OpenMD  2.5
Molecular Dynamics in the Open
OpenMD::HBondJump Class Reference

#include <HBondJump.hpp>

Inheritance diagram for OpenMD::HBondJump:
OpenMD::MultipassCorrFunc< RealType > OpenMD::DynamicProperty

Public Member Functions

 HBondJump (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, double OOCut, double thetaCut, double OHCut, int order)
 
- Public Member Functions inherited from OpenMD::MultipassCorrFunc< RealType >
 MultipassCorrFunc (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, int storageLayout)
 
virtual ~MultipassCorrFunc ()
 
virtual void doCorrelate ()
 
const std::string & getCorrFuncType () const
 
void setCorrFuncType (const std::string &type)
 
void setParameterString (const std::string &params)
 
- Public Member Functions inherited from OpenMD::DynamicProperty
 DynamicProperty ()
 
virtual ~DynamicProperty ()
 
void setOutputName (const std::string &filename)
 
const std::string & getOutputFileName () const
 

Private Member Functions

virtual void correlation ()
 
virtual void computeFrame (int istep)
 
virtual int computeProperty1 (int frame, StuntDouble *sd)
 
virtual int computeProperty2 (int frame, StuntDouble *sd)
 
virtual RealType calcCorrVal (int frame1, int frame2, int id1, int id2)
 
virtual void postCorrelate ()
 

Private Attributes

std::vector< std::vector< int > > GIDtoDonor_
 
std::vector< std::vector< int > > DonorToGID_
 
std::vector< std::vector< int > > acceptor_
 
std::vector< std::vector< int > > acceptorStartFrame_
 
std::vector< std::vector< Vector3d > > rOO_
 
std::vector< std::vector< RealType > > rOHprojection_
 
RealType OOCut_
 
RealType thetaCut_
 
RealType OHCut_
 
int order_
 

Additional Inherited Members

- Protected Member Functions inherited from OpenMD::MultipassCorrFunc< RealType >
virtual void preCorrelate ()
 
virtual void validateSelection (SelectionManager &seleMan)
 
virtual void correlateFrames (int frame1, int frame2, int timeBin)
 
virtual void writeCorrelate ()
 
void writeCorrelate ()
 
void writeCorrelate ()
 
- Protected Attributes inherited from OpenMD::MultipassCorrFunc< RealType >
int storageLayout_
 
RealType deltaTime_
 
int nTimeBins_
 
int nFrames_
 
std::vector< RealType > histogram_
 
std::vector< int > count_
 
std::vector< RealType > times_
 
bool uniqueSelections_
 
SimInfoinfo_
 
DumpReaderreader_
 
std::string dumpFilename_
 
SelectionManager seleMan1_
 
SelectionManager seleMan2_
 
SnapshotcurrentSnapshot_
 
std::string selectionScript1_
 
std::string selectionScript2_
 
SelectionEvaluator evaluator1_
 
SelectionEvaluator evaluator2_
 
bool autoCorrFunc_
 
std::string corrFuncType_
 
std::string paramString_
 
std::vector< std::vector< int > > sele1ToIndex_
 
std::vector< std::vector< int > > sele2ToIndex_
 
- Protected Attributes inherited from OpenMD::DynamicProperty
std::string outputFilename_
 

Detailed Description

Definition at line 48 of file HBondJump.hpp.

Constructor & Destructor Documentation

◆ HBondJump()

OpenMD::HBondJump::HBondJump ( SimInfo info,
const std::string &  filename,
const std::string &  sele1,
const std::string &  sele2,
double  OOCut,
double  thetaCut,
double  OHCut,
int  order 
)

Member Function Documentation

◆ calcCorrVal()

virtual RealType OpenMD::HBondJump::calcCorrVal ( int  frame1,
int  frame2,
int  id1,
int  id2 
)
inlineprivatevirtual

Implements OpenMD::MultipassCorrFunc< RealType >.

Definition at line 60 of file HBondJump.hpp.

References postCorrelate().

◆ computeFrame()

◆ computeProperty1()

virtual int OpenMD::HBondJump::computeProperty1 ( int  frame,
StuntDouble sd 
)
inlineprivatevirtual

Implements OpenMD::MultipassCorrFunc< RealType >.

Definition at line 58 of file HBondJump.hpp.

◆ computeProperty2()

virtual int OpenMD::HBondJump::computeProperty2 ( int  frame,
StuntDouble sd 
)
inlineprivatevirtual

Implements OpenMD::MultipassCorrFunc< RealType >.

Definition at line 59 of file HBondJump.hpp.

◆ correlation()

◆ postCorrelate()

void OpenMD::HBondJump::postCorrelate ( )
privatevirtual

Member Data Documentation

◆ acceptor_

std::vector<std::vector<int> > OpenMD::HBondJump::acceptor_
private

Definition at line 65 of file HBondJump.hpp.

Referenced by computeFrame(), correlation(), and HBondJump().

◆ acceptorStartFrame_

std::vector<std::vector<int> > OpenMD::HBondJump::acceptorStartFrame_
private

Definition at line 66 of file HBondJump.hpp.

Referenced by computeFrame(), correlation(), and HBondJump().

◆ DonorToGID_

std::vector<std::vector<int> > OpenMD::HBondJump::DonorToGID_
private

Definition at line 64 of file HBondJump.hpp.

Referenced by computeFrame(), correlation(), and HBondJump().

◆ GIDtoDonor_

std::vector<std::vector<int> > OpenMD::HBondJump::GIDtoDonor_
private

Definition at line 63 of file HBondJump.hpp.

Referenced by computeFrame(), correlation(), and HBondJump().

◆ OHCut_

RealType OpenMD::HBondJump::OHCut_
private

Definition at line 72 of file HBondJump.hpp.

Referenced by computeFrame(), and HBondJump().

◆ OOCut_

RealType OpenMD::HBondJump::OOCut_
private

Definition at line 70 of file HBondJump.hpp.

Referenced by computeFrame(), and HBondJump().

◆ order_

int OpenMD::HBondJump::order_
private

Definition at line 73 of file HBondJump.hpp.

Referenced by HBondJump().

◆ rOHprojection_

std::vector<std::vector<RealType> > OpenMD::HBondJump::rOHprojection_
private

Definition at line 68 of file HBondJump.hpp.

Referenced by computeFrame(), and HBondJump().

◆ rOO_

std::vector<std::vector<Vector3d> > OpenMD::HBondJump::rOO_
private

Definition at line 67 of file HBondJump.hpp.

Referenced by computeFrame(), and HBondJump().

◆ thetaCut_

RealType OpenMD::HBondJump::thetaCut_
private

Definition at line 71 of file HBondJump.hpp.

Referenced by computeFrame(), and HBondJump().


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