Provides the keyword NLINKS More...

Inheritance diagram for PLMD::multicolvar::NumberOfLinks:

[legend]

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

typedef std::set< FILE * >::iterator	files_iterator

Public Member Functions
	NumberOfLinks (const ActionOptions &)

void	calculateWeight (AtomValuePack &myatoms) const
	Do the stuff with the switching functions. More...

double	compute (const unsigned &tindex, AtomValuePack &myatoms) const
	Actually do the calculation. More...

bool	isPeriodic ()
	Is the variable periodic. More...

virtual void	updateActiveAtoms (AtomValuePack &myatoms) const
	Update the atoms that are active. More...

void	calculate ()
	Regular calculate. More...

void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Calculate the numerical derivatives for this action. More...

Vector	getPositionOfAtomForLinkCells (const unsigned &iatom) const
	This is used in MultiColvarBase only - it is used to setup the link cells. More...

virtual bool	isCurrentlyActive (const unsigned &bno, const unsigned &code)
	Some things can be inactive in functions. More...

virtual void	turnOnDerivatives ()
	Turn on the derivatives. More...

bool	usesPbc () const
	Do we use pbc to calculate this quantity. More...

void	applyPbc (std::vector< Vector > &dlist, unsigned max_index=0) const
	Apply PBCs over a set of distance vectors. More...

virtual void	performTask (const unsigned &, const unsigned &, MultiValue &) const
	Prepare for the calculation Perform one of the tasks. More...

virtual double	doCalculation (const unsigned &tindex, AtomValuePack &myatoms) const
	And a virtual function which actually computes the colvar. More...

virtual void	apply ()
	Apply the forces from this action. More...

virtual unsigned	getNumberOfDerivatives ()
	Get the number of derivatives for this action. More...

virtual CatomPack	getCentralAtomPack (const unsigned &basn, const unsigned &curr)

virtual Vector	getCentralAtomPos (const unsigned &curr)
	Get the index where the central atom is stored. More...

virtual bool	isDensity () const
	Get the list of indices that have derivatives. More...

bool	storedValueIsActive (const unsigned &iatom)
	Store central atoms so that this can be used in a function. More...

virtual bool	hasDifferentiableOrientation () const
	This is true if multicolvar is calculating a vector or if the multicolvar is the density. More...

virtual void	doNotCalculateDirector ()
	This makes sure we are not calculating the director when we do LocalAverage. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
	Parse a list of atoms without a numbered keyword. 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	changeBox (const Tensor &newbox)
	Change the box shape. More...

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

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

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

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

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

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

void	clearOutputForces ()

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

void	retrieveAtoms ()

void	applyForces ()

void	lockRequests ()

void	unlockRequests ()

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual void	update ()
	Update. More...

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

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

virtual std::string	getDocumentation () const

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

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

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

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

virtual void	clearOptions ()

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual void	checkFieldsAllowed ()

void	unlockContributors ()

void	lockContributors ()

virtual void	finishTaskListUpdate ()

virtual void	deactivate_task (const unsigned &task_index)
	Activate the jth colvar Deactivate the current task in future loops. More...

bool	derivativesAreRequired () const
	Are derivatives required for this quantity. More...

virtual void	finishComputations (const std::vector< double > &buffer)
	Finish running all the calculations. More...

virtual void	retrieveDomain (std::string &min, std::string &max)
	What are the domains of the base quantities. More...

virtual unsigned	getNumberOfQuantities ()
	Get the number of quantities that are calculated during each task. More...

void	activateTheseTasks (std::vector< unsigned > &addtionalTasks)
	Get the list of indices that have derivatives. More...

virtual void	doJobsRequiredBeforeTaskList ()
	Do any jobs that are required before the task list is undertaken. More...

unsigned	getFullNumberOfTasks () const
	Get the full size of the taskList dynamic list. More...

unsigned	getPositionInFullTaskList (const unsigned &ii) const
	Get the position of the ith active task in the full list. More...

unsigned	getTaskCode (const unsigned &ii) const
	Get the code for the ii th task in the list. More...

virtual void	transformBridgedDerivatives (const unsigned &current, MultiValue &invals, MultiValue &outvals) const
	Do the task if we have a bridge. More...

StoreDataVessel *	buildDataStashes (const bool &allow_wcutoff, const double &wtol)
	Ensure that data required in other vessels is stored. More...

virtual void	applyBridgeForces (const std::vector< double > &bb)
	Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. More...

Vessel *	getVesselWithName (const std::string &mynam)
	These are overwritten in MultiColvarFunction. More...

bool	weightWithDerivatives () const
	Does the weight have derivatives. More...

Static Public Member Functions
static void	registerKeywords (Keywords &keys)

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

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

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

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

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

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

Protected Member Functions
unsigned	getFullNumberOfBaseTasks () const
	Get the total number of tasks that this calculation is based on. More...

CatomPack	getCentralAtomPackFromInput (const unsigned &ind) const
	Get the derivatives for the central atom with index ind. More...

void	getVectorForTask (const unsigned &ind, const bool &normed, std::vector< double > &orient0) const

void	getVectorDerivatives (const unsigned &ind, const bool &normed, MultiValue &myder0) const

void	mergeVectorDerivatives (const unsigned &ival, const unsigned &start, const unsigned &end, const unsigned &jatom, const std::vector< double > &der, MultiValue &myder, AtomValuePack &myatoms) const

unsigned	convertToLocalIndex (const unsigned &index, const unsigned &mcv_code) const
	Convert an index in the global array to an index in the individual base colvars. More...

void	buildSets ()
	Build sets by taking one multicolvar from each base. More...

void	buildSymmetryFunctionLists ()
	Build colvars for atoms as if they were symmetry functions. More...

void	buildAtomListWithPairs (const bool &allow_intra_group)
	Build a colvar for each pair of atoms. More...

unsigned	getNumberOfBaseMultiColvars () const
	Get the number of base multicolvars. More...

MultiColvarBase *	getBaseMultiColvar (const unsigned &icolv) const
	Get an example of the underlying multicolvar. More...

unsigned	getBaseColvarNumber (const unsigned &iatom) const
	Return the base multicolvar index that this colvar is a part of. More...

void	addTaskToList (const unsigned &taskCode)
	Add a task to the list of tasks. More...

void	setupMultiColvarBase ()
	Finish setting up the multicolvar base. More...

void	setAtomsForCentralAtom (const std::vector< bool > &catom_ind)
	Set which atoms are to be used to calculate the central atom position. More...

void	setLinkCellCutoff (const double &lcut)
	Set the value of the cutoff for the link cells. More...

void	setupLinkCells ()
	Setup link cells in order to make this calculation faster. More...

Vector	getSeparation (const Vector &vec1, const Vector &vec2) const
	Get the separation between a pair of vectors. More...

bool	setupCurrentAtomList (const unsigned &taskCode, AtomValuePack &myatoms) const
	This sets up the list of atoms that are involved in this colvar. More...

void	decodeIndexToAtoms (const unsigned &taskCode, std::vector< unsigned > &atoms) const
	Decode indices if there are 2 or 3 atoms involved. More...

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

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

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

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

void	addVessel (const std::string &name, const std::string &input, const int numlab=0)
	Add a vessel to the list of vessels. More...

void	addVessel (Vessel *vv)

BridgeVessel *	addBridgingVessel (ActionWithVessel *tome)
	Add a bridging vessel to the list of vessels. More...

void	readVesselKeywords ()
	Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...

void	needsDerivatives ()
	Turn on the derivatives in the vessel. More...

double	getTolerance () const
	Return the value of the tolerance. More...

double	getNLTolerance () const
	Return the value for the neighbor list tolerance. More...

unsigned	getNumberOfVessels () const
	Get the number of vessels. More...

Vessel *	getPntrToVessel (const unsigned &i)
	Get a pointer to the ith vessel. More...

void	runAllTasks ()
	Calculate the values of all the vessels. More...

void	resizeFunctions ()
	Resize all the functions when the number of derivatives change. More...

bool	calculateAllVessels (const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)
	This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More...

bool	getForcesFromVessels (std::vector< double > &forcesToApply)
	Retrieve the forces from all the vessels (used in apply) More...

bool	serialCalculation () const
	Is the calculation being done in serial. More...

bool	usingLowMem () const
	Are we using low memory. More...

void	setLowMemOption (const bool &)
	Set that we are using low memory. More...

unsigned	getCurrentNumberOfActiveTasks () const
	Get the number of tasks that are currently active. More...

unsigned	getActiveTask (const unsigned &ii) const
	Get the ith of the currently active tasks. More...

void	deactivateAllTasks ()
	Deactivate all the tasks in the task list. More...

void	deactivateTasksInRange (const unsigned &lower, const unsigned &upper)
	Deactivate all tasks with i in lower \(\le\) i < upper. More...

unsigned	getSizeOfBuffer (unsigned &bufsize)
	Get the size of the buffer. More...

Protected Attributes
bool	usespecies
	Using the species keyword to read in atoms. More...

unsigned	nblock
	Number of atoms in each block. More...

std::vector< unsigned >	decoder
	This is used when turning cvcodes into atom numbers. More...

std::vector< std::vector< unsigned > >	ablocks
	Blocks of atom numbers. More...

Atoms &	atoms

bool	contributorsAreUnlocked
	The terms in the series are locked. More...

bool	weightHasDerivatives
	Does the weight have derivatives. More...

unsigned	bridgeVariable
	This is used for numerical derivatives of bridge variables. More...

Private Attributes
std::vector< double >	orient0
	The values of the quantities in the dot products. More...

std::vector< double >	orient1

SwitchingFunction	switchingFunction
	The switching function that tells us if atoms are close enough together. More...

Detailed Description

Provides the keyword NLINKS

Member Typedef Documentation

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

inherited

typedef std::set<FILE*>::iterator PLMD::Action::files_iterator

inherited

Constructor & Destructor Documentation

PLMD::multicolvar::NumberOfLinks::NumberOfLinks ( const ActionOptions & ao )

explicit

Member Function Documentation

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

void PLMD::vesselbase::ActionWithVessel::activateTheseTasks ( std::vector< unsigned > & addtionalTasks )

inherited

Get the list of indices that have derivatives.

Switch on additional tasks

BridgeVessel * PLMD::vesselbase::ActionWithVessel::addBridgingVessel ( ActionWithVessel * tome )

protectedinherited

Add a bridging vessel to the list of vessels.

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

inherited

Add a value with a name like label.name.

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

inherited

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

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

inherited

Specify that this Action depends on another one.

void PLMD::multicolvar::MultiColvarBase::addTaskToList ( const unsigned & taskCode )

protectedinherited

Add a task to the list of tasks.

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

void PLMD::vesselbase::ActionWithVessel::addVessel	(	const std::string &	name,
		const std::string &	input,
		const int	numlab = `0`
	)

protectedinherited

Add a vessel to the list of vessels.

void PLMD::vesselbase::ActionWithVessel::addVessel ( Vessel * vv )

protectedinherited

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )

inlineinherited

Allow calls to modifyGlobalForce()

void PLMD::multicolvar::MultiColvarBase::apply ( )

virtualinherited

Apply the forces from this action.

Implements PLMD::Action.

Reimplemented in PLMD::multicolvar::Sprint, and PLMD::multicolvar::BridgedMultiColvarFunction.

virtual void PLMD::vesselbase::ActionWithVessel::applyBridgeForces ( const std::vector< double > & bb )

inlinevirtualinherited

Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.

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

void ActionAtomistic::applyForces ( )

inherited

void PLMD::multicolvar::MultiColvarBase::applyPbc	(	std::vector< Vector > &	dlist,
		unsigned	max_index = `0`
	)		const

inherited

Apply PBCs over a set of distance vectors.

void PLMD::multicolvar::MultiColvarFunction::buildAtomListWithPairs ( const bool & allow_intra_group )

protectedinherited

Build a colvar for each pair of atoms.

StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes	(	const bool &	allow_wcutoff,
		const double &	wtol
	)

inherited

Ensure that data required in other vessels is stored.

void PLMD::multicolvar::MultiColvarFunction::buildSets ( )

protectedinherited

Build sets by taking one multicolvar from each base.

void PLMD::multicolvar::MultiColvarFunction::buildSymmetryFunctionLists ( )

protectedinherited

Build colvars for atoms as if they were symmetry functions.

void PLMD::multicolvar::MultiColvarFunction::calculate ( )

virtualinherited

Regular calculate.

Implements PLMD::Action.

bool PLMD::vesselbase::ActionWithVessel::calculateAllVessels	(	const unsigned &	taskCode,
		MultiValue &	myvals,
		MultiValue &	bvals,
		std::vector< double > &	buffer,
		std::vector< unsigned > &	der_list
	)

protectedinherited

This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.

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

inherited

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

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

void PLMD::multicolvar::MultiColvarFunction::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtualinherited

Calculate the numerical derivatives for this action.

Reimplemented from PLMD::ActionAtomistic.

void PLMD::multicolvar::NumberOfLinks::calculateWeight ( AtomValuePack & myatoms ) const

virtual

Do the stuff with the switching functions.

Reimplemented from PLMD::multicolvar::MultiColvarBase.

void ActionAtomistic::changeBox ( const Tensor & newbox )

inherited

Change the box shape.

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap.

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

inlinevirtualinherited

Check if the action needs gradient.

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

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

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

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

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

inherited

Cite a paper see PlumedMain::cite.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

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

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

void PLMD::Action::clearOptions ( )

virtualinherited

void ActionAtomistic::clearOutputForces ( )

inherited

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

inherited

Set your value component to have no periodicity.

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.

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

staticinherited

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

double PLMD::multicolvar::NumberOfLinks::compute	(	const unsigned &	tindex,
		AtomValuePack &	myatoms
	)		const

virtual

Actually do the calculation.

Implements PLMD::multicolvar::MultiColvarBase.

unsigned PLMD::multicolvar::MultiColvarFunction::convertToLocalIndex	(	const unsigned &	index,
		const unsigned &	mcv_code
	)		const

inlineprotectedinherited

Convert an index in the global array to an index in the individual base colvars.

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.

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.

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

void PLMD::vesselbase::ActionWithVessel::deactivate_task ( const unsigned & task_index )

virtualinherited

Activate the jth colvar Deactivate the current task in future loops.

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

void PLMD::vesselbase::ActionWithVessel::deactivateAllTasks ( )

protectedinherited

Deactivate all the tasks in the task list.

void PLMD::vesselbase::ActionWithVessel::deactivateTasksInRange	(	const unsigned &	lower,
		const unsigned &	upper
	)

protectedinherited

Deactivate all tasks with i in lower \(\le\) i < upper.

void PLMD::multicolvar::MultiColvarBase::decodeIndexToAtoms	(	const unsigned &	taskCode,
		std::vector< unsigned > &	atoms
	)		const

protectedinherited

Decode indices if there are 2 or 3 atoms involved.

bool PLMD::vesselbase::ActionWithVessel::derivativesAreRequired ( ) const

inlineinherited

Are derivatives required for this quantity.

double PLMD::multicolvar::MultiColvarBase::doCalculation	(	const unsigned &	tindex,
		AtomValuePack &	myatoms
	)		const

virtualinherited

And a virtual function which actually computes the colvar.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

void PLMD::vesselbase::ActionWithVessel::doJobsRequiredBeforeTaskList ( )

virtualinherited

Do any jobs that are required before the task list is undertaken.

Reimplemented in PLMD::multicolvar::AdjacencyMatrixAction, PLMD::manyrestraints::ManyRestraintsBase, PLMD::multicolvar::VolumeGradientBase, and PLMD::multicolvar::MultiColvarFilter.

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlineinherited

Are we not calculating derivatives.

virtual void PLMD::multicolvar::MultiColvarBase::doNotCalculateDirector ( )

inlinevirtualinherited

This makes sure we are not calculating the director when we do LocalAverage.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

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.

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.

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

inherited

Crash calculation and print documentation.

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.

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

inherited

Exit with error code c.

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

inherited

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

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

void PLMD::vesselbase::ActionWithVessel::finishComputations ( const std::vector< double > & buffer )

virtualinherited

Finish running all the calculations.

virtual void PLMD::vesselbase::ActionWithVessel::finishTaskListUpdate ( )

inlinevirtualinherited

Reimplemented in PLMD::secondarystructure::SecondaryStructureRMSD.

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)

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

inlineinherited

Get the absolute index of an atom.

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

inlineinherited

Get the vector of absolute indexes.

unsigned PLMD::vesselbase::ActionWithVessel::getActiveTask ( const unsigned & ii ) const

inlineprotectedinherited

Get the ith of the currently active tasks.

unsigned PLMD::multicolvar::MultiColvarFunction::getBaseColvarNumber ( const unsigned & iatom ) const

inlineprotectedinherited

Return the base multicolvar index that this colvar is a part of.

MultiColvarBase * PLMD::multicolvar::MultiColvarFunction::getBaseMultiColvar ( const unsigned & icolv ) const

inlineprotectedinherited

Get an example of the underlying multicolvar.

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

inlineinherited

Get box shape.

CatomPack PLMD::multicolvar::MultiColvarBase::getCentralAtomPack	(	const unsigned &	basn,
		const unsigned &	curr
	)

virtualinherited

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

CatomPack PLMD::multicolvar::MultiColvarFunction::getCentralAtomPackFromInput ( const unsigned & ind ) const

inlineprotectedinherited

Get the derivatives for the central atom with index ind.

Vector PLMD::multicolvar::MultiColvarBase::getCentralAtomPos ( const unsigned & curr )

virtualinherited

Get the index where the central atom is stored.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

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

inlineinherited

Get charge of i-th atom.

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

inherited

get a string that contains all the available components

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

inherited

get a vector that contains the label for all the components

unsigned PLMD::vesselbase::ActionWithVessel::getCurrentNumberOfActiveTasks ( ) const

inlineprotectedinherited

Get the number of tasks that are currently active.

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

inlineinherited

Return dependencies.

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

virtualinherited

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

inlineinherited

Get energy.

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

bool PLMD::vesselbase::ActionWithVessel::getForcesFromVessels ( std::vector< double > & forcesToApply )

protectedinherited

Retrieve the forces from all the vessels (used in apply)

unsigned PLMD::multicolvar::MultiColvarFunction::getFullNumberOfBaseTasks ( ) const

inlineprotectedinherited

Get the total number of tasks that this calculation is based on.

unsigned PLMD::vesselbase::ActionWithVessel::getFullNumberOfTasks ( ) const

inlineinherited

Get the full size of the taskList dynamic list.

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

inlineinherited

Returns the label.

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

inlineinherited

Get mass of i-th atom.

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

inlineinherited

Returns the name.

double PLMD::vesselbase::ActionWithVessel::getNLTolerance ( ) const

inlineprotectedinherited

Return the value for the neighbor list tolerance.

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

unsigned PLMD::multicolvar::MultiColvarFunction::getNumberOfBaseMultiColvars ( ) const

inlineprotectedinherited

Get the number of base multicolvars.

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

unsigned PLMD::multicolvar::MultiColvarBase::getNumberOfDerivatives ( )

inlinevirtualinherited

Get the number of derivatives for this action.

Implements PLMD::ActionWithValue.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfQuantities ( )

inlinevirtualinherited

Get the number of quantities that are calculated during each task.

Reimplemented in PLMD::multicolvar::LocalAverage, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::crystallization::VectorMultiColvar, PLMD::crystallization::DFSClustering, PLMD::multicolvar::ActionVolume, PLMD::crystallisation::Gradient, and PLMD::multicolvar::MultiColvarFilter.

unsigned PLMD::vesselbase::ActionWithVessel::getNumberOfVessels ( ) const

inlineprotectedinherited

Get the number of vessels.

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

inlineinherited

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

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)

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

inlineinherited

Get reference to Pbc.

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

protectedinherited

Return a pointer to the component by index.

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

protectedinherited

Return a pointer to the value by name.

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

Vessel * PLMD::vesselbase::ActionWithVessel::getPntrToVessel ( const unsigned & i )

inlineprotectedinherited

Get a pointer to the ith vessel.

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

inlineinherited

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

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

inlineinherited

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

With direct access to the global atom array

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInFullTaskList ( const unsigned & ii ) const

inlineinherited

Get the position of the ith active task in the full list.

Vector PLMD::multicolvar::MultiColvarFunction::getPositionOfAtomForLinkCells ( const unsigned & iatom ) const

inlinevirtualinherited

This is used in MultiColvarBase only - it is used to setup the link cells.

Implements PLMD::multicolvar::MultiColvarBase.

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

inlineinherited

Get the array of all positions.

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

Vector PLMD::multicolvar::MultiColvarBase::getSeparation	(	const Vector &	vec1,
		const Vector &	vec2
	)		const

protectedinherited

Get the separation between a pair of vectors.

unsigned PLMD::vesselbase::ActionWithVessel::getSizeOfBuffer ( unsigned & bufsize )

protectedinherited

Get the size of the buffer.

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

inherited

Return the present timestep.

unsigned PLMD::vesselbase::ActionWithVessel::getTaskCode ( const unsigned & ii ) const

inlineinherited

Get the code for the ii th task in the list.

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

double PLMD::vesselbase::ActionWithVessel::getTolerance ( ) const

inlineprotectedinherited

Return the value of the tolerance.

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inlineinherited

Get total number of atoms, including virtual ones.

Can be used to make a loop on modifyPosition or getPosition(AtomNumber)

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

inlineinherited

void PLMD::multicolvar::MultiColvarFunction::getVectorDerivatives	(	const unsigned &	ind,
		const bool &	normed,
		MultiValue &	myder0
	)		const

protectedinherited

void PLMD::multicolvar::MultiColvarFunction::getVectorForTask	(	const unsigned &	ind,
		const bool &	normed,
		std::vector< double > &	orient0
	)		const

inlineprotectedinherited

Vessel * PLMD::vesselbase::ActionWithVessel::getVesselWithName ( const std::string & mynam )

inherited

These are overwritten in MultiColvarFunction.

Return a particular named vessel

virtual bool PLMD::multicolvar::MultiColvarBase::hasDifferentiableOrientation ( ) const

inlinevirtualinherited

This is true if multicolvar is calculating a vector or if the multicolvar is the density.

Reimplemented in PLMD::crystallization::VectorMultiColvar, and PLMD::multicolvar::Density.

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

bool PLMD::multicolvar::MultiColvarFunction::isCurrentlyActive	(	const unsigned &	bno,
		const unsigned &	code
	)

inlinevirtualinherited

Some things can be inactive in functions.

Implements PLMD::multicolvar::MultiColvarBase.

virtual bool PLMD::multicolvar::MultiColvarBase::isDensity ( ) const

inlinevirtualinherited

Get the list of indices that have derivatives.

Is this a density?

Reimplemented in PLMD::multicolvar::Density.

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

inlineinherited

Check if an option is on.

bool PLMD::multicolvar::NumberOfLinks::isPeriodic ( )

inlinevirtual

Is the variable periodic.

Implements PLMD::vesselbase::ActionWithVessel.

void PLMD::vesselbase::ActionWithVessel::lockContributors ( )

inherited

void PLMD::ActionAtomistic::lockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::PCAVars, and PLMD::mapping::Mapping.

void ActionAtomistic::makeWhole ( )

inherited

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

void PLMD::multicolvar::MultiColvarFunction::mergeVectorDerivatives	(	const unsigned &	ival,
		const unsigned &	start,
		const unsigned &	end,
		const unsigned &	jatom,
		const std::vector< double > &	der,
		MultiValue &	myder,
		AtomValuePack &	myatoms
	)		const

protectedinherited

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

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

inlineinherited

Get a reference to forces array.

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

inlineinherited

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

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

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inlineinherited

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

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

inlineinherited

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

Should be used by action that need to modify the stored atomic coordinates

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

void PLMD::vesselbase::ActionWithVessel::needsDerivatives ( )

protectedinherited

Turn on the derivatives in the vessel.

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.

template<class T >

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

inherited

Parse one keyword as generic type.

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

inherited

Parse a list of atoms without a numbered keyword.

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

inherited

Parse an list of atom with a numbred keyword.

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

inherited

Parse one keyword as boolean flag.

template<class T >

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

inherited

Parse one numbered keyword as generic type.

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.

template<class T >

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

inherited

Parse one keyword as std::vector.

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

inherited

Applies PBCs to a seriens of positions or distances.

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

inherited

Compute the pbc distance between two positions.

void PLMD::multicolvar::MultiColvarBase::performTask	(	const unsigned &	task_index,
		const unsigned &	current,
		MultiValue &	myvals
	)		const

virtualinherited

Prepare for the calculation Perform one of the tasks.

Implements PLMD::vesselbase::ActionWithVessel.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

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::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::mapping::Mapping, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::Read, PLMD::generic::Print, PLMD::colvar::Energy, and PLMD::colvar::CoordinationBase.

void ActionAtomistic::readAtomsFromPDB ( const PDB & pdb )

virtualinherited

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

Reimplemented from PLMD::Action.

void PLMD::vesselbase::ActionWithVessel::readVesselKeywords ( )

protectedinherited

Complete the setup of this object (this routine must be called after construction of ActionWithValue)

void PLMD::multicolvar::NumberOfLinks::registerKeywords ( Keywords & keys )

static

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

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

void PLMD::vesselbase::ActionWithVessel::resizeFunctions ( )

protectedinherited

Resize all the functions when the number of derivatives change.

void ActionAtomistic::retrieveAtoms ( )

inherited

void PLMD::vesselbase::ActionWithVessel::retrieveDomain	(	std::string &	min,
		std::string &	max
	)

virtualinherited

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::Torsions.

void PLMD::vesselbase::ActionWithVessel::runAllTasks ( )

protectedinherited

Calculate the values of all the vessels.

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

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

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

Reimplemented in PLMD::analysis::Analysis.

bool PLMD::vesselbase::ActionWithVessel::serialCalculation ( ) const

inlineprotectedinherited

Is the calculation being done in serial.

void PLMD::multicolvar::MultiColvarBase::setAtomsForCentralAtom ( const std::vector< bool > & catom_ind )

protectedinherited

Set which atoms are to be used to calculate the central atom position.

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

inherited

Add the forces to the atoms.

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

void PLMD::multicolvar::MultiColvarBase::setLinkCellCutoff ( const double & lcut )

protectedinherited

Set the value of the cutoff for the link cells.

void PLMD::vesselbase::ActionWithVessel::setLowMemOption ( const bool & l )

inlineprotectedinherited

Set that we are using low memory.

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

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

virtualinherited

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

inherited

Set the value to be periodic with a particular domain.

bool PLMD::multicolvar::MultiColvarBase::setupCurrentAtomList	(	const unsigned &	taskCode,
		AtomValuePack &	myatoms
	)		const

protectedinherited

This sets up the list of atoms that are involved in this colvar.

void PLMD::multicolvar::MultiColvarBase::setupLinkCells ( )

protectedinherited

Setup link cells in order to make this calculation faster.

void PLMD::multicolvar::MultiColvarBase::setupMultiColvarBase ( )

protectedinherited

Finish setting up the multicolvar base.

void PLMD::ActionWithValue::setValue ( const double & d )

inlineprotectedinherited

Set the default value (the one without name)

void PLMD::ActionWithValue::setValue	(	Value *	,
		double
	)

inherited

Set the value.

bool PLMD::multicolvar::MultiColvarBase::storedValueIsActive ( const unsigned & iatom )

inherited

Store central atoms so that this can be used in a function.

Calculate and store getElementValue(uder)/getElementValue(vder) and its derivatives in getElementValue(iout) Activate the atoms that have derivatives from a storeDataVessel Add central atom derivatives to a multicolvar function Get the value for this task Used to accumulate values Used for calculating weighted averages Add derivatives to the orientations Is the iatom'th stored value currently active

void PLMD::vesselbase::ActionWithVessel::transformBridgedDerivatives	(	const unsigned &	current,
		MultiValue &	invals,
		MultiValue &	outvals
	)		const

virtualinherited

Do the task if we have a bridge.

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

void PLMD::multicolvar::MultiColvarBase::turnOnDerivatives ( )

virtualinherited

Turn on the derivatives.

Reimplemented from PLMD::ActionWithValue.

Reimplemented in PLMD::crystallization::DFSClustering, and PLMD::crystallization::DFSClusterDiameter.

void PLMD::vesselbase::ActionWithVessel::unlockContributors ( )

inherited

void PLMD::ActionAtomistic::unlockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::PCAVars, and PLMD::mapping::Mapping.

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::bias::PBMetaD, PLMD::analysis::Analysis, PLMD::bias::ExtendedLagrangian, PLMD::multicolvar::VolumeCavity, PLMD::generic::DumpAtoms, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::DumpMassCharge, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvarDensity, PLMD::generic::Print, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::multicolvar::VolumeTetrapore, and PLMD::generic::DumpProjections.

void PLMD::multicolvar::MultiColvarFunction::updateActiveAtoms ( AtomValuePack & myatoms ) const

virtualinherited

Update the atoms that are active.

Implements PLMD::multicolvar::MultiColvarBase.

Reimplemented in PLMD::crystallization::DFSClustering.

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

staticinherited

The components in the action will depend on the user.

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

bool PLMD::multicolvar::MultiColvarBase::usesPbc ( ) const

inlineinherited

Do we use pbc to calculate this quantity.

bool PLMD::vesselbase::ActionWithVessel::usingLowMem ( ) const

inlineprotectedinherited

Are we using low memory.

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

inherited

Issue a warning.

bool PLMD::vesselbase::ActionWithVessel::weightWithDerivatives ( ) const

inlineinherited

Does the weight have derivatives.

Member Data Documentation

std::vector< std::vector<unsigned> > PLMD::multicolvar::MultiColvarBase::ablocks

protectedinherited

Blocks of atom numbers.

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protectedinherited

This is used for numerical derivatives of bridge variables.

Communicator& PLMD::Action::comm

inherited

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protectedinherited

The terms in the series are locked.

std::vector<unsigned> PLMD::multicolvar::MultiColvarBase::decoder

protectedinherited

This is used when turning cvcodes into atom numbers.

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

inherited

const Keywords& PLMD::Action::keywords

inherited

Log& PLMD::Action::log

inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm

inherited

unsigned PLMD::multicolvar::MultiColvarBase::nblock

protectedinherited

Number of atoms in each block.

std::vector<double> PLMD::multicolvar::NumberOfLinks::orient0

private

The values of the quantities in the dot products.

std::vector<double> PLMD::multicolvar::NumberOfLinks::orient1

private

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

SwitchingFunction PLMD::multicolvar::NumberOfLinks::switchingFunction

private

The switching function that tells us if atoms are close enough together.

bool PLMD::multicolvar::MultiColvarBase::usespecies

protectedinherited

Using the species keyword to read in atoms.

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

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

multicolvar/NumberOfLinks.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation