Generalized Coordinate Number Sequence. More...

#include <GCNSeq.hpp>

Inheritance diagram for OpenMD::GCNSeq:

Public Member Functions
	GCNSeq (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, RealType rCut, int bins)
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 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)

Additional Inherited Members
Protected Member Functions inherited from OpenMD::SequentialAnalyzer
virtual void	preSequence ()
virtual void	postSequence ()
Protected Attributes inherited from OpenMD::SequentialAnalyzer
SimInfo *	info_ {nullptr}
Snapshot *	currentSnapshot_
std::string	dumpFilename_
SelectionManager	seleMan1_
std::string	selectionScript1_
SelectionEvaluator	evaluator1_
SelectionManager	seleMan2_
std::string	selectionScript2_
SelectionEvaluator	evaluator2_
int	step_
std::string	outputFilename_
int	frame_
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 76 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 )

Definition at line 60 of file GCNSeq.cpp.

Member Function Documentation

◆ doFrame()

void OpenMD::GCNSeq::doFrame ( int istep )

virtual

Implements OpenMD::SequentialAnalyzer.

Definition at line 80 of file GCNSeq.cpp.

◆ writeSequence()

void OpenMD::GCNSeq::writeSequence ( )

virtual

Reimplemented from OpenMD::SequentialAnalyzer.

Definition at line 177 of file GCNSeq.cpp.

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

applications/sequentialProps/GCNSeq.hpp
applications/sequentialProps/GCNSeq.cpp