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::set< Action * >	Dependencies

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

Public Member Functions
	Analysis (const ActionOptions &)

	~Analysis ()

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 ()

virtual void	performAnalysis ()=0

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 ()

virtual 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...

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...

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

void	lockRequests ()

void	unlockRequests ()

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

double	retrieveNorm () const
	This retrieves the value of norm from the analysis action. More...

Private Attributes
bool	single_run
	Are we running only once for the whole trajectory. More...

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...

std::vector< Value * >	biases
	The biases we are using in reweighting and the args we store them separately. More...

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

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

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

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

std::vector< double >	weights

bool	firstAnalysisDone
	Have we analyzed the data for the first time. More...

double	norm
	The value of the old normalization constant. More...

double	old_norm

std::string	ofmt
	The format to use in output files. 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.

Definition at line 40 of file Analysis.h.

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

Definition at line 75 of file Analysis.cpp.

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

Definition at line 253 of file Analysis.cpp.

Member Function Documentation

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

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 ( )

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.

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 ( )

virtual

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 )

protected

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 ( )

inlineprotected

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

inlineprotected

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

protected

Return the normalization constant.

Definition at line 324 of file Analysis.cpp.

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

inlineprotected

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

inlineprotected

Return the number of data points.

Definition at line 131 of file Analysis.h.

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

inlineprotected

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
	)

protected

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
	)

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.

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.

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

pure virtual

Implemented in PLMD::analysis::Histogram.

void PLMD::analysis::Analysis::prepare ( )

virtual

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::Analysis::readDataFromFile ( const std::string & filename )

private

Read in data from a file.

Definition at line 176 of file Analysis.cpp.

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

static

Definition at line 55 of file Analysis.cpp.

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

inherited

Setup the dependencies.

Definition at line 206 of file ActionWithArguments.cpp.

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

inlineprivate

This retrieves the value of norm from the analysis action.

It is only used to transfer data from one analysis action to another. You should never need to use it. If you think you need it you probably need getNormalization()

Definition at line 167 of file Analysis.h.

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

Definition at line 296 of file Analysis.cpp.

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.

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 ( )

virtual

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

inlineprotected

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::Analysis::args

private

Tempory vector to store values of arguments.

Definition at line 72 of file Analysis.h.

std::vector<Value*> PLMD::analysis::Analysis::biases

private

The biases we are using in reweighting and the args we store them separately.

Definition at line 68 of file Analysis.h.

Communicator& PLMD::Action::comm

inherited

Definition at line 158 of file Action.h.

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

private

The data we are going to analyze.

Definition at line 74 of file Analysis.h.

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

inherited

Definition at line 139 of file Action.h.

bool PLMD::analysis::Analysis::firstAnalysisDone

private

Have we analyzed the data for the first time.

Definition at line 78 of file Analysis.h.

unsigned PLMD::analysis::Analysis::freq

private

The frequency with which we are performing analysis.

Definition at line 58 of file Analysis.h.

unsigned PLMD::analysis::Analysis::idata

private

The piece of data we are inserting.

Definition at line 70 of file Analysis.h.

bool PLMD::analysis::Analysis::ignore_reweight

private

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

Definition at line 54 of file Analysis.h.

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.

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

private

The weights of all the data points.

Definition at line 76 of file Analysis.h.

Communicator& PLMD::Action::multi_sim_comm

inherited

Definition at line 159 of file Action.h.

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

private

The Analysis action that we are reusing data from.

Definition at line 56 of file Analysis.h.

unsigned PLMD::analysis::Analysis::ndata

private

Number of data point we need to run analysis.

Definition at line 60 of file Analysis.h.

bool PLMD::analysis::Analysis::needeng

private

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

Definition at line 66 of file Analysis.h.

bool PLMD::analysis::Analysis::nomemory

private

Are we treating each block of data separately.

Definition at line 48 of file Analysis.h.

double PLMD::analysis::Analysis::norm

private

The value of the old normalization constant.

Definition at line 80 of file Analysis.h.

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

private

The format to use in output files.

Definition at line 82 of file Analysis.h.

double PLMD::analysis::Analysis::old_norm

private

Definition at line 80 of file Analysis.h.

PlumedMain& PLMD::Action::plumed

inherited

Reference to main plumed object.

Definition at line 90 of file Action.h.

bool PLMD::analysis::Analysis::reusing_data

private

Are we reusing data stored by another analysis action.

Definition at line 52 of file Analysis.h.

OFile PLMD::analysis::Analysis::rfile

private

The checkpoint file.

Definition at line 84 of file Analysis.h.

double PLMD::analysis::Analysis::rtemp

private

The temperature at which we want the histogram.

Definition at line 64 of file Analysis.h.

double PLMD::analysis::Analysis::simtemp

private

The temperature at which we are running the calculation.

Definition at line 62 of file Analysis.h.

bool PLMD::analysis::Analysis::single_run

private

Are we running only once for the whole trajectory.

Definition at line 46 of file Analysis.h.

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

private

Definition at line 76 of file Analysis.h.

bool PLMD::analysis::Analysis::write_chq

private

Are we writing a checkpoint file.

Definition at line 50 of file Analysis.h.

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

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation