This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box. More...

#include <ActionVolume.h>

Inheritance diagram for PLMD::multicolvar::ActionVolume:

[legend]

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

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

Public Member Functions
	ActionVolume (const ActionOptions &)

void	clearDerivatives ()
	Don't actually clear the derivatives when this is called from plumed main. More...

void	finishTaskListUpdate ()

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

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

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

bool	isPeriodic ()
	Is the output quantity periodic. More...

void	prepare ()
	Jobs to be done when the action is activated. More...

void	doJobsRequiredBeforeTaskList ()
	Do jobs required before tasks are undertaken. More...

void	performTask ()
	This calculates all the vessels and is called from within a bridge vessel. More...

void	deactivate_task ()
	Routines that have to be defined so as not to have problems with virtual methods. More...

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

void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	We need our own calculate numerical derivatives here. More...

virtual void	setupRegion ()=0

virtual double	calculateNumberInside (const Vector &cpos, HistogramBead &bead, Vector &derivatives)=0

void	applyBridgeForces (const std::vector< double > &bb)
	Forces here are applied through the bridge. More...

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

void	mergeDerivatives (const unsigned &ider, const double &df)
	These routines replace the virtual routines in ActionWithVessel for code optimization. More...

void	clearDerivativesAfterTask (const unsigned &ider)

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 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...

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...

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	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...

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...

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	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...

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...

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

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

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

virtual void	checkFieldsAllowed ()

void	unlockContributors ()

void	lockContributors ()

void	chainRuleForElementDerivatives (const unsigned &, const unsigned &, const double &, Vessel *)
	Merge the derivatives. More...

void	chainRuleForElementDerivatives (const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *)

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

virtual void	finishComputations ()
	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 void	getIndexList (const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices)
	Get the list of indices that have derivatives. More...

void	activateTheseTasks (std::vector< bool > &addtionalTasks)
	Switch on additional tasks. More...

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

void	setElementDerivative (const unsigned &, const double &)
	Set the derivative of the jth element wrt to a numbered element. More...

void	addElementDerivative (const unsigned &, const double &)
	Add some derivative of the quantity in the sum wrt to a numbered element. More...

void	setElementValue (const unsigned &, const double &)
	Set the value of the element. More...

void	addElementValue (const unsigned &, const double &)
	Add to an element value. More...

double	getElementValue (const unsigned &ival) const
	Get the value of this element. More...

double	getElementDerivative (const unsigned &) const
	Retrieve the derivative of the quantity in the sum wrt to a numbered element. More...

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

virtual void	activateIndexes (const unsigned &, const unsigned &, const std::vector< unsigned > &)
	These are overwritten in MultiColvarFunction. More...

Vessel *	getVesselWithName (const std::string &mynam)
	Return a particular named vessel. More...

virtual void	addBridgeForces (const std::vector< double > &bb)
	Apply forces from the bridge. 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
double	getSigma () const

const Tensor &	getBox () const
	Get the cell box. More...

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

Vector	pbcDistance (const Vector &v1, const Vector &v2) const
	Calculate distance between two points. More...

const Vector &	getPosition (int iatom)
	Get position of atom. More...

void	requestAtoms (const std::vector< AtomNumber > &atoms)
	Request the atoms. More...

MultiColvarBase *	getPntrToMultiColvar ()

void	addReferenceAtomDerivatives (const unsigned &iatom, const Vector &der)
	Add derivatinve to one of the reference atoms here. More...

void	addBoxDerivatives (const Tensor &vir)
	Add derivatives wrt to the virial. 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	setMaximumNumberOfDerivatives (const unsigned &)
	Set the maximum number of derivatives. 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 ()
	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...

void	accumulateDerivative (const unsigned &ider, const double &df)
	This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives. More...

void	clearAfterTask ()
	Clear tempory data that is calculated for each task. 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...

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

unsigned	getCurrentPositionInTaskList () const
	Get the current task's position in the task list. More...

unsigned	getCurrentTask () const
	Return the number that provides instructions for the current task. 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...

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

void	readArgument (const std::string &type)
	What type of arguments are we reading in. More...

Vessel *	getPntrToArgument ()
	Return a pointer to specific argument. More...

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

Protected Attributes
Atoms &	atoms

std::vector< bool >	thisval_wasset
	A boolean that makes sure we don't accumulate very wrong derivatives. More...

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
double	sigma
	The value of sigma. More...

bool	not_in
	Are we interested in the area outside the colvar. More...

Vector	tmp_p
	This is used for storing positions properly. More...

HistogramBead	bead
	The bead for the histogram. More...

MultiColvarBase *	mycolv
	The action that is calculating the colvars of interest. More...

vesselbase::BridgeVessel *	myBridgeVessel
	The vessel that bridges. More...

bool	firsttime
	Everything for controlling the updating of neighbor lists. More...

int	updateFreq

DynamicList< unsigned >	activeAtoms
	Fast merging of derivatives (automatic skips of zero contributions) More...

std::vector< double >	tmpforces
	This is used to store forces temporarily in apply. More...

Friends
class	MultiColvarBase

Detailed Description

This is the abstract base class to use for implementing a new way of definining a particular region of the simulation box.

You can use this to calculate the number of atoms inside that part or the average value of a quantity like the coordination number inside that part of the cell.

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::ActionVolume::ActionVolume ( const ActionOptions & ao )

Member Function Documentation

void PLMD::vesselbase::ActionWithVessel::accumulateDerivative	(	const unsigned &	ider,
		const double &	df
	)

inlineprotectedinherited

This is used to accumulate the derivatives when we merge using chainRuleForElementDerivatives.

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

virtual void PLMD::vesselbase::ActionWithVessel::activateIndexes	(	const unsigned &	,
		const unsigned &	,
		const std::vector< unsigned > &
	)

inlinevirtualinherited

These are overwritten in MultiColvarFunction.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

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

inherited

Switch on additional tasks.

void PLMD::multicolvar::ActionVolume::addBoxDerivatives ( const Tensor & vir )

inlineprotected

Add derivatives wrt to the virial.

virtual void PLMD::vesselbase::ActionWithInputVessel::addBridgeForces ( const std::vector< double > & bb )

inlinevirtualinherited

Apply forces from the bridge.

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::vesselbase::ActionWithVessel::addElementDerivative	(	const unsigned &	ider,
		const double &	der
	)

inlineinherited

Add some derivative of the quantity in the sum wrt to a numbered element.

void PLMD::vesselbase::ActionWithVessel::addElementValue	(	const unsigned &	ival,
		const double &	val
	)

inlineinherited

Add to an element value.

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

protectedinherited

Add forces to arguments (used in apply)

void PLMD::multicolvar::ActionVolume::addReferenceAtomDerivatives	(	const unsigned &	iatom,
		const Vector &	der
	)

inlineprotected

Add derivatinve to one of the reference atoms here.

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

protectedinherited

Add a task to the full list.

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::multicolvar::ActionVolume::apply ( )

inlinevirtual

Apply an Action.

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

Implements PLMD::Action.

void PLMD::multicolvar::ActionVolume::applyBridgeForces ( const std::vector< double > & bb )

virtual

Forces here are applied through the bridge.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

void ActionAtomistic::applyForces ( )

inherited

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

virtualinherited

Ensure that data required in other vessels is stored.

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

void PLMD::multicolvar::ActionVolume::calculate ( )

inlinevirtual

Calculate an Action.

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

Implements PLMD::Action.

bool PLMD::vesselbase::ActionWithVessel::calculateAllVessels ( )

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

virtual double PLMD::multicolvar::ActionVolume::calculateNumberInside	(	const Vector &	cpos,
		HistogramBead &	bead,
		Vector &	derivatives
	)

pure virtual

Implemented in PLMD::multicolvar::VolumeAround.

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

virtual

We need our own calculate numerical derivatives here.

Reimplemented from PLMD::ActionAtomistic.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives	(	const unsigned &	iout,
		const unsigned &	ider,
		const double &	df,
		Vessel *	valout
	)

inherited

Merge the derivatives.

void PLMD::vesselbase::ActionWithVessel::chainRuleForElementDerivatives	(	const unsigned &	iout,
		const unsigned &	ider,
		const unsigned &	stride,
		const unsigned &	off,
		const double &	df,
		Vessel *	valout
	)

inherited

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

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

inherited

Cite a paper see PlumedMain::cite.

void PLMD::vesselbase::ActionWithVessel::clearAfterTask ( )

protectedinherited

Clear tempory data that is calculated for each task.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

void PLMD::multicolvar::ActionVolume::clearDerivatives ( )

inlinevirtual

Don't actually clear the derivatives when this is called from plumed main.

They are calculated inside another action and clearing them would be bad

Reimplemented from PLMD::ActionWithValue.

void PLMD::multicolvar::ActionVolume::clearDerivativesAfterTask ( const unsigned & ider )

virtual

Reimplemented from PLMD::vesselbase::ActionWithVessel.

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.

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::multicolvar::ActionVolume::deactivate_task ( )

virtual

Routines that have to be defined so as not to have problems with virtual methods.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

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.

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

inlineinherited

Are derivatives required for this quantity.

void PLMD::multicolvar::ActionVolume::doJobsRequiredBeforeTaskList ( )

virtual

Do jobs required before tasks are undertaken.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlineinherited

Are we not calculating derivatives.

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 ( )

virtualinherited

Finish running all the calculations.

void PLMD::multicolvar::ActionVolume::finishTaskListUpdate ( )

virtual

Reimplemented from PLMD::vesselbase::ActionWithVessel.

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.

const Tensor & PLMD::multicolvar::ActionVolume::getBox ( ) const

inlineprotected

Get the cell box.

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.

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

inlineprotectedinherited

Get the current task's position in the task list.

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

inlineprotectedinherited

Return the number that provides instructions for the current task.

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

inlineinherited

Return dependencies.

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

virtualinherited

double PLMD::vesselbase::ActionWithVessel::getElementDerivative ( const unsigned & ider ) const

inlineinherited

Retrieve the derivative of the quantity in the sum wrt to a numbered element.

double PLMD::vesselbase::ActionWithVessel::getElementValue ( const unsigned & ival ) const

inlineinherited

Get the value of this element.

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::vesselbase::ActionWithVessel::getFullNumberOfTasks ( ) const

inlineinherited

Get the full size of the taskList dynamic list.

void PLMD::vesselbase::ActionWithVessel::getIndexList	(	const unsigned &	ntotal,
		const unsigned &	jstore,
		const unsigned &	maxder,
		std::vector< unsigned > &	indices
	)

virtualinherited

Get the list of indices that have derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase, and PLMD::multicolvar::Density.

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.

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

unsigned PLMD::multicolvar::ActionVolume::getNumberOfDerivatives ( )

inlinevirtual

Get the number of derivatives for this action.

Implements PLMD::ActionWithValue.

unsigned PLMD::multicolvar::ActionVolume::getNumberOfQuantities ( )

inlinevirtual

Get the number of quantities that are calculated each time.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

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::multicolvar::ActionVolume::getPbc ( ) const

inlineprotected

Get reference to Pbc.

Vessel * PLMD::vesselbase::ActionWithInputVessel::getPntrToArgument ( )

inlineprotectedinherited

Return a pointer to specific argument.

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.

MultiColvarBase * PLMD::multicolvar::ActionVolume::getPntrToMultiColvar ( )

inlineprotected

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

const Vector & PLMD::multicolvar::ActionVolume::getPosition ( int iatom )

inlineprotected

Get position of atom.

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

inlineprotectedinherited

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

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

inlineinherited

Get the array of all positions.

double PLMD::multicolvar::ActionVolume::getSigma ( ) const

inlineprotected

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

inherited

Return the present timestep.

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

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

inherited

Return a particular named vessel.

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

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

inlineinherited

Check if an option is on.

bool PLMD::multicolvar::ActionVolume::isPeriodic ( )

virtual

Is the output quantity periodic.

Implements PLMD::vesselbase::ActionWithVessel.

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

inherited

void PLMD::ActionAtomistic::lockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in PLMD::mapping::Mapping.

void PLMD::multicolvar::ActionVolume::mergeDerivatives	(	const unsigned &	ider,
		const double &	df
	)

virtual

These routines replace the virtual routines in ActionWithVessel for code optimization.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

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).

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

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.

Vector PLMD::multicolvar::ActionVolume::pbcDistance	(	const Vector &	v1,
		const Vector &	v2
	)		const

inlineprotected

Calculate distance between two points.

void PLMD::multicolvar::ActionVolume::performTask ( )

virtual

This calculates all the vessels and is called from within a bridge vessel.

Implements PLMD::vesselbase::ActionWithVessel.

void PLMD::multicolvar::ActionVolume::prepare ( )

virtual

Jobs to be done when the action is activated.

Reimplemented from PLMD::Action.

void PLMD::vesselbase::ActionWithInputVessel::readArgument ( const std::string & type )

protectedinherited

What type of arguments are we reading in.

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::ActionVolume::registerKeywords ( Keywords & keys )

static

void PLMD::multicolvar::ActionVolume::requestAtoms ( const std::vector< AtomNumber > & atoms )

protected

Request the 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::vesselbase::ActionWithVessel::setElementDerivative	(	const unsigned &	ider,
		const double &	der
	)

inlineinherited

Set the derivative of the jth element wrt to a numbered element.

void PLMD::vesselbase::ActionWithVessel::setElementValue	(	const unsigned &	ival,
		const double &	val
	)

inlineinherited

Set the value of the element.

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

inlineprotectedinherited

Set that we are using low memory.

void PLMD::vesselbase::ActionWithVessel::setMaximumNumberOfDerivatives ( const unsigned & )

protectedinherited

Set the maximum number of derivatives.

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.

virtual void PLMD::multicolvar::ActionVolume::setupRegion ( )

pure virtual

Implemented in PLMD::multicolvar::VolumeAround.

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.

void PLMD::multicolvar::ActionVolume::turnOnDerivatives ( )

virtual

Turn on the derivatives.

Reimplemented from PLMD::ActionWithValue.

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

inherited

void PLMD::ActionAtomistic::unlockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

Reimplemented in 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::analysis::Analysis, PLMD::generic::DumpAtoms, PLMD::generic::Read, PLMD::multicolvar::DumpMultiColvar, PLMD::generic::Print, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, and PLMD::generic::DumpProjections.

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::vesselbase::ActionWithVessel::usingLowMem ( ) const

inlineprotectedinherited

Are we using low memory.

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

inherited

Issue a warning.

Friends And Related Function Documentation

friend class MultiColvarBase

friend

Member Data Documentation

DynamicList<unsigned> PLMD::multicolvar::ActionVolume::activeAtoms

private

Fast merging of derivatives (automatic skips of zero contributions)

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

HistogramBead PLMD::multicolvar::ActionVolume::bead

private

The bead for the histogram.

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

inherited

bool PLMD::multicolvar::ActionVolume::firsttime

private

Everything for controlling the updating of neighbor lists.

const Keywords& PLMD::Action::keywords

inherited

Log& PLMD::Action::log

inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm

inherited

vesselbase::BridgeVessel* PLMD::multicolvar::ActionVolume::myBridgeVessel

private

The vessel that bridges.

MultiColvarBase* PLMD::multicolvar::ActionVolume::mycolv

private

The action that is calculating the colvars of interest.

bool PLMD::multicolvar::ActionVolume::not_in

private

Are we interested in the area outside the colvar.

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

double PLMD::multicolvar::ActionVolume::sigma

private

The value of sigma.

std::vector<bool> PLMD::vesselbase::ActionWithVessel::thisval_wasset

protectedinherited

A boolean that makes sure we don't accumulate very wrong derivatives.

Vector PLMD::multicolvar::ActionVolume::tmp_p

private

This is used for storing positions properly.

std::vector<double> PLMD::multicolvar::ActionVolume::tmpforces

private

This is used to store forces temporarily in apply.

int PLMD::multicolvar::ActionVolume::updateFreq

private

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

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

multicolvar/ActionVolume.h
multicolvar/ActionVolume.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation