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

Tetrahedrality ParameterZ. More...

#include <TetrahedralityParamZ.hpp>

Inheritance diagram for OpenMD::TetrahedralityParamZ:
OpenMD::StaticAnalyser

Public Member Functions

 TetrahedralityParamZ (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, double rCut, int nzbins, int axis=2)
 
int getNZBins ()
 
virtual ~TetrahedralityParamZ ()
 
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

void writeQz ()
 

Private Attributes

SnapshotcurrentSnapshot_
 
std::string selectionScript1_
 
std::string selectionScript2_
 
SelectionManager seleMan1_
 
SelectionManager seleMan2_
 
SelectionEvaluator evaluator1_
 
SelectionEvaluator evaluator2_
 
RealType rCut_
 
int nZBins_
 
std::vector< RealType > zBox_
 
std::vector< RealType > sliceQ_
 
std::vector< int > sliceCount_
 
int axis_
 
std::string axisLabel_
 

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 ParameterZ.

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 81 of file TetrahedralityParamZ.hpp.

Constructor & Destructor Documentation

◆ TetrahedralityParamZ()

OpenMD::TetrahedralityParamZ::TetrahedralityParamZ ( SimInfo info,
const std::string &  filename,
const std::string &  sele1,
const std::string &  sele2,
double  rCut,
int  nzbins,
int  axis = 2 
)

◆ ~TetrahedralityParamZ()

OpenMD::TetrahedralityParamZ::~TetrahedralityParamZ ( )
virtual

Definition at line 98 of file TetrahedralityParamZ.cpp.

References sliceCount_, sliceQ_, and zBox_.

Referenced by getNZBins().

Member Function Documentation

◆ getNZBins()

int OpenMD::TetrahedralityParamZ::getNZBins ( )
inline

Definition at line 86 of file TetrahedralityParamZ.hpp.

References nZBins_, process(), writeQz(), and ~TetrahedralityParamZ().

◆ process()

◆ writeQz()

void OpenMD::TetrahedralityParamZ::writeQz ( )
private

Member Data Documentation

◆ axis_

int OpenMD::TetrahedralityParamZ::axis_
private

Definition at line 108 of file TetrahedralityParamZ.hpp.

Referenced by process(), and TetrahedralityParamZ().

◆ axisLabel_

std::string OpenMD::TetrahedralityParamZ::axisLabel_
private

Definition at line 109 of file TetrahedralityParamZ.hpp.

Referenced by TetrahedralityParamZ(), and writeQz().

◆ currentSnapshot_

Snapshot* OpenMD::TetrahedralityParamZ::currentSnapshot_
private

Definition at line 96 of file TetrahedralityParamZ.hpp.

Referenced by process().

◆ evaluator1_

SelectionEvaluator OpenMD::TetrahedralityParamZ::evaluator1_
private

Definition at line 101 of file TetrahedralityParamZ.hpp.

Referenced by process(), and TetrahedralityParamZ().

◆ evaluator2_

SelectionEvaluator OpenMD::TetrahedralityParamZ::evaluator2_
private

Definition at line 102 of file TetrahedralityParamZ.hpp.

Referenced by process(), and TetrahedralityParamZ().

◆ nZBins_

int OpenMD::TetrahedralityParamZ::nZBins_
private

Definition at line 104 of file TetrahedralityParamZ.hpp.

Referenced by getNZBins().

◆ rCut_

RealType OpenMD::TetrahedralityParamZ::rCut_
private

Definition at line 103 of file TetrahedralityParamZ.hpp.

Referenced by process(), and TetrahedralityParamZ().

◆ selectionScript1_

std::string OpenMD::TetrahedralityParamZ::selectionScript1_
private

Definition at line 97 of file TetrahedralityParamZ.hpp.

Referenced by writeQz().

◆ selectionScript2_

std::string OpenMD::TetrahedralityParamZ::selectionScript2_
private

Definition at line 98 of file TetrahedralityParamZ.hpp.

Referenced by writeQz().

◆ seleMan1_

SelectionManager OpenMD::TetrahedralityParamZ::seleMan1_
private

Definition at line 99 of file TetrahedralityParamZ.hpp.

Referenced by process(), and TetrahedralityParamZ().

◆ seleMan2_

SelectionManager OpenMD::TetrahedralityParamZ::seleMan2_
private

Definition at line 100 of file TetrahedralityParamZ.hpp.

Referenced by process(), and TetrahedralityParamZ().

◆ sliceCount_

std::vector<int> OpenMD::TetrahedralityParamZ::sliceCount_
private

◆ sliceQ_

std::vector<RealType> OpenMD::TetrahedralityParamZ::sliceQ_
private

◆ zBox_

std::vector<RealType> OpenMD::TetrahedralityParamZ::zBox_
private

Definition at line 105 of file TetrahedralityParamZ.hpp.

Referenced by process(), writeQz(), and ~TetrahedralityParamZ().


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