gmx::EnergyTerm Class Reference

#include <gromacs/energyanalysis/energyterm.h>

Description

Class describing the whole time series of an energy term.

Public Member Functions
	EnergyTerm (unsigned int indexWithinEnergyFile, bool bStoreData, const std::string &energyTerm, const std::string &energyUnit)
	Constructor. More...
unsigned int	fileIndex () const
	Return the index in the file to the function type stored here.
std::string	name () const
	Return the name corresponding to the energy term.
std::string	unit () const
	Return the name corresponding to the energy unit.
void	setStoreData (bool bStoreData)
	Tell the class to store or not to store data. More...
bool	storeData () const
	Returns whether any data has been stored from the analyzed frame.
bool	termIsEnergy () const
	Is this a true energy or e.g. Temperature.
EnergyAnalysisFrameIterator	begin () const
	Return iterator to begin looping over energy frames.
EnergyAnalysisFrameIterator	end () const
	Return iterator to end looping over energy frames.
EnergyAnalysisFrameIterator	findFrame (int64_t frameIndex) const
	Return the stored energy frame corresponding to a certain input frame. More...
void	addFrame (double time, int64_t step, int numIntermediateStepsSum, double energySumOverNumSteps, double energyVarianceOverNumSteps, double energyAtTime)
	Add a data frame to this EnergyTerm. More...
double	average () const
	Return the average energy.
double	standardDeviation () const
	Return the standard deviation.
std::optional< real >	errorEstimate (unsigned int numBlocks) const
	Compute an error estimate based on block averaging. Requires that the energies have been stored. More...
std::optional< real >	slopeOfLinearFit () const
	Calculate the slope of linear fit of energy. More...
int64_t	numFrames () const
	Return the number of points stored.
double	timeSpan () const
	Return the length of the data set in time.
double	timeBegin () const
	Return the begin time of the data set.
double	timeEnd () const
	Return the end time of the data set.
int64_t	numSteps () const
	Return the length of the data set in steps.
int64_t	stepBegin () const
	Return the begin step of the data set.
int64_t	stepEnd () const
	Return the end step of the data set.

Constructor & Destructor Documentation

gmx::EnergyTerm::EnergyTerm	(	unsigned int	indexWithinEnergyFile,
		bool	bStoreData,
		const std::string &	energyTerm,
		const std::string &	energyUnit
	)

Constructor.

Parameters

[in]	indexWithinEnergyFile	File index (in the energies stored)
[in]	bStoreData	boolean indicating whether to store the data
[in]	energyTerm	String describing the energy
[in]	energyUnit	String describing the energy unit

Member Function Documentation

void gmx::EnergyTerm::addFrame	(	double	time,
		int64_t	step,
		int	numIntermediateStepsSum,
		double	energySumOverNumSteps,
		double	energyVarianceOverNumSteps,
		double	energyAtTime
	)

Add a data frame to this EnergyTerm.

Parameters

[in]	time	The time in the simulation
[in]	step	The simulation step
[in]	numIntermediateStepsSum	The number of intermediate steps for the sums
[in]	energySumOverNumSteps	The sum of energies over the last nsum steps
[in]	energyVarianceOverNumSteps	The variance of the energies over the last nsum steps
[in]	energyAtTime	The energy at this point in time (trajectory)

std::optional< real > gmx::EnergyTerm::errorEstimate

(

unsigned int

numBlocks

)

const

Compute an error estimate based on block averaging. Requires that the energies have been stored.

Parameters

[in]

numBlocks

Number of blocks

Returns

Optional error estimate

EnergyAnalysisFrameIterator gmx::EnergyTerm::findFrame

(

int64_t

frameIndex

)

const

Return the stored energy frame corresponding to a certain input frame.

Parameters

[in]

frameIndex

The frame number to search the storage for.

Returns

the actual EnergyFrameIterator, or end() if not found

void gmx::EnergyTerm::setStoreData ( bool  bStoreData )

inline

Tell the class to store or not to store data.

Parameters

[in]

bStoreData

Boolean

std::optional< real > gmx::EnergyTerm::slopeOfLinearFit

(

)

const

Calculate the slope of linear fit of energy.

This energy drift calculation can only be done when the data is stored. This is done by fitting the data to a line y = ax + b.

Returns

Optional slope of the line when calculated

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

• src/gromacs/energyanalysis/energyterm.h
• src/gromacs/energyanalysis/energyterm.cpp