

virtual ActionShortcut *	castToActionShortcut () noexcept

virtual ActionToGetData *	castToActionToGetData () noexcept

virtual ActionToPutData *	castToActionToPutData () noexcept

virtual ActionWithArguments *	castToActionWithArguments () noexcept

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

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

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

virtual DomainDecomposition *	castToDomainDecomposition () noexcept

virtual PbcAction *	castToPbcAction () noexcept

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

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

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

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

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

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

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

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

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

virtual void	clearInputForces (const bool &force=false)
	Clear the forces on the values. More...

virtual void	clearOptions ()

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

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

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

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

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

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...

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

unsigned int	get_n_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...

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

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

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

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

Vector	getForce (const std::pair< std::size_t, std::size_t > &a) const
	Get the force acting on a particular atom. More...

Vector	getGlobalPosition (const std::pair< std::size_t, std::size_t > &) const
	Get position of i-th atom (access by absolute AtomNumber). More...

void	getGradient (const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const
	Transfer the gradients. More...

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

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

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

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

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

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

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

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

unsigned	getNumberOfDerivatives () override

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

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

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

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 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::vector< AtomNumber > &	getUnique () const

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

Tensor	getVirial () const
	Get the virial that is acting. More...

void	interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
	Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this. More...

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	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...

virtual void	optimize ()=0
	Optimal values needed for biasing are computed by methods overridding the optimize 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...

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

virtual void	retrieveAtoms (const bool &force=false)

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_label (const std::string &)

void	set_n_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)
	Add the forces to the atoms. More...

void	setForcesOnCell (const double *forcesToApply, std::size_t size, unsigned &ind)
	Add the virial forces (span-like syntax) More...

void	setForcesOnCell (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the virial forces. More...

void	setGlobalPosition (const std::pair< std::size_t, std::size_t > &, const Vector &pos)
	Modify position of i-th atom (access by absolute AtomNumber). More...

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

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

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

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

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

Static Public Member Functions
static void	getAtomValuesFromPlumedObject (const PlumedMain &plumed, std::vector< Value * > &xpos, std::vector< Value * > &ypos, std::vector< Value * > &zpos, std::vector< Value * > &masv, std::vector< Value * > &chargev)
	This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges. More...

static void	interpretAtomList (std::vector< std::string > &strings, const std::vector< Value * > &xpos, Action *action, std::vector< AtomNumber > &t)
	Convert a set of read in strings into an atom list (this is used in parseAtomList) 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	setBoxDerivativesNoPbc (const std::vector< Vector > &pos, std::vector< std::vector< Vector > > &derivs, std::vector< Tensor > &virial)

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

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

const Tensor &	getBoxDerivatives () const

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

const double &	getForce () const

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

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

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

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

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

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

std::pair< std::size_t, std::size_t >	getValueIndices (const AtomNumber &i) const
	Used to interpret whether this index is a virtual atom or a real atom. 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...

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

Protected Attributes
bool	chargesWereSet

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

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

bool	massesWereSet

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

unsigned int	n_threads_

std::unique_ptr< 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...

unsigned int	stride_

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

void	updateUniqueLocal (const bool &useunique, const std::vector< int > &g2l)

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

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

std::vector< std::pair< std::size_t, std::size_t > >	atom_value_ind

std::vector< std::pair< std::size_t, std::vector< std::size_t > > >	atom_value_ind_grouped

Value *	boxValue

std::vector< double >	charges

std::vector< Value * >	chargev

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

bool	doCheckPoint

bool	donotforce

bool	donotretrieve

double	energy

bool	first_time_

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

double	forceOnEnergy

double	forceOnExtraCV

std::vector< Vector >	forces

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

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

std::vector< Value * >	masv

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

bool	never_activate

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

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

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

Pbc &	pbc =*pbc_fwd

ForwardDecl< Pbc >	pbc_fwd

std::vector< Vector >	positions

int	replica_index

bool	restart

bool	serial_

double	timestep
	Save the timestep here. More...

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

std::vector< AtomNumber >	unique_local

bool	unique_local_needs_update
	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< unsigned >	valsToForce

std::vector< std::size_t >	value_depends

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

std::vector< Loss * >	vec_loss_

std::vector< Value * >	xpos
	Values that hold information about atom positions and charges. More...

std::vector< Value * >	ypos

std::vector< Value * >	zpos

Detailed Description

Base class for implementing optimizers for ligand unbinding.

An optimizer is defined as a colvar that can be passed to Optimizer_Bias.

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ Optimizer()

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

explicit

PLMD constructor.

Parameters

[in] ao PLMD::ActionOptions&

◆ ~Optimizer()

PLMD::maze::Optimizer::~Optimizer ( )

inline

Destructor.

Member Function Documentation

◆ actionHasForces()

bool PLMD::ActionAtomistic::actionHasForces ( )

virtualinherited

Reimplemented in PLMD::generic::FitToTemplate, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::DumpAtoms, PLMD::generic::WholeMolecules, PLMD::generic::DumpMassCharge, and PLMD::generic::PrintNDX.

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addComponent()

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

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

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

virtualinherited

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

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

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addForce()

void PLMD::ActionAtomistic::addForce	(	const std::pair< std::size_t, std::size_t > &	a,
		const Vector &	f
	)

inlineinherited

Add force to an atom.

◆ addValue()

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

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

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

virtualinherited

Add a value with the name label that has derivatives.

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

◆ apply()

void PLMD::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.

◆ 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 ( )

virtual

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::ActionWithVector, PLMD::generic::DumpAtoms, PLMD::generic::PrintNDX, PLMD::isdb::EMMI, and PLMD::isdb::MetainferenceBase.

◆ calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )

virtualinherited

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

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

◆ castToActionAtomistic()

ActionAtomistic* PLMD::ActionAtomistic::castToActionAtomistic ( )

inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

◆ castToActionForInterface()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

◆ castToActionShortcut()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

◆ castToActionToGetData()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

◆ castToActionToPutData()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

◆ castToActionWithArguments()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

◆ castToActionWithValue() [1/2]

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

inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ castToActionWithValue() [2/2]

ActionWithValue* PLMD::ActionWithValue::castToActionWithValue ( )

inlinefinalvirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented from PLMD::Action.

◆ castToActionWithVirtualAtom()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

◆ castToDomainDecomposition()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

◆ castToPbcAction()

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

◆ center_of_mass()

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

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.

◆ checkForDependency()

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

inherited

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

◆ checkForForces()

bool PLMD::ActionWithValue::checkForForces ( )

protectedinherited

Accumulate the forces from the Values.

◆ checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkNumericalDerivatives() [2/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

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

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

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

virtualinherited

Clear the derivatives of values wrt parameters.

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

◆ clearInputForces()

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

virtualinherited

Clear the forces on the values.

Reimplemented in PLMD::ActionWithVector.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ componentIsNotPeriodic()

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

inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

◆ copyOutput() [1/2]

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

inherited

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

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

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

inherited

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

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

◆ 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_label()

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

inline

Getters and setters.

◆ get_n_iterations()

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

inline

◆ get_n_threads_openmp()

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

inline

◆ get_nl_cutofff()

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

inline

◆ get_nl_stride()

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

inline

◆ get_opt()

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

inline

◆ get_opt_value()

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

inline

◆ get_optimizer_stride()

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

inline

◆ get_rank_openmp()

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

inline

◆ get_sampling_radius()

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

inline

◆ get_stride_openmp()

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

inline

◆ 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.

◆ getAtomValuesFromPlumedObject()

void PLMD::ActionAtomistic::getAtomValuesFromPlumedObject	(	const PlumedMain &	plumed,
		std::vector< Value * > &	xpos,
		std::vector< Value * > &	ypos,
		std::vector< Value * > &	zpos,
		std::vector< Value * > &	masv,
		std::vector< Value * > &	chargev
	)

staticinherited

This gets std::vector that contain the PLMD::Value objects that contain xpositions, ypositions, zpositions, masses and charges.

◆ 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

◆ getConstPntrToComponent()

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

protectedinherited

Get a const pointer to the ith component.

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getDefaultString()

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

inlineinherited

Get the defaults.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ 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() [1/2]

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

protectedinherited

◆ getForce() [2/2]

Vector PLMD::ActionAtomistic::getForce ( const std::pair< std::size_t, std::size_t > & a ) const

inlineinherited

Get the force acting on a particular atom.

◆ getForcesToApply()

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

inlineprotectedinherited

Get the forces to apply.

◆ getGlobalPosition()

Vector PLMD::ActionAtomistic::getGlobalPosition ( const std::pair< std::size_t, std::size_t > & a ) 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.

◆ getGradient()

void PLMD::ActionAtomistic::getGradient	(	const unsigned &	ind,
		Vector &	deriv,
		std::map< AtomNumber, Vector > &	gradients
	)		const

inherited

Transfer the gradients.

◆ getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const

protectedinherited

Get the value of Boltzmann's constant.

◆ getkBT()

double PLMD::Action::getkBT ( )

inherited

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

◆ getKeyword()

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

inherited

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

◆ getLabel()

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

inlineinherited

Returns the label.

◆ getMass()

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

inlineinherited

Get mass of i-th atom.

◆ getMatrixColumnTitles()

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

virtualinherited

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

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

◆ getName()

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

inlineinherited

Returns the name.

◆ 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.

◆ getOutputComponentDescription()

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

virtualinherited

Get the description of this component.

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

◆ getOutputQuantity() [1/2]

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

inlineinherited

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

◆ getOutputQuantity() [2/2]

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

inlineinherited

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

◆ 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 ( )

inlineprotectedinherited

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 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

inherited

Get total number of atoms, including virtual ones.

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

◆ getUnique()

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

inlineinherited

◆ getUniqueLocal()

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

inlineinherited

◆ getUnits()

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

protectedinherited

Get the units that we are operating in.

◆ getValueIndices()

std::pair< std::size_t, std::size_t > PLMD::ActionAtomistic::getValueIndices ( const AtomNumber & i ) const

protectedinherited

Used to interpret whether this index is a virtual atom or a real atom.

◆ getVirial()

Tensor PLMD::ActionAtomistic::getVirial ( ) const

inherited

Get the virial that is acting.

◆ interpretAtomList() [1/2]

void PLMD::ActionAtomistic::interpretAtomList	(	std::vector< std::string > &	strings,
		const std::vector< Value * > &	xpos,
		Action *	action,
		std::vector< AtomNumber > &	t
	)

staticinherited

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

◆ interpretAtomList() [2/2]

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

inherited

Interpret the atom selection. Just a wrapper to the static function with four arguments called interpretAtomList that passes xpos and this.

◆ is_pbc_on()

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

inline

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isOptionOn()

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

inlineinherited

Check if an option is on.

◆ lockRequests()

void PLMD::ActionAtomistic::lockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, and PLMD::generic::PrintNDX.

◆ makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )

inherited

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

◆ modifyForceOnEnergy()

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

◆ 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()

virtual void PLMD::maze::Optimizer::optimize ( )

pure virtual

Optimal values needed for biasing are computed by methods overridding the optimize function.

Implemented in PLMD::maze::Simulated_Annealing, PLMD::maze::Random_Walk, PLMD::maze::Random_Acceleration_MD, PLMD::maze::Steered_MD, and PLMD::maze::Memetic.

◆ pairing()

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

virtual

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 ( )

inline

◆ pbc_on()

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

inline

◆ 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

inlineinherited

Compute the pbc distance between two positions.

◆ prepare()

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

virtual

Prepare the neighbor list.

Reimplemented from PLMD::Action.

◆ 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::Optimizer::registerKeywords ( Keywords & keys )

static

Registers PLMD keywords.

Parameters

[in] keys PLMD 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

◆ resetStoredTimestep()

void PLMD::Action::resetStoredTimestep ( )

inherited

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

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( const bool & force = false )

virtualinherited

Reimplemented in PLMD::ActionWithVector.

◆ 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.

◆ sampling_radius()

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

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 ( )

Score a ligand-protein configuration.

Returns: score

◆ set_label()

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

inline

◆ set_n_iterations()

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

inline

◆ set_n_threads_openmp()

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

inline

◆ set_nl_cutoff()

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

inline

◆ set_nl_stride()

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

inline

◆ set_opt()

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

inline

◆ set_opt_value()

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

inline

◆ set_optimizer_stride()

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

inline

◆ set_rank_openmp()

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

inline

◆ set_sampling_radius()

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

inline

◆ set_stride_openmp()

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

inline

◆ 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() [1/3]

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() [2/3]

void PLMD::Colvar::setBoxDerivativesNoPbc	(	const std::vector< Vector > &	pos,
		std::vector< std::vector< Vector > > &	derivs,
		std::vector< Tensor > &	virial
	)

staticinherited

◆ setBoxDerivativesNoPbc() [3/3]

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

protectedinherited

◆ setExtraCV()

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

protectedinherited

◆ setForcesOnAtoms()

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

inherited

Add the forces to the atoms.

◆ setForcesOnCell() [1/2]

void PLMD::ActionAtomistic::setForcesOnCell	(	const double *	forcesToApply,
		std::size_t	size,
		unsigned &	ind
	)

inherited

Add the virial forces (span-like syntax)

◆ setForcesOnCell() [2/2]

void PLMD::ActionAtomistic::setForcesOnCell	(	const std::vector< double > &	forcesToApply,
		unsigned &	ind
	)

inherited

Add the virial forces.

◆ setGlobalPosition()

void PLMD::ActionAtomistic::setGlobalPosition	(	const std::pair< std::size_t, std::size_t > &	a,
		const Vector &	pos
	)

inlineinherited

Modify 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.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

virtualinherited

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

Reimplemented in PLMD::ActionForInterface.

◆ 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.

◆ setupConstantValues()

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

inherited

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

◆ 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.

◆ start_step_0()

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

inline

◆ start_step_stride()

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

inline

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

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

◆ unlockRequests()

void PLMD::ActionAtomistic::unlockRequests ( )

inlineoverridevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::DumpAtoms, PLMD::ActionWithVector, and PLMD::generic::PrintNDX.

◆ 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::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::volumes::VolumeTetrapore, PLMD::volumes::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpPDB, PLMD::generic::DumpProjections, PLMD::generic::PrintNDX, PLMD::generic::Accumulate, PLMD::generic::Collect, PLMD::generic::DumpVector, PLMD::contour::DumpContour, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::mapping::PathReparameterization, and PLMD::mapping::PathDisplacements.

◆ update_nl()

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

Load new positions of atoms in the neighbor list.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal	(	const bool &	useunique,
		const std::vector< int > &	g2l
	)

privateinherited

◆ 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.

◆ usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const

protectedinherited

Are we using natural units.

◆ warning()

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

inherited

Issue a warning.

◆ writeInGraph()

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

virtualinherited

Get the info on what to calculate.

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

Member Data Documentation

◆ active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

◆ after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

◆ atom_value_ind

std::vector<std::pair<std::size_t, std::size_t > > PLMD::ActionAtomistic::atom_value_ind

privateinherited

◆ atom_value_ind_grouped

std::vector<std::pair<std::size_t,std::vector<std::size_t> > > PLMD::ActionAtomistic::atom_value_ind_grouped

privateinherited

◆ boxValue

Value* PLMD::ActionAtomistic::boxValue

privateinherited

◆ charges

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

privateinherited

◆ chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet

protectedinherited

◆ chargev

std::vector<Value*> PLMD::ActionAtomistic::chargev

privateinherited

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

◆ doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

◆ donotforce

bool PLMD::ActionAtomistic::donotforce

privateinherited

◆ donotretrieve

bool PLMD::ActionAtomistic::donotretrieve

privateinherited

◆ energy

double PLMD::ActionAtomistic::energy

privateinherited

◆ files

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

inherited

◆ first_step_

bool PLMD::maze::Optimizer::first_step_

protected

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

◆ first_time_

bool PLMD::maze::Optimizer::first_time_

private

◆ firststep

bool PLMD::ActionWithValue::firststep

privateinherited

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

◆ forceOnEnergy

double PLMD::ActionAtomistic::forceOnEnergy

privateinherited

◆ forceOnExtraCV

double PLMD::ActionAtomistic::forceOnExtraCV

privateinherited

◆ forces

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

privateinherited

◆ forcesForApply

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

privateinherited

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

◆ indexes

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

privateinherited

◆ 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_

protected

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.

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ loss_

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

private

Pointer to the loss function.

◆ masses

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

privateinherited

◆ massesWereSet

bool PLMD::ActionAtomistic::massesWereSet

protectedinherited

◆ masv

std::vector<Value*> PLMD::ActionAtomistic::masv

privateinherited

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ n_iter_

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

protected

Number of global iterations.

◆ n_threads_

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

protected

◆ name

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

privateinherited

Name of the directive in the plumed.dat file.

◆ neighbor_list_

std::unique_ptr<NeighborList> PLMD::maze::Optimizer::neighbor_list_

protected

Neighbor list of ligand-protein atom pairs.

◆ never_activate

bool PLMD::Action::never_activate

privateinherited

◆ nl_cutoff_

double PLMD::maze::Optimizer::nl_cutoff_

protected

Neighbor list cut-off.

◆ nl_stride_

int PLMD::maze::Optimizer::nl_stride_

protected

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_

protected

Biasing direction.

◆ opt_value_

double PLMD::maze::Optimizer::opt_value_

protected

Current loss function value.

◆ optimizer_stride_

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

protected

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_

protected

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_

protected

OpenMP.

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ sampling_r_

double PLMD::maze::Optimizer::sampling_r_

protected

Sampling radius.

◆ serial_

bool PLMD::maze::Optimizer::serial_

private

◆ stride_

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

protected

◆ timestep

double PLMD::Action::timestep

privateinherited

Save the timestep here.

◆ unique

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

privateinherited

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

◆ unique_local

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

privateinherited

◆ unique_local_needs_update

bool PLMD::ActionAtomistic::unique_local_needs_update

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_

private

◆ valsToForce

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

privateinherited

◆ value_action_

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

Loss value.

◆ value_depends

std::vector<std::size_t> PLMD::ActionAtomistic::value_depends

privateinherited

◆ value_sampling_radius_

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

Sampling radiues value.

◆ value_x_

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

Biased cv.

◆ value_y_

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

◆ value_z_

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

◆ 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_

private

◆ xpos

std::vector<Value*> PLMD::ActionAtomistic::xpos

privateinherited

Values that hold information about atom positions and charges.

◆ ypos

std::vector<Value*> PLMD::ActionAtomistic::ypos

privateinherited

◆ zpos

std::vector<Value*> PLMD::ActionAtomistic::zpos

privateinherited

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

maze/Optimizer.h
maze/Optimizer.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

◆ Optimizer()

◆ ~Optimizer()

Member Function Documentation

◆ actionHasForces()

◆ activate()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForce()

◆ addValue()

◆ addValueWithDerivatives()

◆ apply()

◆ beforeUpdate()

◆ calculate()

◆ calculateAtomicNumericalDerivatives()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ calculateOnUpdate()

◆ castToActionAtomistic()

◆ castToActionForInterface()

◆ castToActionShortcut()

◆ castToActionToGetData()

◆ castToActionToPutData()

◆ castToActionWithArguments()

◆ castToActionWithValue() [1/2]

◆ castToActionWithValue() [2/2]

◆ castToActionWithVirtualAtom()

◆ castToDomainDecomposition()

◆ castToPbcAction()

◆ center_of_mass()

◆ changeBox()

◆ checkFieldsAllowed()

◆ checkForDependency()

◆ checkForForces()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ doNotCalculateDerivatives()

◆ doNotForce()

◆ doNotRetrieve()

◆ error()

◆ exists()

◆ exit()

◆ fclose()

◆ fflush()

◆ fopen()

◆ get_label()

◆ get_n_iterations()

◆ get_n_threads_openmp()

◆ get_nl_cutofff()

◆ get_nl_stride()

◆ get_opt()

◆ get_opt_value()

◆ get_optimizer_stride()

◆ get_rank_openmp()

◆ get_sampling_radius()