Provides the keyword WHOLEMOLECULES More...

Inheritance diagram for PLMD::generic::WholeMolecules:

[legend]

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

Public Member Functions
	WholeMolecules (const ActionOptions &ao)

bool	actionHasForces () override

virtual void	activate ()
	Set action to active. 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	apply () override
	Apply an Action. More...

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

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

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

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

virtual ActionAtomistic *	castToActionAtomistic () noexcept

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...

virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept

virtual DomainDecomposition *	castToDomainDecomposition () noexcept

virtual PbcAction *	castToPbcAction () noexcept

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

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...

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	clearOptions ()

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

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...

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...

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...

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

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

int	getStride () const
	Get the stride. 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	isActive () const
	Check if action is active. More...

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

virtual void	lockRequests ()

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

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

void	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	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...

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

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

void	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...

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	setOption (const std::string &s)

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

virtual void	unlockRequests ()

void	unlockRequests () override

virtual void	update ()
	Update. 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	registerKeywords (Keywords &keys)

Public Attributes
Communicator &	comm

std::set< FILE * >	files

const Keywords &	keywords

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

Communicator &	multi_sim_comm

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

Protected Member Functions
double	getKBoltzmann () const
	Get the value of Boltzmann's constant. 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	setExtraCV (const std::string &name)

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

Protected Attributes
bool	chargesWereSet

bool	massesWereSet

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

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

bool	addref

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	doemst

bool	donotforce

bool	donotretrieve

double	energy

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

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

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

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

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

Pbc &	pbc =*pbc_fwd

ForwardDecl< Pbc >	pbc_fwd

std::vector< Vector >	positions

std::vector< Vector >	refs

int	replica_index

bool	restart

int	stride

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...

std::vector< std::size_t >	value_depends

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

std::vector< Value * >	ypos

std::vector< Value * >	zpos

Detailed Description

Provides the keyword WHOLEMOLECULES

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ WholeMolecules()

PLMD::generic::WholeMolecules::WholeMolecules ( const ActionOptions & ao )

explicit

Member Function Documentation

◆ actionHasForces()

bool PLMD::generic::WholeMolecules::actionHasForces ( )

inlineoverridevirtual

Reimplemented from PLMD::ActionAtomistic.

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ 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.

◆ apply()

void PLMD::generic::WholeMolecules::apply ( )

inlineoverridevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ 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::generic::WholeMolecules::calculate ( )

overridevirtual

Calculate an Action.

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

Implements PLMD::Action.

◆ 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() [1/2]

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

virtualinherited

Perform calculation using numerical derivatives N.B.

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

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

◆ calculateNumericalDerivatives() [2/2]

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.

◆ castToActionAtomistic() [1/2]

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

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionAtomistic.

◆ castToActionAtomistic() [2/2]

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()

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

inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

◆ 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.

◆ changeBox()

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

inherited

Change the box shape.

◆ checkForDependency()

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

inherited

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

◆ 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()

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

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

inherited

Cite a paper see PlumedMain::cite.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ 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.

◆ 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)

◆ 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.

◆ getCharge()

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

inlineinherited

Get charge of i-th atom.

◆ 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()

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

inlineinherited

Get the force acting on a particular atom.

◆ 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.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

◆ getPbc()

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

inlineinherited

Get reference to Pbc.

◆ 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.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ 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.

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isOptionOn()

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

inlineinherited

Check if an option is on.

◆ lockRequests() [1/2]

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

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

◆ lockRequests() [2/2]

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.

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ 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.

◆ 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::Action::prepare ( )

virtualinherited

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

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

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

◆ readAtomsFromPDB() [1/2]

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

inlinevirtualinherited

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

Reimplemented in PLMD::ActionAtomistic.

◆ readAtomsFromPDB() [2/2]

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::generic::WholeMolecules::registerKeywords ( Keywords & keys )

static

◆ requestAtoms()

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.

◆ 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.

◆ setOption()

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

virtualinherited

◆ setStride()

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

inherited

Set the value of the stride.

◆ 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.

◆ unlockRequests() [1/2]

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

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

◆ unlockRequests() [2/2]

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.

◆ updateUniqueLocal()

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

privateinherited

◆ 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.

◆ addref

bool PLMD::generic::WholeMolecules::addref

private

◆ 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

◆ doemst

bool PLMD::generic::WholeMolecules::doemst

private

◆ 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

◆ 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

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ label

std::string PLMD::Action::label

privateinherited

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

◆ line

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

privateinherited

Directive line.

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

◆ lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms

privateinherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ 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

◆ name

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

privateinherited

Name of the directive in the plumed.dat file.

◆ never_activate

bool PLMD::Action::never_activate

privateinherited

◆ options

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

privateinherited

Option that you might have enabled.

◆ p_groups

std::vector<std::vector<std::pair<std::size_t,std::size_t> > > PLMD::generic::WholeMolecules::p_groups

private

◆ p_roots

std::vector<std::vector<std::pair<std::size_t,std::size_t> > > PLMD::generic::WholeMolecules::p_roots

private

◆ pbc

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

privateinherited

◆ 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

◆ refs

std::vector<Vector> PLMD::generic::WholeMolecules::refs

private

◆ replica_index

int PLMD::Action::replica_index

privateinherited

◆ restart

bool PLMD::Action::restart

privateinherited

◆ stride

int PLMD::ActionPilot::stride

privateinherited

◆ 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.

◆ value_depends

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

privateinherited

◆ 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 file:

generic/WholeMolecules.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

◆ WholeMolecules()

Member Function Documentation

◆ actionHasForces()

◆ activate()

◆ addDependency()

◆ addForce()

◆ apply()

◆ beforeUpdate()

◆ calculate()

◆ calculateAtomicNumericalDerivatives()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives() [1/2]

◆ calculateNumericalDerivatives() [2/2]

◆ castToActionAtomistic() [1/2]

◆ castToActionAtomistic() [2/2]

◆ castToActionForInterface()

◆ castToActionShortcut()

◆ castToActionToGetData()

◆ castToActionToPutData()

◆ castToActionWithArguments()

◆ castToActionWithValue()

◆ castToActionWithVirtualAtom()

◆ castToDomainDecomposition()

◆ castToPbcAction()

◆ changeBox()

◆ checkForDependency()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives()

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearDependencies()

◆ clearOptions()

◆ deactivate()

◆ doNotForce()

◆ doNotRetrieve()

◆ error()

◆ exit()

◆ fclose()

◆ fflush()

◆ fopen()

◆ getAbsoluteIndex()

◆ getAbsoluteIndexes()

◆ getAtomValuesFromPlumedObject()

◆ getBox()

◆ getCharge()

◆ getCPT()

◆ getDefaultString()

◆ getDependencies()

◆ getEnergy()

◆ getExchangeStep()

◆ getForce()

◆ getGlobalPosition()

◆ getGradient()

◆ getKBoltzmann()

◆ getkBT()

◆ getKeyword()

◆ getLabel()

◆ getMass()

◆ getName()

◆ getNumberOfAtoms()

◆ getPbc()

◆ getPosition()

◆ getPositions()

◆ getRestart()

◆ getStep()

◆ getStride()

◆ getTime()