OpenMD 3.2
Molecular Dynamics in the Open
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OpenMD::HBondJump Class Reference
Inheritance diagram for OpenMD::HBondJump:

Public Member Functions

 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 &params)
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 ()

Protected Member Functions

virtual void correlation ()
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)
virtual void postCorrelate ()
virtual int registerHydrogen (int frame, int hIndex)
virtual void findHBonds (int frame)
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

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 57 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 )

Definition at line 57 of file HBondJump.cpp.

Member Function Documentation

◆ calcCorrVal() [1/2]

virtual RealType OpenMD::HBondJump::calcCorrVal ( int ,
int  )
inlineprotectedvirtual

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 77 of file HBondJump.hpp.

◆ calcCorrVal() [2/2]

virtual RealType OpenMD::HBondJump::calcCorrVal ( int ,
int ,
int ,
int  )
inlineprotectedvirtual

Definition at line 76 of file HBondJump.hpp.

◆ computeFrame()

void OpenMD::HBondJump::computeFrame ( int istep)
protectedvirtual

Reimplemented from OpenMD::TimeCorrFunc< RealType >.

Definition at line 104 of file HBondJump.cpp.

◆ computeProperty1() [1/4]

virtual void OpenMD::HBondJump::computeProperty1 ( int )
inlineprotectedvirtual

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 67 of file HBondJump.hpp.

◆ computeProperty1() [2/4]

virtual int OpenMD::HBondJump::computeProperty1 ( int ,
Bond *  )
inlineprotectedvirtual

Definition at line 71 of file HBondJump.hpp.

◆ computeProperty1() [3/4]

virtual int OpenMD::HBondJump::computeProperty1 ( int ,
Molecule *  )
inlineprotectedvirtual

Definition at line 69 of file HBondJump.hpp.

◆ computeProperty1() [4/4]

virtual int OpenMD::HBondJump::computeProperty1 ( int ,
StuntDouble *  )
inlineprotectedvirtual

Definition at line 70 of file HBondJump.hpp.

◆ computeProperty2() [1/4]

virtual void OpenMD::HBondJump::computeProperty2 ( int )
inlineprotectedvirtual

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 68 of file HBondJump.hpp.

◆ computeProperty2() [2/4]

virtual int OpenMD::HBondJump::computeProperty2 ( int ,
Bond *  )
inlineprotectedvirtual

Definition at line 74 of file HBondJump.hpp.

◆ computeProperty2() [3/4]

virtual int OpenMD::HBondJump::computeProperty2 ( int ,
Molecule *  )
inlineprotectedvirtual

Definition at line 72 of file HBondJump.hpp.

◆ computeProperty2() [4/4]

virtual int OpenMD::HBondJump::computeProperty2 ( int ,
StuntDouble *  )
inlineprotectedvirtual

Definition at line 73 of file HBondJump.hpp.

◆ correlation()

void OpenMD::HBondJump::correlation ( )
protectedvirtual

Reimplemented from OpenMD::TimeCorrFunc< RealType >.

Definition at line 130 of file HBondJump.cpp.

◆ findHBonds()

void OpenMD::HBondJump::findHBonds ( int frame)
protectedvirtual

Definition at line 341 of file HBondJump.cpp.

◆ isHBond()

bool OpenMD::HBondJump::isHBond ( Vector3d donorPos,
Vector3d hPos,
Vector3d acceptorPos )
protected

Definition at line 411 of file HBondJump.cpp.

◆ postCorrelate()

void OpenMD::HBondJump::postCorrelate ( )
protectedvirtual

Reimplemented from OpenMD::TimeCorrFunc< RealType >.

Definition at line 221 of file HBondJump.cpp.

◆ processNonOverlapping()

void OpenMD::HBondJump::processNonOverlapping ( int frame,
SelectionManager & sman1,
SelectionManager & sman2 )
protected

Definition at line 232 of file HBondJump.cpp.

◆ processOverlapping()

void OpenMD::HBondJump::processOverlapping ( int frame,
SelectionManager & sman )
protected

Definition at line 285 of file HBondJump.cpp.

◆ registerHydrogen()

int OpenMD::HBondJump::registerHydrogen ( int frame,
int hIndex )
protectedvirtual

Definition at line 437 of file HBondJump.cpp.

◆ registerHydrogenBond()

void OpenMD::HBondJump::registerHydrogenBond ( int frame,
int index,
int hIndex,
int aIndex )
protected

Definition at line 465 of file HBondJump.cpp.

Member Data Documentation

◆ acceptor_

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

Definition at line 91 of file HBondJump.hpp.

◆ acceptorStartFrame_

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

Definition at line 94 of file HBondJump.hpp.

◆ common_

SelectionManager OpenMD::HBondJump::common_
protected

Definition at line 102 of file HBondJump.hpp.

◆ GIDtoH_

std::vector<std::vector<int> > OpenMD::HBondJump::GIDtoH_
protected

Definition at line 89 of file HBondJump.hpp.

◆ hydrogen_

std::vector<std::vector<int> > OpenMD::HBondJump::hydrogen_
protected

Definition at line 90 of file HBondJump.hpp.

◆ lastAcceptor_

std::vector<std::vector<int> > OpenMD::HBondJump::lastAcceptor_
protected

Definition at line 92 of file HBondJump.hpp.

◆ OHCut_

RealType OpenMD::HBondJump::OHCut_
protected

Definition at line 98 of file HBondJump.hpp.

◆ OOCut_

RealType OpenMD::HBondJump::OOCut_
protected

Definition at line 96 of file HBondJump.hpp.

◆ sele1_minus_common_

SelectionManager OpenMD::HBondJump::sele1_minus_common_
protected

Definition at line 100 of file HBondJump.hpp.

◆ sele2_minus_common_

SelectionManager OpenMD::HBondJump::sele2_minus_common_
protected

Definition at line 101 of file HBondJump.hpp.

◆ selected_

std::vector<std::vector<bool> > OpenMD::HBondJump::selected_
protected

Definition at line 93 of file HBondJump.hpp.

◆ thetaCut_

RealType OpenMD::HBondJump::thetaCut_
protected

Definition at line 97 of file HBondJump.hpp.

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