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gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData Class Reference
+ Inheritance diagram for gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData:
+ Collaboration diagram for gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData:

Description

Temporary memory for use within a single-frame calculation.

Public Member Functions

 PairDistanceModuleData (TrajectoryAnalysisModule *module, const AnalysisDataParallelOptions &opt, const SelectionCollection &selections, int refGroupCount, const Selection &refSel, int maxGroupCount)
 Reserves memory for the frame-local data.
 
void finish () override
 Performs any finishing actions after all frames have been processed. More...
 
void initRefCountArray (const Selection &refSel)
 Computes the number of positions in each group in refSel and stores them into refCountArray_.
 
- Public Member Functions inherited from gmx::TrajectoryAnalysisModuleData
AnalysisDataHandle dataHandle (const AnalysisData &data)
 Returns a data handle for a given dataset. More...
 
Selection parallelSelection (const Selection &selection)
 Returns a selection that corresponds to the given selection. More...
 
SelectionList parallelSelections (const SelectionList &selections)
 Returns a set of selection that corresponds to the given selections. More...
 

Public Attributes

std::vector< realdistArray_
 Squared distance between each group. More...
 
std::vector< int > countArray_
 Number of pairs within the cutoff that have contributed to the value in distArray_. More...
 
std::vector< int > refCountArray_
 Number of positions within each reference group. More...
 

Additional Inherited Members

- 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...
 

Member Function Documentation

void gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData::finish ( )
inlineoverridevirtual

Performs any finishing actions after all frames have been processed.

Exceptions
unspecifiedImplementation 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<int> gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData::countArray_

Number of pairs within the cutoff that have contributed to the value in distArray_.

This is needed to identify whether there were any pairs inside the cutoff and whether there were additional pairs outside the cutoff that were not covered by the neihborhood search.

std::vector<real> gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData::distArray_

Squared distance between each group.

One entry for each group pair for the current selection. Enough memory is allocated to fit the largest calculation selection. This is needed to support neighborhood searching, which may not return the pairs in order: for each group pair, we need to search through all the position pairs and update this array to find the minimum/maximum distance between them.

std::vector<int> gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData::refCountArray_

Number of positions within each reference group.

This is used to more efficiently compute the total number of pairs (for comparison with countArray_), as otherwise these numbers would need to be recomputed for each selection.


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