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Gromacs
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Inheritance diagram for gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData: Collaboration diagram for gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData: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... | |
Public Attributes | |
| std::vector< real > | distArray_ |
| 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 | |
| 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... | |
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inlineoverridevirtual |
Performs any finishing actions after all frames have been processed.
| 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.
| 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.
1.8.5