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
SimInfoinfo_
 
std::string dumpFilename_
 
std::string outputFilename_
 
int step_
 
std::string analysisType_
 
std::string paramString_
 
unsigned int nBins_
 
OutputDatacounts_
 
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). http://dx.doi.org/10.1126/science.aab3501

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 ( )
virtual

Definition at line 282 of file CoordinationNumber.cpp.

Member Function Documentation

◆ computeCoordination()

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

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: