gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData Class Reference

Inheritance diagram for gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData:

Collaboration diagram for gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData:

Description

Temporary memory for use within a single-frame calculation.

Public Member Functions
	RdfModuleData (TrajectoryAnalysisModule *module, const AnalysisDataParallelOptions &opt, const SelectionCollection &selections, int surfaceGroupCount)
	Reserves memory for the frame-local data. More...
void	finish () override
	Performs any finishing actions after all frames have been processed. More...
Public Member Functions inherited from gmx::TrajectoryAnalysisModuleData
AnalysisDataHandle	dataHandle (const AnalysisData &data)
	Returns a data handle for a given dataset. More...

Public Attributes
std::vector< real >	surfaceDist2_
	Minimum distance to each surface group. More...

Additional Inherited Members
Static Public Member Functions inherited from gmx::TrajectoryAnalysisModuleData
static Selection	parallelSelection (const Selection &selection)
	Returns a selection that corresponds to the given selection. More...
static SelectionList	parallelSelections (const SelectionList &selections)
	Returns a set of selection that corresponds to the given selections. More...
Protected Member Functions inherited from gmx::TrajectoryAnalysisModuleData
	TrajectoryAnalysisModuleData (TrajectoryAnalysisModule *module, const AnalysisDataParallelOptions &opt, const SelectionCollection &selections)
	Initializes thread-local storage for data handles and selections. More...
void	finishDataHandles ()
	Calls finishData() on all data handles. More...

Constructor & Destructor Documentation

gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData::RdfModuleData ( TrajectoryAnalysisModule *  module, const AnalysisDataParallelOptions &  opt, const SelectionCollection &  selections, int  surfaceGroupCount  )

inline

Reserves memory for the frame-local data.

surfaceGroupCount will be zero if -surf is not specified.

Member Function Documentation

void gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData::finish ( )

inlineoverridevirtual

Performs any finishing actions after all frames have been processed.

Exceptions

unspecified

Implementation may throw exceptions to indicate errors.

This function is called immediately before the destructor, after TrajectoryAnalysisModule::finishFrames(). Derived classes should implement any final operations that need to be done after successful analysis. All implementations should call finishDataHandles().

Implements gmx::TrajectoryAnalysisModuleData.

Member Data Documentation

std::vector<real> gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData::surfaceDist2_

Minimum distance to each surface group.

One entry for each group (residue/molecule, per -surf) in the reference selection. This is needed to support neighborhood searching, which may not return the reference positions in order: for each position, we need to search through all the reference positions and update this array to find the minimum distance to each surface group, and then compute the RDF from these numbers.

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

• src/gromacs/trajectoryanalysis/modules/rdf.cpp