PLMD::ActionWithVector Class Reference

#include <ActionWithVector.h>

Inheritance diagram for PLMD::ActionWithVector:

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

Public Member Functions
	ActionWithVector (const ActionOptions &)
virtual	~ActionWithVector ()
virtual bool	actionHasForces ()
bool	actionInChain () const
	Are we running this command in a chain. More...
virtual void	activate ()
	Set action to active. More...
void	addComponent (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with a name like label.name. More...
virtual void	addComponentWithDerivatives (const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with a name like label.name that has derivatives. More...
void	addDependency (Action *)
	Specify that this Action depends on another one. More...
void	addForce (const std::pair< std::size_t, std::size_t > &a, const Vector &f)
	Add force to an atom. More...
void	addForcesOnArguments (const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c)
	Add forces to arguments (used in apply) More...
void	addValue (const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with the name label. More...
virtual void	addValueWithDerivatives (const std::vector< unsigned > &shape=std::vector< unsigned >())
	Add a value with the name label that has derivatives. More...
virtual void	apply ()
	Apply the forces on this data. More...
virtual void	areAllTasksRequired (std::vector< ActionWithVector * > &task_reducing_actions)
	Do we always need to do all the tasks for this action. More...
virtual void	beforeUpdate ()
	Before Update. More...
double	bringBackInPbc (int i, double d1) const
	Takes one value and brings it back into the pbc of argument i. More...
virtual void	calculate ()=0
	Calculate an Action. More...
void	calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
	Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...
virtual bool	calculateConstantValues (const bool &have_atoms)
	Used to calculate constant values in startup. More...
void	calculateFromPDB (const PDB &)
	Calculate the action given a pdb file as input. More...
void	calculateNumericalDerivatives (ActionWithValue *av) override
	N.B. More...
virtual bool	calculateOnUpdate ()
	This is used to check if we run calculate during the update step. More...
virtual bool	canBeAfterInChain (ActionWithVector *av)
	Check if we can be after another ActionWithVector. More...
ActionAtomistic *	castToActionAtomistic () noexcept final
virtual ActionForInterface *	castToActionForInterface () noexcept
virtual ActionShortcut *	castToActionShortcut () noexcept
virtual ActionToGetData *	castToActionToGetData () noexcept
virtual ActionToPutData *	castToActionToPutData () noexcept
virtual ActionWithArguments *	castToActionWithArguments () noexcept
ActionWithArguments *	castToActionWithArguments () noexcept final
virtual ActionWithValue *	castToActionWithValue () noexcept
	Specialized casts, to make PlumedMain run faster. More...
ActionWithValue *	castToActionWithValue () noexcept final
	Specialized casts, to make PlumedMain run faster. More...
virtual ActionWithVirtualAtom *	castToActionWithVirtualAtom () noexcept
virtual DomainDecomposition *	castToDomainDecomposition () noexcept
virtual PbcAction *	castToPbcAction () noexcept
void	changeBox (const Tensor &newbox)
	Change the box shape. More...
virtual void	checkFieldsAllowed ()
bool	checkForDependency (Action *)
	Check that this action does not depend on the action in the argument. More...
virtual bool	checkForTaskForce (const unsigned &itask, const Value *myval) const
	Check if there is a force that needs to be accumulated on the ith task. More...
virtual bool	checkNeedsGradients () const
	Check if the action needs gradient. More...
virtual bool	checkNumericalDerivatives () const
	Check if numerical derivatives should be performed. More...
bool	checkNumericalDerivatives () const override
	Check if numerical derivatives should be used. More...
void	checkRead ()
	Check if Action was properly read. More...
virtual int	checkTaskStatus (const unsigned &taskno, int &flag) const
	Check the status of the ith task. More...
bool	checkUpdate () const
	Check if action should be updated. More...
std::string	cite (const std::string &s)
	Cite a paper see PlumedMain::cite. More...
void	clearDependencies ()
	Clear the dependence list for this Action. More...
void	clearDerivatives (const bool &force=false) override
	We override clearDerivatives here to prevent data in streams from being deleted. More...
void	clearInputForces (const bool &force=false) override
	We override clearInputForces here to ensure that forces are deleted from all values. More...
virtual void	clearOptions ()
void	componentIsNotPeriodic (const std::string &name)
	Set your value component to have no periodicity. More...
void	componentIsPeriodic (const std::string &name, const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...
Value *	copyOutput (const std::string &name) const
	Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
Value *	copyOutput (const unsigned &n) const
	Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions) You should NEVER use this routine to refer to the components of your PLMD::Action. More...
virtual void	deactivate ()
	Set action to inactive. More...
double	difference (int, double, double) const
	Takes the difference taking into account pbc for arg i. More...
virtual bool	doNotCalculateDerivatives () const
	Are we not calculating derivatives. More...
void	doNotForce ()
	Skip atom forces - use with care. More...
void	doNotRetrieve ()
	Skip atom retrieval - use with care. More...
void	error (const std::string &msg) const
	Crash calculation and print documentation. More...
bool	exists (const std::string &name) const
	Check if a value with a particular name is present. More...
void	exit (int c=0)
	Exit with error code c. More...
int	fclose (FILE *fp)
	Closes a file opened with Action::fclose(). More...
void	fflush ()
	Tell to the Action to flush open files. More...
virtual void	finishChainBuild (ActionWithVector *act)
	This is overwritten within ActionWithMatrix and is used to build the chain of just matrix actions. More...
void	finishComputations (const std::vector< double > &buf)
	This is to transfer data from the buffer to the final value. More...
FILE *	fopen (const char *path, const char *mode)
	Opens a file. More...
virtual void	gatherForcesOnStoredValue (const Value *myval, const unsigned &itask, const MultiValue &myvals, std::vector< double > &forces) const
	Gather the forces on a particular value. More...
virtual void	gatherProcesses (std::vector< double > &buffer)
	Gather all the data from the MPI processes. More...
virtual void	gatherStoredValue (const unsigned &valindex, const unsigned &code, const MultiValue &myvals, const unsigned &bufstart, std::vector< double > &buffer) const
	Gather the values that we intend to store in the buffer. More...
virtual void	gatherThreads (const unsigned &nt, const unsigned &bufsize, const std::vector< double > &omp_buffer, std::vector< double > &buffer, MultiValue &myvals)
	Gather the data from all the OpenMP threads. More...
AtomNumber	getAbsoluteIndex (int i) const
	Get the absolute index of an atom. More...
virtual const std::vector< AtomNumber > &	getAbsoluteIndexes () const
	Get the vector of absolute indexes. More...
virtual void	getAdditionalTasksRequired (ActionWithVector *action, std::vector< unsigned > &atasks)
	Get the additional tasks that are required here. More...
void	getAllActionLabelsInChain (std::vector< std::string > &mylabels) const
	Get every the label of every value that is calculated in this chain. More...
virtual void	getAllActionLabelsInMatrixChain (std::vector< std::string > &matchain) const
	This is overridden in ActionWithMatrix. More...
double	getArgument (const unsigned n) const
	Returns the value of an argument. More...
virtual const std::vector< Value * > &	getArguments () const
	Returns an array of pointers to the arguments. More...
const Tensor &	getBox () const
	Get box shape. More...
double	getCharge (int i) const
	Get charge of i-th atom. More...
std::string	getComponentsList () const
	get a string that contains all the available components More...
std::vector< std::string >	getComponentsVector () const
	get a vector that contains the label for all the components More...
bool	getCPT () const
	Return true if we are doing at a checkpoint step. More...
std::string	getDefaultString () const
	Get the defaults. More...
const Dependencies &	getDependencies () const
	Return dependencies. More...
const double &	getEnergy () const
	Get energy. More...
bool	getExchangeStep () const
	Check if we are on an exchange step. More...
ActionWithVector *	getFirstActionInChain ()
const ActionWithVector *	getFirstActionInChain () const
	Return a pointer to the first action in the chain. More...
Vector	getForce (const std::pair< std::size_t, std::size_t > &a) const
	Get the force acting on a particular atom. More...
Vector	getGlobalPosition (const std::pair< std::size_t, std::size_t > &) const
	Get position of i-th atom (access by absolute AtomNumber). More...
void	getGradient (const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const
	Transfer the gradients. More...
double	getkBT ()
	Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code. More...
std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string. More...
const std::string &	getLabel () const
	Returns the label. More...
double	getMass (int i) const
	Get mass of i-th atom. More...
virtual void	getMatrixColumnTitles (std::vector< std::string > &argnames) const
	Get the titles to use for the columns of the matrix. More...
const std::string &	getName () const
	Returns the name. More...
virtual unsigned	getNumberOfArguments () const
	Returns the number of arguments. More...
unsigned	getNumberOfAtoms () const
	Get number of available atoms. More...
int	getNumberOfComponents () const
	Returns the number of values defined. More...
virtual unsigned	getNumberOfDerivatives ()=0
void	getNumberOfStreamedDerivatives (unsigned &nderivatives, Value *stopat)
	Get the number of derivatives in the stream. More...
virtual void	getNumberOfTasks (unsigned &ntasks)
	Find out how many tasks we need to perform in this loop. 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...
double	getOutputQuantity (const unsigned j) const
	Get the value of one of the components of the PLMD::Action. More...
const Pbc &	getPbc () const
	Get reference to Pbc. More...
Value *	getPntrToArgument (const unsigned n) const
	Return a pointer to specific argument. More...
const Vector &	getPosition (int) const
	Get position of i-th atom (access by relative index) More...
const std::vector< Vector > &	getPositions () const
	Get the array of all positions. More...
double	getProjection (unsigned i, unsigned j) const
	Get the scalar product between the gradients of two variables. More...
bool	getRestart () const
	Return true if we are doing a restart. More...
long long int	getStep () const
	Return the present timestep. More...
double	getTime () const
	Return the present time. More...
double	getTimeStep () const
	Return the timestep. More...
unsigned	getTotAtoms () const
	Get total number of atoms, including virtual ones. More...
const std::vector< AtomNumber > &	getUnique () const
const std::vector< AtomNumber > &	getUniqueLocal () const
Tensor	getVirial () const
	Get the virial that is acting. More...
bool	hasStoredArguments () const
	Check if there are any stored values in arguments. More...
void	interpretAtomList (std::vector< std::string > &strings, std::vector< AtomNumber > &t)
	Convert a set of read in strings into an atom list (this is used in parseAtomList) More...
bool	isActive () const
	Check if action is active. More...
virtual bool	isInSubChain (unsigned &nder)
	Check if we are in a subchain. More...
bool	isOptionOn (const std::string &s) const
	Check if an option is on. More...
void	lockRequests () override
void	makeWhole ()
	Make atoms whole, assuming they are in the proper order. More...
double &	modifyForceOnEnergy ()
	Get a reference to force on energy. More...
template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. More...
bool	parseArgumentList (const std::string &key, int i, std::vector< Value * > &args)
	Parse a numbered list of arguments. More...
void	parseArgumentList (const std::string &key, std::vector< Value * > &args)
	Parse a list of arguments. 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	parseAtomList (const std::string &key, std::vector< AtomNumber > &t)
	Parse a list of atoms without a numbered keyword. More...
void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...
template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...
template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...
template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...
void	pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
	Applies PBCs to a seriens of positions or distances. More...
Vector	pbcDistance (const Vector &, const Vector &) const
	Compute the pbc distance between two positions. More...
virtual void	performTask (const unsigned &current, MultiValue &myvals) const =0
	This we override to perform each individual task. More...
virtual void	prepare () override
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...
void	readAtomsFromPDB (const PDB &pdb) override
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...
void	requestArguments (const std::vector< Value * > &arg)
	Setup the dependencies. More...
void	requestAtoms (const std::vector< AtomNumber > &a, const bool clearDep=true)
	Request an array of atoms. More...
void	requestExtraDependencies (const std::vector< Value * > &extra)
void	retrieveAtoms (const bool &force=false) override
virtual void	runFinalJobs ()
	RunFinalJobs This method is called once at the very end of the calculation. More...
void	setForcesOnAtoms (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the forces to the atoms. More...
void	setForcesOnCell (const double *forcesToApply, std::size_t size, unsigned &ind)
	Add the virial forces (span-like syntax) More...
void	setForcesOnCell (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the virial forces. More...
void	setGlobalPosition (const std::pair< std::size_t, std::size_t > &, const Vector &pos)
	Modify position of i-th atom (access by absolute AtomNumber). More...
void	setGradients (Value *myval, unsigned &start) const
	Get the gradient for this action. More...
virtual void	setGradientsIfNeeded ()
	Calculate the gradients and store them for all the values (need for projections) More...
void	setNotPeriodic ()
	Set your default value to have no periodicity. More...
virtual void	setOption (const std::string &s)
void	setPeriodic (const std::string &min, const std::string &max)
	Set the value to be periodic with a particular domain. More...
void	setupConstantValues (const bool &have_atoms)
	This calculates any values that are constant and ensures that we don't calculate these actions on every timestep. More...
virtual void	setupStreamedComponents (const std::string &headstr, unsigned &nquants, unsigned &nmat, unsigned &maxcol, unsigned &nbookeeping)
	setup the streamed quantities More...
void	setValue (Value *, double)
	Set the value. More...
virtual void	switchTaskReduction (const bool &task_reduction, ActionWithVector *aselect)
	Can be used to reduce the number of tasks that are performed when you use an ation from elsewhere. More...
virtual void	turnOnDerivatives ()
	Activate the calculation of derivatives. More...
void	unlockRequests () override
virtual void	update ()
	Update. More...
virtual void	updateAdditionalIndices (const unsigned &ostrn, MultiValue &myvals) const
	This is used to ensure that all indices are updated when you do local average. More...
virtual void	updateForceTasksFromValue (const Value *myval, std::vector< unsigned > &force_tasks) const
	Get the force tasks that are active for this action. More...
void	useNumericalDerivatives ()
	This forces the class to use numerical derivatives. More...
void	warning (const std::string &msg)
	Issue a warning. More...
virtual std::string	writeInGraph () const
	Get the info on what to calculate. More...

Static Public Member Functions
static void	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...
static void	interpretArgumentList (const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg)
	Convert a list of argument names into a list of pointers to the values. More...
static void	noAnalyticalDerivatives (Keywords &keys)
	Insist that numerical derivatives should always be used for an action and make this fact appear in the manual. More...
static void	registerKeywords (Keywords &keys)
static void	useCustomisableComponents (Keywords &keys)
	The components in the action will depend on the user. More...

Public Attributes
Communicator &	comm
std::set< FILE * >	files
const Keywords &	keywords
Log &	log
	Reference to the log stream. More...
Communicator &	multi_sim_comm
PlumedMain &	plumed
	Reference to main plumed object. More...

Protected Member Functions
bool	argumentDependsOn (const std::string &headstr, ActionWithVector *faction, Value *thearg)
	Check if the arguments of this action depend on thearg. More...
unsigned	buildArgumentStore (const unsigned &argstart)
	This sets up the arguments at the start of the calculation. More...
bool	checkForForces ()
	Accumulate the forces from the Values. More...
void	expandArgKeywordInPDB (const PDB &pdb)
	This changes the arg keyword in the pdb file. More...
const Value *	getConstPntrToComponent (int i) const
	Get a const pointer to the ith component. More...
const std::vector< double > &	getForcesToApply () const
	Get the forces to apply. More...
double	getKBoltzmann () const
	Get the value of Boltzmann's constant. More...
std::vector< unsigned > &	getListOfActiveTasks (ActionWithVector *action)
	Get the list of tasks that are active. More...
Value *	getPntrToComponent (const std::string &name)
	Return a pointer to the value by name. More...
Value *	getPntrToComponent (int i)
	Return a pointer to the component by index. More...
Value *	getPntrToValue ()
	Get a pointer to the default value. More...
const Units &	getUnits () const
	Get the units that we are operating in. More...
std::pair< std::size_t, std::size_t >	getValueIndices (const AtomNumber &i) const
	Used to interpret whether this index is a virtual atom or a real atom. More...
void	runAllTasks ()
	Run all the tasks in the list. More...
bool	runInSerial () const
	Run all calculations in serial. More...
void	setExtraCV (const std::string &name)
void	setValue (const double &d)
	Set the default value (the one without name) More...
void	updateTaskListReductionStatus ()
	This updates whether or not we are using all the task reduction stuff. More...
bool	usingNaturalUnits () const
	Are we using natural units. More...

Protected Attributes
std::vector< unsigned >	arg_deriv_starts
	A vector that contains the start point for the argument derivatives. More...
bool	chargesWereSet
bool	done_in_chain
	Assert if this action is part of a chain. More...

Private Member Functions
bool	addActionToChain (const std::vector< std::string > &alabels, ActionWithVector *act)
	Add this action to the recursive chain. More...
void	addForcesToInput (const std::vector< double > &forcesToApply, unsigned &ind)
	Add the gathered forces to the inputs across the whole chain. More...
void	broadcastThatTasksAreReduced (ActionWithVector *aselect)
	Send information to arguments that tasks are reduced in depedent actions. More...
void	canReduceTasks (std::vector< ActionWithVector * > &task_reducing_actions)
	Check if this ation can reduce the number of tasks we perform. More...
bool	checkChainForNonScalarForces () const
	Check the chain for non scalar forces. More...
bool	checkComponentsForForce () const
	Check if a force has been added on one of the components of this action. More...
bool	checkForGrids (unsigned &nder) const
	Check if there are any grids in the stream. More...
void	gatherAccumulators (const unsigned &taskCode, const MultiValue &myvals, std::vector< double > &buffer) const
	Gather the values that we intend to store in the buffer. More...
void	gatherForces (const unsigned &i, const MultiValue &myvals, std::vector< double > &forces) const
	Gather the forces on non-scalar quantities. More...
ActionWithVector *	getActionWithDerivatives (ActionWithVector *depaction)
	Work backwards through the chain to find an action that has either stored arguments or derivatives. More...
int	getComponent (const std::string &name) const
	Return the index for the component named name. More...
void	getForceTasks (std::vector< unsigned > &force_tasks) const
	Get the tasks that we need for forces. More...
bool	getNumberOfStoredValues (Value *startat, unsigned &nvals, const unsigned &astart, const std::vector< Value * > &stopat)
	Get the number of stored values in the stream. More...
void	getNumberOfStreamedQuantities (const std::string &headstr, unsigned &nquants, unsigned &nmat, unsigned &maxcol, unsigned &nbookeeping)
	Get the number of quantities in the stream. More...
void	getSizeOfBuffer (const unsigned &nactive_tasks, unsigned &bufsize)
	Get the size of the buffer array that holds the data we are gathering over the MPI loop. More...
unsigned	reallyBuildArgumentStore (const unsigned &argstart)
	This is used to build the argument store when we cannot use the chain. More...
void	runTask (const unsigned &taskno, MultiValue &myvals) const
	Run the task. More...
void	taskIsActive (const unsigned &current, int &flag) const
	Check if a particular task is active at this time. More...
void	updateTaskReductionFlag (bool &head_reduce_tasks)
	Turn on task reduction flag in dependent actions. More...
void	updateUniqueLocal (const bool &useunique, const std::vector< int > &g2l)

Private Attributes
ActionWithVector *	action_to_do_after
	Actions that must be done after this one. More...
ActionWithVector *	action_to_do_before
	Action that must be done before this one. More...
bool	active
	Switch to activate Action on this step. More...
std::vector< unsigned >	active_tasks
	The list of active tasks. More...
Dependencies	after
	Actions on which this Action depends. More...
std::vector< Value * >	arguments
std::vector< std::pair< std::size_t, std::size_t > >	atom_value_ind
std::vector< std::pair< std::size_t, std::vector< std::size_t > > >	atom_value_ind_grouped
bool	atomsWereRetrieved
	Were the atoms retrieved in some earlier action. More...
Value *	boxValue
std::vector< double >	buffer
	The buffer that we use (we keep a copy here to avoid resizing) More...
std::vector< double >	charges
std::vector< Value * >	chargev
std::string	defaults
	The set of default arguments that we are using. More...
bool	doCheckPoint
bool	donotforce
bool	donotretrieve
double	energy
bool	firststep
	This finishes setup on first step to check if actions are calculated during update. More...
double	forceOnEnergy
double	forceOnExtraCV
std::vector< Vector >	forces
std::vector< double >	forcesForApply
	A vector that is used to hold the forces that we will apply on the input quantities. More...
std::vector< AtomNumber >	indexes
std::string	label
	Label of the Action, as set with LABEL= in the plumed.dat file. More...
std::vector< std::string >	line
	Directive line. More...
bool	lockRequestArguments
bool	lockRequestAtoms
std::vector< double >	masses
std::vector< Value * >	masv
const std::string	name
	Name of the directive in the plumed.dat file. More...
bool	never_activate
bool	never_reduce_tasks
	This is turned on if there is some action that needs all the tasks. More...
bool	noderiv
	Are we skipping the calculation of the derivatives. More...
bool	numericalDerivatives
	Are we using numerical derivatives to differentiate. More...
std::set< std::string >	options
	Option that you might have enabled. More...
Pbc &	pbc =*pbc_fwd
ForwardDecl< Pbc >	pbc_fwd
std::vector< Vector >	positions
bool	reduce_tasks
	Are we allowed to reduce the number of tasks being performed. More...
int	replica_index
bool	restart
bool	serial
	Is the calculation to be done in serial. More...
std::vector< ActionWithVector * >	task_control_list
	This is the list of actions that control the tasks that we do here. More...
double	timestep
	Save the timestep here. More...
std::vector< AtomNumber >	unique
	unique should be an ordered set since we later create a vector containing the corresponding indexes More...
std::vector< AtomNumber >	unique_local
bool	unique_local_needs_update
	unique_local should be an ordered set since we later create a vector containing the corresponding indexes More...
double	update_from
	Update only after this time. More...
double	update_until
	Update only until this time. More...
std::vector< unsigned >	valsToForce
std::vector< std::size_t >	value_depends
std::vector< std::unique_ptr< Value > >	values
	An array containing the values for this action. More...
std::vector< Value * >	xpos
	Values that hold information about atom positions and charges. More...
std::vector< Value * >	ypos
std::vector< Value * >	zpos

Friends
class	Value

Member Typedef Documentation

Dependencies

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

inherited

Constructor & Destructor Documentation

ActionWithVector()

PLMD::ActionWithVector::ActionWithVector ( const ActionOptions &  ao )

explicit

~ActionWithVector()

PLMD::ActionWithVector::~ActionWithVector ( )

virtual

Member Function Documentation

actionHasForces()

bool PLMD::ActionAtomistic::actionHasForces ( )

virtualinherited

Reimplemented in PLMD::generic::FitToTemplate, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::DumpAtoms, PLMD::generic::WholeMolecules, PLMD::generic::DumpMassCharge, and PLMD::generic::PrintNDX.

actionInChain()

bool PLMD::ActionWithVector::actionInChain ( ) const

inline

Are we running this command in a chain.

activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

addActionToChain()

bool PLMD::ActionWithVector::addActionToChain ( const std::vector< std::string > &  alabels, ActionWithVector *  act  )

private

Add this action to the recursive chain.

addComponent()

void PLMD::ActionWithValue::addComponent ( const std::string &  name, const std::vector< unsigned > &  shape = std::vector<unsigned>()  )

inherited

Add a value with a name like label.name.

addComponentWithDerivatives()

void PLMD::ActionWithValue::addComponentWithDerivatives ( const std::string &  name, const std::vector< unsigned > &  shape = std::vector<unsigned>()  )

virtualinherited

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

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

addDependency()

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

inherited

Specify that this Action depends on another one.

addForce()

void PLMD::ActionAtomistic::addForce ( const std::pair< std::size_t, std::size_t > &  a, const Vector &  f  )

inlineinherited

Add force to an atom.

addForcesOnArguments()

void PLMD::ActionWithArguments::addForcesOnArguments ( const unsigned &  argstart, const std::vector< double > &  forces, unsigned &  ind, const std::string &  c  )

inherited

Add forces to arguments (used in apply)

addForcesToInput()

void PLMD::ActionWithVector::addForcesToInput ( const std::vector< double > &  forcesToApply, unsigned &  ind  )

private

Add the gathered forces to the inputs across the whole chain.

addValue()

void PLMD::ActionWithValue::addValue ( const std::vector< unsigned > &  shape = std::vector<unsigned>() )

inherited

Add a value with the name label.

addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( const std::vector< unsigned > &  shape = std::vector<unsigned>() )

virtualinherited

Add a value with the name label that has derivatives.

Reimplemented in PLMD::colvar::MultiColvarTemplate< T >.

apply()

void PLMD::ActionWithVector::apply ( )

virtual

Apply the forces on this data.

Implements PLMD::Action.

Reimplemented in PLMD::dimred::ProjectPoints, PLMD::gridtools::FunctionOfGrid< T >, and PLMD::colvar::RMSDVector.

areAllTasksRequired()

virtual void PLMD::ActionWithVector::areAllTasksRequired ( std::vector< ActionWithVector * > &  task_reducing_actions )

inlinevirtual

Do we always need to do all the tasks for this action.

Reimplemented in PLMD::gridtools::KDE, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::volumes::ActionVolume, PLMD::contour::FindContour, and PLMD::function::FunctionOfVector< T >.

argumentDependsOn()

bool PLMD::ActionWithVector::argumentDependsOn ( const std::string &  headstr, ActionWithVector *  faction, Value *  thearg  )

protected

Check if the arguments of this action depend on thearg.

beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

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

Reimplemented in PLMD::generic::UpdateIf.

bringBackInPbc()

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

inlineinherited

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

broadcastThatTasksAreReduced()

void PLMD::ActionWithVector::broadcastThatTasksAreReduced ( ActionWithVector *  aselect )

private

Send information to arguments that tasks are reduced in depedent actions.

buildArgumentStore()

unsigned PLMD::ActionWithVector::buildArgumentStore ( const unsigned &  argstart )

protected

This sets up the arguments at the start of the calculation.

calculate()

virtual void PLMD::Action::calculate ( )

pure virtualinherited

Calculate an Action.

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

Implemented in PLMD::bias::MetaD, PLMD::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::EMMI, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::function::FuncPathMSD, PLMD::generic::FitToTemplate, PLMD::function::FuncSumHills, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::BasisFunctions, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::generic::WrapAround, PLMD::generic::Include, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::vatom::Center, PLMD::colvar::Distance, PLMD::colvar::Dimer, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::colvar::Torsion, PLMD::bias::MovingRestraint, PLMD::bias::External, PLMD::colvar::ContactMap, PLMD::generic::WholeMolecules, PLMD::colvar::ERMSD, PLMD::colvar::Angle, PLMD::crystdistrib::Quaternion, PLMD::isdb::Shadow, PLMD::colvar::Position, PLMD::generic::ResetCell, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::colvar::EEFSolv, PLMD::generic::Read, PLMD::colvar::Dipole, PLMD::vatom::FixedAtom, PLMD::colvar::PathMSDBase, PLMD::colvar::SelectMassCharge, PLMD::adjmat::ActionWithMatrix, PLMD::analysis::Wham, PLMD::bias::ABMD, PLMD::clusters::ClusterDistribution, PLMD::generic::DumpMassCharge, PLMD::colvar::Gyration, PLMD::isdb::FretEfficiency, PLMD::ves::OutputBasisFunctions, PLMD::generic::UpdateIf, PLMD::generic::Print, PLMD::ves::OutputTargetDistribution, PLMD::isdb::PRE, PLMD::membranefusion::memFusionP, PLMD::fourier::FourierTransform, PLMD::membranefusion::fusionPoreNucleationP, PLMD::function::LocalEnsemble, PLMD::bias::LWalls, PLMD::bias::UWalls, PLMD::membranefusion::fusionPoreExpansionP, PLMD::generic::RandomExchanges, PLMD::bias::BiasValue, PLMD::contour::DistanceFromContour, PLMD::isdb::NOE, PLMD::maze::Loss, PLMD::bias::Restraint, PLMD::colvar::DihedralCorrelation, PLMD::colvar::Puckering, PLMD::colvar::Plane, PLMD::analysis::Committor, PLMD::ActionForInterface, PLMD::generic::Flush, PLMD::isdb::Selector, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::function::FunctionOfVector< T >, PLMD::function::Ensemble, PLMD::generic::Constant, PLMD::function::Stats, PLMD::GenericMolInfo, PLMD::dimred::ArrangePoints, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::EndPlumed, PLMD::vatom::Ghost, PLMD::generic::Debug, PLMD::gridtools::FindGridOptimum, PLMD::clusters::ClusterWeights, PLMD::generic::DumpProjections, PLMD::generic::DumpPDB, PLMD::analysis::Accumulate, PLMD::analysis::Collect, PLMD::dimred::ProjectPoints, PLMD::valtools::SelectWithMask, PLMD::colvar::Template, PLMD::vatom::ArgsToVatom, PLMD::generic::DumpVector, PLMD::colvar::Cell, PLMD::adjmat::DiagonalizeMatrix, PLMD::opes::ExpansionCVs, PLMD::valtools::Concatenate, PLMD::analysis::CreateMask, PLMD::clusters::ClusteringBase, PLMD::ActionShortcut, PLMD::adjmat::InvertMatrix, PLMD::colvar::RMSDVector, PLMD::contour::DumpContour, PLMD::colvar::MultiColvarTemplate< T >, PLMD::colvar::Volume, PLMD::function::FunctionOfScalar< T >, PLMD::generic::PrintNDX, PLMD::generic::Time, PLMD::valtools::Flatten, PLMD::adjmat::TransposeMatrix, PLMD::analysis::FarthestPointSampling, PLMD::colvar::ColvarFake, PLMD::mapping::GeometricPath, PLMD::symfunc::ThreeBodyGFunctions, PLMD::colvar::CoordinationBase, PLMD::bias::ReweightBase, PLMD::refdist::MatrixProductDiagonal, PLMD::colvar::PCARMSD, PLMD::ActionAnyorder, PLMD::ActionSetup, PLMD::colvar::RMSD, PLMD::gridtools::ActionWithGrid, PLMD::Group, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::piv::PIV, PLMD::sasa::SASA_HASEL, PLMD::sasa::SASA_LCPO, PLMD::fisst::FISST, PLMD::isdb::Rescale, PLMD::maze::OptimizerBias, PLMD::funnel::Funnel, PLMD::function::FuncPathGeneral, PLMD::funnel::FUNNEL_PS, PLMD::function::annfunc::ANN, PLMD::isdb::Caliber, PLMD::maze::Optimizer, PLMD::s2cm::S2ContactModel, PLMD::colvar::ProjectionOnAxis, PLMD::isdb::Select, PLMD::mapping::PathReparameterization, PLMD::volumes::ActionVolume, PLMD::mapping::PathDisplacements, PLMD::ActionToGetData, PLMD::analysis::GatherReplicas, and PLMD::contour::DistanceFromSphericalContour.

calculateAtomicNumericalDerivatives()

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

inherited

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

calculateConstantValues()

bool PLMD::ActionWithArguments::calculateConstantValues ( const bool &  have_atoms )

virtualinherited

Used to calculate constant values in startup.

Reimplemented in PLMD::analysis::Accumulate, and PLMD::analysis::Collect.

calculateFromPDB()

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

inherited

Calculate the action given a pdb file as input.

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

calculateNumericalDerivatives()

void PLMD::ActionWithVector::calculateNumericalDerivatives ( ActionWithValue *  a )

overridevirtual

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.

calculateOnUpdate()

bool PLMD::ActionWithValue::calculateOnUpdate ( )

virtualinherited

This is used to check if we run calculate during the update step.

Reimplemented in PLMD::analysis::Accumulate, and PLMD::analysis::Collect.

canBeAfterInChain()

virtual bool PLMD::ActionWithVector::canBeAfterInChain ( ActionWithVector *  av )

inlinevirtual

Check if we can be after another ActionWithVector.

Reimplemented in PLMD::adjmat::Neighbors.

canReduceTasks()

void PLMD::ActionWithVector::canReduceTasks ( std::vector< ActionWithVector * > &  task_reducing_actions )

private

Check if this ation can reduce the number of tasks we perform.

castToActionAtomistic()

ActionAtomistic* PLMD::ActionAtomistic::castToActionAtomistic ( )

inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

castToActionForInterface()

virtual ActionForInterface* PLMD::Action::castToActionForInterface ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionForInterface.

castToActionShortcut()

virtual ActionShortcut* PLMD::Action::castToActionShortcut ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionShortcut.

castToActionToGetData()

virtual ActionToGetData* PLMD::Action::castToActionToGetData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToGetData.

castToActionToPutData()

virtual ActionToPutData* PLMD::Action::castToActionToPutData ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionToPutData.

castToActionWithArguments() [1/2]

virtual ActionWithArguments* PLMD::Action::castToActionWithArguments ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithArguments.

castToActionWithArguments() [2/2]

ActionWithArguments* PLMD::ActionWithArguments::castToActionWithArguments ( )

inlinefinalvirtualnoexceptinherited

Reimplemented from PLMD::Action.

castToActionWithValue() [1/2]

virtual ActionWithValue* PLMD::Action::castToActionWithValue ( )

inlinevirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented in PLMD::ActionWithValue.

castToActionWithValue() [2/2]

ActionWithValue* PLMD::ActionWithValue::castToActionWithValue ( )

inlinefinalvirtualnoexceptinherited

Specialized casts, to make PlumedMain run faster.

Reimplemented from PLMD::Action.

castToActionWithVirtualAtom()

virtual ActionWithVirtualAtom* PLMD::Action::castToActionWithVirtualAtom ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::ActionWithVirtualAtom.

castToDomainDecomposition()

virtual DomainDecomposition* PLMD::Action::castToDomainDecomposition ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::DomainDecomposition.

castToPbcAction()

virtual PbcAction* PLMD::Action::castToPbcAction ( )

inlinevirtualnoexceptinherited

Reimplemented in PLMD::PbcAction.

changeBox()

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

inherited

Change the box shape.

checkChainForNonScalarForces()

bool PLMD::ActionWithVector::checkChainForNonScalarForces ( ) const

private

Check the chain for non scalar forces.

checkComponentsForForce()

bool PLMD::ActionWithVector::checkComponentsForForce ( ) const

private

Check if a force has been added on one of the components of this action.

checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

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

checkForDependency()

bool PLMD::Action::checkForDependency ( Action *  action )

inherited

Check that this action does not depend on the action in the argument.

checkForForces()

bool PLMD::ActionWithVector::checkForForces ( )

protected

Accumulate the forces from the Values.

checkForGrids()

bool PLMD::ActionWithVector::checkForGrids ( unsigned &  nder ) const

private

Check if there are any grids in the stream.

checkForTaskForce()

bool PLMD::ActionWithVector::checkForTaskForce ( const unsigned &  itask, const Value *  myval  ) const

virtual

Check if there is a force that needs to be accumulated on the ith task.

Reimplemented in PLMD::adjmat::ActionWithMatrix, and PLMD::colvar::RMSDVector.

checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

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

checkNumericalDerivatives() [1/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

checkNumericalDerivatives() [2/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlineoverridevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

checkTaskStatus()

virtual int PLMD::ActionWithVector::checkTaskStatus ( const unsigned &  taskno, int &  flag  ) const

inlinevirtual

Check the status of the ith task.

Reimplemented in PLMD::gridtools::KDE, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::volumes::ActionVolume, and PLMD::contour::FindContour.

checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

cite()

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

inherited

Cite a paper see PlumedMain::cite.

clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

clearDerivatives()

void PLMD::ActionWithVector::clearDerivatives ( const bool &  force = false )

overridevirtual

We override clearDerivatives here to prevent data in streams from being deleted.

Reimplemented from PLMD::ActionWithValue.

clearInputForces()

void PLMD::ActionWithVector::clearInputForces ( const bool &  force = false )

overridevirtual

We override clearInputForces here to ensure that forces are deleted from all values.

Reimplemented from PLMD::ActionWithValue.

clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

componentIsNotPeriodic()

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

inherited

Set your value component to have no periodicity.

componentIsPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

componentsAreNotOptional()

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

staticinherited

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

copyOutput() [1/2]

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

inherited

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

Use getPntrToComponent instead.

copyOutput() [2/2]

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

inherited

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

Use getPntrToComponent instead.

deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

difference()

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

inlineinherited

Takes the difference taking into account pbc for arg i.

doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

doNotForce()

void PLMD::ActionAtomistic::doNotForce ( )

inlineinherited

Skip atom forces - use with care.

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

doNotRetrieve()

void PLMD::ActionAtomistic::doNotRetrieve ( )

inlineinherited

Skip atom retrieval - use with care.

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

error()

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

inherited

Crash calculation and print documentation.

exists()

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

inherited

Check if a value with a particular name is present.

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

exit()

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

inherited

Exit with error code c.

expandArgKeywordInPDB()

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

protectedinherited

This changes the arg keyword in the pdb file.

fclose()

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

inherited

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

fflush()

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

finishChainBuild()

void PLMD::ActionWithVector::finishChainBuild ( ActionWithVector *  act )

virtual

This is overwritten within ActionWithMatrix and is used to build the chain of just matrix actions.

Reimplemented in PLMD::adjmat::ActionWithMatrix.

finishComputations()

void PLMD::ActionWithVector::finishComputations

(

const std::vector< double > &

buf

)

This is to transfer data from the buffer to the final value.

fopen()

FILE * PLMD::Action::fopen ( const char *  path, const char *  mode  )

inherited

Opens a file.

This is similar to plain fopen, but with some extra functionality.

• When opened for writing, processors other than the one with rank 0 just open /dev/null
• PlumedMain::fopen is used, so that other tricks may appear (see PlumedMain::fopen)

gatherAccumulators()

void PLMD::ActionWithVector::gatherAccumulators ( const unsigned &  taskCode, const MultiValue &  myvals, std::vector< double > &  buffer  ) const

private

Gather the values that we intend to store in the buffer.

gatherForces()

void PLMD::ActionWithVector::gatherForces ( const unsigned &  i, const MultiValue &  myvals, std::vector< double > &  forces  ) const

private

Gather the forces on non-scalar quantities.

gatherForcesOnStoredValue()

void PLMD::ActionWithVector::gatherForcesOnStoredValue ( const Value *  myval, const unsigned &  itask, const MultiValue &  myvals, std::vector< double > &  forces  ) const

virtual

Gather the forces on a particular value.

Reimplemented in PLMD::adjmat::ActionWithMatrix, PLMD::gridtools::KDE, PLMD::gridtools::InterpolateGrid, and PLMD::colvar::RMSDVector.

gatherProcesses()

void PLMD::ActionWithVector::gatherProcesses ( std::vector< double > &  buffer )

virtual

Gather all the data from the MPI processes.

Reimplemented in PLMD::adjmat::ActionWithMatrix.

gatherStoredValue()

void PLMD::ActionWithVector::gatherStoredValue ( const unsigned &  valindex, const unsigned &  code, const MultiValue &  myvals, const unsigned &  bufstart, std::vector< double > &  buffer  ) const

virtual

Gather the values that we intend to store in the buffer.

Reimplemented in PLMD::contour::FindSphericalContour, PLMD::contour::FindContourSurface, PLMD::gridtools::KDE, PLMD::adjmat::ActionWithMatrix, PLMD::gridtools::FunctionOfGrid< T >, PLMD::adjmat::Voronoi, PLMD::colvar::RMSDVector, and PLMD::gridtools::InterpolateGrid.

gatherThreads()

void PLMD::ActionWithVector::gatherThreads ( const unsigned &  nt, const unsigned &  bufsize, const std::vector< double > &  omp_buffer, std::vector< double > &  buffer, MultiValue &  myvals  )

virtual

Gather the data from all the OpenMP threads.

Reimplemented in PLMD::adjmat::ActionWithMatrix.

getAbsoluteIndex()

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

inlineinherited

Get the absolute index of an atom.

getAbsoluteIndexes()

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

inlinevirtualinherited

Get the vector of absolute indexes.

getActionWithDerivatives()

ActionWithVector * PLMD::ActionWithVector::getActionWithDerivatives ( ActionWithVector *  depaction )

private

Work backwards through the chain to find an action that has either stored arguments or derivatives.

getAdditionalTasksRequired()

void PLMD::ActionWithVector::getAdditionalTasksRequired ( ActionWithVector *  action, std::vector< unsigned > &  atasks  )

virtual

Get the additional tasks that are required here.

Reimplemented in PLMD::adjmat::MatrixTimesMatrix, and PLMD::adjmat::AdjacencyMatrixBase.

getAllActionLabelsInChain()

void PLMD::ActionWithVector::getAllActionLabelsInChain

(

std::vector< std::string > &

mylabels

)

const

Get every the label of every value that is calculated in this chain.

getAllActionLabelsInMatrixChain()

virtual void PLMD::ActionWithVector::getAllActionLabelsInMatrixChain ( std::vector< std::string > &  matchain ) const

inlinevirtual

This is overridden in ActionWithMatrix.

Reimplemented in PLMD::adjmat::ActionWithMatrix.

getArgument()

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

inlineinherited

Returns the value of an argument.

getArguments()

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

inlinevirtualinherited

Returns an array of pointers to the arguments.

getBox()

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

inlineinherited

Get box shape.

getCharge()

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

inlineinherited

Get charge of i-th atom.

getComponent()

int PLMD::ActionWithValue::getComponent ( const std::string &  name ) const

privateinherited

Return the index for the component named name.

getComponentsList()

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

inherited

get a string that contains all the available components

getComponentsVector()

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

inherited

get a vector that contains the label for all the components

getConstPntrToComponent()

const Value * PLMD::ActionWithValue::getConstPntrToComponent ( int  i ) const

protectedinherited

Get a const pointer to the ith component.

getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

getDefaultString()

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

inlineinherited

Get the defaults.

getDependencies()

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

inlineinherited

Return dependencies.

getEnergy()

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

inlineinherited

Get energy.

getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

getFirstActionInChain() [1/2]

ActionWithVector* PLMD::ActionWithVector::getFirstActionInChain

(

)

getFirstActionInChain() [2/2]

ActionWithVector * PLMD::ActionWithVector::getFirstActionInChain

(

)

const

Return a pointer to the first action in the chain.

getForce()

Vector PLMD::ActionAtomistic::getForce ( const std::pair< std::size_t, std::size_t > &  a ) const

inlineinherited

Get the force acting on a particular atom.

getForcesToApply()

const std::vector< double > & PLMD::ActionWithValue::getForcesToApply ( ) const

inlineprotectedinherited

Get the forces to apply.

getForceTasks()

void PLMD::ActionWithVector::getForceTasks ( std::vector< unsigned > &  force_tasks ) const

private

Get the tasks that we need for forces.

getGlobalPosition()

Vector PLMD::ActionAtomistic::getGlobalPosition ( const std::pair< std::size_t, std::size_t > &  a ) const

inlineinherited

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

With direct access to the global atom array.

Warning

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

getGradient()

void PLMD::ActionAtomistic::getGradient ( const unsigned &  ind, Vector &  deriv, std::map< AtomNumber, Vector > &  gradients  ) const

inherited

Transfer the gradients.

getKBoltzmann()

double PLMD::Action::getKBoltzmann ( ) const

protectedinherited

Get the value of Boltzmann's constant.

getkBT()

double PLMD::Action::getkBT ( )

inherited

Get the value of kBT by either reading the TEMP keyword and multiplying the temperature by Boltzmann's constant or get it fro the MD code.

getKeyword()

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

inherited

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

getLabel()

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

inlineinherited

Returns the label.

getListOfActiveTasks()

std::vector< unsigned > & PLMD::ActionWithVector::getListOfActiveTasks ( ActionWithVector *  action )

protected

Get the list of tasks that are active.

getMass()

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

inlineinherited

Get mass of i-th atom.

getMatrixColumnTitles()

void PLMD::ActionWithValue::getMatrixColumnTitles ( std::vector< std::string > &  argnames ) const

virtualinherited

Get the titles to use for the columns of the matrix.

Reimplemented in PLMD::adjmat::VStack, and PLMD::valtools::SelectWithMask.

getName()

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

inlineinherited

Returns the name.

getNumberOfArguments()

unsigned PLMD::ActionWithArguments::getNumberOfArguments ( ) const

inlinevirtualinherited

Returns the number of arguments.

getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

getNumberOfDerivatives()

virtual unsigned PLMD::ActionWithValue::getNumberOfDerivatives ( )

pure virtualinherited

Implemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::FitToTemplate, PLMD::ves::Optimizer, PLMD::generic::Plumed, PLMD::contour::FindSphericalContour, PLMD::generic::Read, PLMD::contour::FindContourSurface, PLMD::clusters::ClusterDistribution, PLMD::fourier::FourierTransform, PLMD::gridtools::KDE, PLMD::Colvar, PLMD::generic::Constant, PLMD::gridtools::InterpolateGrid, PLMD::gridtools::ReadGridInSetup, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::dimred::ArrangePoints, PLMD::bias::Bias, PLMD::adjmat::FunctionOfMatrix< T >, PLMD::function::FunctionOfVector< T >, PLMD::contour::DistanceFromContourBase, PLMD::gridtools::FindGridOptimum, PLMD::clusters::ClusterWeights, PLMD::opes::ExpansionCVs, PLMD::adjmat::AdjacencyMatrixBase, PLMD::vatom::ArgsToVatom, PLMD::ActionForInterface, PLMD::function::Function, PLMD::generic::Time, PLMD::valtools::Concatenate, PLMD::valtools::SelectWithMask, PLMD::analysis::CreateMask, PLMD::clusters::ClusteringBase, PLMD::adjmat::DiagonalizeMatrix, PLMD::adjmat::InvertMatrix, PLMD::valtools::Flatten, PLMD::symfunc::ThreeBodyGFunctions, PLMD::adjmat::VStack, PLMD::analysis::FarthestPointSampling, PLMD::mapping::GeometricPath, PLMD::colvar::MultiColvarTemplate< T >, PLMD::colvar::RMSDVector, PLMD::adjmat::Neighbors, PLMD::adjmat::TransposeMatrix, PLMD::gridtools::FunctionOfGrid< T >, PLMD::adjmat::Voronoi, PLMD::refdist::MatrixProductDiagonal, PLMD::bias::ReweightBase, PLMD::contour::FindContour, PLMD::analysis::Wham, PLMD::ActionWithVirtualAtom, PLMD::adjmat::MatrixTimesMatrix, PLMD::volumes::ActionVolume, PLMD::analysis::Accumulate, PLMD::analysis::Collect, PLMD::dimred::ProjectPoints, PLMD::mapping::PathDisplacements, PLMD::crystdistrib::QuaternionBondProductMatrix, PLMD::analysis::GatherReplicas, PLMD::adjmat::OuterProduct, PLMD::adjmat::MatrixTimesVector, PLMD::adjmat::TorsionsMatrix, and PLMD::crystdistrib::QuaternionProductMatrix.

getNumberOfStoredValues()

bool PLMD::ActionWithVector::getNumberOfStoredValues ( Value *  startat, unsigned &  nvals, const unsigned &  astart, const std::vector< Value * > &  stopat  )

private

Get the number of stored values in the stream.

getNumberOfStreamedDerivatives()

void PLMD::ActionWithVector::getNumberOfStreamedDerivatives	(	unsigned &	nderivatives,
		Value *	stopat
	)

Get the number of derivatives in the stream.

getNumberOfStreamedQuantities()

void PLMD::ActionWithVector::getNumberOfStreamedQuantities ( const std::string &  headstr, unsigned &  nquants, unsigned &  nmat, unsigned &  maxcol, unsigned &  nbookeeping  )

private

Get the number of quantities in the stream.

getNumberOfTasks()

void PLMD::ActionWithVector::getNumberOfTasks ( unsigned &  ntasks )

virtual

Find out how many tasks we need to perform in this loop.

Reimplemented in PLMD::gridtools::KDE, PLMD::volumes::ActionVolume, and PLMD::contour::FindContour.

getOutputQuantity() [1/2]

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

inlineinherited

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

getOutputQuantity() [2/2]

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

inlineinherited

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

getPbc()

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

inlineinherited

Get reference to Pbc.

getPntrToArgument()

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

inlineinherited

Return a pointer to specific argument.

getPntrToComponent() [1/2]

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

protectedinherited

Return a pointer to the value by name.

getPntrToComponent() [2/2]

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

protectedinherited

Return a pointer to the component by index.

getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

inlineprotectedinherited

Get a pointer to the default value.

getPosition()

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

inlineinherited

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

getPositions()

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

inlineinherited

Get the array of all positions.

getProjection()

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

inherited

Get the scalar product between the gradients of two variables.

getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

getSizeOfBuffer()

void PLMD::ActionWithVector::getSizeOfBuffer ( const unsigned &  nactive_tasks, unsigned &  bufsize  )

private

Get the size of the buffer array that holds the data we are gathering over the MPI loop.

getStep()

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

inherited

Return the present timestep.

getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

getTotAtoms()

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inherited

Get total number of atoms, including virtual ones.

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

getUnique()

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

inlineinherited

getUniqueLocal()

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

inlineinherited

getUnits()

const Units & PLMD::Action::getUnits ( ) const

protectedinherited

Get the units that we are operating in.

getValueIndices()

std::pair< std::size_t, std::size_t > PLMD::ActionAtomistic::getValueIndices ( const AtomNumber &  i ) const

protectedinherited

Used to interpret whether this index is a virtual atom or a real atom.

getVirial()

Tensor PLMD::ActionAtomistic::getVirial ( ) const

inherited

Get the virial that is acting.

hasStoredArguments()

bool PLMD::ActionWithVector::hasStoredArguments

(

)

const

Check if there are any stored values in arguments.

interpretArgumentList()

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

staticinherited

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

interpretAtomList()

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

inherited

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

isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

isInSubChain()

virtual bool PLMD::ActionWithVector::isInSubChain ( unsigned &  nder )

inlinevirtual

Check if we are in a subchain.

Reimplemented in PLMD::volumes::ActionVolume, and PLMD::adjmat::MatrixTimesVector.

isOptionOn()

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

inlineinherited

Check if an option is on.

lockRequests()

void PLMD::ActionWithVector::lockRequests ( )

overridevirtual

Reimplemented from PLMD::ActionAtomistic.

makeWhole()

void PLMD::ActionAtomistic::makeWhole ( )

inherited

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

modifyForceOnEnergy()

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

noAnalyticalDerivatives()

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

staticinherited

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

parse()

template<class T >

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

inherited

Parse one keyword as generic type.

parseArgumentList() [1/2]

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

inherited

Parse a numbered list of arguments.

parseArgumentList() [2/2]

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

inherited

Parse a list of arguments.

parseAtomList() [1/2]

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

inherited

Parse an list of atom with a numbred keyword.

parseAtomList() [2/2]

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

inherited

Parse a list of atoms without a numbered keyword.

parseFlag()

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

inherited

Parse one keyword as boolean flag.

parseNumbered()

template<class T >

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

inherited

Parse one numbered keyword as generic type.

parseNumberedVector()

template<class T >

bool PLMD::Action::parseNumberedVector ( const std::string &  key, const int  no, std::vector< T > &  t  )

inherited

Parse a vector with a number.

parseVector()

template<class T >

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

inherited

Parse one keyword as std::vector.

pbcApply()

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

inherited

Applies PBCs to a seriens of positions or distances.

pbcDistance()

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

inlineinherited

Compute the pbc distance between two positions.

performTask()

virtual void PLMD::ActionWithVector::performTask ( const unsigned &  current, MultiValue &  myvals  ) const

pure virtual

This we override to perform each individual task.

Implemented in PLMD::adjmat::ActionWithMatrix, PLMD::symfunc::ThreeBodyGFunctions, PLMD::refdist::MatrixProductDiagonal, PLMD::contour::FindSphericalContour, PLMD::contour::FindContourSurface, PLMD::gridtools::KDE, PLMD::fourier::FourierTransform, PLMD::function::FunctionOfVector< T >, PLMD::gridtools::InterpolateGrid, PLMD::gridtools::ReadGridInSetup, PLMD::gridtools::FindGridOptimum, PLMD::dimred::ProjectPoints, PLMD::gridtools::FunctionOfGrid< T >, PLMD::mapping::GeometricPath, PLMD::colvar::RMSDVector, PLMD::contour::FindContour, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::colvar::MultiColvarTemplate< T >, and PLMD::volumes::ActionVolume.

prepare()

void PLMD::ActionWithVector::prepare ( )

overridevirtual

Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation.

Typical case is for collective variables which would like to change their list of requested atoms. By default (if not overridden) does nothing.

Reimplemented from PLMD::Action.

Reimplemented in PLMD::adjmat::FunctionOfMatrix< T >, PLMD::function::FunctionOfVector< T >, PLMD::adjmat::AdjacencyMatrixBase, PLMD::adjmat::MatrixTimesMatrix, PLMD::dimred::ProjectPoints, PLMD::adjmat::OuterProduct, PLMD::adjmat::VStack, PLMD::adjmat::MatrixTimesVector, and PLMD::adjmat::Voronoi.

readAtomsFromPDB()

void PLMD::ActionAtomistic::readAtomsFromPDB ( const PDB &  pdb )

overridevirtualinherited

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

Reimplemented from PLMD::Action.

reallyBuildArgumentStore()

unsigned PLMD::ActionWithVector::reallyBuildArgumentStore ( const unsigned &  argstart )

private

This is used to build the argument store when we cannot use the chain.

registerKeywords()

void PLMD::ActionWithVector::registerKeywords ( Keywords &  keys )

static

requestArguments()

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

inherited

Setup the dependencies.

requestAtoms()

void PLMD::ActionAtomistic::requestAtoms ( const std::vector< AtomNumber > &  a, const bool  clearDep = true  )

inherited

Request an array of atoms.

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

requestExtraDependencies()

void PLMD::ActionWithArguments::requestExtraDependencies ( const std::vector< Value * > &  extra )

inherited

retrieveAtoms()

void PLMD::ActionWithVector::retrieveAtoms ( const bool &  force = false )

overridevirtual

Reimplemented from PLMD::ActionAtomistic.

runAllTasks()

void PLMD::ActionWithVector::runAllTasks ( )

protected

Run all the tasks in the list.

runFinalJobs()

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.

runInSerial()

bool PLMD::ActionWithVector::runInSerial ( ) const

inlineprotected

Run all calculations in serial.

runTask()

void PLMD::ActionWithVector::runTask ( const unsigned &  taskno, MultiValue &  myvals  ) const

private

Run the task.

setExtraCV()

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

protectedinherited

setForcesOnAtoms()

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

inherited

Add the forces to the atoms.

setForcesOnCell() [1/2]

void PLMD::ActionAtomistic::setForcesOnCell ( const double *  forcesToApply, std::size_t  size, unsigned &  ind  )

inherited

Add the virial forces (span-like syntax)

setForcesOnCell() [2/2]

void PLMD::ActionAtomistic::setForcesOnCell ( const std::vector< double > &  forcesToApply, unsigned &  ind  )

inherited

Add the virial forces.

setGlobalPosition()

void PLMD::ActionAtomistic::setGlobalPosition ( const std::pair< std::size_t, std::size_t > &  a, const Vector &  pos  )

inlineinherited

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

Warning

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

setGradients()

void PLMD::ActionWithArguments::setGradients ( Value *  myval, unsigned &  start  ) const

inherited

Get the gradient for this action.

setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

virtualinherited

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

Reimplemented in PLMD::ActionForInterface.

setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

setOption()

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

virtualinherited

setPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

setupConstantValues()

void PLMD::Action::setupConstantValues ( const bool &  have_atoms )

inherited

This calculates any values that are constant and ensures that we don't calculate these actions on every timestep.

setupStreamedComponents()

void PLMD::ActionWithVector::setupStreamedComponents ( const std::string &  headstr, unsigned &  nquants, unsigned &  nmat, unsigned &  maxcol, unsigned &  nbookeeping  )

virtual

setup the streamed quantities

Reimplemented in PLMD::adjmat::ActionWithMatrix, PLMD::function::FunctionOfVector< T >, PLMD::adjmat::FunctionOfMatrix< T >, and PLMD::colvar::MultiColvarTemplate< T >.

setValue() [1/2]

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

inlineprotectedinherited

Set the default value (the one without name)

setValue() [2/2]

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

inherited

Set the value.

switchTaskReduction()

virtual void PLMD::ActionWithVector::switchTaskReduction ( const bool &  task_reduction, ActionWithVector *  aselect  )

inlinevirtual

Can be used to reduce the number of tasks that are performed when you use an ation from elsewhere.

taskIsActive()

void PLMD::ActionWithVector::taskIsActive ( const unsigned &  current, int &  flag  ) const

private

Check if a particular task is active at this time.

turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

Reimplemented in PLMD::isdb::EMMI, PLMD::isdb::MetainferenceBase, PLMD::generic::Read, PLMD::adjmat::FunctionOfMatrix< T >, PLMD::function::FunctionOfVector< T >, PLMD::function::FunctionOfScalar< T >, PLMD::adjmat::Neighbors, PLMD::eds::EDS, and PLMD::fisst::FISST.

unlockRequests()

void PLMD::ActionWithVector::unlockRequests ( )

overridevirtual

Reimplemented from PLMD::ActionAtomistic.

update()

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::isdb::CS2Backbone, PLMD::isdb::SAXS, PLMD::bias::PBMetaD, PLMD::ves::VesLinearExpansion, PLMD::isdb::Metainference, PLMD::opes::OPESmetad< mode >, PLMD::isdb::RDC, PLMD::ves::Optimizer, PLMD::gridtools::DumpGrid, PLMD::ves::TargetDistribution, PLMD::opes::OPESexpanded, PLMD::ves::VesDeltaF, PLMD::generic::Plumed, PLMD::bias::MaxEnt, PLMD::generic::DumpAtoms, PLMD::volumes::VolumeTetrapore, PLMD::volumes::VolumeCavity, PLMD::generic::EffectiveEnergyDrift, PLMD::bias::ExtendedLagrangian, PLMD::ves::OutputFesBias, PLMD::isdb::JCoupling, PLMD::generic::Read, PLMD::generic::DumpMassCharge, PLMD::generic::Print, PLMD::isdb::PRE, PLMD::isdb::NOE, PLMD::generic::Flush, PLMD::generic::DumpDerivatives, PLMD::generic::DumpForces, PLMD::generic::DumpProjections, PLMD::generic::DumpPDB, PLMD::analysis::Accumulate, PLMD::analysis::Collect, PLMD::generic::PrintNDX, PLMD::generic::DumpVector, PLMD::contour::DumpContour, PLMD::logmfd::LogMFD, PLMD::eds::EDS, PLMD::fisst::FISST, PLMD::mapping::PathReparameterization, and PLMD::mapping::PathDisplacements.

updateAdditionalIndices()

virtual void PLMD::ActionWithVector::updateAdditionalIndices ( const unsigned &  ostrn, MultiValue &  myvals  ) const

inlinevirtual

This is used to ensure that all indices are updated when you do local average.

Reimplemented in PLMD::adjmat::MatrixTimesVector.

updateForceTasksFromValue()

void PLMD::ActionWithVector::updateForceTasksFromValue ( const Value *  myval, std::vector< unsigned > &  force_tasks  ) const

virtual

Get the force tasks that are active for this action.

Reimplemented in PLMD::gridtools::KDE.

updateTaskListReductionStatus()

void PLMD::ActionWithVector::updateTaskListReductionStatus ( )

protected

This updates whether or not we are using all the task reduction stuff.

updateTaskReductionFlag()

void PLMD::ActionWithVector::updateTaskReductionFlag ( bool &  head_reduce_tasks )

private

Turn on task reduction flag in dependent actions.

updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( const bool &  useunique, const std::vector< int > &  g2l  )

privateinherited

useCustomisableComponents()

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

staticinherited

The components in the action will depend on the user.

useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

usingNaturalUnits()

bool PLMD::Action::usingNaturalUnits ( ) const

protectedinherited

Are we using natural units.

warning()

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

inherited

Issue a warning.

writeInGraph()

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

virtualinherited

Get the info on what to calculate.

Reimplemented in PLMD::generic::Print, PLMD::adjmat::ContactMatrix, PLMD::function::FunctionOfVector< T >, PLMD::adjmat::FunctionOfMatrix< T >, PLMD::generic::PrintNDX, PLMD::function::FunctionOfScalar< T >, and PLMD::gridtools::FunctionOfGrid< T >.

Friends And Related Function Documentation

Value

friend class Value

friend

Member Data Documentation

action_to_do_after

ActionWithVector* PLMD::ActionWithVector::action_to_do_after

private

Actions that must be done after this one.

action_to_do_before

ActionWithVector* PLMD::ActionWithVector::action_to_do_before

private

Action that must be done before this one.

active

bool PLMD::Action::active

privateinherited

Switch to activate Action on this step.

active_tasks

std::vector<unsigned> PLMD::ActionWithVector::active_tasks

private

The list of active tasks.

after

Dependencies PLMD::Action::after

privateinherited

Actions on which this Action depends.

arg_deriv_starts

std::vector<unsigned> PLMD::ActionWithVector::arg_deriv_starts

protected

A vector that contains the start point for the argument derivatives.

arguments

std::vector<Value*> PLMD::ActionWithArguments::arguments

privateinherited

atom_value_ind

std::vector<std::pair<std::size_t, std::size_t > > PLMD::ActionAtomistic::atom_value_ind

privateinherited

atom_value_ind_grouped

std::vector<std::pair<std::size_t,std::vector<std::size_t> > > PLMD::ActionAtomistic::atom_value_ind_grouped

privateinherited

atomsWereRetrieved

bool PLMD::ActionWithVector::atomsWereRetrieved

private

Were the atoms retrieved in some earlier action.

boxValue

Value* PLMD::ActionAtomistic::boxValue

privateinherited

buffer

std::vector<double> PLMD::ActionWithVector::buffer

private

The buffer that we use (we keep a copy here to avoid resizing)

charges

std::vector<double> PLMD::ActionAtomistic::charges

privateinherited

chargesWereSet

bool PLMD::ActionAtomistic::chargesWereSet

protectedinherited

chargev

std::vector<Value*> PLMD::ActionAtomistic::chargev

privateinherited

comm

Communicator& PLMD::Action::comm

inherited

defaults

std::string PLMD::Action::defaults

privateinherited

The set of default arguments that we are using.

doCheckPoint

bool PLMD::Action::doCheckPoint

privateinherited

done_in_chain

bool PLMD::ActionWithVector::done_in_chain

protected

Assert if this action is part of a chain.

donotforce

bool PLMD::ActionAtomistic::donotforce

privateinherited

donotretrieve

bool PLMD::ActionAtomistic::donotretrieve

privateinherited

energy

double PLMD::ActionAtomistic::energy

privateinherited

files

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

inherited

firststep

bool PLMD::ActionWithValue::firststep

privateinherited

This finishes setup on first step to check if actions are calculated during update.

forceOnEnergy

double PLMD::ActionAtomistic::forceOnEnergy

privateinherited

forceOnExtraCV

double PLMD::ActionAtomistic::forceOnExtraCV

privateinherited

forces

std::vector<Vector> PLMD::ActionAtomistic::forces

privateinherited

forcesForApply

std::vector<double> PLMD::ActionWithValue::forcesForApply

privateinherited

A vector that is used to hold the forces that we will apply on the input quantities.

indexes

std::vector<AtomNumber> PLMD::ActionAtomistic::indexes

privateinherited

keywords

const Keywords& PLMD::Action::keywords

inherited

label

std::string PLMD::Action::label

privateinherited

Label of the Action, as set with LABEL= in the plumed.dat file.

line

std::vector<std::string> PLMD::Action::line

privateinherited

Directive line.

This line is progressively erased during Action construction so as to check if all the present keywords are correct.

lockRequestArguments

bool PLMD::ActionWithArguments::lockRequestArguments

privateinherited

lockRequestAtoms

bool PLMD::ActionAtomistic::lockRequestAtoms

privateinherited

log

Log& PLMD::Action::log

inherited

Reference to the log stream.

masses

std::vector<double> PLMD::ActionAtomistic::masses

privateinherited

masv

std::vector<Value*> PLMD::ActionAtomistic::masv

privateinherited

multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

name

const std::string PLMD::Action::name

privateinherited

Name of the directive in the plumed.dat file.

never_activate

bool PLMD::Action::never_activate

privateinherited

never_reduce_tasks

bool PLMD::ActionWithVector::never_reduce_tasks

private

This is turned on if there is some action that needs all the tasks.

noderiv

bool PLMD::ActionWithValue::noderiv

privateinherited

Are we skipping the calculation of the derivatives.

numericalDerivatives

bool PLMD::ActionWithValue::numericalDerivatives

privateinherited

Are we using numerical derivatives to differentiate.

options

std::set<std::string> PLMD::Action::options

privateinherited

Option that you might have enabled.

pbc

Pbc& PLMD::ActionAtomistic::pbc =*pbc_fwd

privateinherited

pbc_fwd

ForwardDecl<Pbc> PLMD::ActionAtomistic::pbc_fwd

privateinherited

plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

positions

std::vector<Vector> PLMD::ActionAtomistic::positions

privateinherited

reduce_tasks

bool PLMD::ActionWithVector::reduce_tasks

private

Are we allowed to reduce the number of tasks being performed.

replica_index

int PLMD::Action::replica_index

privateinherited

restart

bool PLMD::Action::restart

privateinherited

serial

bool PLMD::ActionWithVector::serial

private

Is the calculation to be done in serial.

task_control_list

std::vector<ActionWithVector*> PLMD::ActionWithVector::task_control_list

private

This is the list of actions that control the tasks that we do here.

timestep

double PLMD::Action::timestep

privateinherited

Save the timestep here.

unique

std::vector<AtomNumber> PLMD::ActionAtomistic::unique

privateinherited

unique should be an ordered set since we later create a vector containing the corresponding indexes

unique_local

std::vector<AtomNumber> PLMD::ActionAtomistic::unique_local

privateinherited

unique_local_needs_update

bool PLMD::ActionAtomistic::unique_local_needs_update

privateinherited

unique_local should be an ordered set since we later create a vector containing the corresponding indexes

update_from

double PLMD::Action::update_from

privateinherited

Update only after this time.

update_until

double PLMD::Action::update_until

privateinherited

Update only until this time.

valsToForce

std::vector<unsigned> PLMD::ActionWithValue::valsToForce

privateinherited

value_depends

std::vector<std::size_t> PLMD::ActionAtomistic::value_depends

privateinherited

values

std::vector<std::unique_ptr<Value> > PLMD::ActionWithValue::values

privateinherited

An array containing the values for this action.

xpos

std::vector<Value*> PLMD::ActionAtomistic::xpos

privateinherited

Values that hold information about atom positions and charges.

ypos

std::vector<Value*> PLMD::ActionAtomistic::ypos

privateinherited

zpos

std::vector<Value*> PLMD::ActionAtomistic::zpos

privateinherited

---

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

• core/ActionWithVector.h
• core/ActionWithVector.cpp