This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames. More...

#include <ActionWithAveraging.h>

Inheritance diagram for PLMD::vesselbase::ActionWithAveraging:

[legend]

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

Public Member Functions
	ActionWithAveraging (const ActionOptions &)

virtual void	accumulateAverage (MultiValue &myvals) const

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

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

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

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

void	addForcesOnArguments (const std::vector< double > &forces)
	Add forces to arguments (used in apply) More...

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

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

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

virtual void	apply ()=0
	Apply an Action. More...

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

void	applyForces ()

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

double	bringBackInPbc (int i, double d1) const
	Takes one value and brings it back into the pbc of argument i. More...

StoreDataVessel *	buildDataStashes (ActionWithVessel *actionThatUses)
	Ensure that data required in other vessels is stored. More...

virtual void	calculate ()=0
	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...

void	calculateNumericalDerivatives (PLMD::ActionWithValue *)
	N.B. More...

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

virtual void	checkFieldsAllowed ()

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

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

virtual void	clearAverage ()
	This does the clearing of the action. More...

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

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

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

virtual void	clearOptions ()

void	clearOutputForces ()

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

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

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

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

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

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

double	difference (int, double, double) const
	Takes the difference taking into account pbc for arg i. More...

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

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

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

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

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

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

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

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

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

virtual void	finishAveraging ()
	This is done once the averaging is finished. More...

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

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

double	getArgument (const unsigned n) const
	Returns the value of an argument. More...

virtual const std::vector< Value * > &	getArguments () const
	Returns an array of pointers to the arguments. More...

virtual const std::vector< Value *> &	getArguments () const
	Overwrite ActionWithArguments getArguments() so that we don't return the bias. More...

std::vector< Value * >	getArguments ()

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

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

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

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

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

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

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

virtual std::string	getDocumentation () const

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

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

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

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

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

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

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

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

unsigned	getNumberOfArguments () const
	Returns the number of arguments. More...

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

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

virtual unsigned	getNumberOfDerivatives ()

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

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

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

Value *	getPntrToArgument (const unsigned n)
	Return a pointer to specific argument. More...

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

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

unsigned	getPositionInCurrentTaskList (const unsigned &myind) const
	Return the position in the current task list. More...

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

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

double	getProjection (unsigned i, unsigned j) const
	Get the scalar product between the gradients of two variables. More...

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

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

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

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

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

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

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

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

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

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

bool	ignoreNormalization () const

void	interpretArgumentList (const std::vector< std::string > &c, std::vector< Value *> &arg)
	Convert a list of argument names into a list of pointers to the values. More...

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

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

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

virtual bool	isPeriodic ()=0
	Are the base quantities periodic. More...

void	lockContributors ()

void	lockRequests ()

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

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

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

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

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

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

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

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

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

virtual void	normalizeVector (std::vector< double > &vals) const
	These normalizes vectors and is used in StoreDataVessel. More...

virtual void	normalizeVectorDerivatives (MultiValue &myvals) const

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	parseArgumentList (const std::string &key, std::vector< Value *> &args)
	Parse a list of arguments. More...

bool	parseArgumentList (const std::string &key, int i, std::vector< Value *> &args)
	Parse a numbered list of arguments. 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	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	performOperations (const bool &from_update)
	This does the averaging operation. More...

virtual void	performTask (const unsigned &task_index, const unsigned &current, MultiValue &myvals) const
	Does the calculation. 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	prepareForAveraging ()
	This is done before the averaging comences. More...

void	readAtomsFromPDB (const PDB &pdb)
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. 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	requestArguments (const std::vector< Value *> &arg)
	Setup the dependencies. More...

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

virtual void	retrieveAtoms ()

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

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

virtual void	runTask (const unsigned &current, MultiValue &myvals) const

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

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

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

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

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

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

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

bool	taskIsCurrentlyActive (const unsigned &index) const
	Check whether or not a particular task is currently active. More...

virtual bool	threadSafe () const
	Is this action thread safe. More...

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

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

void	unlockRequests ()

void	update ()
	Update. More...

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

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

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

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

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

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

static void	registerKeywords (Keywords &keys)

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

Public Attributes
Communicator &	comm

std::set< FILE * >	files

const Keywords &	keywords

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

Communicator &	multi_sim_comm

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

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

void	addTaskToList (const unsigned &taskCode)
	Add a task to the full list. 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 (std::unique_ptr< Vessel > vv)

void	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...

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

void	expandArgKeywordInPDB (PDB &pdb)
	This changes the arg keyword in the pdb file. More...

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

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

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

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

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

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

bool	noNormalization () const
	Check if we are using the normalization condition when calculating this quantity. More...

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

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

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

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

void	setAveragingAction (std::unique_ptr< AveragingVessel > av_vessel, const bool &usetasks)
	Set the averaging action. More...

void	setExtraCV (const std::string &name)

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

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

bool	storeThenAverage () const
	Are we storing data then averaging. More...

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

Protected Attributes
Atoms &	atoms

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

unsigned	clearstride
	The frequency with which to clear the grid. More...

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

double	cweight

bool	dertime
	This is also used to minimise computational expense in complex functions. More...

double	lweight
	The current weight and its logarithm. More...

StoreDataVessel *	mydata
	A pointer to the object that stores data. More...

std::vector< unsigned >	taskFlags
	This list is used to update the neighbor list. More...

bool	useRunAllTasks
	This ensures runAllTasks is used. More...

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

Private Types
enum	{ t, f, ndata }

Private Attributes
bool	activated
	Are we accumulated the unormalized quantity. More...

analysis::AnalysisBase *	my_analysis_object
	An object in which analysis data has been stored. More...

AveragingVessel *	myaverage
	The vessel which is used to compute averages. More...

enum PLMD::vesselbase::ActionWithAveraging:: { ... }	normalization

std::vector< Value * >	weights
	The weights we are going to use for reweighting. More...

Friends
class	AveragingVessel

Detailed Description

This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames.

Notice that we use the word average very broadly here and state that even dimensionality reduction algorithms calculate an "average." In other words, what we mean by average is that the method is going to take in data from each trajectory frame and only calculate the final quantity once a certain amount of data has been collected.

Member Typedef Documentation

◆ Dependencies

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

inherited

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

private

Enumerator
t
f
ndata

Constructor & Destructor Documentation

◆ ActionWithAveraging()

PLMD::vesselbase::ActionWithAveraging::ActionWithAveraging ( const ActionOptions & ao )

explicit

Member Function Documentation

◆ accumulateAverage()

virtual void PLMD::vesselbase::ActionWithAveraging::accumulateAverage ( MultiValue & myvals ) const

inlinevirtual

Reimplemented in PLMD::analysis::Average.

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addBridgingVessel()

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

protectedinherited

Add a bridging vessel to the list of vessels.

◆ addComponent()

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

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

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

inherited

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

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments ( const std::vector< double > & forces )

inherited

Add forces to arguments (used in apply)

◆ addTaskToList()

void PLMD::vesselbase::ActionWithVessel::addTaskToList ( const unsigned & taskCode )

protectedinherited

Add a task to the full list.

◆ addValue()

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

◆ addVessel() [1/2]

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.

◆ addVessel() [2/2]

void PLMD::vesselbase::ActionWithVessel::addVessel ( std::unique_ptr< Vessel > vv )

protectedinherited

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )

inlineinherited

Allow calls to modifyGlobalForce()

◆ apply()

virtual void PLMD::Action::apply ( )

pure virtualinherited

Apply an Action.

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

Implemented in PLMD::analysis::Histogram, PLMD::generic::FitToTemplate, PLMD::isdb::MetainferenceBase, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::multicolvar::MultiColvarBase, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::ves::VesBias, PLMD::generic::DumpAtoms, PLMD::generic::Group, PLMD::generic::EffectiveEnergyDrift, PLMD::generic::WholeMolecules, PLMD::generic::ResetCell, PLMD::generic::DumpMassCharge, PLMD::multicolvar::MultiColvarDensity, PLMD::adjmat::Sprint, PLMD::analysis::Average, PLMD::generic::Read, PLMD::mapping::Mapping, PLMD::analysis::AnalysisBase, PLMD::multicolvar::DistanceFromContour, PLMD::generic::UpdateIf, PLMD::ves::OutputFesBias, PLMD::generic::Print, PLMD::ves::OutputBasisFunctions, PLMD::ves::OutputTargetDistribution, PLMD::adjmat::OutputCluster, PLMD::generic::RandomExchanges, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::manyrestraints::ManyRestraintsBase, PLMD::generic::DumpProjections, PLMD::generic::Debug, PLMD::Colvar, PLMD::adjmat::DumpGraph, PLMD::adjmat::ClusteringBase, PLMD::bias::Bias, PLMD::generic::Time, PLMD::function::Function, PLMD::bias::ReweightBase, PLMD::ActionShortcut, PLMD::ActionWithVirtualAtom, PLMD::gridtools::ActionWithInputGrid, PLMD::gridtools::ActionWithIntegral, PLMD::ActionAnyorder, PLMD::ActionSetup, and PLMD::gridtools::GridPrintingBase.

◆ applyBridgeForces()

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.

◆ applyForces()

void PLMD::ActionAtomistic::applyForces ( )

inherited

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

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

Reimplemented in PLMD::generic::UpdateIf.

◆ bringBackInPbc()

double PLMD::ActionWithArguments::bringBackInPbc	(	int	i,
		double	d1
	)		const

inlineinherited

Takes one value and brings it back into the pbc of argument i.

◆ buildDataStashes()

StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes ( ActionWithVessel * actionThatUses )

inherited

Ensure that data required in other vessels is stored.

◆ calculate()

virtual void PLMD::Action::calculate ( )

pure virtualinherited

Calculate an Action.

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

Implemented in PLMD::isdb::CS2Backbone, PLMD::bias::MetaD, PLMD::logmfd::LogMFD, PLMD::ves::VesLinearExpansion, PLMD::bias::PBMetaD, PLMD::isdb::Metainference, PLMD::eds::EDS, PLMD::function::FuncPathMSD, PLMD::piv::PIV, PLMD::isdb::EMMI, PLMD::function::FuncSumHills, PLMD::generic::FitToTemplate, PLMD::mapping::PCAVars, PLMD::ves::Optimizer, PLMD::isdb::RDC, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::function::Custom, PLMD::multicolvar::MultiColvarBase, PLMD::bias::MaxEnt, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::isdb::Rescale, PLMD::generic::Include, PLMD::generic::DumpAtoms, PLMD::isdb::SAXS, PLMD::generic::Group, PLMD::colvar::Dimer, PLMD::vatom::Center, PLMD::bias::ExtendedLagrangian, PLMD::bias::External, PLMD::colvar::DRMSD, PLMD::colvar::ContactMap, PLMD::colvar::Distance, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::MovingRestraint, PLMD::colvar::ERMSD, PLMD::generic::WholeMolecules, PLMD::function::Target, PLMD::generic::ResetCell, PLMD::generic::DumpMassCharge, PLMD::mapping::AdaptivePath, PLMD::isdb::JCoupling, PLMD::adjmat::Sprint, PLMD::colvar::Torsion, PLMD::generic::Read, PLMD::colvar::EEFSolv, PLMD::analysis::Average, PLMD::analysis::AnalysisBase, PLMD::isdb::Caliber, PLMD::multicolvar::CenterOfMultiColvar, PLMD::vatom::FixedAtom, PLMD::colvar::Gyration, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::colvar::PathMSDBase, PLMD::isdb::FretEfficiency, PLMD::ves::OutputFesBias, PLMD::generic::UpdateIf, PLMD::multicolvar::DistanceFromContour, PLMD::ves::OutputBasisFunctions, PLMD::function::Combine, PLMD::isdb::PRE, PLMD::generic::Print, PLMD::colvar::Position, PLMD::ves::OutputTargetDistribution, PLMD::function::LocalEnsemble, PLMD::adjmat::OutputCluster, PLMD::bias::BiasValue, PLMD::isdb::NOE, PLMD::colvar::Puckering, PLMD::generic::RandomExchanges, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::multicolvar::DumpMultiColvar, PLMD::adjmat::ClusterDistribution, PLMD::function::Piecewise, PLMD::bias::LWalls, PLMD::isdb::Select, PLMD::bias::UWalls, PLMD::adjmat::ClusterDiameter, PLMD::analysis::Committor, PLMD::adjmat::ClusterSize, PLMD::colvar::Dipole, PLMD::colvar::Energy, PLMD::bias::Restraint, PLMD::colvar::Constant, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::adjmat::ClusterProperties, PLMD::function::Ensemble, PLMD::function::Stats, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::colvar::ExtraCV, PLMD::generic::Debug, PLMD::colvar::Template, PLMD::generic::DumpProjections, PLMD::manyrestraints::ManyRestraintsBase, PLMD::vatom::Ghost, PLMD::colvar::Cell, PLMD::adjmat::DumpGraph, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::generic::Time, PLMD::gridtools::ActionWithGrid, PLMD::adjmat::ClusteringBase, PLMD::colvar::MultiRMSD, PLMD::colvar::PCARMSD, PLMD::colvar::RMSD, PLMD::ActionShortcut, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::gridtools::GridPrintingBase, and PLMD::mapping::PathBase.

◆ calculateAllVessels()

void 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.

◆ calculateAtomicNumericalDerivatives()

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

inherited

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

◆ calculateFromPDB()

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

inherited

Calculate the action given a pdb file as input.

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

◆ calculateNumericalDerivatives()

void PLMD::vesselbase::ActionWithAveraging::calculateNumericalDerivatives ( PLMD::ActionWithValue * a )

virtual

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::ActionAtomistic.

◆ changeBox()

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

inherited

Change the box shape.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

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

◆ checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

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

inherited

Cite a paper see PlumedMain::cite.

◆ clearAverage()

void PLMD::vesselbase::ActionWithAveraging::clearAverage ( )

virtual

This does the clearing of the action.

Reimplemented in PLMD::multicolvar::MultiColvarDensity, PLMD::gridtools::FindContourSurface, PLMD::gridtools::FourierTransform, and PLMD::gridtools::ActionWithInputGrid.

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

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

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )

inherited

◆ componentIsNotPeriodic()

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

inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

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

staticinherited

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

◆ copyOutput() [1/2]

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

inherited

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

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

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

inherited

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

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ deactivateAllTasks()

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

protectedinherited

Deactivate all the tasks in the task list.

◆ derivativesAreRequired()

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

inlineinherited

Are derivatives required for this quantity.

◆ difference()

double PLMD::ActionWithArguments::difference	(	int	i,
		double	d1,
		double	d2
	)		const

inlineinherited

Takes the difference taking into account pbc for arg i.

◆ doJobsRequiredBeforeTaskList()

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

virtualinherited

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

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

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ doNotForce()

void PLMD::ActionAtomistic::doNotForce ( )

inlineinherited

Skip atom forces - use with care.

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

◆ doNotRetrieve()

void PLMD::ActionAtomistic::doNotRetrieve ( )

inlineinherited

Skip atom retrieval - use with care.

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

◆ error()

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

inherited

Crash calculation and print documentation.

◆ exists()

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

inherited

Check if a value with a particular name is present.

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

◆ exit()

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

inherited

Exit with error code c.

◆ expandArgKeywordInPDB()

void PLMD::ActionWithArguments::expandArgKeywordInPDB ( PDB & pdb )

protectedinherited

This changes the arg keyword in the pdb file.

◆ 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.

◆ finishAveraging()

virtual void PLMD::vesselbase::ActionWithAveraging::finishAveraging ( )

inlinevirtual

This is done once the averaging is finished.

Reimplemented in PLMD::analysis::Histogram, PLMD::gridtools::FindContour, PLMD::gridtools::FindContourSurface, and PLMD::analysis::Average.

◆ finishComputations()

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

virtualinherited

Finish running all the calculations.

◆ 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.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ getActiveTask()

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

inlineinherited

Get the ith of the currently active tasks.

◆ getArgument()

double PLMD::ActionWithArguments::getArgument ( const unsigned n ) const

inlineinherited

Returns the value of an argument.

◆ getArguments() [1/3]

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments ( ) const

inlinevirtualinherited

Returns an array of pointers to the arguments.

◆ getArguments() [2/3]

const std::vector< Value * > & PLMD::ActionWithArguments::getArguments

inline

Overwrite ActionWithArguments getArguments() so that we don't return the bias.

◆ getArguments() [3/3]

std::vector< Value * > PLMD::vesselbase::ActionWithAveraging::getArguments ( )

inline

◆ 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.

◆ getComponentsList()

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

inherited

get a string that contains all the available components

◆ getComponentsVector()

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

inherited

get a vector that contains the label for all the components

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getCurrentNumberOfActiveTasks()

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

inlineinherited

Get the number of tasks that are currently active.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ getDocumentation()

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

virtualinherited

◆ getEnergy()

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

inlineinherited

Get energy.

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getForcesFromVessels()

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

protectedinherited

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

◆ getFullNumberOfTasks()

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

inlineinherited

Get the full size of the taskList dynamic list.

◆ getGlobalPosition()

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

inlineinherited

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

With direct access to the global atom array.

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

◆ getKeyword()

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

inherited

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

◆ getLabel()

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

inlineinherited

Returns the label.

◆ getMass()

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

inlineinherited

Get mass of i-th atom.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNLTolerance()

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

inlineprotectedinherited

Return the value for the neighbor list tolerance.

◆ getNumberOfArguments()

unsigned PLMD::vesselbase::ActionWithAveraging::getNumberOfArguments ( ) const

inlinevirtual

Returns the number of arguments.

Reimplemented from PLMD::ActionWithArguments.

◆ getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDerivatives()

virtual unsigned PLMD::vesselbase::ActionWithAveraging::getNumberOfDerivatives ( )

inlinevirtual

Implements PLMD::ActionWithValue.

Reimplemented in PLMD::analysis::Histogram, PLMD::gridtools::ContourFindingBase, and PLMD::gridtools::ActionWithIntegral.

◆ getNumberOfQuantities()

unsigned PLMD::vesselbase::ActionWithAveraging::getNumberOfQuantities ( ) const

virtual

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

Reimplemented from PLMD::vesselbase::ActionWithVessel.

Reimplemented in PLMD::analysis::Histogram, PLMD::gridtools::FindSphericalContour, PLMD::gridtools::FindContour, PLMD::multicolvar::MultiColvarDensity, PLMD::gridtools::FindContourSurface, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::InterpolateGrid.

◆ getNumberOfVessels()

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

inlineinherited

Get the number of vessels.

◆ getOutputQuantity() [1/2]

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

inlineinherited

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

◆ getOutputQuantity() [2/2]

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

inlineinherited

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

◆ getPbc()

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

inlineinherited

Get reference to Pbc.

◆ getPntrToArgument()

Value * PLMD::ActionWithArguments::getPntrToArgument ( const unsigned n )

inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

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

protectedinherited

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

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

protectedinherited

Return a pointer to the value by name.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

◆ getPntrToVessel()

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

inlineinherited

Get a pointer to the ith vessel.

◆ getPosition()

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

inlineinherited

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

◆ getPositionInCurrentTaskList()

unsigned PLMD::vesselbase::ActionWithVessel::getPositionInCurrentTaskList ( const unsigned & myind ) const

inlineinherited

Return the position in the current task list.

◆ getPositionInFullTaskList()

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

inlineinherited

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

◆ getPositions()

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

inlineinherited

Get the array of all positions.

◆ getProjection()

double PLMD::ActionWithArguments::getProjection	(	unsigned	i,
		unsigned	j
	)		const

inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getSizeOfBuffer()

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

protectedinherited

Get the size of the buffer.

◆ getStep()

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

inherited

Return the present timestep.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

◆ getTaskCode()

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

inlineinherited

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

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getTolerance()

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

inlineprotectedinherited

Return the value of the tolerance.

◆ getTotAtoms()

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inlineinherited

Get total number of atoms, including virtual ones.

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

◆ getUnique()

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

inlineinherited

◆ getUniqueLocal()

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

inlineinherited

◆ getVesselWithName()

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

inherited

These are overwritten in MultiColvarFunction.

Return a particular named vessel

◆ ignoreNormalization()

bool PLMD::vesselbase::ActionWithAveraging::ignoreNormalization ( ) const

◆ interpretArgumentList()

void PLMD::ActionWithArguments::interpretArgumentList	(	const std::vector< std::string > &	c,
		std::vector< Value *> &	arg
	)

inherited

Convert a list of argument names into a list of pointers to the values.

◆ interpretAtomList()

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

inherited

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

◆ 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.

◆ isPeriodic()

virtual bool PLMD::vesselbase::ActionWithVessel::isPeriodic ( )

pure virtualinherited

Are the base quantities periodic.

◆ lockContributors()

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

inherited

◆ lockRequests()

void PLMD::vesselbase::ActionWithAveraging::lockRequests ( )

virtual

Reimplemented from PLMD::ActionAtomistic.

◆ 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.

◆ modifyForceOnExtraCV()

double & PLMD::ActionAtomistic::modifyForceOnExtraCV ( )

inlineinherited

Get a reference to force on extraCV.

◆ modifyForces()

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

inlineinherited

Get a reference to forces array.

◆ modifyGlobalForce()

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

inlineinherited

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

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

◆ modifyGlobalPbc()

Pbc & PLMD::ActionAtomistic::modifyGlobalPbc ( )

inlineinherited

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

◆ modifyGlobalPosition()

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

inlineinherited

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

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

◆ modifyGlobalVirial()

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inlineinherited

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

◆ modifyVirial()

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

◆ needsDerivatives()

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

protectedinherited

Turn on the derivatives in the vessel.

◆ noAnalyticalDerivatives()

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

staticinherited

Insist that numerical derivatives should always be used for an action and make this fact appear in the manual.

◆ noNormalization()

bool PLMD::vesselbase::ActionWithAveraging::noNormalization ( ) const

inlineprotected

Check if we are using the normalization condition when calculating this quantity.

◆ normalizeVector()

virtual void PLMD::vesselbase::ActionWithVessel::normalizeVector ( std::vector< double > & vals ) const

inlinevirtualinherited

These normalizes vectors and is used in StoreDataVessel.

Reimplemented in PLMD::multicolvar::LocalAverage, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::crystallization::VectorMultiColvar, and PLMD::crystallization::MoleculeOrientation.

◆ normalizeVectorDerivatives()

virtual void PLMD::vesselbase::ActionWithVessel::normalizeVectorDerivatives ( MultiValue & myvals ) const

inlinevirtualinherited

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::crystallization::VectorMultiColvar, and PLMD::crystallization::MoleculeOrientation.

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

void PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		std::vector< Value *> &	args
	)

inherited

Parse a list of arguments.

◆ parseArgumentList() [2/2]

bool PLMD::ActionWithArguments::parseArgumentList	(	const std::string &	key,
		int	i,
		std::vector< Value *> &	args
	)

inherited

Parse a numbered list of arguments.

◆ parseAtomList() [1/2]

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

inherited

Parse a list of atoms without a numbered keyword.

◆ parseAtomList() [2/2]

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.

◆ 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

inherited

Compute the pbc distance between two positions.

◆ performOperations()

void PLMD::vesselbase::ActionWithAveraging::performOperations ( const bool & from_update )

virtual

This does the averaging operation.

Reimplemented in PLMD::analysis::Histogram, PLMD::analysis::Average, PLMD::gridtools::FourierTransform, and PLMD::gridtools::ActionWithInputGrid.

◆ performTask()

void PLMD::vesselbase::ActionWithAveraging::performTask	(	const unsigned &	task_index,
		const unsigned &	current,
		MultiValue &	myvals
	)		const

virtual

Does the calculation.

Implements PLMD::vesselbase::ActionWithVessel.

Reimplemented in PLMD::analysis::Average.

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

◆ prepareForAveraging()

virtual void PLMD::vesselbase::ActionWithAveraging::prepareForAveraging ( )

inlinevirtual

This is done before the averaging comences.

Reimplemented in PLMD::analysis::Histogram, PLMD::gridtools::FindContour, PLMD::multicolvar::MultiColvarDensity, PLMD::gridtools::FindContourSurface, PLMD::gridtools::ConvertToFES, and PLMD::gridtools::ActionWithInputGrid.

◆ readAtomsFromPDB() [1/2]

void PLMD::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.

◆ readAtomsFromPDB() [2/2]

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.

◆ readVesselKeywords()

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

protectedinherited

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

◆ registerKeywords()

void PLMD::vesselbase::ActionWithAveraging::registerKeywords ( Keywords & keys )

static

◆ requestArguments()

void PLMD::ActionWithArguments::requestArguments ( const std::vector< Value *> & arg )

inherited

Setup the dependencies.

◆ 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

◆ resizeFunctions()

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

protectedinherited

Resize all the functions when the number of derivatives change.

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( )

virtualinherited

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ retrieveDomain()

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

virtualinherited

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::XYTorsion, PLMD::crystallization::InterMolecularTorsions, and PLMD::multicolvar::Torsions.

◆ runAllTasks()

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

protectedinherited

Calculate the values of all the vessels.

◆ runFinalJobs()

void PLMD::vesselbase::ActionWithAveraging::runFinalJobs ( )

virtual

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 from PLMD::Action.

◆ runTask()

virtual void PLMD::vesselbase::ActionWithAveraging::runTask	(	const unsigned &	current,
		MultiValue &	myvals
	)		const

inlinevirtual

Reimplemented in PLMD::gridtools::ActionWithGrid.

◆ serialCalculation()

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

inlineprotectedinherited

Is the calculation being done in serial.

◆ setAveragingAction()

void PLMD::vesselbase::ActionWithAveraging::setAveragingAction	(	std::unique_ptr< AveragingVessel >	av_vessel,
		const bool &	usetasks
	)

protected

Set the averaging action.

◆ setExtraCV()

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

inlineprotectedinherited

◆ setForcesOnAtoms()

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

inherited

Add the forces to the atoms.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

◆ setLowMemOption()

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

inlineprotectedinherited

Set that we are using low memory.

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

◆ setOption()

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

virtualinherited

◆ setPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

◆ setStride()

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

inherited

Set the value of the stride.

◆ setValue() [1/2]

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

inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

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

inherited

Set the value.

◆ storeThenAverage()

bool PLMD::vesselbase::ActionWithAveraging::storeThenAverage ( ) const

inlineprotected

Are we storing data then averaging.

◆ taskIsCurrentlyActive()

bool PLMD::vesselbase::ActionWithVessel::taskIsCurrentlyActive ( const unsigned & index ) const

inherited

Check whether or not a particular task is currently active.

◆ threadSafe()

virtual bool PLMD::vesselbase::ActionWithVessel::threadSafe ( ) const

inlinevirtualinherited

Is this action thread safe.

Reimplemented in PLMD::analysis::Histogram, and PLMD::multicolvar::MultiColvarBase.

◆ transformBridgedDerivatives()

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.

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

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

◆ unlockRequests()

void PLMD::vesselbase::ActionWithAveraging::unlockRequests ( )

virtual

Reimplemented from PLMD::ActionAtomistic.

◆ update()

void PLMD::vesselbase::ActionWithAveraging::update ( )

virtual

Update.

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

Reimplemented from PLMD::Action.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( )

inherited

updates local unique atoms

◆ useCustomisableComponents()

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

staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ usingLowMem()

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

inlineprotectedinherited

Are we using low memory.

◆ warning()

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

inherited

Issue a warning.

◆ weightWithDerivatives()

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

inlineinherited

Does the weight have derivatives.

Friends And Related Function Documentation

◆ AveragingVessel

friend class AveragingVessel

friend

Member Data Documentation

◆ activated

bool PLMD::vesselbase::ActionWithAveraging::activated

private

Are we accumulated the unormalized quantity.

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

◆ bridgeVariable

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protectedinherited

This is used for numerical derivatives of bridge variables.

◆ clearstride

unsigned PLMD::vesselbase::ActionWithAveraging::clearstride

protected

The frequency with which to clear the grid.

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ contributorsAreUnlocked

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protectedinherited

The terms in the series are locked.

◆ cweight

double PLMD::vesselbase::ActionWithAveraging::cweight

protected

◆ dertime

bool PLMD::vesselbase::ActionWithVessel::dertime

protectedinherited

This is also used to minimise computational expense in complex functions.

◆ files

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

inherited

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ lweight

double PLMD::vesselbase::ActionWithAveraging::lweight

protected

The current weight and its logarithm.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ my_analysis_object

analysis::AnalysisBase* PLMD::vesselbase::ActionWithAveraging::my_analysis_object

private

An object in which analysis data has been stored.

◆ myaverage

AveragingVessel* PLMD::vesselbase::ActionWithAveraging::myaverage

private

The vessel which is used to compute averages.

◆ mydata

StoreDataVessel* PLMD::vesselbase::ActionWithVessel::mydata

protectedinherited

A pointer to the object that stores data.

◆ normalization

enum { ... } PLMD::vesselbase::ActionWithAveraging::normalization

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ taskFlags

std::vector<unsigned> PLMD::vesselbase::ActionWithVessel::taskFlags

protectedinherited

This list is used to update the neighbor list.

◆ useRunAllTasks

bool PLMD::vesselbase::ActionWithAveraging::useRunAllTasks

protected

This ensures runAllTasks is used.

◆ weightHasDerivatives

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

◆ weights

std::vector<Value*> PLMD::vesselbase::ActionWithAveraging::weights

private

The weights we are going to use for reweighting.

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

vesselbase/ActionWithAveraging.h
vesselbase/ActionWithAveraging.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Types

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ Dependencies

Member Enumeration Documentation

◆ anonymous enum

Constructor & Destructor Documentation

◆ ActionWithAveraging()

Member Function Documentation

◆ accumulateAverage()

◆ activate()

◆ addBridgingVessel()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addTaskToList()

◆ addValue()

◆ addValueWithDerivatives()

◆ addVessel() [1/2]

◆ addVessel() [2/2]

◆ allowToAccessGlobalForces()

◆ apply()

◆ applyBridgeForces()

◆ applyForces()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ buildDataStashes()

◆ calculate()

◆ calculateAllVessels()

◆ calculateAtomicNumericalDerivatives()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ changeBox()

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearAverage()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ clearOutputForces()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ deactivateAllTasks()

◆ derivativesAreRequired()

◆ difference()

◆ doJobsRequiredBeforeTaskList()

◆ doNotCalculateDerivatives()

◆ doNotForce()

◆ doNotRetrieve()

◆ error()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ finishAveraging()

◆ finishComputations()

◆ fopen()

◆ getAbsoluteIndex()

◆ getAbsoluteIndexes()

◆ getActiveTask()