OpenMD 3.0
Molecular Dynamics in the Open
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Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
OpenMD::CoordinationNumber Class Reference

CoordinationNumber. More...

#include <CoordinationNumber.hpp>

+ Inheritance diagram for OpenMD::CoordinationNumber:

Public Member Functions

 CoordinationNumber (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, RealType rCut, int bins)
 
virtual void process ()
 
virtual void writeOutput ()
 
- Public Member Functions inherited from OpenMD::StaticAnalyser
 StaticAnalyser (SimInfo *info, const std::string &filename, unsigned int nbins)
 
void setOutputName (const std::string &filename)
 
const std::string & getOutputFileName () const
 
void setStep (int step)
 
int getStep () const
 
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 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
SimInfo * info_ {nullptr}
 
std::string dumpFilename_
 
int step_
 
unsigned int nBins_
 
std::string outputFilename_
 
std::string analysisType_
 
std::string paramString_
 
std::vector< OutputData > data_
 
std::vector< AtomType * > outputTypes_
 

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 72 of file CoordinationNumber.hpp.

Constructor & Destructor Documentation

◆ CoordinationNumber()

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

Definition at line 57 of file CoordinationNumber.cpp.

Member Function Documentation

◆ computeCoordination()

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

Definition at line 207 of file CoordinationNumber.cpp.

◆ process()

void OpenMD::CoordinationNumber::process ( )
virtual

Implements OpenMD::StaticAnalyser.

Definition at line 90 of file CoordinationNumber.cpp.

◆ writeOutput()

void OpenMD::CoordinationNumber::writeOutput ( )
virtual

Reimplemented from OpenMD::StaticAnalyser.

Definition at line 212 of file CoordinationNumber.cpp.

Member Data Documentation

◆ bins_

int OpenMD::CoordinationNumber::bins_
protected

Definition at line 85 of file CoordinationNumber.hpp.

◆ count_

int OpenMD::CoordinationNumber::count_
protected

Definition at line 99 of file CoordinationNumber.hpp.

◆ delta_

RealType OpenMD::CoordinationNumber::delta_
protected

Definition at line 98 of file CoordinationNumber.hpp.

◆ evaluator1_

SelectionEvaluator OpenMD::CoordinationNumber::evaluator1_
protected

Definition at line 89 of file CoordinationNumber.hpp.

◆ evaluator2_

SelectionEvaluator OpenMD::CoordinationNumber::evaluator2_
protected

Definition at line 93 of file CoordinationNumber.hpp.

◆ histogram_

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

Definition at line 100 of file CoordinationNumber.hpp.

◆ nnMax_

int OpenMD::CoordinationNumber::nnMax_
protected

Definition at line 97 of file CoordinationNumber.hpp.

◆ rCut_

RealType OpenMD::CoordinationNumber::rCut_
protected

Definition at line 84 of file CoordinationNumber.hpp.

◆ sele1_

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

Definition at line 87 of file CoordinationNumber.hpp.

◆ sele2_

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

Definition at line 91 of file CoordinationNumber.hpp.

◆ selectionCount1_

int OpenMD::CoordinationNumber::selectionCount1_
protected

Definition at line 95 of file CoordinationNumber.hpp.

◆ selectionCount2_

int OpenMD::CoordinationNumber::selectionCount2_
protected

Definition at line 96 of file CoordinationNumber.hpp.

◆ seleMan1_

SelectionManager OpenMD::CoordinationNumber::seleMan1_
protected

Definition at line 88 of file CoordinationNumber.hpp.

◆ seleMan2_

SelectionManager OpenMD::CoordinationNumber::seleMan2_
protected

Definition at line 92 of file CoordinationNumber.hpp.

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