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

Generalized Coordinate Number. More...

#include <CoordinationNumber.hpp>

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

Public Member Functions

 GCN (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, RealType rCut, int bins)
virtual ~GCN ()
virtual RealType computeCoordination (int a, vector< vector< int > > neighbors)
- Public Member Functions inherited from OpenMD::CoordinationNumber
 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)

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::CoordinationNumber
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
std::string dumpFilename_
std::string outputFilename_
int step_
std::string analysisType_
std::string paramString_
unsigned int nBins_
vector< OutputData * > data_

Detailed Description

Generalized Coordinate Number.

Computes a distribution of generalized coordinate numbers as described in:

"Finding optimal surface sites on heterogeneous catalysts by counting nearest neighbors," by F. Calle-Vallejo et al., Science 350(6257) pp. 185-189 (2015).

Definition at line 129 of file CoordinationNumber.hpp.

Constructor & Destructor Documentation

◆ GCN()

OpenMD::GCN::GCN ( SimInfo info,
const std::string &  filename,
const std::string &  sele1,
const std::string &  sele2,
RealType  rCut,
int  bins 

◆ ~GCN()

OpenMD::GCN::~GCN ( )

Definition at line 282 of file CoordinationNumber.cpp.

Member Function Documentation

◆ computeCoordination()

RealType OpenMD::GCN::computeCoordination ( int  a,
vector< vector< int > >  neighbors 

Reimplemented from OpenMD::CoordinationNumber.

Definition at line 285 of file CoordinationNumber.cpp.

References OpenMD::CoordinationNumber::nnMax_.

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