AMDAT: Amorphous Molecular Dynamics Analysis Toolkit

Robust, standardized, efficient analysis of molecular simulation trajectories is a crosscutting need in polymer molecular dynamics simulations. Here we describe the Amorphous Molecular Dynamics Analysis Toolkit – the outcome of a 15-year development process for a unified, well-validated MD analysis package targeting analysis of polymer and soft matter molecular simulations. AMDAT is built to work with multiple LAMMPS trajectory output styles. It has built-in and well-validated tools to compute a wide range of static and dynamic properties from molecular dynamics trajectories, such as such as clustering, spatial decomposition, and calculating time-resolved structure factors, mean-square displacements, radial distribution functions, and intermediate scattering functions. It allows highly refined selections of particles by identity, spatial location, distance to other particles, mobility, and other particle properties, facilitating spatially resolved and property-resolved analysis. Designed with high-molecular weight polymers and glass-forming systems in mind, AMDAT facilitates analysis of simulations spanning many decades of dynamical phenomena. In addition to standard linearly spaced trajectories, it analyzes exponentially spaced trajectories that allow efficient computation of dynamical properties across many orders of magnitude in time, and it comes packaged with a template LAMMPS input script to produce trajectories of this kind. AMDAT is publicly available at https://github.com/dssimmons-codes/AMDAT.