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

Tetrahedrality Hydrogen Bonding Matrix. More...

#include <TetrahedralityHBMatrix.hpp>

Inheritance diagram for OpenMD::TetrahedralityHBMatrix:
OpenMD::StaticAnalyser

Public Member Functions

 TetrahedralityHBMatrix (SimInfo *info, const std::string &filename, const std::string &sele, double rCut, double OOCut, double thetaCut, double OHCut, int nbins)
 
virtual ~TetrahedralityHBMatrix ()
 
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 (RealType q1, RealType q2)
 
void writeOutput ()
 

Private Attributes

SnapshotcurrentSnapshot_
 
std::string selectionScript_
 
SelectionManager seleMan_
 
SelectionEvaluator evaluator_
 
RealType rCut_
 
RealType OOCut_
 
RealType thetaCut_
 
RealType OHCut_
 
unsigned int count_
 
int frameCounter_
 
RealType MinQ_
 
RealType MaxQ_
 
RealType deltaQ_
 
std::vector< RealType > Q_
 
std::vector< std::vector< unsigned int > > Q_histogram_
 

Additional Inherited Members

- Protected Member Functions inherited from OpenMD::StaticAnalyser
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

Tetrahedrality Hydrogen Bonding Matrix.

Computes hydrogen-bonding probabilities for molecules that are categorized by the local tetrahedral order parameter Q as introduced in:

"A new order parameter for tetrahedral configurations," by P.-L. Chau and A.J. Hardwick, Mol. Phys. 93, pp. 511-518 (1998).

Note that we use a rescaled version of the tetrahedral order parameter 'Q' such that a perfectly tetrahedral configuration has a Q value of 1 and an ideal gas configuration has a Q value of 0. This rescaled version of the tetrahedrality parameter was first introduced in:

"Relationship between structural order and the anomalies of liquid water," by J.R. Errington and P.G. Debenedetti, Nature 409, pp. 318-321 (2001).

Definition at line 74 of file TetrahedralityHBMatrix.hpp.

Constructor & Destructor Documentation

◆ TetrahedralityHBMatrix()

◆ ~TetrahedralityHBMatrix()

OpenMD::TetrahedralityHBMatrix::~TetrahedralityHBMatrix ( )
virtual

Definition at line 98 of file TetrahedralityHBMatrix.cpp.

References OpenMD::StaticAnalyser::nBins_, and Q_histogram_.

Member Function Documentation

◆ collectHistogram()

void OpenMD::TetrahedralityHBMatrix::collectHistogram ( RealType  q1,
RealType  q2 
)
privatevirtual

Definition at line 320 of file TetrahedralityHBMatrix.cpp.

References count_, deltaQ_, MaxQ_, MinQ_, and Q_histogram_.

Referenced by process().

◆ initializeHistogram()

void OpenMD::TetrahedralityHBMatrix::initializeHistogram ( )
privatevirtual

Definition at line 105 of file TetrahedralityHBMatrix.cpp.

References OpenMD::StaticAnalyser::nBins_, and Q_histogram_.

◆ process()

◆ writeOutput()

Member Data Documentation

◆ count_

unsigned int OpenMD::TetrahedralityHBMatrix::count_
private

Definition at line 97 of file TetrahedralityHBMatrix.hpp.

Referenced by collectHistogram(), and writeOutput().

◆ currentSnapshot_

Snapshot* OpenMD::TetrahedralityHBMatrix::currentSnapshot_
private

Definition at line 88 of file TetrahedralityHBMatrix.hpp.

Referenced by process().

◆ deltaQ_

RealType OpenMD::TetrahedralityHBMatrix::deltaQ_
private

Definition at line 102 of file TetrahedralityHBMatrix.hpp.

Referenced by collectHistogram(), and TetrahedralityHBMatrix().

◆ evaluator_

SelectionEvaluator OpenMD::TetrahedralityHBMatrix::evaluator_
private

Definition at line 91 of file TetrahedralityHBMatrix.hpp.

Referenced by process(), and TetrahedralityHBMatrix().

◆ frameCounter_

int OpenMD::TetrahedralityHBMatrix::frameCounter_
private

Definition at line 99 of file TetrahedralityHBMatrix.hpp.

◆ MaxQ_

RealType OpenMD::TetrahedralityHBMatrix::MaxQ_
private

Definition at line 101 of file TetrahedralityHBMatrix.hpp.

Referenced by collectHistogram(), and TetrahedralityHBMatrix().

◆ MinQ_

RealType OpenMD::TetrahedralityHBMatrix::MinQ_
private

Definition at line 100 of file TetrahedralityHBMatrix.hpp.

Referenced by collectHistogram(), and TetrahedralityHBMatrix().

◆ OHCut_

RealType OpenMD::TetrahedralityHBMatrix::OHCut_
private

Definition at line 96 of file TetrahedralityHBMatrix.hpp.

Referenced by process(), and TetrahedralityHBMatrix().

◆ OOCut_

RealType OpenMD::TetrahedralityHBMatrix::OOCut_
private

Definition at line 94 of file TetrahedralityHBMatrix.hpp.

Referenced by process(), and TetrahedralityHBMatrix().

◆ Q_

std::vector<RealType> OpenMD::TetrahedralityHBMatrix::Q_
private

Definition at line 104 of file TetrahedralityHBMatrix.hpp.

Referenced by process().

◆ Q_histogram_

std::vector<std::vector<unsigned int> > OpenMD::TetrahedralityHBMatrix::Q_histogram_
private

◆ rCut_

RealType OpenMD::TetrahedralityHBMatrix::rCut_
private

Definition at line 93 of file TetrahedralityHBMatrix.hpp.

Referenced by process(), and TetrahedralityHBMatrix().

◆ selectionScript_

std::string OpenMD::TetrahedralityHBMatrix::selectionScript_
private

Definition at line 89 of file TetrahedralityHBMatrix.hpp.

Referenced by writeOutput().

◆ seleMan_

SelectionManager OpenMD::TetrahedralityHBMatrix::seleMan_
private

Definition at line 90 of file TetrahedralityHBMatrix.hpp.

Referenced by process(), and TetrahedralityHBMatrix().

◆ thetaCut_

RealType OpenMD::TetrahedralityHBMatrix::thetaCut_
private

Definition at line 95 of file TetrahedralityHBMatrix.hpp.

Referenced by process(), and TetrahedralityHBMatrix().


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