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

CoordinationNumber. More...

#include <CoordinationNumber.hpp>

Inheritance diagram for OpenMD::CoordinationNumber:
OpenMD::StaticAnalyser OpenMD::GCN OpenMD::SCN

Public Member Functions

 CoordinationNumber (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, RealType rCut, int bins)
 
virtual ~CoordinationNumber ()
 
virtual void process ()
 
virtual void writeOutput ()
 
- 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)
 

Protected Member Functions

virtual RealType computeCoordination (int a, vector< vector< int > > neighbors)
 
- 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

RealType rCut_
 
int bins_
 
std::string sele1_
 
SelectionManager seleMan1_
 
SelectionEvaluator evaluator1_
 
std::string sele2_
 
SelectionManager seleMan2_
 
SelectionEvaluator evaluator2_
 
int selectionCount1_
 
int selectionCount2_
 
int nnMax_
 
RealType delta_
 
int count_
 
std::vector< RealType > histogram_
 
- 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

CoordinationNumber.

Computes a distribution of coordination numbers defined as the number of atoms in sele2 that are within rCut of the atom in sele1

Note that extra parameters must be declared:

Parameters
rCutcutoff radius for finding lists of nearest neighbors
sele1selection of StuntDoubles used for the distribution
sele2selection of StuntDoubles used for nearest neighbor computation

Definition at line 67 of file CoordinationNumber.hpp.

Constructor & Destructor Documentation

◆ CoordinationNumber()

◆ ~CoordinationNumber()

OpenMD::CoordinationNumber::~CoordinationNumber ( )
virtual

Definition at line 88 of file CoordinationNumber.cpp.

References histogram_.

Member Function Documentation

◆ computeCoordination()

RealType OpenMD::CoordinationNumber::computeCoordination ( int  a,
vector< vector< int > >  neighbors 
)
protectedvirtual

Reimplemented in OpenMD::GCN, and OpenMD::SCN.

Definition at line 211 of file CoordinationNumber.cpp.

Referenced by process().

◆ process()

◆ writeOutput()

Member Data Documentation

◆ bins_

int OpenMD::CoordinationNumber::bins_
protected

Definition at line 81 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), and process().

◆ count_

int OpenMD::CoordinationNumber::count_
protected

Definition at line 95 of file CoordinationNumber.hpp.

Referenced by process().

◆ delta_

RealType OpenMD::CoordinationNumber::delta_
protected

Definition at line 94 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), process(), and writeOutput().

◆ evaluator1_

SelectionEvaluator OpenMD::CoordinationNumber::evaluator1_
protected

Definition at line 85 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), and process().

◆ evaluator2_

SelectionEvaluator OpenMD::CoordinationNumber::evaluator2_
protected

Definition at line 89 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), and process().

◆ histogram_

std::vector<RealType> OpenMD::CoordinationNumber::histogram_
protected

Definition at line 96 of file CoordinationNumber.hpp.

Referenced by process(), writeOutput(), and ~CoordinationNumber().

◆ nnMax_

int OpenMD::CoordinationNumber::nnMax_
protected

Definition at line 93 of file CoordinationNumber.hpp.

Referenced by OpenMD::GCN::computeCoordination(), and CoordinationNumber().

◆ rCut_

RealType OpenMD::CoordinationNumber::rCut_
protected

Definition at line 80 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), and process().

◆ sele1_

std::string OpenMD::CoordinationNumber::sele1_
protected

Definition at line 83 of file CoordinationNumber.hpp.

Referenced by writeOutput().

◆ sele2_

std::string OpenMD::CoordinationNumber::sele2_
protected

Definition at line 87 of file CoordinationNumber.hpp.

Referenced by writeOutput().

◆ selectionCount1_

int OpenMD::CoordinationNumber::selectionCount1_
protected

Definition at line 91 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), and process().

◆ selectionCount2_

int OpenMD::CoordinationNumber::selectionCount2_
protected

Definition at line 92 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), and process().

◆ seleMan1_

SelectionManager OpenMD::CoordinationNumber::seleMan1_
protected

Definition at line 84 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), and process().

◆ seleMan2_

SelectionManager OpenMD::CoordinationNumber::seleMan2_
protected

Definition at line 88 of file CoordinationNumber.hpp.

Referenced by CoordinationNumber(), and process().


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