Visualization and Analysis Strategies for Atomistic Simulations

Abstract

An important aspect of many molecular dynamics studies is the meaningful visualization of computed atomic configurations and trajectories, often contributing a lot to the understanding of the investigated phenomena. This chapter introduces visualization programs and analysis tools that have been developed for working with the output of classical molecular dynamics and other atomistic simulation models. Basic analysis techniques relevant for nanomechanics problems are described, which help to reveal structural phases, defects, and local deformations in materials. Furthermore, this chapter gives an overview of the dislocation extraction algorithm, which is a computational method for the automated detection and identification of dislocation lines in atomistic crystal models.