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

Hydrogen Bonding statistics using geometric criteria. More...

#include <HBondGeometric.hpp>

Inheritance diagram for OpenMD::HBondGeometric:
OpenMD::StaticAnalyser

Public Member Functions

 HBondGeometric (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, double rCut, double thetaCut, int nbins)
 
virtual ~HBondGeometric ()
 
virtual void process ()
 
- Public Member Functions inherited from OpenMD::StaticAnalyser
 StaticAnalyser (SimInfo *info, const std::string &filename, unsigned int nbins)
 
virtual ~StaticAnalyser ()
 
void setOutputName (const std::string &filename)
 
const std::string & getOutputFileName () const
 
void setStep (int step)
 
int getStep ()
 
const std::string & getAnalysisType () const
 
void setAnalysisType (const std::string &type)
 
void setParameterString (const std::string &params)
 

Private Member Functions

virtual void initializeHistogram ()
 
virtual void collectHistogram (int nHB, int nD, int nA)
 
void writeHistogram ()
 

Private Attributes

SnapshotcurrentSnapshot_
 
std::string selectionScript1_
 
SelectionManager seleMan1_
 
SelectionEvaluator evaluator1_
 
std::string selectionScript2_
 
SelectionManager seleMan2_
 
SelectionEvaluator evaluator2_
 
ForceFieldff_
 
RealType rCut_
 
RealType thetaCut_
 
int frameCounter_
 
int nBins_
 
std::vector< int > nHBonds_
 
std::vector< int > nDonor_
 
std::vector< int > nAcceptor_
 
int nSelected_
 

Additional Inherited Members

- Protected Member Functions inherited from OpenMD::StaticAnalyser
virtual void writeOutput ()
 
virtual void writeData (ostream &os, OutputData *dat, unsigned int bin)
 
virtual void writeErrorBars (ostream &os, OutputData *dat, unsigned int bin)
 
OutputDatabeginOutputData (vector< OutputData *>::iterator &i)
 
OutputDatanextOutputData (vector< OutputData *>::iterator &i)
 
- Protected Attributes inherited from OpenMD::StaticAnalyser
SimInfoinfo_
 
std::string dumpFilename_
 
std::string outputFilename_
 
int step_
 
std::string analysisType_
 
std::string paramString_
 
unsigned int nBins_
 
OutputDatacounts_
 
vector< OutputData * > data_
 

Detailed Description

Hydrogen Bonding statistics using geometric criteria.

Computes hydrogen bonding statistics using structural information:

"Hydrogen-bond dynamics for the extended simple point-carge model of water" by F. W. Starr, J. K. Nielsen, and H. E. Stanley, Phys. Rev. E 62(1), 579-587 (2000).

Definition at line 66 of file HBondGeometric.hpp.

Constructor & Destructor Documentation

◆ HBondGeometric()

◆ ~HBondGeometric()

OpenMD::HBondGeometric::~HBondGeometric ( )
virtual

Definition at line 88 of file HBondGeometric.cpp.

References nAcceptor_, nDonor_, and nHBonds_.

Member Function Documentation

◆ collectHistogram()

void OpenMD::HBondGeometric::collectHistogram ( int  nHB,
int  nD,
int  nA 
)
privatevirtual

Definition at line 222 of file HBondGeometric.cpp.

References nAcceptor_, nDonor_, nHBonds_, and nSelected_.

Referenced by process().

◆ initializeHistogram()

void OpenMD::HBondGeometric::initializeHistogram ( )
privatevirtual

Definition at line 94 of file HBondGeometric.cpp.

References nAcceptor_, nDonor_, nHBonds_, and nSelected_.

Referenced by HBondGeometric().

◆ process()

◆ writeHistogram()

void OpenMD::HBondGeometric::writeHistogram ( )
private

Member Data Documentation

◆ currentSnapshot_

Snapshot* OpenMD::HBondGeometric::currentSnapshot_
private

Definition at line 82 of file HBondGeometric.hpp.

Referenced by process().

◆ evaluator1_

SelectionEvaluator OpenMD::HBondGeometric::evaluator1_
private

Definition at line 85 of file HBondGeometric.hpp.

Referenced by HBondGeometric(), and process().

◆ evaluator2_

SelectionEvaluator OpenMD::HBondGeometric::evaluator2_
private

Definition at line 88 of file HBondGeometric.hpp.

Referenced by HBondGeometric(), and process().

◆ ff_

ForceField* OpenMD::HBondGeometric::ff_
private

Definition at line 89 of file HBondGeometric.hpp.

Referenced by HBondGeometric().

◆ frameCounter_

int OpenMD::HBondGeometric::frameCounter_
private

Definition at line 93 of file HBondGeometric.hpp.

Referenced by process().

◆ nAcceptor_

std::vector<int> OpenMD::HBondGeometric::nAcceptor_
private

◆ nBins_

int OpenMD::HBondGeometric::nBins_
private

Definition at line 94 of file HBondGeometric.hpp.

Referenced by HBondGeometric(), and writeHistogram().

◆ nDonor_

std::vector<int> OpenMD::HBondGeometric::nDonor_
private

◆ nHBonds_

std::vector<int> OpenMD::HBondGeometric::nHBonds_
private

◆ nSelected_

int OpenMD::HBondGeometric::nSelected_
private

Definition at line 99 of file HBondGeometric.hpp.

Referenced by collectHistogram(), initializeHistogram(), and writeHistogram().

◆ rCut_

RealType OpenMD::HBondGeometric::rCut_
private

Definition at line 91 of file HBondGeometric.hpp.

Referenced by HBondGeometric(), and process().

◆ selectionScript1_

std::string OpenMD::HBondGeometric::selectionScript1_
private

Definition at line 83 of file HBondGeometric.hpp.

Referenced by writeHistogram().

◆ selectionScript2_

std::string OpenMD::HBondGeometric::selectionScript2_
private

Definition at line 86 of file HBondGeometric.hpp.

Referenced by writeHistogram().

◆ seleMan1_

SelectionManager OpenMD::HBondGeometric::seleMan1_
private

Definition at line 84 of file HBondGeometric.hpp.

Referenced by HBondGeometric(), and process().

◆ seleMan2_

SelectionManager OpenMD::HBondGeometric::seleMan2_
private

Definition at line 87 of file HBondGeometric.hpp.

Referenced by HBondGeometric(), and process().

◆ thetaCut_

RealType OpenMD::HBondGeometric::thetaCut_
private

Definition at line 92 of file HBondGeometric.hpp.

Referenced by HBondGeometric(), and process().


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