Provides the keyword CLASSICAL_MDS More...

Inheritance diagram for PLMD::analysis::ClassicalMultiDimensionalScaling:

[legend]

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

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

Public Member Functions
	ClassicalMultiDimensionalScaling (const ActionOptions &ao)

	~ClassicalMultiDimensionalScaling ()

void	analyzeLandmarks ()

void	performAnalysis ()
	Do the analysis. More...

void	performTask (const unsigned &, const unsigned &, MultiValue &) const
	This does nothing. More...

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

void	prepare ()
	Prepare an Action for calculation This can be used by Action if they need some special preparation before calculation. More...

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

void	update ()
	Update. More...

void	accumulate ()

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

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

void	runAnalysis ()

void	lockRequests ()

void	unlockRequests ()

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

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

unsigned	getNumberOfDerivatives ()
	Get the number of derivatives for final calculated quantity. More...

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

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...

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

virtual std::string	getDocumentation () const

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

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

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

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

virtual void	clearOptions ()

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

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

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

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

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

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

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

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

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

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...

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...

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

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

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

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

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

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

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

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

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

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

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

void	clearOutputForces ()

void	calculateAtomicNumericalDerivatives (ActionWithValue *a, const unsigned &startnum)
	Numerical derivative routine to use when using Actions that inherit from BOTH ActionWithArguments and ActionAtomistic. More...

void	retrieveAtoms ()

void	applyForces ()

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

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...

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	unlockContributors ()

void	lockContributors ()

virtual void	finishTaskListUpdate ()

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

bool	derivativesAreRequired () const
	Are derivatives required for this quantity. 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 ()
	Get the number of quantities that are calculated during each task. More...

void	activateTheseTasks (std::vector< unsigned > &addtionalTasks)
	Get the list of indices that have derivatives. 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...

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

StoreDataVessel *	buildDataStashes (const bool &allow_wcutoff, const double &wtol)
	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...

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

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	setDataToAnalyze (MultiReferenceBase *mydata)
	Set the data that needs to be analyzed. More...

unsigned	getNumberOfLandmarks () const
	Return the number of landmarks we are selecting. More...

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	getNumberOfArguments () const
	Return the number of arguments (this overwrites the one in ActionWithArguments) 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...

double	getNormalization () const
	Return the normalization constant. More...

double	getTemp () const
	Return the set temperature (N.B. k_B T is what is returned by this function) More...

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

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

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

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

int	getStride () const

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

void	addVessel (const std::string &name, const std::string &input, const int numlab=0)
	Add a vessel to the list of vessels. More...

void	addVessel (Vessel *vv)

BridgeVessel *	addBridgingVessel (ActionWithVessel *tome)
	Add a bridging vessel to the list of vessels. More...

void	readVesselKeywords ()
	Complete the setup of this object (this routine must be called after construction of ActionWithValue) More...

void	needsDerivatives ()
	Turn on the derivatives in the vessel. More...

double	getTolerance () const
	Return the value of the tolerance. More...

double	getNLTolerance () const
	Return the value for the neighbor list tolerance. More...

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

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

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

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

bool	calculateAllVessels (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...

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

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

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

void	deactivateTasksInRange (const unsigned &lower, const unsigned &upper)
	Deactivate all tasks with i in lower \(\le\) i < upper. More...

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

Atoms &	atoms

bool	contributorsAreUnlocked
	The terms in the series are locked. More...

bool	weightHasDerivatives
	Does the weight have derivatives. More...

unsigned	bridgeVariable
	This is used for numerical derivatives of bridge variables. More...

Private Attributes
unsigned	nlow

std::string	ofilename

std::string	efilename

PointWiseMapping *	myembedding

Detailed Description

Provides the keyword CLASSICAL_MDS

Member Typedef Documentation

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

inherited

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

inherited

Constructor & Destructor Documentation

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

explicit

PLMD::analysis::ClassicalMultiDimensionalScaling::~ClassicalMultiDimensionalScaling ( )

Member Function Documentation

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

inherited

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

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

inherited

Get the list of indices that have derivatives.

Switch on additional tasks

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

protectedinherited

Add a bridging vessel to the list of vessels.

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

inherited

Specify that this Action depends on another one.

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

inherited

Add forces to arguments (used in apply)

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

protectedinherited

Add a task to the full list.

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

protectedinherited

Add a vessel to the list of vessels.

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

protectedinherited

void PLMD::ActionAtomistic::allowToAccessGlobalForces ( )

inlineinherited

Allow calls to modifyGlobalForce()

void PLMD::analysis::ClassicalMultiDimensionalScaling::analyzeLandmarks ( )

virtual

Implements PLMD::analysis::AnalysisWithLandmarks.

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

inlinevirtualinherited

Apply an Action.

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

Implements PLMD::Action.

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

inlinevirtualinherited

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

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

void ActionAtomistic::applyForces ( )

inherited

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

inlineinherited

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

StoreDataVessel * PLMD::vesselbase::ActionWithVessel::buildDataStashes	(	const bool &	allow_wcutoff,
		const double &	wtol
	)

inherited

Ensure that data required in other vessels is stored.

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

virtualinherited

Calculate an Action.

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

Implements PLMD::Action.

bool PLMD::vesselbase::ActionWithVessel::calculateAllVessels	(	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.

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

inherited

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

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

inherited

Calculate the action given a pdb file as input.

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

void PLMD::analysis::Analysis::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

inlinevirtualinherited

N.B.

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

Reimplemented from PLMD::ActionAtomistic.

void ActionAtomistic::changeBox ( const Tensor & newbox )

inherited

Change the box shape.

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

inlinevirtualinherited

Check if the action needs gradient.

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

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

void PLMD::Action::checkRead ( )

inherited

Check if Action was properly read.

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

bool PLMD::Action::checkUpdate ( ) const

inherited

Check if action should be updated.

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

inherited

Cite a paper see PlumedMain::cite.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

void PLMD::Action::clearOptions ( )

virtualinherited

void ActionAtomistic::clearOutputForces ( )

inherited

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

void PLMD::vesselbase::ActionWithVessel::deactivate_task ( const unsigned & task_index )

virtualinherited

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

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

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

protectedinherited

Deactivate all the tasks in the task list.

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

protectedinherited

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

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

inlineinherited

Are derivatives required for this quantity.

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

inlineinherited

Takes the difference taking into account pbc for arg i.

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

virtualinherited

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

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

void PLMD::ActionAtomistic::doNotForce ( )

inlineinherited

Skip atom forces - use with care.

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

void PLMD::ActionAtomistic::doNotRetrieve ( )

inlineinherited

Skip atom retrieval - use with care.

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

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

inherited

Crash calculation and print documentation.

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

inherited

Exit with error code c.

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

protectedinherited

This changes the arg keyword in the pdb file.

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

inherited

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

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

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

protectedinherited

Convert the stored log weights to proper weights.

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

virtualinherited

Finish running all the calculations.

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

inlinevirtualinherited

Reimplemented in PLMD::secondarystructure::SecondaryStructureRMSD.

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

inherited

Opens a file.

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

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

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

inlineinherited

Get the absolute index of an atom.

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

inlineinherited

Get the vector of absolute indexes.

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

inlineprotectedinherited

Get the ith of the currently active tasks.

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

inlineinherited

Returns the value of an argument.

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

inlineinherited

Returns an array of pointers to the arguments.

std::vector< Value * > PLMD::analysis::Analysis::getArguments ( )

inlineprotectedinherited

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

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

inlineinherited

Get box shape.

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

inlineinherited

Get charge of i-th atom.

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

inlineprotectedinherited

Get the number of tasks that are currently active.

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

protectedinherited

Retrieve the ith point.

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

inlineinherited

Return dependencies.

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

virtualinherited

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

inlineinherited

Get energy.

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

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

protectedinherited

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

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

inlineinherited

Get the full size of the taskList dynamic list.

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

inlineinherited

Returns the label.

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

inlineinherited

Get mass of i-th atom.

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

inlineprotectedinherited

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

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

inlineinherited

Returns the name.

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

inlineprotectedinherited

Return the value for the neighbor list tolerance.

double PLMD::analysis::Analysis::getNormalization ( ) const

protectedinherited

Return the normalization constant.

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

inlineprotectedinherited

Return the number of arguments (this overwrites the one in ActionWithArguments)

unsigned PLMD::ActionAtomistic::getNumberOfAtoms ( ) const

inlineinherited

Get number of available atoms.

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

inlineprotectedinherited

Return the number of data points.

unsigned PLMD::analysis::Analysis::getNumberOfDerivatives ( )

inlinevirtualinherited

Get the number of derivatives for final calculated quantity.

Implements PLMD::vesselbase::ActionWithVessel.

unsigned PLMD::analysis::AnalysisWithLandmarks::getNumberOfLandmarks ( ) const

protectedinherited

Return the number of landmarks we are selecting.

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

inlinevirtualinherited

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

Reimplemented in PLMD::multicolvar::LocalAverage, PLMD::secondarystructure::SecondaryStructureRMSD, PLMD::crystallization::VectorMultiColvar, PLMD::crystallization::DFSClustering, PLMD::multicolvar::ActionVolume, PLMD::crystallisation::Gradient, and PLMD::multicolvar::MultiColvarFilter.

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

inlineprotectedinherited

Get the number of vessels.

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

inlineprotectedinherited

Return the format to use for numbers in output files.

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

inlineinherited

Get reference to Pbc.

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

protectedinherited

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

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

inlineinherited

Return a pointer to specific argument.

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

inlineprotectedinherited

Get a pointer to the ith vessel.

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

inlineinherited

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

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

inlineinherited

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

With direct access to the global atom array

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

inlineinherited

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

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

inlineinherited

Get the array of all positions.

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

inherited

Get the scalar product between the gradients of two variables.

bool PLMD::Action::getRestart ( ) const

inlineinherited

Return true if we are doing a restart.

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

protectedinherited

Get the size of the buffer.

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

inherited

Return the present timestep.

int PLMD::ActionPilot::getStride ( ) const

protectedinherited

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

inlineinherited

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

double PLMD::analysis::Analysis::getTemp ( ) const

protectedinherited

Return the set temperature (N.B. k_B T is what is returned by this function)

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

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

inlineprotectedinherited

Return the value of the tolerance.

unsigned PLMD::ActionAtomistic::getTotAtoms ( ) const

inlineinherited

Get total number of atoms, including virtual ones.

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

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

inlineinherited

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

inherited

These are overwritten in MultiColvarFunction.

Return a particular named vessel

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

protectedinherited

Return the weight of the ith point.

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

inherited

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

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

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

inlineinherited

Check if an option is on.

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

inlinevirtualinherited

Are the base quantities periodic.

Implements PLMD::vesselbase::ActionWithVessel.

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

inherited

void PLMD::analysis::Analysis::lockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

void ActionAtomistic::makeWhole ( )

inherited

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

double & PLMD::ActionAtomistic::modifyForceOnEnergy ( )

inlineinherited

Get a reference to force on energy.

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

inlineinherited

Get a reference to forces array.

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

inlineinherited

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

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!

Tensor & PLMD::ActionAtomistic::modifyGlobalVirial ( )

inlineinherited

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

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

inlineinherited

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

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

Tensor & PLMD::ActionAtomistic::modifyVirial ( )

inlineinherited

Get a reference to virial array.

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

protectedinherited

Turn on the derivatives in the vessel.

bool PLMD::ActionPilot::onStep ( ) const

inherited

Check if the action is active on this step.

template<class T >

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

inherited

Parse one keyword as generic type.

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

inherited

Parse a list of arguments.

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

inherited

Parse a list of atoms without a numbered keyword.

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

inherited

Parse an list of atom with a numbred keyword.

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

inherited

Parse one keyword as boolean flag.

template<class T >

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

inherited

Parse one numbered keyword as generic type.

template<class T >

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

inherited

Parse a vector with a number.

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

protectedinherited

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.

template<class T >

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

inherited

Parse one keyword as std::vector.

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

inherited

Applies PBCs to a seriens of positions or distances.

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

inherited

Compute the pbc distance between two positions.

void PLMD::analysis::AnalysisWithLandmarks::performAnalysis ( )

virtualinherited

Do the analysis.

Implements PLMD::analysis::Analysis.

void PLMD::analysis::AnalysisWithLandmarks::performTask	(	const unsigned &	taskIndex,
		const unsigned &	current,
		MultiValue &	myvals
	)		const

virtualinherited

This does nothing.

Implements PLMD::vesselbase::ActionWithVessel.

void PLMD::analysis::Analysis::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 from PLMD::Action.

void ActionAtomistic::readAtomsFromPDB ( const PDB & pdb )

virtualinherited

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

Reimplemented from PLMD::Action.

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.

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

protectedinherited

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

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

static

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

inherited

Setup the dependencies.

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

inherited

Request an array of atoms.

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

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

protectedinherited

Resize all the functions when the number of derivatives change.

void ActionAtomistic::retrieveAtoms ( )

inherited

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

virtualinherited

What are the domains of the base quantities.

Reimplemented in PLMD::multicolvar::Torsions.

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

protectedinherited

Calculate the values of all the vessels.

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

inherited

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

virtualinherited

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.

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

inlineprotectedinherited

Is the calculation being done in serial.

void PLMD::analysis::AnalysisWithLandmarks::setDataToAnalyze ( MultiReferenceBase * mydata )

protectedinherited

Set the data that needs to be analyzed.

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

inherited

Add the forces to the atoms.

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

inlineprotectedinherited

Set that we are using low memory.

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

virtualinherited

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.

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

inherited

void PLMD::analysis::Analysis::unlockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

void PLMD::analysis::Analysis::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.

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

inlineprotectedinherited

Are we using low memory.

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

inlineprotectedinherited

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

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

inherited

Issue a warning.

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

inlineinherited

Does the weight have derivatives.

Member Data Documentation

Atoms& PLMD::ActionAtomistic::atoms

protectedinherited

unsigned PLMD::vesselbase::ActionWithVessel::bridgeVariable

protectedinherited

This is used for numerical derivatives of bridge variables.

Communicator& PLMD::Action::comm

inherited

bool PLMD::vesselbase::ActionWithVessel::contributorsAreUnlocked

protectedinherited

The terms in the series are locked.

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

protectedinherited

The data we are going to analyze.

std::string PLMD::analysis::ClassicalMultiDimensionalScaling::efilename

private

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

inherited

const Keywords& PLMD::Action::keywords

inherited

Log& PLMD::Action::log

inherited

Reference to the log stream.

Communicator& PLMD::Action::multi_sim_comm

inherited

PointWiseMapping* PLMD::analysis::ClassicalMultiDimensionalScaling::myembedding

private

unsigned PLMD::analysis::ClassicalMultiDimensionalScaling::nlow

private

std::string PLMD::analysis::ClassicalMultiDimensionalScaling::ofilename

private

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

bool PLMD::vesselbase::ActionWithVessel::weightHasDerivatives

protectedinherited

Does the weight have derivatives.

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

analysis/ClassicalMultiDimensionalScaling.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation