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

#include <SurfaceDiffusion.hpp>

Inheritance diagram for OpenMD::SurfaceDiffusion:
OpenMD::StaticAnalyser

Public Member Functions

 SurfaceDiffusion (SimInfo *info, const std::string &filename, const std::string &sele, RealType len)
 
virtual ~SurfaceDiffusion ()
 
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

double round (double r)
 
void solventAccessible ()
 
void mobileAtomsFirst ()
 
void mobileAtomsLast ()
 
void mobileAtoms ()
 
void positionCorrelation ()
 

Private Attributes

SnapshotcurrentSnapshot_
 
int nProcessed_
 
std::string selectionScript_
 
SelectionEvaluator evaluator_
 
SelectionManager seleMan1_
 
string filename_
 
int bins_
 
int selectionCount_
 
double singleMoveDistance_
 
int frames_
 
bool doSolvent_
 
std::vector< std::vector< Vector3d > > positions_
 
std::vector< std::vector< Vector3d > > positions2_
 
std::vector< std::vector< bool > > moBool_
 
std::vector< std::vector< bool > > moBool2_
 
std::vector< std::vector< StuntDouble * > > gridSD_
 
std::vector< StuntDouble * > gridHighZ_
 
std::vector< StuntDouble * > gridLowZ_
 
std::vector< StuntDouble * > forIndex_
 
std::vector< Vector3dfirstPosition_
 
std::vector< Vector3dlastPosition_
 
std::vector< int > SAIndices_
 
std::vector< int > mobileIndices_
 
std::vector< int > indices_
 
std::vector< int > count_
 
std::vector< RealType > xHist_
 
std::vector< RealType > yHist_
 
std::vector< RealType > rHist_
 
RealType minDistance_
 
RealType probe_
 

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

Definition at line 58 of file SurfaceDiffusion.hpp.

Constructor & Destructor Documentation

◆ SurfaceDiffusion()

◆ ~SurfaceDiffusion()

OpenMD::SurfaceDiffusion::~SurfaceDiffusion ( )
virtual

Definition at line 83 of file SurfaceDiffusion.cpp.

Member Function Documentation

◆ mobileAtoms()

void OpenMD::SurfaceDiffusion::mobileAtoms ( )
private

◆ mobileAtomsFirst()

void OpenMD::SurfaceDiffusion::mobileAtomsFirst ( )
private

◆ mobileAtomsLast()

void OpenMD::SurfaceDiffusion::mobileAtomsLast ( )
private

◆ positionCorrelation()

void OpenMD::SurfaceDiffusion::positionCorrelation ( )
private

◆ process()

◆ round()

double OpenMD::SurfaceDiffusion::round ( double  r)
private

◆ solventAccessible()

void OpenMD::SurfaceDiffusion::solventAccessible ( )
private

Member Data Documentation

◆ bins_

int OpenMD::SurfaceDiffusion::bins_
private

Definition at line 83 of file SurfaceDiffusion.hpp.

◆ count_

std::vector<int> OpenMD::SurfaceDiffusion::count_
private

Definition at line 116 of file SurfaceDiffusion.hpp.

Referenced by positionCorrelation().

◆ currentSnapshot_

Snapshot* OpenMD::SurfaceDiffusion::currentSnapshot_
private

Definition at line 75 of file SurfaceDiffusion.hpp.

Referenced by process().

◆ doSolvent_

bool OpenMD::SurfaceDiffusion::doSolvent_
private

Definition at line 87 of file SurfaceDiffusion.hpp.

◆ evaluator_

SelectionEvaluator OpenMD::SurfaceDiffusion::evaluator_
private

Definition at line 79 of file SurfaceDiffusion.hpp.

Referenced by SurfaceDiffusion().

◆ filename_

string OpenMD::SurfaceDiffusion::filename_
private

Definition at line 82 of file SurfaceDiffusion.hpp.

Referenced by process(), and SurfaceDiffusion().

◆ firstPosition_

std::vector<Vector3d> OpenMD::SurfaceDiffusion::firstPosition_
private

Definition at line 109 of file SurfaceDiffusion.hpp.

◆ forIndex_

std::vector<StuntDouble*> OpenMD::SurfaceDiffusion::forIndex_
private

Definition at line 108 of file SurfaceDiffusion.hpp.

◆ frames_

int OpenMD::SurfaceDiffusion::frames_
private

Definition at line 86 of file SurfaceDiffusion.hpp.

Referenced by process().

◆ gridHighZ_

std::vector<StuntDouble*> OpenMD::SurfaceDiffusion::gridHighZ_
private

Definition at line 106 of file SurfaceDiffusion.hpp.

◆ gridLowZ_

std::vector<StuntDouble*> OpenMD::SurfaceDiffusion::gridLowZ_
private

Definition at line 107 of file SurfaceDiffusion.hpp.

◆ gridSD_

std::vector< std::vector<StuntDouble*> > OpenMD::SurfaceDiffusion::gridSD_
private

Definition at line 105 of file SurfaceDiffusion.hpp.

◆ indices_

std::vector<int> OpenMD::SurfaceDiffusion::indices_
private

Definition at line 115 of file SurfaceDiffusion.hpp.

◆ lastPosition_

std::vector<Vector3d> OpenMD::SurfaceDiffusion::lastPosition_
private

Definition at line 110 of file SurfaceDiffusion.hpp.

◆ minDistance_

RealType OpenMD::SurfaceDiffusion::minDistance_
private

Definition at line 122 of file SurfaceDiffusion.hpp.

◆ mobileIndices_

std::vector<int> OpenMD::SurfaceDiffusion::mobileIndices_
private

Definition at line 114 of file SurfaceDiffusion.hpp.

◆ moBool2_

std::vector< std::vector<bool> > OpenMD::SurfaceDiffusion::moBool2_
private

Definition at line 103 of file SurfaceDiffusion.hpp.

Referenced by positionCorrelation(), and process().

◆ moBool_

std::vector< std::vector<bool> > OpenMD::SurfaceDiffusion::moBool_
private

Definition at line 102 of file SurfaceDiffusion.hpp.

Referenced by process(), and SurfaceDiffusion().

◆ nProcessed_

int OpenMD::SurfaceDiffusion::nProcessed_
private

Definition at line 77 of file SurfaceDiffusion.hpp.

Referenced by process().

◆ positions2_

std::vector< std::vector<Vector3d> > OpenMD::SurfaceDiffusion::positions2_
private

Definition at line 94 of file SurfaceDiffusion.hpp.

Referenced by positionCorrelation(), and process().

◆ positions_

std::vector< std::vector<Vector3d> > OpenMD::SurfaceDiffusion::positions_
private

Definition at line 93 of file SurfaceDiffusion.hpp.

Referenced by process(), and SurfaceDiffusion().

◆ probe_

RealType OpenMD::SurfaceDiffusion::probe_
private

Definition at line 123 of file SurfaceDiffusion.hpp.

◆ rHist_

std::vector<RealType> OpenMD::SurfaceDiffusion::rHist_
private

Definition at line 120 of file SurfaceDiffusion.hpp.

Referenced by positionCorrelation(), and process().

◆ SAIndices_

std::vector<int> OpenMD::SurfaceDiffusion::SAIndices_
private

Definition at line 113 of file SurfaceDiffusion.hpp.

◆ selectionCount_

int OpenMD::SurfaceDiffusion::selectionCount_
private

Definition at line 84 of file SurfaceDiffusion.hpp.

Referenced by process(), and SurfaceDiffusion().

◆ selectionScript_

std::string OpenMD::SurfaceDiffusion::selectionScript_
private

Definition at line 78 of file SurfaceDiffusion.hpp.

◆ seleMan1_

SelectionManager OpenMD::SurfaceDiffusion::seleMan1_
private

Definition at line 80 of file SurfaceDiffusion.hpp.

Referenced by process(), and SurfaceDiffusion().

◆ singleMoveDistance_

double OpenMD::SurfaceDiffusion::singleMoveDistance_
private

Definition at line 85 of file SurfaceDiffusion.hpp.

Referenced by process(), and SurfaceDiffusion().

◆ xHist_

std::vector<RealType> OpenMD::SurfaceDiffusion::xHist_
private

Definition at line 118 of file SurfaceDiffusion.hpp.

Referenced by positionCorrelation(), and process().

◆ yHist_

std::vector<RealType> OpenMD::SurfaceDiffusion::yHist_
private

Definition at line 119 of file SurfaceDiffusion.hpp.

Referenced by positionCorrelation(), and process().


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