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OpenMD::HBondJumpZ Class Reference
Inheritance diagram for OpenMD::HBondJumpZ:
Public Member Functions | |
| HBondJumpZ (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, double OOCut, double thetaCut, double OHCut, int nZbins, int axis=2) | |
| virtual int | registerHydrogen (int frame, int hIndex) |
| virtual void | findHBonds (int frame) |
| virtual void | correlation () |
| virtual void | postCorrelate () |
| virtual void | writeCorrelate () |
| Public Member Functions inherited from OpenMD::HBondJump | |
| HBondJump (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, double OOCut, double thetaCut, double OHCut) | |
| Public Member Functions inherited from OpenMD::TimeCorrFunc< RealType > | |
| TimeCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2) | |
| virtual void | doCorrelate () |
| const std::string & | getCorrFuncType () const |
| void | setCorrFuncType (const std::string &type) |
| void | setParameterString (const std::string ¶ms) |
| void | setLabelString (const std::string &label) |
| void | setWindowingParameters (RealType tcorr_fs, int nStart, RealType tsep_fs) |
| Public Member Functions inherited from OpenMD::DynamicProperty | |
| void | setOutputName (const std::string &filename) |
| const std::string & | getOutputFileName () const |
| void | setSelectionModeRestart () |
Additional Inherited Members | |
| Protected Member Functions inherited from OpenMD::HBondJump | |
| virtual void | computeFrame (int istep) |
| virtual void | computeProperty1 (int) |
| virtual void | computeProperty2 (int) |
| virtual int | computeProperty1 (int, Molecule *) |
| virtual int | computeProperty1 (int, StuntDouble *) |
| virtual int | computeProperty1 (int, Bond *) |
| virtual int | computeProperty2 (int, Molecule *) |
| virtual int | computeProperty2 (int, StuntDouble *) |
| virtual int | computeProperty2 (int, Bond *) |
| virtual RealType | calcCorrVal (int, int, int, int) |
| virtual RealType | calcCorrVal (int, int) |
| bool | isHBond (Vector3d donorPos, Vector3d hPos, Vector3d acceptorPos) |
| void | registerHydrogenBond (int frame, int index, int hIndex, int aIndex) |
| void | processNonOverlapping (int frame, SelectionManager &sman1, SelectionManager &sman2) |
| void | processOverlapping (int frame, SelectionManager &sman) |
| Protected Member Functions inherited from OpenMD::TimeCorrFunc< RealType > | |
| void | writeCorrelate () |
| void | writeCorrelate () |
| void | writeCorrelate () |
| void | writeCorrelate () |
| virtual void | preCorrelate () |
| virtual void | validateSelection (SelectionManager &seleMan) |
| virtual void | correlateFrames (int frame1, int frame2, int timeBin) |
| Protected Attributes inherited from OpenMD::HBondJump | |
| std::vector< std::vector< int > > | GIDtoH_ |
| std::vector< std::vector< int > > | hydrogen_ |
| std::vector< std::vector< int > > | acceptor_ |
| std::vector< std::vector< int > > | lastAcceptor_ |
| std::vector< std::vector< bool > > | selected_ |
| std::vector< std::vector< int > > | acceptorStartFrame_ |
| RealType | OOCut_ |
| RealType | thetaCut_ |
| RealType | OHCut_ |
| SelectionManager | sele1_minus_common_ |
| SelectionManager | sele2_minus_common_ |
| SelectionManager | common_ |
| Protected Attributes inherited from OpenMD::TimeCorrFunc< RealType > | |
| RealType | deltaTime_ |
| unsigned int | nTimeBins_ |
| int | nFrames_ |
| std::vector< RealType > | histogram_ |
| std::vector< int > | count_ |
| std::vector< RealType > | times_ |
| RealType | dtMean_ |
| RealType | dtSigma_ |
| SimInfo * | info_ |
| DumpReader * | reader_ |
| std::string | dumpFilename_ |
| SelectionManager | seleMan1_ |
| SelectionManager | seleMan2_ |
| Snapshot * | currentSnapshot_ |
| std::string | selectionScript1_ |
| std::string | selectionScript2_ |
| SelectionEvaluator | evaluator1_ |
| SelectionEvaluator | evaluator2_ |
| bool | uniqueSelections_ |
| bool | autoCorrFunc_ |
| bool | doSystemProperties_ |
| bool | doMolecularProperties_ |
| bool | doObjectProperties_ |
| bool | doAtomicProperties_ |
| bool | doBondProperties_ |
| bool | allowTimeFuzz_ |
| std::string | corrFuncType_ |
| std::string | paramString_ |
| std::string | labelString_ |
| std::vector< std::vector< int > > | sele1ToIndex_ |
| std::vector< std::vector< int > > | sele2ToIndex_ |
| ProgressBarPtr | progressBar_ |
| std::vector< std::vector< int > > | GIDtoSele1_ |
| std::vector< std::vector< int > > | GIDtoSele2_ |
| std::vector< std::vector< int > > | selection1StartFrame_ |
| std::vector< std::vector< int > > | selection2StartFrame_ |
| int | nStart_ |
| int | nSep_ |
| int | nStride_ |
| int | navg_ |
| bool | useWindowing_ |
| Protected Attributes inherited from OpenMD::DynamicProperty | |
| std::string | outputFilename_ |
| bool | selectionModeRestart_ |
Detailed Description
Definition at line 105 of file HBondJump.hpp.
Constructor & Destructor Documentation
◆ HBondJumpZ()
| OpenMD::HBondJumpZ::HBondJumpZ | ( | SimInfo * | info, |
| const std::string & | filename, | ||
| const std::string & | sele1, | ||
| const std::string & | sele2, | ||
| double | OOCut, | ||
| double | thetaCut, | ||
| double | OHCut, | ||
| int | nZbins, | ||
| int | axis = 2 ) |
Definition at line 483 of file HBondJump.cpp.
Member Function Documentation
◆ correlation()
|
virtual |
Reimplemented from OpenMD::HBondJump.
Definition at line 630 of file HBondJump.cpp.
◆ findHBonds()
|
virtual |
Reimplemented from OpenMD::HBondJump.
Definition at line 516 of file HBondJump.cpp.
◆ postCorrelate()
|
virtual |
Reimplemented from OpenMD::HBondJump.
Definition at line 716 of file HBondJump.cpp.
◆ registerHydrogen()
|
virtual |
Reimplemented from OpenMD::HBondJump.
Definition at line 601 of file HBondJump.cpp.
◆ writeCorrelate()
|
virtual |
Definition at line 729 of file HBondJump.cpp.
The documentation for this class was generated from the following files:
- applications/dynamicProps/HBondJump.hpp
- applications/dynamicProps/HBondJump.cpp
