A Set of Tutorials for the LAMMPS Simulation Package

Abstract

The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While molecular simulations thus become accessible to a larger audience, the `black box' nature of such software packages and wide array of options and features can make it challenging to use them correctly, particularly for beginners in the topic of MD simulations. LAMMPS is one such versatile molecular simulation code, designed for modeling particle-based systems across a broad range of materials science and computational chemistry applications, including atomistic, coarse-grained, mesoscale, grid-free continuum, and discrete element models. LAMMPS is capable of efficiently running simulations of varying sizes from small desktop computers to large-scale supercomputing environments. Its flexibility and extensibility make it ideal for complex and extensive simulations of atomic and molecular systems, and beyond. This article introduces a suite of tutorials designed to make learning LAMMPS more accessible to new users. The first four tutorials cover the basics of running molecular simulations in LAMMPS with systems of varying complexities. The second four tutorials address more advanced molecular simulation techniques, specifically the use of a reactive force field, grand canonical Monte Carlo, enhanced sampling, and the REACTER protocol. In addition, we introduce LAMMPS-GUI, an enhanced cross-platform graphical text editor specifically designed for use with LAMMPS and able to run LAMMPS directly on the edited input. LAMMPS-GUI is used as the primary tool in the tutorials to edit inputs, run LAMMPS, extract data, and visualize the simulated systems.