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

Generalized Coordinate Number Sequence. More...

#include <GCNSeq.hpp>

Inheritance diagram for OpenMD::GCNSeq:
OpenMD::SequentialAnalyzer

Public Member Functions

 GCNSeq (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, RealType rCut, int bins)
 
virtual ~GCNSeq ()
 
virtual void doFrame (int istep)
 
virtual void writeSequence ()
 
- Public Member Functions inherited from OpenMD::SequentialAnalyzer
 SequentialAnalyzer (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2)
 
virtual ~SequentialAnalyzer ()
 
virtual void doSequence ()
 
void setOutputName (const std::string &filename)
 
const std::string & getOutputFileName () const
 
void setStep (int step)
 
int getStep ()
 
const std::string & getSequenceType () const
 
void setSequenceType (const std::string &type)
 
void setParameterString (const std::string &params)
 

Private Attributes

RealType rCut_
 
int bins_
 
bool usePBC_
 
int nnMax_
 
RealType delta_
 
int selectionCount1_
 
int selectionCount2_
 
std::vector< int > count_
 
std::vector< std::vector< RealType > > histogram_
 

Additional Inherited Members

- Protected Member Functions inherited from OpenMD::SequentialAnalyzer
virtual void preSequence ()
 
virtual void postSequence ()
 
- Protected Attributes inherited from OpenMD::SequentialAnalyzer
SimInfoinfo_
 
SnapshotcurrentSnapshot_
 
std::string dumpFilename_
 
SelectionManager seleMan1_
 
std::string selectionScript1_
 
SelectionEvaluator evaluator1_
 
SelectionManager seleMan2_
 
std::string selectionScript2_
 
SelectionEvaluator evaluator2_
 
int step_
 
std::string outputFilename_
 
int frame_
 
int storageLayout_
 
std::vector< RealType > times_
 
std::vector< RealType > values_
 
std::string sequenceType_
 
std::string paramString_
 

Detailed Description

Generalized Coordinate Number Sequence.

Computes a frame-by-frame sequence of distributions 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

Note that extra parameters mussed be declared:

rCut = cutoff radius for finding lists of nearest neighbors sele1 = selection of StuntDoubles used for the GCN distribution sele2 = selection of StuntDoubles used for nearest neighbor computation

Definition at line 69 of file GCNSeq.hpp.

Constructor & Destructor Documentation

◆ GCNSeq()

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

◆ ~GCNSeq()

OpenMD::GCNSeq::~GCNSeq ( )
virtual

Definition at line 74 of file GCNSeq.cpp.

References histogram_.

Member Function Documentation

◆ doFrame()

◆ writeSequence()

Member Data Documentation

◆ bins_

int OpenMD::GCNSeq::bins_
private

Definition at line 82 of file GCNSeq.hpp.

Referenced by doFrame(), and GCNSeq().

◆ count_

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

Definition at line 90 of file GCNSeq.hpp.

Referenced by doFrame(), and writeSequence().

◆ delta_

RealType OpenMD::GCNSeq::delta_
private

Definition at line 86 of file GCNSeq.hpp.

Referenced by doFrame(), GCNSeq(), and writeSequence().

◆ histogram_

std::vector<std::vector<RealType> > OpenMD::GCNSeq::histogram_
private

Definition at line 91 of file GCNSeq.hpp.

Referenced by doFrame(), writeSequence(), and ~GCNSeq().

◆ nnMax_

int OpenMD::GCNSeq::nnMax_
private

Definition at line 85 of file GCNSeq.hpp.

Referenced by doFrame(), and GCNSeq().

◆ rCut_

RealType OpenMD::GCNSeq::rCut_
private

Definition at line 81 of file GCNSeq.hpp.

Referenced by doFrame(), and GCNSeq().

◆ selectionCount1_

int OpenMD::GCNSeq::selectionCount1_
private

Definition at line 87 of file GCNSeq.hpp.

Referenced by doFrame().

◆ selectionCount2_

int OpenMD::GCNSeq::selectionCount2_
private

Definition at line 88 of file GCNSeq.hpp.

Referenced by doFrame().

◆ usePBC_

bool OpenMD::GCNSeq::usePBC_
private

Definition at line 84 of file GCNSeq.hpp.

Referenced by doFrame(), and GCNSeq().


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