Tetrahedral order parameter Q field, output frame-by-frame as OpenDX volumetric data files. More...

#include <Qsurf.hpp>

Inheritance diagram for OpenMD::Qsurf:

Public Member Functions
	Qsurf (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2, RealType rCut, RealType voxelSize, RealType gaussWidth)
virtual void	doSequence () override
Public Member Functions inherited from OpenMD::SequentialAnalyzer
	SequentialAnalyzer (SimInfo *info, const std::string &filename, const std::string &sele1, const std::string &sele2)
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)

Protected Member Functions
virtual void	doFrame (int) override
Protected Member Functions inherited from OpenMD::SequentialAnalyzer
virtual void	preSequence ()
virtual void	postSequence ()
virtual void	writeSequence ()

Additional Inherited Members
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

Tetrahedral order parameter Q field, output frame-by-frame as OpenDX volumetric data files.

For each frame, computes the Errington-Debenedetti rescaled tetrahedrality parameter Q for every molecule in sele1 (using neighbors from sele2), Gaussian-coarse-grains Q onto a 3D voxel grid, and writes the resulting scalar field to a numbered OpenDX (.dx) file.

Output is a series of per-frame .dx files plus a Tcl script for loading the entire series into VMD as an animated isosurface. The user can interactively adjust the isovalue threshold in VMD's Isosurface representation.

Definition at line 72 of file Qsurf.hpp.

Constructor & Destructor Documentation

◆ Qsurf()

OpenMD::Qsurf::Qsurf	(	SimInfo *	info,
		const std::string &	filename,
		const std::string &	sele1,
		const std::string &	sele2,
		RealType	rCut,
		RealType	voxelSize,
		RealType	gaussWidth )

Definition at line 65 of file Qsurf.cpp.

Member Function Documentation

◆ doFrame()

virtual void OpenMD::Qsurf::doFrame ( int )

inlineoverrideprotectedvirtual

Implements OpenMD::SequentialAnalyzer.

Definition at line 81 of file Qsurf.hpp.

◆ doSequence()

void OpenMD::Qsurf::doSequence ( )

overridevirtual

Reimplemented from OpenMD::SequentialAnalyzer.

Definition at line 86 of file Qsurf.cpp.

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

applications/sequentialProps/Qsurf.hpp
applications/sequentialProps/Qsurf.cpp

Public Member Functions