Provides the keyword TETRAHEDRAL More...

Inheritance diagram for PLMD::crystallization::Tetrahedral:

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

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

Public Member Functions
	Tetrahedral (const ActionOptions &)

virtual double	compute ()
	This is replaced once we have a function to calculate the cv. More...

Vector	getCentralAtom ()
	Get the position of the central atom. More...

bool	isPeriodic ()
	Returns the number of coordinates of the field. More...

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

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

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

void	finishTaskListUpdate ()
	Finish the update of the task list. More...

virtual void	calculate ()
	Calculate the multicolvar. More...

void	updateActiveAtoms ()
	Update the atoms that have derivatives. More...

Vector	calculateCentralAtomPosition ()
	Calculate the position of the central atom. More...

double	getMass (unsigned) const
	Get the mass of atom iatom. More...

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

double	getCharge (unsigned) const
	Get the charge of atom iatom. More...

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

AtomNumber	getAbsoluteIndex (unsigned) const
	Get the absolute index of atom iatom. More...

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

unsigned	getBaseQuantityIndex (const unsigned &code)
	Get base quantity index. More...

bool	isCurrentlyActive (const unsigned &)
	Is this atom currently being copied. More...

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

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

void	prepare ()
	Prepare for the calculation. More...

void	performTask ()
	Perform one of the tasks. More...

virtual double	doCalculation ()
	And a virtual function which actually computes the colvar. More...

void	mergeDerivatives (const unsigned &ider, const double &df)
	These replace the functions in ActionWithVessel to make the code faster. More...

void	clearDerivativesAfterTask (const unsigned &ider)

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

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

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

Vector	retrieveCentralAtomPos ()
	Retrieve the position of the central atom. More...

virtual void	calculateWeight ()
	You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations. More...

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

virtual bool	isDensity ()
	Is this a density? More...

virtual vesselbase::StoreDataVessel *	buildDataStashes ()
	Store central atoms so that this can be used in a function. More...

void	copyAtomListToFunction (MultiColvarBase *myfunction)
	Copy the list of atoms involved to a second MultiColvarBase (used by functions) More...

void	quotientRule (const unsigned &uder, const unsigned &vder, const unsigned &iout)
	Calculate and store getElementValue(uder)/getElementValue(vder) and its derivatives in getElementValue(iout) More...

unsigned	getInternalIndex (const AtomNumber &iatom) const
	Return the number of the colvar in which iatom is the first atom. More...

void	copyActiveAtomsToFunction (MultiColvarBase *myfunction, const unsigned &start)
	Make sure the same list of atoms is active in a function. More...

void	activateIndexes (const unsigned &istart, const unsigned &number, const std::vector< unsigned > &indexes)
	Activate the atoms that have derivatives from a storeDataVessel. More...

Vector	getCentralAtomPosition (const unsigned &iatom) const
	Get the position of the iatom th central atom (used in multicolvarfunction) More...

void	addCentralAtomDerivativeToFunction (const unsigned &iatom, const unsigned &jout, const unsigned &base_cv_no, const Vector &der, MultiColvarFunction *func)
	Add central atom derivatives to a multicolvar function. More...

virtual void	getValueForTask (const unsigned &iatom, std::vector< double > &vals)
	Get the value for this task. More...

virtual void	copyElementsToBridgedColvar (const double &weight, ActionVolume *)

virtual void	addWeightedValueDerivatives (const unsigned &iatom, const unsigned &base_cv_no, const double &weight, MultiColvarFunction *func)
	Used to accumulate values. More...

virtual void	finishWeightedAverageCalculation (MultiColvarFunction *func)
	Used for calculating weighted averages. More...

virtual void	addOrientationDerivativesToBase (const unsigned &iatom, const unsigned &jstore, const unsigned &base_cv_no, const std::vector< double > &weight, MultiColvarFunction *func)
	Add derivatives to the orientations. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
	Parse a list of atoms without a numbered keyword. More...

void	parseAtomList (const std::string &key, const int num, std::vector< AtomNumber > &t)
	Parse an list of atom with a numbred keyword. More...

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

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

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

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

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

void	clearOutputForces ()

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual void	checkFieldsAllowed ()

void	unlockContributors ()

void	lockContributors ()

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

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...

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

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

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

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

Vessel *	getVesselWithName (const std::string &mynam)
	Return a particular named vessel. 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
void	readAtoms (int &natoms)
	Read in all the keywords that can be used to define atoms. More...

void	readAtomsLikeKeyword (const std::string &key, int &natoms)
	Read in ATOMS keyword. More...

void	readTwoGroups (const std::string &key1, const std::string &key2)
	Read two group keywords. More...

void	readThreeGroups (const std::string &key1, const std::string &key2, const std::string &key3, const bool &allow2)
	Read three groups. More...

void	threeBodyNeighborList (const SwitchingFunction &sf)
	This is used to make neighbor list update fast when three atoms are involved in the colvar (e.g. ANGLES, WATERBRIDGE) More...

void	addColvar (const std::vector< unsigned > &newatoms)
	Add a collective variable. More...

void	addAtomsDerivatives (const int &, const Vector &)
	Add some derivatives for an atom. More...

void	addAtomsDerivatives (const unsigned &, const unsigned &, const Vector &)
	Add some derivatives for an atom. More...

void	addAtomsDerivativeOfWeight (const unsigned &i, const Vector &wder)
	Set the derivative of the weight (used in MEAN and HISTOGRAM) More...

void	addCentralAtomDerivatives (const unsigned &iatom, const Tensor &der)
	Add derivatives to the central atom position. More...

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

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

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

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

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

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

void	addBoxDerivatives (const unsigned &, const Tensor &)
	Add some derivatives for a box. More...

void	addBoxDerivatives (const Tensor &)
	Add some derivatives of the value to the virial. More...

double	getCentralAtomDerivative (const unsigned &iatom, const unsigned &jcomp, const Vector &df)
	Retrieve derivative of central atom position wrt jcomp'th component of position of iatom'th atom. More...

void	setWeight (const double &weight)
	Set a weight for this colvar (used in MEAN and HISTOGRAM) More...

void	addBoxDerivativesOfWeight (const Tensor &vir)
	Set the derivative of the weight (used in MEAN and HISTOGRAM) More...

unsigned	getNAtoms () const
	Get the number of atoms in this particular colvar. More...

void	getCentralAtomIndexList (const unsigned &ntotal, const unsigned &jstore, const unsigned &maxder, std::vector< unsigned > &indices) const
	Get the indices for the central atom. More...

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

Protected Attributes
DynamicList< unsigned >	atoms_with_derivatives
	A dynamic list containing those atoms with derivatives. More...

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

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

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

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

unsigned	natomsper
	Number of atoms in the cv - set at start of calculation. More...

std::vector< unsigned >	current_atoms
	Vector containing the indices of the current atoms. More...

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
SwitchingFunction	switchingFunction

Detailed Description

Provides the keyword TETRAHEDRAL

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::crystallization::Tetrahedral::Tetrahedral ( 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.

void PLMD::multicolvar::MultiColvarBase::activateIndexes	(	const unsigned &	istart,
		const unsigned &	number,
		const std::vector< unsigned > &	indexes
	)

virtualinherited

Activate the atoms that have derivatives from a storeDataVessel.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

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

inherited

Switch on additional tasks.

void PLMD::multicolvar::MultiColvar::addAtomsDerivativeOfWeight	(	const unsigned &	i,
		const Vector &	wder
	)

inlineprotectedinherited

Set the derivative of the weight (used in MEAN and HISTOGRAM)

void PLMD::multicolvar::MultiColvar::addAtomsDerivatives	(	const int &	iatom,
		const Vector &	der
	)

inlineprotectedinherited

Add some derivatives for an atom.

void PLMD::multicolvar::MultiColvarBase::addAtomsDerivatives	(	const unsigned &	ielem,
		const unsigned &	iatom,
		const Vector &	der
	)

inlineprotectedinherited

Add some derivatives for an atom.

void PLMD::multicolvar::MultiColvarBase::addBoxDerivatives	(	const unsigned &	ielem,
		const Tensor &	vir
	)

inlineprotectedinherited

Add some derivatives for a box.

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

inlineprotectedinherited

Add some derivatives of the value to the virial.

void PLMD::multicolvar::MultiColvarBase::addBoxDerivativesOfWeight ( const Tensor & vir )

inlineprotectedinherited

Set the derivative of the weight (used in MEAN and HISTOGRAM)

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

protectedinherited

Add a bridging vessel to the list of vessels.

void PLMD::multicolvar::MultiColvar::addCentralAtomDerivatives	(	const unsigned &	iatom,
		const Tensor &	der
	)

inlineprotectedinherited

Add derivatives to the central atom position.

void PLMD::multicolvar::MultiColvarBase::addCentralAtomDerivativeToFunction	(	const unsigned &	iatom,
		const unsigned &	jout,
		const unsigned &	base_cv_no,
		const Vector &	der,
		MultiColvarFunction *	func
	)

inherited

Add central atom derivatives to a multicolvar function.

void PLMD::multicolvar::MultiColvar::addColvar ( const std::vector< unsigned > & newatoms )

protectedinherited

Add a collective variable.

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::multicolvar::MultiColvarBase::addOrientationDerivativesToBase	(	const unsigned &	iatom,
		const unsigned &	jstore,
		const unsigned &	base_cv_no,
		const std::vector< double > &	weight,
		MultiColvarFunction *	func
	)

virtualinherited

Add derivatives to the orientations.

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

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

protectedinherited

Add a task to the list of tasks.

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

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

protectedinherited

Add a vessel to the list of vessels.

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

protectedinherited

void PLMD::multicolvar::MultiColvarBase::addWeightedValueDerivatives	(	const unsigned &	iatom,
		const unsigned &	base_cv_no,
		const double &	weight,
		MultiColvarFunction *	func
	)

virtualinherited

Used to accumulate values.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

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

virtualinherited

Apply the forces from this action.

Implements PLMD::Action.

Reimplemented in PLMD::multicolvar::Sprint.

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::ActionVolume, and PLMD::manyrestraints::ManyRestraintsBase.

void ActionAtomistic::applyForces ( )

inherited

vesselbase::StoreDataVessel * PLMD::multicolvar::MultiColvarBase::buildDataStashes ( )

virtualinherited

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

Reimplemented from PLMD::vesselbase::ActionWithVessel.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

void PLMD::multicolvar::MultiColvar::calculate ( )

virtualinherited

Calculate the multicolvar.

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.

Vector PLMD::multicolvar::MultiColvar::calculateCentralAtomPosition ( )

virtualinherited

Calculate the position of the central atom.

Implements PLMD::multicolvar::MultiColvarBase.

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

inherited

Calculate the action given a pdb file as input.

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

void ActionAtomistic::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtualinherited

N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing. The default will be correct for the vast majority of cases

Reimplemented from PLMD::Action.

Reimplemented in PLMD::analysis::Analysis, PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarFunction, and PLMD::mapping::Mapping.

void PLMD::multicolvar::MultiColvarBase::calculateWeight ( )

inlinevirtualinherited

You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations.

Reimplemented in PLMD::multicolvar::Angles, PLMD::multicolvar::NumberOfLinks, PLMD::multicolvar::Bridge, PLMD::multicolvar::AdjacencyMatrixAction, and PLMD::crystallization::OrientationSphere.

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::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

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

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

virtualinherited

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.

double PLMD::crystallization::Tetrahedral::compute ( )

virtual

This is replaced once we have a function to calculate the cv.

Implements PLMD::multicolvar::MultiColvarBase.

void PLMD::multicolvar::MultiColvarBase::copyActiveAtomsToFunction	(	MultiColvarBase *	myfunction,
		const unsigned &	start
	)

inherited

Make sure the same list of atoms is active in a function.

void PLMD::multicolvar::MultiColvarBase::copyAtomListToFunction ( MultiColvarBase * myfunction )

inherited

Copy the list of atoms involved to a second MultiColvarBase (used by functions)

void PLMD::multicolvar::MultiColvarBase::copyElementsToBridgedColvar	(	const double &	weight,
		ActionVolume *	func
	)

virtualinherited

Reimplemented in PLMD::crystallization::VectorMultiColvar.

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

inherited

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

Use getPntrToComponent instead.

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

inherited

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

Use getPntrToComponent instead.

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

void PLMD::vesselbase::ActionWithVessel::deactivate_task ( )

virtualinherited

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

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

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

protectedinherited

Deactivate all the tasks in the task list.

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

protectedinherited

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

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

inlineinherited

Are derivatives required for this quantity.

double PLMD::multicolvar::MultiColvarBase::doCalculation ( )

virtualinherited

And a virtual function which actually computes the colvar.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

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

virtualinherited

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

Reimplemented in PLMD::multicolvar::ActionVolume, PLMD::multicolvar::Angles, PLMD::multicolvar::Bridge, PLMD::multicolvar::AdjacencyMatrixAction, and PLMD::manyrestraints::ManyRestraintsBase.

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlineinherited

Are we not calculating derivatives.

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

inlinevirtualinherited

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

Reimplemented in PLMD::crystallization::VectorMultiColvar.

void PLMD::ActionAtomistic::doNotForce ( )

inlineinherited

Skip atom forces - use with care.

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

void PLMD::ActionAtomistic::doNotRetrieve ( )

inlineinherited

Skip atom retrieval - use with care.

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

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

inherited

Crash calculation and print documentation.

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

inherited

Check if a value with a particular name is present.

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

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

inherited

Exit with error code c.

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

inherited

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

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

void PLMD::vesselbase::ActionWithVessel::finishComputations ( )

virtualinherited

Finish running all the calculations.

void PLMD::multicolvar::MultiColvar::finishTaskListUpdate ( )

virtualinherited

Finish the update of the task list.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

void PLMD::multicolvar::MultiColvarBase::finishWeightedAverageCalculation ( MultiColvarFunction * func )

virtualinherited

Used for calculating weighted averages.

Reimplemented in PLMD::crystallization::VectorMultiColvar.

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::multicolvar::MultiColvar::getAbsoluteIndex ( unsigned iatom ) const

inlineinherited

Get the absolute index of atom iatom.

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

inlineinherited

Get the absolute index of an atom.

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

inlineinherited

Get the vector of absolute indexes.

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

inlineprotectedinherited

Get the ith of the currently active tasks.

unsigned PLMD::multicolvar::MultiColvar::getBaseQuantityIndex ( const unsigned & code )

inlinevirtualinherited

Get base quantity index.

Implements PLMD::multicolvar::MultiColvarBase.

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

inlineinherited

Get box shape.

Vector PLMD::crystallization::Tetrahedral::getCentralAtom ( )

virtual

Get the position of the central atom.

Implements PLMD::multicolvar::MultiColvar.

double PLMD::multicolvar::MultiColvarBase::getCentralAtomDerivative	(	const unsigned &	iatom,
		const unsigned &	jcomp,
		const Vector &	df
	)

protectedinherited

Retrieve derivative of central atom position wrt jcomp'th component of position of iatom'th atom.

void PLMD::multicolvar::MultiColvarBase::getCentralAtomIndexList	(	const unsigned &	ntotal,
		const unsigned &	jstore,
		const unsigned &	maxder,
		std::vector< unsigned > &	indices
	)		const

protectedinherited

Get the indices for the central atom.

Vector PLMD::multicolvar::MultiColvarBase::getCentralAtomPosition ( const unsigned & iatom ) const

inherited

Get the position of the iatom th central atom (used in multicolvarfunction)

double PLMD::multicolvar::MultiColvar::getCharge ( unsigned iatom ) const

inlineinherited

Get the charge of atom iatom.

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::multicolvar::MultiColvarBase::getIndexList	(	const unsigned &	ntotal,
		const unsigned &	jstore,
		const unsigned &	maxder,
		std::vector< unsigned > &	indices
	)

virtualinherited

Get the list of indices that have derivatives.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

unsigned PLMD::multicolvar::MultiColvarBase::getInternalIndex ( const AtomNumber & iatom ) const

inherited

Return the number of the colvar in which iatom is the first atom.

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

inlineinherited

Returns the label.

double PLMD::multicolvar::MultiColvar::getMass ( unsigned iatom ) const

inlineinherited

Get the mass of atom iatom.

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.

unsigned PLMD::multicolvar::MultiColvarBase::getNAtoms ( ) const

inlineprotectedinherited

Get the number of atoms in this particular colvar.

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::MultiColvarBase::getNumberOfDerivatives ( )

inlinevirtualinherited

Get the number of derivatives for this action.

Implements PLMD::ActionWithValue.

unsigned PLMD::multicolvar::MultiColvarBase::getNumberOfQuantities ( )

inlinevirtualinherited

Get the number of quantities that are calculated each time.

Reimplemented from PLMD::vesselbase::ActionWithVessel.

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

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

inlineprotectedinherited

Get the number of vessels.

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

inlineinherited

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

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

inlineinherited

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

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

inlineinherited

Get reference to Pbc.

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

protectedinherited

Return a pointer to the component by index.

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

protectedinherited

Return a pointer to the value by name.

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

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

inlineprotectedinherited

Get a pointer to the ith vessel.

const Vector & PLMD::multicolvar::MultiColvar::getPosition ( unsigned iatom ) const

inlineinherited

Get the position of atom iatom.

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

inlineinherited

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

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

inlineinherited

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

With direct access to the global atom array

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

inlineprotectedinherited

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

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

inlinevirtualinherited

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

Implements PLMD::multicolvar::MultiColvarBase.

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

inlineinherited

Get the array of all positions.

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

protectedinherited

Get the separation between a pair of vectors.

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

void PLMD::multicolvar::MultiColvarBase::getValueForTask	(	const unsigned &	iatom,
		std::vector< double > &	vals
	)

virtualinherited

Get the value for this task.

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

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

inherited

Return a particular named vessel.

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

inlinevirtualinherited

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

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

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

bool PLMD::multicolvar::MultiColvar::isCurrentlyActive ( const unsigned & code )

inlinevirtualinherited

Is this atom currently being copied.

Implements PLMD::multicolvar::MultiColvarBase.

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

inlinevirtualinherited

Is this a density?

Reimplemented in PLMD::multicolvar::Density.

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

inlineinherited

Check if an option is on.

bool PLMD::crystallization::Tetrahedral::isPeriodic ( )

inlinevirtual

Returns the number of coordinates of the field.

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::MultiColvarBase::mergeDerivatives	(	const unsigned &	ider,
		const double &	df
	)

virtualinherited

These replace the functions in ActionWithVessel to make the code faster.

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

inherited

Compute the pbc distance between two positions.

void PLMD::multicolvar::MultiColvarBase::performTask ( )

virtualinherited

Perform one of the tasks.

Implements PLMD::vesselbase::ActionWithVessel.

void PLMD::multicolvar::MultiColvarBase::prepare ( )

virtualinherited

Prepare for the calculation.

Reimplemented from PLMD::Action.

void PLMD::multicolvar::MultiColvarBase::quotientRule	(	const unsigned &	uder,
		const unsigned &	vder,
		const unsigned &	iout
	)

inherited

Calculate and store getElementValue(uder)/getElementValue(vder) and its derivatives in getElementValue(iout)

void PLMD::multicolvar::MultiColvar::readAtoms ( int & natoms )

protectedinherited

Read in all the keywords that can be used to define atoms.

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::multicolvar::MultiColvar::readAtomsLikeKeyword	(	const std::string &	key,
		int &	natoms
	)

protectedinherited

Read in ATOMS keyword.

void PLMD::multicolvar::MultiColvar::readThreeGroups	(	const std::string &	key1,
		const std::string &	key2,
		const std::string &	key3,
		const bool &	allow2
	)

protectedinherited

Read three groups.

void PLMD::multicolvar::MultiColvar::readTwoGroups	(	const std::string &	key1,
		const std::string &	key2
	)

protectedinherited

Read two group keywords.

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

protectedinherited

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

void PLMD::crystallization::Tetrahedral::registerKeywords ( Keywords & keys )

static

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

inherited

Request an array of atoms.

This method is used to ask for a list of atoms. Atoms should be asked for by number. If this routine is called during the simulation, atoms will be available at the next step MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC LISTS OF ATOMS

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

protectedinherited

Resize all the functions when the number of derivatives change.

void ActionAtomistic::retrieveAtoms ( )

inherited

Vector PLMD::multicolvar::MultiColvarBase::retrieveCentralAtomPos ( )

inherited

Retrieve the position of the central atom.

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

protectedinherited

Set the value of the cutoff for the link cells.

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

inlineprotectedinherited

Set that we are using low memory.

void PLMD::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.

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

protectedinherited

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

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

protectedinherited

Setup link cells in order to make this calculation faster.

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

protectedinherited

Finish setting up the multicolvar base.

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

inlineprotectedinherited

Set the default value (the one without name)

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

inherited

Set the value.

void PLMD::multicolvar::MultiColvarBase::setWeight ( const double & weight )

inlineprotectedinherited

Set a weight for this colvar (used in MEAN and HISTOGRAM)

void PLMD::multicolvar::MultiColvar::threeBodyNeighborList ( const SwitchingFunction & sf )

protectedinherited

This is used to make neighbor list update fast when three atoms are involved in the colvar (e.g. ANGLES, WATERBRIDGE)

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

virtualinherited

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::multicolvar::MultiColvar::updateActiveAtoms ( )

virtualinherited

Update the atoms that have derivatives.

Implements PLMD::multicolvar::MultiColvarBase.

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

staticinherited

The components in the action will depend on the user.

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

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

inlineprotectedinherited

Do we use pbc to calculate this quantity.

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

inlineprotectedinherited

Are we using low memory.

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

inherited

Issue a warning.

Member Data Documentation

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

protectedinherited

Blocks of atom numbers.

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

DynamicList<unsigned> PLMD::multicolvar::MultiColvarBase::atoms_with_derivatives

protectedinherited

A dynamic list containing those atoms with derivatives.

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protectedinherited

This is used for numerical derivatives of bridge variables.

Communicator& PLMD::Action::comm

inherited

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protectedinherited

The terms in the series are locked.

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

protectedinherited

Vector containing the indices of the current atoms.

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

protectedinherited

This is used when turning cvcodes into atom numbers.

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

inherited

const Keywords& PLMD::Action::keywords

inherited

Log& PLMD::Action::log

inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm

inherited

unsigned PLMD::multicolvar::MultiColvarBase::natomsper

protectedinherited

Number of atoms in the cv - set at start of calculation.

unsigned PLMD::multicolvar::MultiColvarBase::nblock

protectedinherited

Number of atoms in each block.

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

SwitchingFunction PLMD::crystallization::Tetrahedral::switchingFunction

private

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

protectedinherited

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

bool PLMD::multicolvar::MultiColvarBase::usespecies

protectedinherited

Using the species keyword to read in atoms.

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

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

crystallization/Tetrahedral.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation