Inheritance diagram for PLMD::analysis::Histogram:

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

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

Public Member Functions
	Histogram (const ActionOptions &ao)

void	performAnalysis ()

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 ()

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

void	addDependency (Action *)
	Specify that this Action depends on another one. More...

void	clearDependencies ()
	Clear the dependence list for this Action. More...

long int	getStep () const
	Return the present timestep. More...

double	getTime () const
	Return the present time. More...

double	getTimeStep () const
	Return the timestep. More...

template<class T >
void	parse (const std::string &key, T &t)
	Parse one keyword as generic type. More...

template<class T >
bool	parseNumbered (const std::string &key, const int no, T &t)
	Parse one numbered keyword as generic type. More...

template<class T >
void	parseVector (const std::string &key, std::vector< T > &t)
	Parse one keyword as std::vector. More...

template<class T >
bool	parseNumberedVector (const std::string &key, const int no, std::vector< T > &t)
	Parse a vector with a number. More...

void	parseFlag (const std::string &key, bool &t)
	Parse one keyword as boolean flag. More...

void	error (const std::string &msg) const
	Crash calculation and print documentation. More...

void	warning (const std::string &msg)
	Issue a warning. More...

void	exit (int c=0)
	Exit with error code c. More...

void	checkRead ()
	Check if Action was properly read. More...

virtual void	lockRequests ()

void	lockRequests ()

virtual void	unlockRequests ()

void	unlockRequests ()

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...

virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Perform calculation using numerical derivatives N.B. More...

virtual void	calculateNumericalDerivatives (ActionWithValue *a=NULL)
	Calculate the numerical derivatives N.B. 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...

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

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

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

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

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

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...

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

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...

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...

Private Attributes
std::vector< std::string >	gmin

std::vector< std::string >	gmax

std::vector< double >	point

std::vector< double >	bw

std::vector< unsigned >	gbin

std::string	gridfname

std::string	kerneltype

Detailed Description

Provides the keyword HISTOGRAM

Definition at line 89 of file Histogram.cpp.

Member Typedef Documentation

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

inherited

Definition at line 75 of file Action.h.

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

inherited

Definition at line 140 of file Action.h.

Constructor & Destructor Documentation

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

Definition at line 115 of file Histogram.cpp.

Member Function Documentation

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

inherited

Definition at line 215 of file Analysis.cpp.

void PLMD::Action::activate ( )

virtualinherited

Set action to active.

Definition at line 127 of file Action.cpp.

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

inherited

Specify that this Action depends on another one.

Definition at line 123 of file Action.cpp.

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

inherited

Add forces to arguments (used in apply)

Definition at line 276 of file ActionWithArguments.cpp.

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.

Definition at line 125 of file Analysis.h.

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

inlineinherited

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

Definition at line 108 of file ActionWithArguments.h.

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.

Definition at line 211 of file Analysis.cpp.

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

Definition at line 205 of file Action.cpp.

void PLMD::ActionWithArguments::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtualinherited

Calculate the numerical derivatives N.B.

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

Reimplemented from PLMD::Action.

Definition at line 242 of file ActionWithArguments.cpp.

void PLMD::Action::calculateNumericalDerivatives ( ActionWithValue * a = NULL )

virtualinherited

Perform calculation using numerical derivatives N.B.

only pass an ActionWithValue to this routine if you know exactly what you are doing.

Reimplemented in PLMD::ActionAtomistic, PLMD::multicolvar::ActionVolume, PLMD::ActionWithArguments, and PLMD::multicolvar::MultiColvarFunction.

Definition at line 187 of file Action.cpp.

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

inlinevirtualinherited

Check if the action needs gradient.

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

Definition at line 230 of file Action.h.

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

inlinevirtualinherited

Check if numerical derivatives should be performed.

Reimplemented in PLMD::ActionWithValue.

Definition at line 227 of file Action.h.

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

Definition at line 161 of file Action.cpp.

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

inherited

Cite a paper see PlumedMain::cite.

Definition at line 221 of file Action.cpp.

void PLMD::Action::clearDependencies ( )

inherited

Clear the dependence list for this Action.

Definition at line 153 of file Action.cpp.

void PLMD::Action::clearOptions ( )

virtualinherited

Definition at line 147 of file Action.cpp.

void PLMD::Action::deactivate ( )

inlinevirtualinherited

Set action to inactive.

Definition at line 369 of file Action.h.

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

inlineinherited

Takes the difference taking into account pbc for arg i.

Definition at line 103 of file ActionWithArguments.h.

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

inherited

Crash calculation and print documentation.

Definition at line 195 of file Action.cpp.

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

inherited

Exit with error code c.

Definition at line 183 of file Action.cpp.

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

protectedinherited

This changes the arg keyword in the pdb file.

Definition at line 193 of file ActionWithArguments.cpp.

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

inherited

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

Definition at line 93 of file Action.cpp.

void PLMD::Action::fflush ( )

inherited

Tell to the Action to flush open files.

Definition at line 98 of file Action.cpp.

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

protectedinherited

Convert the stored log weights to proper weights.

Definition at line 257 of file Analysis.cpp.

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)

Definition at line 83 of file Action.cpp.

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

inlineinherited

Returns the value of an argument.

Definition at line 93 of file ActionWithArguments.h.

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

inlineprotectedinherited

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

Definition at line 172 of file Analysis.h.

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

inlineprotectedinherited

Retrieve the ith point.

Definition at line 141 of file Analysis.h.

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

inlineinherited

Return dependencies.

Definition at line 224 of file Action.h.

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

virtualinherited

Definition at line 157 of file Action.cpp.

bool PLMD::Action::getExchangeStep ( ) const

inherited

Check if we are on an exchange step.

Definition at line 217 of file Action.cpp.

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

inlineinherited

Returns the label.

Definition at line 263 of file Action.h.

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

inlineinherited

Returns the name.

Definition at line 268 of file Action.h.

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

protectedinherited

Return the normalization constant.

Definition at line 324 of file Analysis.cpp.

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

inlineprotectedinherited

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

Definition at line 161 of file Analysis.h.

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

inlineprotectedinherited

Return the number of data points.

Definition at line 131 of file Analysis.h.

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

inlineprotectedinherited

Return the format to use for numbers in output files.

Definition at line 179 of file Analysis.h.

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.

Definition at line 337 of file Analysis.cpp.

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

inlineinherited

Return a pointer to specific argument.

Definition at line 88 of file ActionWithArguments.h.

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

inherited

Get the scalar product between the gradients of two variables.

Definition at line 268 of file ActionWithArguments.cpp.

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

inherited

Return the present timestep.

Definition at line 169 of file Action.cpp.

int PLMD::ActionPilot::getStride ( ) const

protectedinherited

Definition at line 42 of file ActionPilot.cpp.

double PLMD::Action::getTime ( ) const

inherited

Return the present time.

Definition at line 173 of file Action.cpp.

double PLMD::Action::getTimeStep ( ) const

inherited

Return the timestep.

Definition at line 177 of file Action.cpp.

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.

Definition at line 44 of file ActionWithArguments.cpp.

bool PLMD::Action::isActive ( ) const

inlineinherited

Check if action is active.

Definition at line 375 of file Action.h.

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

inlineinherited

Check if an option is on.

Definition at line 380 of file Action.h.

void PLMD::ActionWithArguments::lockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

Definition at line 113 of file ActionWithArguments.h.

virtual void PLMD::Action::lockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::ActionAtomistic, and PLMD::ActionWithArguments.

Definition at line 172 of file Action.h.

bool PLMD::ActionPilot::onStep ( ) const

inherited

Check if the action is active on this step.

Definition at line 38 of file ActionPilot.cpp.

template<class T >

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

inherited

Parse one keyword as generic type.

Definition at line 273 of file Action.h.

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

inherited

Parse a list of arguments.

Definition at line 40 of file ActionWithArguments.cpp.

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

inherited

Parse one keyword as boolean flag.

Definition at line 104 of file Action.cpp.

template<class T >

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

inherited

Parse one numbered keyword as generic type.

Definition at line 300 of file Action.h.

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.

Definition at line 352 of file Action.h.

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.

Definition at line 198 of file Analysis.cpp.

template<class T >

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

inherited

Parse one keyword as std::vector.

Definition at line 311 of file Action.h.

void PLMD::analysis::Histogram::performAnalysis ( )

virtual

Implements PLMD::analysis::Analysis.

Definition at line 147 of file Histogram.cpp.

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.

Definition at line 207 of file Analysis.cpp.

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.

Definition at line 251 of file Action.h.

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

static

Definition at line 104 of file Histogram.cpp.

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

inherited

Setup the dependencies.

Definition at line 206 of file ActionWithArguments.cpp.

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

inherited

Definition at line 296 of file Analysis.cpp.

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.

Definition at line 343 of file Analysis.cpp.

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

virtualinherited

Definition at line 141 of file Action.cpp.

void PLMD::ActionWithArguments::unlockRequests ( )

inlinevirtualinherited

Reimplemented from PLMD::Action.

Definition at line 118 of file ActionWithArguments.h.

virtual void PLMD::Action::unlockRequests ( )

inlinevirtualinherited

Reimplemented in PLMD::ActionAtomistic, and PLMD::ActionWithArguments.

Definition at line 173 of file Action.h.

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.

Definition at line 329 of file Analysis.cpp.

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

inlineprotectedinherited

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

Definition at line 152 of file Analysis.h.

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

inherited

Issue a warning.

Definition at line 201 of file Action.cpp.

Member Data Documentation

std::vector<double> PLMD::analysis::Histogram::bw

private

Definition at line 92 of file Histogram.cpp.

Communicator& PLMD::Action::comm

inherited

Definition at line 158 of file Action.h.

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

inherited

Definition at line 139 of file Action.h.

std::vector<unsigned> PLMD::analysis::Histogram::gbin

private

Definition at line 93 of file Histogram.cpp.

std::vector<std::string> PLMD::analysis::Histogram::gmax

private

Definition at line 91 of file Histogram.cpp.

std::vector<std::string> PLMD::analysis::Histogram::gmin

private

Definition at line 91 of file Histogram.cpp.

std::string PLMD::analysis::Histogram::gridfname

private

Definition at line 94 of file Histogram.cpp.

std::string PLMD::analysis::Histogram::kerneltype

private

Definition at line 95 of file Histogram.cpp.

const Keywords& PLMD::Action::keywords

inherited

Definition at line 161 of file Action.h.

Log& PLMD::Action::log

inherited

Reference to the log stream.

Definition at line 93 of file Action.h.

Communicator& PLMD::Action::multi_sim_comm

inherited

Definition at line 159 of file Action.h.

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

Definition at line 90 of file Action.h.

std::vector<double> PLMD::analysis::Histogram::point

private

Definition at line 92 of file Histogram.cpp.

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

analysis/Histogram.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation