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

Tetrahedrality Parameter. More...

#include <TetrahedralityParam.hpp>

Inheritance diagram for OpenMD::TetrahedralityParam:
OpenMD::StaticAnalyser

Public Member Functions

 TetrahedralityParam (SimInfo *info, const std::string &filename, const std::string &sele, double rCut, int nbins)
 
virtual ~TetrahedralityParam ()
 
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 Qk)
 
void writeOrderParameter ()
 

Private Attributes

SnapshotcurrentSnapshot_
 
std::string selectionScript_
 
SelectionManager seleMan_
 
SelectionEvaluator evaluator_
 
RealType rCut_
 
int frameCounter_
 
int nBins_
 
RealType MinQ_
 
RealType MaxQ_
 
RealType deltaQ_
 
std::vector< int > Q_histogram_
 
std::vector< StuntDouble * > Distorted_
 
std::vector< StuntDouble * > Tetrahedral_
 

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

Tetrahedrality Parameter.

Computes 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).

Characterization of the spatial correlations of the the local order parameter Q are done according to the procedure outlined in:

"Space-time correlations in the orientational order parameter and the orientational entropy of water," by P. Kumar, S.V. Buldyrev, and H.E. Stanley, arXiv:0807.4699v1 [cond-mat.soft] 29 Jul 2008.

Definition at line 83 of file TetrahedralityParam.hpp.

Constructor & Destructor Documentation

◆ TetrahedralityParam()

OpenMD::TetrahedralityParam::TetrahedralityParam ( SimInfo info,
const std::string &  filename,
const std::string &  sele,
double  rCut,
int  nbins 
)

◆ ~TetrahedralityParam()

OpenMD::TetrahedralityParam::~TetrahedralityParam ( )
virtual

Definition at line 83 of file TetrahedralityParam.cpp.

References Q_histogram_.

Member Function Documentation

◆ collectHistogram()

void OpenMD::TetrahedralityParam::collectHistogram ( RealType  Qk)
privatevirtual

Definition at line 242 of file TetrahedralityParam.cpp.

References deltaQ_, MaxQ_, MinQ_, and Q_histogram_.

Referenced by process().

◆ initializeHistogram()

void OpenMD::TetrahedralityParam::initializeHistogram ( )
privatevirtual

Definition at line 87 of file TetrahedralityParam.cpp.

References Q_histogram_.

◆ process()

◆ writeOrderParameter()

Member Data Documentation

◆ currentSnapshot_

Snapshot* OpenMD::TetrahedralityParam::currentSnapshot_
private

Definition at line 96 of file TetrahedralityParam.hpp.

Referenced by process().

◆ deltaQ_

RealType OpenMD::TetrahedralityParam::deltaQ_
private

◆ Distorted_

std::vector<StuntDouble*> OpenMD::TetrahedralityParam::Distorted_
private

Definition at line 109 of file TetrahedralityParam.hpp.

Referenced by process(), and writeOrderParameter().

◆ evaluator_

SelectionEvaluator OpenMD::TetrahedralityParam::evaluator_
private

Definition at line 99 of file TetrahedralityParam.hpp.

Referenced by process(), and TetrahedralityParam().

◆ frameCounter_

int OpenMD::TetrahedralityParam::frameCounter_
private

Definition at line 102 of file TetrahedralityParam.hpp.

Referenced by process().

◆ MaxQ_

RealType OpenMD::TetrahedralityParam::MaxQ_
private

Definition at line 106 of file TetrahedralityParam.hpp.

Referenced by collectHistogram(), and TetrahedralityParam().

◆ MinQ_

RealType OpenMD::TetrahedralityParam::MinQ_
private

◆ nBins_

int OpenMD::TetrahedralityParam::nBins_
private

Definition at line 103 of file TetrahedralityParam.hpp.

Referenced by TetrahedralityParam(), and writeOrderParameter().

◆ Q_histogram_

std::vector<int> OpenMD::TetrahedralityParam::Q_histogram_
private

◆ rCut_

RealType OpenMD::TetrahedralityParam::rCut_
private

Definition at line 101 of file TetrahedralityParam.hpp.

Referenced by process(), and TetrahedralityParam().

◆ selectionScript_

std::string OpenMD::TetrahedralityParam::selectionScript_
private

Definition at line 97 of file TetrahedralityParam.hpp.

Referenced by writeOrderParameter().

◆ seleMan_

SelectionManager OpenMD::TetrahedralityParam::seleMan_
private

Definition at line 98 of file TetrahedralityParam.hpp.

Referenced by process(), and TetrahedralityParam().

◆ Tetrahedral_

std::vector<StuntDouble*> OpenMD::TetrahedralityParam::Tetrahedral_
private

Definition at line 110 of file TetrahedralityParam.hpp.

Referenced by process(), and writeOrderParameter().


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