OpenMD 3.1
Molecular Dynamics in the Open
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Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
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)
 
- Public Member Functions inherited from OpenMD::DynamicProperty
void setOutputName (const std::string &filename)
 
const std::string & getOutputFileName () const
 

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 >
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

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_
 
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_
 
std::string corrFuncType_
 
std::string paramString_
 
std::string labelString_
 
std::vector< std::vector< int > > sele1ToIndex_
 
std::vector< std::vector< int > > sele2ToIndex_
 
ProgressBarPtr progressBar_
 
- Protected Attributes inherited from OpenMD::DynamicProperty
std::string outputFilename_
 

Detailed Description

Definition at line 54 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 54 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 74 of file HBondJump.hpp.

◆ calcCorrVal() [2/2]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 73 of file HBondJump.hpp.

◆ computeFrame()

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

Reimplemented from OpenMD::TimeCorrFunc< RealType >.

Definition at line 101 of file HBondJump.cpp.

◆ computeProperty1() [1/4]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 64 of file HBondJump.hpp.

◆ computeProperty1() [2/4]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 68 of file HBondJump.hpp.

◆ computeProperty1() [3/4]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 66 of file HBondJump.hpp.

◆ computeProperty1() [4/4]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 67 of file HBondJump.hpp.

◆ computeProperty2() [1/4]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 65 of file HBondJump.hpp.

◆ computeProperty2() [2/4]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 71 of file HBondJump.hpp.

◆ computeProperty2() [3/4]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 69 of file HBondJump.hpp.

◆ computeProperty2() [4/4]

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

Implements OpenMD::TimeCorrFunc< RealType >.

Definition at line 70 of file HBondJump.hpp.

◆ correlation()

void OpenMD::HBondJump::correlation ( )
protectedvirtual

Reimplemented from OpenMD::TimeCorrFunc< RealType >.

Definition at line 127 of file HBondJump.cpp.

◆ findHBonds()

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

Definition at line 331 of file HBondJump.cpp.

◆ isHBond()

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

Definition at line 401 of file HBondJump.cpp.

◆ postCorrelate()

void OpenMD::HBondJump::postCorrelate ( )
protectedvirtual

Reimplemented from OpenMD::TimeCorrFunc< RealType >.

Definition at line 211 of file HBondJump.cpp.

◆ processNonOverlapping()

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

Definition at line 222 of file HBondJump.cpp.

◆ processOverlapping()

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

Definition at line 275 of file HBondJump.cpp.

◆ registerHydrogen()

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

Definition at line 427 of file HBondJump.cpp.

◆ registerHydrogenBond()

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

Definition at line 455 of file HBondJump.cpp.

Member Data Documentation

◆ acceptor_

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

Definition at line 88 of file HBondJump.hpp.

◆ acceptorStartFrame_

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

Definition at line 91 of file HBondJump.hpp.

◆ common_

SelectionManager OpenMD::HBondJump::common_
protected

Definition at line 99 of file HBondJump.hpp.

◆ GIDtoH_

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

Definition at line 86 of file HBondJump.hpp.

◆ hydrogen_

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

Definition at line 87 of file HBondJump.hpp.

◆ lastAcceptor_

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

Definition at line 89 of file HBondJump.hpp.

◆ OHCut_

RealType OpenMD::HBondJump::OHCut_
protected

Definition at line 95 of file HBondJump.hpp.

◆ OOCut_

RealType OpenMD::HBondJump::OOCut_
protected

Definition at line 93 of file HBondJump.hpp.

◆ sele1_minus_common_

SelectionManager OpenMD::HBondJump::sele1_minus_common_
protected

Definition at line 97 of file HBondJump.hpp.

◆ sele2_minus_common_

SelectionManager OpenMD::HBondJump::sele2_minus_common_
protected

Definition at line 98 of file HBondJump.hpp.

◆ selected_

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

Definition at line 90 of file HBondJump.hpp.

◆ thetaCut_

RealType OpenMD::HBondJump::thetaCut_
protected

Definition at line 94 of file HBondJump.hpp.

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