Inheritance diagram for gmx::analysismodules::Msd:

Collaboration diagram for gmx::analysismodules::Msd:

Description

Implements the gmx msd module.

Todo:

Implement -tensor for full MSD tensor calculation

Implement -rmcomm for total-frame COM removal

Implement -pdb for molecule B factors

Public Member Functions
void	initOptions (IOptionsContainer options, TrajectoryAnalysisSettings settings) override
	Initializes options understood by the module. More...

void	optionsFinished (TrajectoryAnalysisSettings *settings) override
	Called after all option values have been set. More...

void	initAfterFirstFrame (const TrajectoryAnalysisSettings &settings, const t_trxframe &fr) override
	Performs additional initialization after reading the first frame. More...

void	initAnalysis (const TrajectoryAnalysisSettings &settings, const TopologyInformation &top) override
	Initializes the analysis. More...

void	analyzeFrame (int frameNumber, const t_trxframe &frame, t_pbc pbc, TrajectoryAnalysisModuleData pdata) override
	Analyzes a single frame. More...

void	finishAnalysis (int nframes) override
	Postprocesses data after frames have been read. More...

void	writeOutput () override
	Writes output into files and/or standard output/error. More...

Public Member Functions inherited from gmx::TrajectoryAnalysisModule
virtual TrajectoryAnalysisModuleDataPointer	startFrames (const AnalysisDataParallelOptions &opt, const SelectionCollection &selections)
	Starts the analysis of frames. More...

virtual void	finishFrames (TrajectoryAnalysisModuleData *pdata)
	Finishes the analysis of frames. More...

int	datasetCount () const
	Returns the number of datasets provided by the module. More...

const std::vector< std::string > &	datasetNames () const
	Returns a vector with the names of datasets provided by the module. More...

AbstractAnalysisData &	datasetFromIndex (int index) const
	Returns a pointer to the data set `index`. More...

AbstractAnalysisData &	datasetFromName (const char *name) const
	Returns a pointer to the data set with name `name`. More...

void	finishFrameSerial (int frameIndex)
	Processes data in AnalysisData objects in serial for each frame. More...

Additional Inherited Members
Protected Member Functions inherited from gmx::TrajectoryAnalysisModule
	TrajectoryAnalysisModule ()
	Initializes the dataset registration mechanism. More...

void	registerBasicDataset (AbstractAnalysisData data, const char name)
	Registers a dataset that exports data. More...

void	registerAnalysisDataset (AnalysisData data, const char name)
	Registers a parallelized dataset that exports data. More...

Member Function Documentation

void gmx::analysismodules::Msd::analyzeFrame	(	int	frnr,
		const t_trxframe &	fr,
		t_pbc *	pbc,
		TrajectoryAnalysisModuleData *	pdata
	)

overridevirtual

Analyzes a single frame.

Parameters

[in]	frnr	Frame number, a zero-based index that uniquely identifies the frame.
[in]	fr	Current frame.
[in]	pbc	Periodic boundary conditions for `fr`.
[in,out]	pdata	Data structure for frame-local data.

This method is called once for each frame to be analyzed, and should analyze the positions provided in the selections. Data handles and selections should be obtained from the pdata structure.

For threaded analysis, this method is called asynchronously in different threads to analyze different frames. The pdata structure is one of the structures created with startFrames(), but no assumptions should be made about which of these data structures is used. It is guaranteed that two instances of analyzeFrame() are not running concurrently with the same pdata data structure. Any access to data structures not stored in pdata should be designed to be thread-safe.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::Msd::finishAnalysis ( int nframes )

overridevirtual

Postprocesses data after frames have been read.

Parameters

[in] nframes Total number of frames processed.

This function is called after all finishFrames() calls have been called. nframes will equal the number of calls to analyzeFrame() that have occurred.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::Msd::initAfterFirstFrame	(	const TrajectoryAnalysisSettings &	settings,
		const t_trxframe &	fr
	)

overridevirtual

Performs additional initialization after reading the first frame.

When this function is called, selections are the same as in initAnalysis(), i.e., they have not been evaluated for the first frame.

It is necessary to override this method only if the module needs to do initialization for which it requires data from the first frame.

The default implementation does nothing.

Reimplemented from gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::Msd::initAnalysis	(	const TrajectoryAnalysisSettings &	settings,
		const TopologyInformation &	top
	)

overridevirtual

Initializes the analysis.

Parameters

[in]	settings	Settings to pass to and from the module.
[in]	top	Topology information.

When this function is called, selections have been initialized based on user input, and a topology has been loaded if provided by the user. For dynamic selections, the selections have been evaluated to the largest possible selection, i.e., the selections passed to analyzeFrame() are always a subset of the selections provided here.

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::Msd::initOptions	(	IOptionsContainer *	options,
		TrajectoryAnalysisSettings *	settings
	)

overridevirtual

Initializes options understood by the module.

Parameters

[in,out]	options	Options object to add the options to.
[in,out]	settings	Settings to pass to and from the module.

This method is called first after the constructor, and it should add options understood by the module to options. Output values from options (including selections) should be stored in member variables.

In addition to initializing the options, this method can also provide information about the module's requirements using the settings object; see TrajectoryAnalysisSettings for more details.

If settings depend on the option values provided by the user, see optionsFinished().

Implements gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::Msd::optionsFinished ( TrajectoryAnalysisSettings * settings )

overridevirtual

Called after all option values have been set.

Parameters

[in,out] settings Settings to pass to and from the module.

This method is called after option values have been assigned (but interactive selection input has not yet been performed).

If the module needs to change settings that affect topology loading (can be done using the settings object) or selection initialization (can be done using SelectionOptionInfo) based on option values, this method has to be overridden.

The default implementation does nothing.

Reimplemented from gmx::TrajectoryAnalysisModule.

void gmx::analysismodules::Msd::writeOutput ( )

overridevirtual

Writes output into files and/or standard output/error.

All output from the module, excluding data written out for each frame during analyzeFrame(), should be confined into this function. This function is guaranteed to be called only after finishAnalysis().

Implements gmx::TrajectoryAnalysisModule.

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

src/gromacs/trajectoryanalysis/modules/msd.cpp

Description

Public Member Functions

Additional Inherited Members

Member Function Documentation