This is the abstract base class to use for implementing new methods for analyzing the trajectory, within it there is information as to how to go about implementing a new analysis method. More...

#include <Analysis.h>

Inheritance diagram for PLMD::analysis::Analysis:

[legend]

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

Public Member Functions
	Analysis (const ActionOptions &)

	~Analysis ()

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

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

void	accumulate ()

void	performOperations (const bool &from_update)
	This does the averaging operation. More...

virtual void	performAnalysis ()=0

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

void	runAnalysis ()

bool	isPeriodic ()
	Are the base quantities periodic. More...

virtual void	finalizeWeights (const bool &ignore_weights)
	Convert the stored log weights to proper weights. More...

void	lockRequests ()

void	unlockRequests ()

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

virtual unsigned	getNumberOfDerivatives ()

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

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

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

void	update ()
	Update. More...

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

virtual void	prepareForAveraging ()
	This is done before the averaging comences. More...

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

virtual bool	onStep () const
	Check if the action is active on this step. More...

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

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

bool	checkUpdate () const
	Check if action should be updated. 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...

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

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

std::string	getKeyword (const std::string &key)
	Just read one of the keywords and return the whole thing as a string. 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	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

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

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

virtual std::string	getDocumentation () const

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

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

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

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

virtual void	clearOptions ()

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

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

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

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

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

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

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

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

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

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

virtual void	readAtomsFromPDB (const PDB &)
	This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code. More...

void	readAtomsFromPDB (const PDB &pdb)
	Read in an input file containing atom positions and calculate the action for the atomic configuration therin. More...

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

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

void	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...

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

void	pbcApply (std::vector< Vector > &dlist, unsigned max_index=0) const
	Applies PBCs to a seriens of positions or distances. More...

virtual 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	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...

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

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

void	updateUniqueLocal ()
	updates local unique atoms 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...

virtual void	retrieveAtoms ()

void	applyForces ()

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

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

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...

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...

bool	parseArgumentList (const std::string &key, int i, std::vector< Value *> &args)
	Parse a numbered 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...

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...

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

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

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

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

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

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

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

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

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

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

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

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

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

virtual void	checkFieldsAllowed ()

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

void	lockContributors ()

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

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

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

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

virtual void	finishComputations (const std::vector< double > &buffer)
	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 () const
	Get the number of quantities that are calculated during each task. More...

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

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

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

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

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

virtual void	performTask (const unsigned &, const unsigned &, MultiValue &) const =0
	Calculate one of the functions in the distribution. More...

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

StoreDataVessel *	buildDataStashes (ActionWithVessel *actionThatUses)
	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...

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

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

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

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

virtual void	normalizeVectorDerivatives (MultiValue &myvals) const

Static Public Member Functions
static void	registerKeywords (Keywords &keys)
	Finalize the weights without using the log sums. 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	componentsAreNotOptional (Keywords &keys)
	Puts a message into the manual that the components always output. More...

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

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

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

std::set< FILE * >	files

Communicator &	comm

Communicator &	multi_sim_comm

const Keywords &	keywords

Protected Member Functions
void	parseOutputFile (const std::string &key, std::string &filename)
	This is used to read in output file names for analysis methods. More...

std::string	getMetricName () const
	Get the name of the metric we are using to measure distances. More...

unsigned	getNumberOfDataPoints () const
	Return the number of data points. More...

double	getWeight (const unsigned &idata) const
	Return the weight of the ith point. More...

void	getDataPoint (const unsigned &idata, std::vector< double > &point, double &weight) const
	Retrieve the ith point. More...

bool	getPeriodicityInformation (const unsigned &i, std::string &dmin, std::string &dmax)
	Returns true if argument i is periodic together with the domain. More...

bool	usingMemory () const
	Are we analyzing each data block separately (if we are not this also returns the old normalization ) More...

std::string	getOutputFormat () const
	Return the format to use for numbers in output files. More...

void	setAveragingAction (AveragingVessel *av_vessel, const bool &usetasks)
	Set the averaging action. More...

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

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

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

void	calculateAllVessels (const unsigned &taskCode, MultiValue &myvals, MultiValue &bvals, std::vector< double > &buffer, std::vector< unsigned > &der_list)
	This loops over all the vessels calculating them and also sets all the element derivatives equal to zero. More...

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

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

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

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

Protected Attributes
std::vector< std::string >	argument_names
	List of argument names. More...

std::vector< ReferenceConfiguration * >	data
	The data we are going to analyze. More...

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

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

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

double	cweight

Atoms &	atoms

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

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

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

Private Member Functions
void	readDataFromFile (const std::string &filename)
	Read in data from a file. More...

std::vector< double >	getMetric () const
	Get the metric if we are using malonobius distance and flexible hill. More...

Private Attributes
bool	nomemory
	Are we treating each block of data separately. More...

bool	write_chq
	Are we writing a checkpoint file. More...

bool	reusing_data
	Are we reusing data stored by another analysis action. More...

bool	ignore_reweight
	If we are reusing data are we ignoring the reweighting in that data. More...

Analysis *	mydatastash
	The Analysis action that we are reusing data from. More...

unsigned	freq
	The frequency with which we are performing analysis. More...

unsigned	ndata
	Number of data point we need to run analysis. More...

double	simtemp
	The temperature at which we are running the calculation. More...

double	rtemp
	The temperature at which we want the histogram. More...

bool	needeng
	Do we need the energy (are we reweighting at a different temperature) More...

unsigned	idata
	The piece of data we are inserting. More...

std::vector< double >	logweights
	The weights of all the data points. More...

std::string	ofmt
	Have we analyzed the data for the first time. More...

std::vector< double >	current_args
	Tempory vector to store values of arguments. More...

std::string	metricname
	The type of metric we are using to measure distances. More...

OFile	rfile
	The checkpoint file. More...

Detailed Description

This is the abstract base class to use for implementing new methods for analyzing the trajectory, within it there is information as to how to go about implementing a new analysis method.

Member Typedef Documentation

◆ Dependencies

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

inherited

Constructor & Destructor Documentation

◆ Analysis()

PLMD::analysis::Analysis::Analysis ( const ActionOptions & ao )

explicit

◆ ~Analysis()

PLMD::analysis::Analysis::~Analysis ( )

Member Function Documentation

◆ accumulate()

void PLMD::analysis::Analysis::accumulate ( )

◆ activate()

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

◆ addBridgingVessel()

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

protectedinherited

Add a bridging vessel to the list of vessels.

◆ addComponent()

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

inherited

Add a value with a name like label.name.

◆ addComponentWithDerivatives()

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

inherited

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

◆ addDependency()

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

inherited

Specify that this Action depends on another one.

◆ addForcesOnArguments()

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

inherited

Add forces to arguments (used in apply)

◆ addTaskToList()

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

protectedinherited

Add a task to the full list.

◆ addValue()

void PLMD::ActionWithValue::addValue ( )

inherited

Add a value with the name label.

◆ addValueWithDerivatives()

void PLMD::ActionWithValue::addValueWithDerivatives ( )

inherited

Add a value with the name label that has derivatives.

◆ addVessel() [1/2]

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

protectedinherited

Add a vessel to the list of vessels.

◆ addVessel() [2/2]

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

protectedinherited

◆ allowToAccessGlobalForces()

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )

inlineinherited

Allow calls to modifyGlobalForce()

◆ apply()

void PLMD::analysis::Analysis::apply ( )

inlinevirtual

Apply an Action.

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

Implements PLMD::Action.

◆ applyBridgeForces()

virtual void PLMD::vesselbase::ActionWithVessel::applyBridgeForces ( const std::vector< double > & bb )

inlinevirtualinherited

Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume.

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

◆ applyForces()

void PLMD::ActionAtomistic::applyForces ( )

inherited

◆ beforeUpdate()

virtual void PLMD::Action::beforeUpdate ( )

inlinevirtualinherited

Before Update.

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

Reimplemented in PLMD::generic::UpdateIf.

◆ bringBackInPbc()

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

inlineinherited

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

◆ buildDataStashes()

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

inherited

Ensure that data required in other vessels is stored.

◆ calculate()

void PLMD::analysis::Analysis::calculate ( )

inlinevirtual

Calculate an Action.

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

Implements PLMD::Action.

◆ calculateAllVessels()

void PLMD::vesselbase::ActionWithVessel::calculateAllVessels	(	const unsigned &	taskCode,
		MultiValue &	myvals,
		MultiValue &	bvals,
		std::vector< double > &	buffer,
		std::vector< unsigned > &	der_list
	)

protectedinherited

This loops over all the vessels calculating them and also sets all the element derivatives equal to zero.

◆ calculateAtomicNumericalDerivatives()

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

inherited

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

◆ calculateFromPDB()

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

inherited

Calculate the action given a pdb file as input.

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

◆ calculateNumericalDerivatives()

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

virtualinherited

N.B.

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

Reimplemented from PLMD::ActionAtomistic.

◆ changeBox()

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

inherited

Change the box shape.

◆ checkFieldsAllowed()

virtual void PLMD::ActionWithValue::checkFieldsAllowed ( )

inlinevirtualinherited

Reimplemented in PLMD::colvar::ContactMap.

◆ checkNeedsGradients()

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

inlinevirtualinherited

Check if the action needs gradient.

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

◆ checkNumericalDerivatives() [1/2]

bool PLMD::ActionWithValue::checkNumericalDerivatives ( ) const

inlinevirtualinherited

Check if numerical derivatives should be used.

Reimplemented from PLMD::Action.

◆ checkNumericalDerivatives() [2/2]

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

◆ checkRead()

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

◆ checkUpdate()

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

◆ cite()

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

inherited

Cite a paper see PlumedMain::cite.

◆ clearAverage()

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

virtualinherited

This does the clearing of the action.

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

◆ clearDependencies()

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

◆ clearDerivatives()

void PLMD::ActionWithValue::clearDerivatives ( )

virtualinherited

Clear the derivatives of values wrt parameters.

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

◆ clearInputForces()

void PLMD::ActionWithValue::clearInputForces ( )

inherited

Clear the forces on the values.

◆ clearOptions()

void PLMD::Action::clearOptions ( )

virtualinherited

◆ clearOutputForces()

void PLMD::ActionAtomistic::clearOutputForces ( )

inherited

◆ componentIsNotPeriodic()

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

inherited

Set your value component to have no periodicity.

◆ componentIsPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

◆ componentsAreNotOptional()

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

staticinherited

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

◆ copyOutput() [1/2]

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

inherited

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

Use getPntrToComponent instead.

◆ copyOutput() [2/2]

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

inherited

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

Use getPntrToComponent instead.

◆ deactivate()

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

◆ deactivateAllTasks()

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

protectedinherited

Deactivate all the tasks in the task list.

◆ derivativesAreRequired()

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

inlineinherited

Are derivatives required for this quantity.

◆ difference()

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

inlineinherited

Takes the difference taking into account pbc for arg i.

◆ doJobsRequiredBeforeTaskList()

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

virtualinherited

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

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

◆ doNotCalculateDerivatives()

bool PLMD::ActionWithValue::doNotCalculateDerivatives ( ) const

inlinevirtualinherited

Are we not calculating derivatives.

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ doNotForce()

void PLMD::ActionAtomistic::doNotForce ( )

inlineinherited

Skip atom forces - use with care.

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

◆ doNotRetrieve()

void PLMD::ActionAtomistic::doNotRetrieve ( )

inlineinherited

Skip atom retrieval - use with care.

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

◆ error()

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

inherited

Crash calculation and print documentation.

◆ exists()

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

inherited

Check if a value with a particular name is present.

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

◆ exit()

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

inherited

Exit with error code c.

◆ expandArgKeywordInPDB()

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

protectedinherited

This changes the arg keyword in the pdb file.

◆ fclose()

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

inherited

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

◆ fflush()

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

◆ finalizeWeights()

void PLMD::analysis::Analysis::finalizeWeights ( const bool & ignore_weights )

virtual

Convert the stored log weights to proper weights.

◆ finishAveraging()

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

inlinevirtualinherited

This is done once the averaging is finished.

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

◆ finishComputations()

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

virtualinherited

Finish running all the calculations.

◆ fopen()

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

inherited

Opens a file.

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

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

◆ getAbsoluteIndex()

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

inlineinherited

Get the absolute index of an atom.

◆ getAbsoluteIndexes()

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

inlinevirtualinherited

Get the vector of absolute indexes.

Reimplemented in PLMD::multicolvar::BridgedMultiColvarFunction.

◆ getActiveTask()

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

inlineinherited

Get the ith of the currently active tasks.

◆ getArgument()

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

inlineinherited

Returns the value of an argument.

◆ getArguments() [1/2]

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

inlineinherited

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

◆ getArguments() [2/2]

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

inlineinherited

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.

◆ getComponentsList()

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

inherited

get a string that contains all the available components

◆ getComponentsVector()

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

inherited

get a vector that contains the label for all the components

◆ getCPT()

bool PLMD::Action::getCPT ( ) const

inherited

Return true if we are doing at a checkpoint step.

◆ getCurrentNumberOfActiveTasks()

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

inlineinherited

Get the number of tasks that are currently active.

◆ getDataPoint()

void PLMD::analysis::Analysis::getDataPoint	(	const unsigned &	idata,
		std::vector< double > &	point,
		double &	weight
	)		const

protected

Retrieve the ith point.

◆ getDependencies()

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

inlineinherited

Return dependencies.

◆ getDocumentation()

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

virtualinherited

◆ getEnergy()

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

inlineinherited

Get energy.

◆ getExchangeStep()

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

◆ getForcesFromVessels()

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

protectedinherited

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

◆ getFullNumberOfTasks()

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

inlineinherited

Get the full size of the taskList dynamic list.

◆ getKeyword()

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

inherited

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

◆ getLabel()

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

inlineinherited

Returns the label.

◆ getMass()

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

inlineinherited

Get mass of i-th atom.

◆ getMetric()

std::vector< double > PLMD::analysis::Analysis::getMetric ( ) const

private

Get the metric if we are using malonobius distance and flexible hill.

◆ getMetricName()

std::string PLMD::analysis::Analysis::getMetricName ( ) const

inlineprotected

Get the name of the metric we are using to measure distances.

◆ getName()

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

inlineinherited

Returns the name.

◆ getNLTolerance()

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

inlineprotectedinherited

Return the value for the neighbor list tolerance.

◆ getNumberOfArguments()

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

inlinevirtualinherited

Returns the number of arguments.

Reimplemented from PLMD::ActionWithArguments.

◆ getNumberOfAtoms()

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

◆ getNumberOfComponents()

int PLMD::ActionWithValue::getNumberOfComponents ( ) const

inlineinherited

Returns the number of values defined.

◆ getNumberOfDataPoints()

unsigned PLMD::analysis::Analysis::getNumberOfDataPoints ( ) const

inlineprotected

Return the number of data points.

◆ getNumberOfDerivatives()

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

inlinevirtualinherited

Implements PLMD::ActionWithValue.

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

◆ getNumberOfQuantities()

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

inlinevirtualinherited

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

Reimplemented in PLMD::analysis::Histogram, PLMD::gridtools::FindSphericalContour, PLMD::gridtools::FindContour, PLMD::multicolvar::MultiColvarDensity, PLMD::gridtools::FindContourSurface, PLMD::multicolvar::LocalAverage, PLMD::multicolvar::DistanceFromContour, PLMD::adjmat::ClusterWithSurface, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::gridtools::ConvertToFES, PLMD::adjmat::TopologyMatrix, PLMD::crystallization::VectorMultiColvar, PLMD::adjmat::ActionWithInputMatrix, PLMD::gridtools::InterpolateGrid, PLMD::multicolvar::ActionVolume, PLMD::adjmat::ClusterAnalysisBase, PLMD::multicolvar::MultiColvarFilter, and PLMD::crystallization::Gradient.

◆ getNumberOfVessels()

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

inlineinherited

Get the number of vessels.

◆ getOutputFormat()

std::string PLMD::analysis::Analysis::getOutputFormat ( ) const

inlineprotected

Return the format to use for numbers in output files.

◆ getOutputQuantity() [1/2]

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

inlineinherited

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

◆ getOutputQuantity() [2/2]

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

inlineinherited

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

◆ getPbc()

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

inlineinherited

Get reference to Pbc.

◆ getPeriodicityInformation()

bool PLMD::analysis::Analysis::getPeriodicityInformation	(	const unsigned &	i,
		std::string &	dmin,
		std::string &	dmax
	)

protected

Returns true if argument i is periodic together with the domain.

◆ getPntrToArgument()

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

inlineinherited

Return a pointer to specific argument.

◆ getPntrToComponent() [1/2]

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

protectedinherited

Return a pointer to the component by index.

◆ getPntrToComponent() [2/2]

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

protectedinherited

Return a pointer to the value by name.

◆ getPntrToValue()

Value * PLMD::ActionWithValue::getPntrToValue ( )

protectedinherited

Get a pointer to the default value.

◆ getPntrToVessel()

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

inlineinherited

Get a pointer to the ith vessel.

◆ getPosition() [1/2]

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

inlineinherited

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

◆ getPosition() [2/2]

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

◆ getPositionInCurrentTaskList()

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

inlineinherited

Return the position in the current task list.

◆ getPositionInFullTaskList()

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

inlineinherited

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

◆ getPositions()

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

inlineinherited

Get the array of all positions.

◆ getProjection()

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

inherited

Get the scalar product between the gradients of two variables.

◆ getRestart()

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

◆ getSizeOfBuffer()

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

protectedinherited

Get the size of the buffer.

◆ getStep()

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

inherited

Return the present timestep.

◆ getStride()

int PLMD::ActionPilot::getStride ( ) const

inherited

Get the stride.

◆ getTaskCode()

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

inlineinherited

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

◆ getTime()

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

◆ getTimeStep()

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

◆ getTolerance()

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

inlineprotectedinherited

Return the value of the tolerance.

◆ getTotAtoms()

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inlineinherited

Get total number of atoms, including virtual ones.

Can be used to make a loop on modifyPosition or getPosition(AtomNumber)

◆ getUnique()

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

inlineinherited

◆ getUniqueLocal()

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

inlineinherited

◆ getVesselWithName()

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

inherited

These are overwritten in MultiColvarFunction.

Return a particular named vessel

◆ getWeight()

double PLMD::analysis::Analysis::getWeight ( const unsigned & idata ) const

protected

Return the weight of the ith point.

◆ interpretArgumentList()

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

inherited

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

◆ interpretAtomList()

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

inherited

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

◆ isActive()

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

◆ isOptionOn()

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

inlineinherited

Check if an option is on.

◆ isPeriodic()

bool PLMD::analysis::Analysis::isPeriodic ( )

inlinevirtual

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

◆ lockContributors()

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

inherited

◆ lockRequests()

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

virtualinherited

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.

◆ modifyForces()

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

inlineinherited

Get a reference to forces array.

◆ modifyGlobalForce()

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

inlineinherited

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

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

◆ modifyGlobalPbc()

Pbc & PLMD::ActionAtomistic::modifyGlobalPbc ( )

inlineinherited

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

◆ modifyGlobalVirial()

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inlineinherited

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

◆ modifyPosition()

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

◆ modifyVirial()

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

◆ needsDerivatives()

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

protectedinherited

Turn on the derivatives in the vessel.

◆ noAnalyticalDerivatives()

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

staticinherited

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

◆ noNormalization()

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

inlineprotectedinherited

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

◆ normalizeVector()

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

inlinevirtualinherited

These normalizes vectors and is used in StoreDataVessel.

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

◆ normalizeVectorDerivatives()

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

inlinevirtualinherited

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

◆ onStep()

bool PLMD::ActionPilot::onStep ( ) const

virtualinherited

Check if the action is active on this step.

Reimplemented in PLMD::gridtools::ConvertToFES.

◆ parse()

template<class T >

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

inherited

Parse one keyword as generic type.

◆ parseArgumentList() [1/2]

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

inherited

Parse a list of arguments.

◆ parseArgumentList() [2/2]

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

inherited

Parse a numbered list of arguments.

◆ parseAtomList() [1/2]

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

inherited

Parse a list of atoms without a numbered keyword.

◆ parseAtomList() [2/2]

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

inherited

Parse an list of atom with a numbred keyword.

◆ parseFlag()

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

inherited

Parse one keyword as boolean flag.

◆ parseNumbered()

template<class T >

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

inherited

Parse one numbered keyword as generic type.

◆ parseNumberedVector()

template<class T >

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

inherited

Parse a vector with a number.

◆ parseOutputFile()

void PLMD::analysis::Analysis::parseOutputFile	(	const std::string &	key,
		std::string &	filename
	)

protected

This is used to read in output file names for analysis methods.

When this method is used and the calculation is not restarted old analysis files are backed up.

◆ parseVector()

template<class T >

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

inherited

Parse one keyword as std::vector.

◆ pbcApply()

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

inherited

Applies PBCs to a seriens of positions or distances.

◆ pbcDistance()

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

inherited

Compute the pbc distance between two positions.

◆ performAnalysis()

virtual void PLMD::analysis::Analysis::performAnalysis ( )

pure virtual

Implemented in PLMD::analysis::PCA, and PLMD::analysis::AnalysisWithLandmarks.

◆ performOperations()

void PLMD::analysis::Analysis::performOperations ( const bool & from_update )

virtual

This does the averaging operation.

Reimplemented from PLMD::vesselbase::ActionWithAveraging.

◆ performTask()

virtual void PLMD::vesselbase::ActionWithVessel::performTask	(	const unsigned &	,
		const unsigned &	,
		MultiValue &
	)		const

pure virtualinherited

Calculate one of the functions in the distribution.

Implemented in PLMD::multicolvar::MultiColvarBase, PLMD::analysis::PCA, PLMD::analysis::Average, PLMD::mapping::AdaptivePath, PLMD::adjmat::ClusterDistribution, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::adjmat::ClusterDiameter, PLMD::adjmat::ClusterSize, PLMD::adjmat::ClusterProperties, PLMD::multicolvar::BridgedMultiColvarFunction, PLMD::manyrestraints::ManyRestraintsBase, PLMD::analysis::AnalysisWithLandmarks, PLMD::gridtools::ActionWithGrid, and PLMD::mapping::PathBase.

◆ prepare()

void PLMD::Action::prepare ( )

virtualinherited

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

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

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

◆ prepareForAveraging()

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

inlinevirtualinherited

This is done before the averaging comences.

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

◆ readAtomsFromPDB() [1/2]

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

virtualinherited

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

Reimplemented from PLMD::Action.

◆ readAtomsFromPDB() [2/2]

virtual void PLMD::Action::readAtomsFromPDB ( const PDB & )

inlinevirtualinherited

This is overwritten in ActionAtomistic so that we can read the atoms from the pdb input file rather than taking them from the MD code.

Reimplemented in PLMD::ActionAtomistic.

◆ readDataFromFile()

void PLMD::analysis::Analysis::readDataFromFile ( const std::string & filename )

private

Read in data from a file.

◆ readVesselKeywords()

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

protectedinherited

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

◆ registerKeywords()

void PLMD::analysis::Analysis::registerKeywords ( Keywords & keys )

static

Finalize the weights without using the log sums.

◆ requestArguments()

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

inherited

Setup the dependencies.

◆ requestAtoms()

void PLMD::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

◆ resizeFunctions()

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

protectedinherited

Resize all the functions when the number of derivatives change.

◆ retrieveAtoms()

void PLMD::ActionAtomistic::retrieveAtoms ( )

virtualinherited

Reimplemented in PLMD::multicolvar::MultiColvarBase.

◆ retrieveDomain()

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

virtualinherited

What are the domains of the base quantities.

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

◆ runAllTasks()

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

protectedinherited

Calculate the values of all the vessels.

◆ runAnalysis()

void PLMD::analysis::Analysis::runAnalysis ( )

◆ runFinalJobs()

void PLMD::analysis::Analysis::runFinalJobs ( )

virtual

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

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

Reimplemented from PLMD::Action.

◆ serialCalculation()

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

inlineprotectedinherited

Is the calculation being done in serial.

◆ setAveragingAction()

void PLMD::vesselbase::ActionWithAveraging::setAveragingAction	(	AveragingVessel *	av_vessel,
		const bool &	usetasks
	)

protectedinherited

Set the averaging action.

◆ setForcesOnAtoms()

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

inherited

Add the forces to the atoms.

◆ setGradientsIfNeeded()

void PLMD::ActionWithValue::setGradientsIfNeeded ( )

inherited

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

◆ setLowMemOption()

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

inlineprotectedinherited

Set that we are using low memory.

◆ setNotPeriodic()

void PLMD::ActionWithValue::setNotPeriodic ( )

inherited

Set your default value to have no periodicity.

◆ setOption()

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

virtualinherited

◆ setPeriodic()

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

inherited

Set the value to be periodic with a particular domain.

◆ setStride()

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

inherited

Set the value of the stride.

◆ setValue() [1/2]

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

inlineprotectedinherited

Set the default value (the one without name)

◆ setValue() [2/2]

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

inherited

Set the value.

◆ taskIsCurrentlyActive()

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

inherited

Check whether or not a particular task is currently active.

◆ threadSafe()

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

inlinevirtualinherited

Is this action thread safe.

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

◆ transformBridgedDerivatives()

void PLMD::vesselbase::ActionWithVessel::transformBridgedDerivatives	(	const unsigned &	current,
		MultiValue &	invals,
		MultiValue &	outvals
	)		const

virtualinherited

Do the task if we have a bridge.

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

◆ turnOnDerivatives()

void PLMD::ActionWithValue::turnOnDerivatives ( )

virtualinherited

Activate the calculation of derivatives.

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

◆ unlockRequests()

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

virtualinherited

Reimplemented from PLMD::ActionAtomistic.

◆ update()

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

virtualinherited

Update.

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

Reimplemented from PLMD::Action.

◆ updateUniqueLocal()

void PLMD::ActionAtomistic::updateUniqueLocal ( )

inherited

updates local unique atoms

◆ useCustomisableComponents()

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

staticinherited

The components in the action will depend on the user.

◆ useNumericalDerivatives()

void PLMD::ActionWithValue::useNumericalDerivatives ( )

inlineinherited

This forces the class to use numerical derivatives.

◆ usingLowMem()

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

inlineprotectedinherited

Are we using low memory.

◆ usingMemory()

bool PLMD::analysis::Analysis::usingMemory ( ) const

inlineprotected

Are we analyzing each data block separately (if we are not this also returns the old normalization )

◆ warning()

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

inherited

Issue a warning.

◆ weightWithDerivatives()

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

inlineinherited

Does the weight have derivatives.

Member Data Documentation

◆ argument_names

std::vector<std::string> PLMD::analysis::Analysis::argument_names

protected

List of argument names.

◆ atoms

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

◆ bridgeVariable

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protectedinherited

This is used for numerical derivatives of bridge variables.

◆ clearstride

unsigned PLMD::vesselbase::ActionWithAveraging::clearstride

protectedinherited

The frequency with which to clear the grid.

◆ comm

Communicator& PLMD::Action::comm

inherited

◆ contributorsAreUnlocked

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protectedinherited

The terms in the series are locked.

◆ current_args

std::vector<double> PLMD::analysis::Analysis::current_args

private

Tempory vector to store values of arguments.

◆ cweight

double PLMD::vesselbase::ActionWithAveraging::cweight

protectedinherited

◆ data

std::vector<ReferenceConfiguration*> PLMD::analysis::Analysis::data

protected

The data we are going to analyze.

◆ dertime

bool PLMD::vesselbase::ActionWithVessel::dertime

protectedinherited

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

◆ files

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

inherited

◆ freq

unsigned PLMD::analysis::Analysis::freq

private

The frequency with which we are performing analysis.

◆ idata

unsigned PLMD::analysis::Analysis::idata

private

The piece of data we are inserting.

◆ ignore_reweight

bool PLMD::analysis::Analysis::ignore_reweight

private

If we are reusing data are we ignoring the reweighting in that data.

◆ keywords

const Keywords& PLMD::Action::keywords

inherited

◆ log

Log& PLMD::Action::log

inherited

Reference to the log stream.

◆ logweights

std::vector<double> PLMD::analysis::Analysis::logweights

private

The weights of all the data points.

◆ lweight

double PLMD::vesselbase::ActionWithAveraging::lweight

protectedinherited

The current weight and its logarithm.

◆ metricname

std::string PLMD::analysis::Analysis::metricname

private

The type of metric we are using to measure distances.

◆ multi_sim_comm

Communicator& PLMD::Action::multi_sim_comm

inherited

◆ mydata

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

protectedinherited

A pointer to the object that stores data.

◆ mydatastash

Analysis* PLMD::analysis::Analysis::mydatastash

private

The Analysis action that we are reusing data from.

◆ ndata

unsigned PLMD::analysis::Analysis::ndata

private

Number of data point we need to run analysis.

◆ needeng

bool PLMD::analysis::Analysis::needeng

private

Do we need the energy (are we reweighting at a different temperature)

◆ nomemory

bool PLMD::analysis::Analysis::nomemory

private

Are we treating each block of data separately.

◆ ofmt

std::string PLMD::analysis::Analysis::ofmt

private

Have we analyzed the data for the first time.

The value of the old normalization constant The format to use in output files

◆ plumed

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

◆ reusing_data

bool PLMD::analysis::Analysis::reusing_data

private

Are we reusing data stored by another analysis action.

◆ rfile

OFile PLMD::analysis::Analysis::rfile

private

The checkpoint file.

◆ rtemp

double PLMD::analysis::Analysis::rtemp

private

The temperature at which we want the histogram.

◆ simtemp

double PLMD::analysis::Analysis::simtemp

private

The temperature at which we are running the calculation.

◆ taskFlags

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

protectedinherited

This list is used to update the neighbor list.

◆ useRunAllTasks

bool PLMD::vesselbase::ActionWithAveraging::useRunAllTasks

protectedinherited

This ensures runAllTasks is used.

◆ weightHasDerivatives

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

◆ write_chq

bool PLMD::analysis::Analysis::write_chq

private

Are we writing a checkpoint file.

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

analysis/Analysis.h
analysis/Analysis.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ Dependencies

Constructor & Destructor Documentation

◆ Analysis()

◆ ~Analysis()

Member Function Documentation

◆ accumulate()

◆ activate()

◆ addBridgingVessel()

◆ addComponent()

◆ addComponentWithDerivatives()

◆ addDependency()

◆ addForcesOnArguments()

◆ addTaskToList()

◆ addValue()

◆ addValueWithDerivatives()

◆ addVessel() [1/2]

◆ addVessel() [2/2]

◆ allowToAccessGlobalForces()

◆ apply()

◆ applyBridgeForces()

◆ applyForces()

◆ beforeUpdate()

◆ bringBackInPbc()

◆ buildDataStashes()

◆ calculate()

◆ calculateAllVessels()

◆ calculateAtomicNumericalDerivatives()

◆ calculateFromPDB()

◆ calculateNumericalDerivatives()

◆ changeBox()

◆ checkFieldsAllowed()

◆ checkNeedsGradients()

◆ checkNumericalDerivatives() [1/2]

◆ checkNumericalDerivatives() [2/2]

◆ checkRead()

◆ checkUpdate()

◆ cite()

◆ clearAverage()

◆ clearDependencies()

◆ clearDerivatives()

◆ clearInputForces()

◆ clearOptions()

◆ clearOutputForces()

◆ componentIsNotPeriodic()

◆ componentIsPeriodic()

◆ componentsAreNotOptional()

◆ copyOutput() [1/2]

◆ copyOutput() [2/2]

◆ deactivate()

◆ deactivateAllTasks()

◆ derivativesAreRequired()

◆ difference()

◆ doJobsRequiredBeforeTaskList()

◆ doNotCalculateDerivatives()

◆ doNotForce()

◆ doNotRetrieve()

◆ error()

◆ exists()

◆ exit()

◆ expandArgKeywordInPDB()

◆ fclose()

◆ fflush()

◆ finalizeWeights()

◆ finishAveraging()

◆ finishComputations()

◆ fopen()

◆ getAbsoluteIndex()

◆ getAbsoluteIndexes()

◆ getActiveTask()

◆ getArgument()