AMDAT: An Open-Source Molecular Dynamics Analysis Toolkit for Supercooled Liquids, Glass-Forming Materials, and Complex Fluids

Abstract

AMDAT (Amorphous Molecular Dynamics Analysis Toolkit) is an open-source C++ toolkit for post-processing molecular dynamics trajectories, focused on high-performance static and dynamic analyses of amorphous, glassy, and polymer materials, including supercooled liquids and complex fluids. In this paper, we describe AMDAT's design for efficient long-timescale analysis via in-memory trajectory handling and exponential time sampling, and we demonstrate representative workflows for widely used observables such as radial distribution functions, structure factors, intermediate scattering functions, and neighbor correlations.