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

Tetrahedrality Parameter XYZ. More...

#include <TetrahedralityParamXYZ.hpp>

Inheritance diagram for OpenMD::TetrahedralityParamXYZ:
OpenMD::StaticAnalyser

Public Member Functions

 TetrahedralityParamXYZ (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, RealType rCut, RealType voxelSize, RealType gaussWidth)
 
virtual ~TetrahedralityParamXYZ ()
 
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 writeQxyz ()
 

Private Attributes

SnapshotcurrentSnapshot_
 
std::string selectionScript1_
 
std::string selectionScript2_
 
SelectionManager seleMan1_
 
SelectionManager seleMan2_
 
SelectionEvaluator evaluator1_
 
SelectionEvaluator evaluator2_
 
RealType rCut_
 
RealType voxelSize_
 
RealType gaussWidth_
 
Vector3i nBins_
 
std::vector< std::vector< std::vector< RealType > > > count_
 
std::vector< std::vector< std::vector< RealType > > > hist_
 

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 XYZ.

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 TetrahedralityParamXYZ.hpp.

Constructor & Destructor Documentation

◆ TetrahedralityParamXYZ()

OpenMD::TetrahedralityParamXYZ::TetrahedralityParamXYZ ( SimInfo info,
const std::string &  filename,
const std::string &  sele1,
const std::string &  sele2,
RealType  rCut,
RealType  voxelSize,
RealType  gaussWidth 
)

◆ ~TetrahedralityParamXYZ()

OpenMD::TetrahedralityParamXYZ::~TetrahedralityParamXYZ ( )
virtual

Definition at line 99 of file TetrahedralityParamXYZ.cpp.

Member Function Documentation

◆ process()

◆ writeQxyz()

Member Data Documentation

◆ count_

std::vector<std::vector<std::vector<RealType> > > OpenMD::TetrahedralityParamXYZ::count_
private

Definition at line 106 of file TetrahedralityParamXYZ.hpp.

Referenced by process(), TetrahedralityParamXYZ(), and writeQxyz().

◆ currentSnapshot_

Snapshot* OpenMD::TetrahedralityParamXYZ::currentSnapshot_
private

Definition at line 93 of file TetrahedralityParamXYZ.hpp.

Referenced by process().

◆ evaluator1_

SelectionEvaluator OpenMD::TetrahedralityParamXYZ::evaluator1_
private

Definition at line 98 of file TetrahedralityParamXYZ.hpp.

Referenced by process(), and TetrahedralityParamXYZ().

◆ evaluator2_

SelectionEvaluator OpenMD::TetrahedralityParamXYZ::evaluator2_
private

Definition at line 99 of file TetrahedralityParamXYZ.hpp.

Referenced by process(), and TetrahedralityParamXYZ().

◆ gaussWidth_

RealType OpenMD::TetrahedralityParamXYZ::gaussWidth_
private

Definition at line 103 of file TetrahedralityParamXYZ.hpp.

Referenced by process().

◆ hist_

std::vector<std::vector<std::vector<RealType> > > OpenMD::TetrahedralityParamXYZ::hist_
private

Definition at line 107 of file TetrahedralityParamXYZ.hpp.

Referenced by process(), TetrahedralityParamXYZ(), and writeQxyz().

◆ nBins_

Vector3i OpenMD::TetrahedralityParamXYZ::nBins_
private

Definition at line 105 of file TetrahedralityParamXYZ.hpp.

Referenced by process(), and TetrahedralityParamXYZ().

◆ rCut_

RealType OpenMD::TetrahedralityParamXYZ::rCut_
private

Definition at line 101 of file TetrahedralityParamXYZ.hpp.

Referenced by process().

◆ selectionScript1_

std::string OpenMD::TetrahedralityParamXYZ::selectionScript1_
private

Definition at line 94 of file TetrahedralityParamXYZ.hpp.

◆ selectionScript2_

std::string OpenMD::TetrahedralityParamXYZ::selectionScript2_
private

Definition at line 95 of file TetrahedralityParamXYZ.hpp.

◆ seleMan1_

SelectionManager OpenMD::TetrahedralityParamXYZ::seleMan1_
private

Definition at line 96 of file TetrahedralityParamXYZ.hpp.

Referenced by process(), and TetrahedralityParamXYZ().

◆ seleMan2_

SelectionManager OpenMD::TetrahedralityParamXYZ::seleMan2_
private

Definition at line 97 of file TetrahedralityParamXYZ.hpp.

Referenced by process(), and TetrahedralityParamXYZ().

◆ voxelSize_

RealType OpenMD::TetrahedralityParamXYZ::voxelSize_
private

Definition at line 102 of file TetrahedralityParamXYZ.hpp.

Referenced by process().


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