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

TL;DR

AMDAT is an open-source C++ toolkit designed for efficient analysis of molecular dynamics trajectories, focusing on amorphous and complex fluid materials, enabling high-performance static and dynamic analyses.

Contribution

The paper introduces AMDAT, a novel open-source toolkit optimized for long-timescale analysis of amorphous materials using in-memory trajectory handling and exponential time sampling.

Findings

Efficient analysis of long-timescale molecular dynamics data.

Support for key observables like radial distribution functions and structure factors.

Demonstrated workflows for analyzing supercooled liquids and glassy materials.

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.