Visual, user-interactive generation of bond networks in 3D particle configurations

TL;DR

PASYVAT is a visualization tool that enables interactive 3D bond network generation in particle systems, aiding structural analysis in molecular dynamics studies.

Contribution

Introduction of PASYVAT, a novel software for visual and interactive bond network analysis in 3D particle configurations from molecular dynamics data.

Findings

Effective visualization of bond networks in 3D particle systems

Applicable to various data sets with defined centers

Facilitates structural analysis in condensed matter physics

Abstract

We present a new program able to perform visual structural analysis on 3D particle systems called PASYVAT (PArticle SYstem Visual Analysis Tool). More specifically, it can select multiple interparticle distance ranges from a radial distribution function (RDF) plot and display them in 3D as bonds between the particles falling within the selected distance range, thus generating a network of bonds. This software can be used with any data set representing a system of points or other objects having a welldefined center of mass or geometric center in 3D space. In this article we describe the program and its internal structure, with emphasis on its applicability in the study of certain particle configurations, obtained from classical molecular dynamics simulation in condensed matter physics.