#include <Mapping.h>

Inheritance diagram for PLMD::mapping::Mapping:

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

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

Public Member Functions
	Mapping (const ActionOptions &)

	~Mapping ()

void	turnOnDerivatives ()
	Overload the virtual functions that appear in both ActionAtomistic and ActionWithArguments. More...

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

void	lockRequests ()

void	unlockRequests ()

bool	isPeriodic ()
	Distance from a point is never periodic. More...

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

virtual double	getLambda ()
	Get the value of lambda for paths and property maps. More...

virtual double	transformHD (const double &dist, double &df)=0
	This does the transformation of the distance by whatever function is required. More...

unsigned	getNumberOfProperties () const
	Get the number of properties we are projecting onto. More...

std::string	getPropertyName (const unsigned &iprop) const
	Get the name of the ith property we are projecting. More...

unsigned	getPropertyIndex (const std::string &name) const
	Get the index of a particular named property. More...

std::string	getArgumentName (unsigned &iarg)
	Get the name of the ith argument. More...

double	getPropertyValue (const unsigned &iprop) const
	Get the value of the ith property for the current frame. More...

double	getCurrentHighDimFunctionValue (const unsigned &ider) const
	Return the current value of the high dimensional function. More...

void	mergeDerivatives (const unsigned &, const double &)
	Perform chain rule for derivatives. More...

void	prepare ()
	Stuff to do before we do the calculation. More...

void	apply ()
	Apply the forces. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	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 ()

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	calculate ()=0
	Calculate an Action. 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...

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

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

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

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

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

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

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

void	requestArguments (const std::vector< Value * > &arg)
	Setup the dependencies. More...

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

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

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

void	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...

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 ()

virtual void	finishTaskListUpdate ()

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 *)

virtual void	clearDerivativesAfterTask (const unsigned &)

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

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...

virtual void	performTask ()=0
	Get the index for a particular numbered task. 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	applyBridgeForces (const std::vector< double > &bb)
	Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume. 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...

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

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

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

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

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

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

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

Protected Member Functions
unsigned	getNumberOfReferencePoints () const
	Get the number of frames in the path. More...

double	calculateDistanceFunction (const unsigned &ifunc, const bool &squared)
	Calculate the value of the distance from the ith frame. More...

void	storeDistanceFunction (const unsigned &ifunc)
	Store the distance function. More...

double	getWeight () const
	Get the value of the weight. More...

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

Protected Attributes
std::vector< double >	fframes
	The (transformed) distance from each frame. 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
std::vector< double >	dfframes

PointWiseMapping *	mymap
	This holds all the reference information. More...

std::vector< double >	forcesToApply
	The forces on each of the derivatives (used in apply) More...

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::mapping::Mapping::Mapping ( const ActionOptions & ao )

PLMD::mapping::Mapping::~Mapping ( )

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.

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

inherited

Add forces to arguments (used in apply)

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::mapping::Mapping::apply ( )

virtual

Apply the forces.

Implements PLMD::Action.

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

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

inlineinherited

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

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

virtualinherited

Ensure that data required in other vessels is stored.

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

virtual void PLMD::Action::calculate ( )

pure virtualinherited

Calculate an Action.

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

Implemented in PLMD::bias::MetaD, PLMD::function::FuncSumHills, PLMD::function::Matheval, PLMD::function::FuncPathMSD, PLMD::analysis::Analysis, PLMD::RDC, PLMD::colvar::Distance, PLMD::bias::MovingRestraint, PLMD::generic::WholeMolecules, PLMD::multicolvar::ActionVolume, PLMD::generic::Group, PLMD::bias::External, PLMD::generic::DumpAtoms, PLMD::generic::FitToTemplate, PLMD::bias::ABMD, PLMD::colvar::Angle, PLMD::multicolvar::MultiColvarFunction, PLMD::colvar::ContactMap, PLMD::function::Combine, PLMD::bias::BiasValue, PLMD::colvar::DRMSD, PLMD::colvar::Gyration, PLMD::colvar::NOE, PLMD::IMD, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::generic::RandomExchanges, PLMD::generic::Read, PLMD::colvar::PathMSDBase, PLMD::function::Piecewise, PLMD::colvar::Position, PLMD::vatom::Center, PLMD::colvar::Torsion, PLMD::multicolvar::DumpMultiColvar, PLMD::multicolvar::MultiColvar, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::generic::Include, PLMD::generic::Print, PLMD::bias::Restraint, PLMD::analysis::Committor, PLMD::generic::Flush, PLMD::vatom::COM, PLMD::colvar::Energy, PLMD::function::Sort, PLMD::generic::DumpDerivatives, PLMD::colvar::Constant, PLMD::generic::DumpForces, PLMD::manyrestraints::ManyRestraintsBase, PLMD::function::Ensemble, PLMD::generic::Debug, PLMD::vatom::Ghost, PLMD::colvar::Dipole, PLMD::colvar::Cell, PLMD::colvar::ColvarFake, PLMD::colvar::Volume, PLMD::colvar::Template, PLMD::function::Target, PLMD::generic::Time, PLMD::generic::DumpProjections, PLMD::colvar::MultiRMSD, PLMD::colvar::RMSD, PLMD::colvar::CoordinationBase, PLMD::ActionSetup, and PLMD::mapping::PathBase.

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.

double PLMD::mapping::Mapping::calculateDistanceFunction	(	const unsigned &	ifunc,
		const bool &	squared
	)

protected

Calculate the value of the distance from the ith frame.

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

inherited

Calculate the action given a pdb file as input.

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

void PLMD::mapping::Mapping::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtual

N.B.

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

Reimplemented from PLMD::ActionAtomistic.

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::vesselbase::ActionWithVessel::clearDerivativesAfterTask ( const unsigned & ider )

virtualinherited

Reimplemented in PLMD::multicolvar::MultiColvarBase, PLMD::multicolvar::ActionVolume, and PLMD::secondarystructure::SecondaryStructureRMSD.

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

inlineinherited

Takes the difference taking into account pbc for arg i.

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.

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.

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

protectedinherited

This changes the arg keyword in the pdb file.

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.

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

inlinevirtualinherited

Reimplemented in PLMD::multicolvar::ActionVolume, PLMD::multicolvar::MultiColvarFunction, PLMD::secondarystructure::SecondaryStructureRMSD, and PLMD::multicolvar::MultiColvar.

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.

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

inlineinherited

Returns the value of an argument.

std::string PLMD::mapping::Mapping::getArgumentName ( unsigned & iarg )

Get the name of the ith argument.

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

inlineinherited

Returns an array of pointers to the arguments.

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

inlineinherited

Get box shape.

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

double PLMD::mapping::Mapping::getCurrentHighDimFunctionValue ( const unsigned & ider ) const

inline

Return the current value of the high dimensional function.

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::mapping::Mapping::getLambda ( )

virtual

Get the value of lambda for paths and property maps.

Reimplemented in PLMD::mapping::PathBase.

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::ActionWithArguments::getNumberOfArguments ( ) const

inlineinherited

Returns the number of arguments.

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::mapping::Mapping::getNumberOfDerivatives ( )

inlinevirtual

Get the number of derivatives for this action.

Implements PLMD::ActionWithValue.

unsigned PLMD::mapping::Mapping::getNumberOfProperties ( ) const

inline

Get the number of properties we are projecting onto.

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

inlinevirtualinherited

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

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

unsigned PLMD::mapping::Mapping::getNumberOfReferencePoints ( ) const

inlineprotected

Get the number of frames in the path.

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::ActionWithArguments::getPntrToArgument ( const unsigned n )

inlineinherited

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.

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

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

inlineprotectedinherited

Get a pointer to the ith vessel.

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

inlineinherited

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

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

inlineinherited

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

With direct access to the global atom array

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

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

inherited

Get the scalar product between the gradients of two variables.

unsigned PLMD::mapping::Mapping::getPropertyIndex ( const std::string & name ) const

Get the index of a particular named property.

std::string PLMD::mapping::Mapping::getPropertyName ( const unsigned & iprop ) const

inline

Get the name of the ith property we are projecting.

double PLMD::mapping::Mapping::getPropertyValue ( const unsigned & iprop ) const

inline

Get the value of the ith property for the current frame.

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.

double PLMD::mapping::Mapping::getWeight ( ) const

inlineprotected

Get the value of the weight.

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

inherited

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

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::mapping::Mapping::isPeriodic ( )

inlinevirtual

Distance from a point is never periodic.

Implements PLMD::vesselbase::ActionWithVessel.

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

inherited

void PLMD::mapping::Mapping::lockRequests ( )

inlinevirtual

Reimplemented from PLMD::ActionAtomistic.

void PLMD::mapping::Mapping::mergeDerivatives	(	const unsigned &	ider,
		const double &	df
	)

virtual

Perform chain rule for derivatives.

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

inherited

Parse a list of arguments.

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.

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

pure virtualinherited

Get the index for a particular numbered task.

Calculate one of the functions in the distribution

Implemented in PLMD::multicolvar::MultiColvarBase, PLMD::analysis::Histogram, PLMD::multicolvar::ActionVolume, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::manyrestraints::UWalls, PLMD::analysis::AnalysisWithLandmarks, and PLMD::mapping::PathBase.

void PLMD::mapping::Mapping::prepare ( )

virtual

Stuff to do before we do the calculation.

Reimplemented from PLMD::Action.

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::mapping::Mapping::registerKeywords ( Keywords & keys )

static

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

inherited

Setup the dependencies.

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

inherited

Request an array of atoms.

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

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

protectedinherited

Resize all the functions when the number of derivatives change.

void ActionAtomistic::retrieveAtoms ( )

inherited

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

virtualinherited

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::Torsions.

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

protectedinherited

Calculate the values of all the vessels.

virtual void PLMD::Action::runFinalJobs ( )

inlinevirtualinherited

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

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

Reimplemented in PLMD::analysis::Analysis.

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

inlineprotectedinherited

Is the calculation being done in serial.

void PLMD::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.

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::mapping::Mapping::storeDistanceFunction ( const unsigned & ifunc )

inlineprotected

Store the distance function.

virtual double PLMD::mapping::Mapping::transformHD	(	const double &	dist,
		double &	df
	)

pure virtual

This does the transformation of the distance by whatever function is required.

Implemented in PLMD::mapping::PathBase.

void PLMD::mapping::Mapping::turnOnDerivatives ( )

virtual

Overload the virtual functions that appear in both ActionAtomistic and ActionWithArguments.

Reimplemented from PLMD::ActionWithValue.

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

inherited

void PLMD::mapping::Mapping::unlockRequests ( )

inlinevirtual

Reimplemented from PLMD::ActionAtomistic.

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.

Member Data Documentation

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protectedinherited

This is used for numerical derivatives of bridge variables.

Communicator& PLMD::Action::comm

inherited

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protectedinherited

The terms in the series are locked.

std::vector<double> PLMD::mapping::Mapping::dfframes

private

std::vector<double> PLMD::mapping::Mapping::fframes

protected

The (transformed) distance from each frame.

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

inherited

std::vector<double> PLMD::mapping::Mapping::forcesToApply

private

The forces on each of the derivatives (used in apply)

const Keywords& PLMD::Action::keywords

inherited

Log& PLMD::Action::log

inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm

inherited

PointWiseMapping* PLMD::mapping::Mapping::mymap

private

This holds all the reference information.

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

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

protectedinherited

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

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

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

mapping/Mapping.h
mapping/Mapping.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation