Molecular Dynamics Simulations of Active Matter using LAMMPS

TL;DR

This paper provides an introduction and practical guidance for using LAMMPS to simulate active matter, focusing on soft active particles and including advanced active Brownian particles simulations.

Contribution

It offers a practical, step-by-step tutorial for researchers to efficiently use LAMMPS for active matter simulations, reducing the learning curve.

Findings

Successful implementation of active Brownian particles in LAMMPS

Guidelines for optimizing soft active matter simulations

Enhanced understanding of molecular dynamics methods for active systems

Abstract

LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main advantage is the optimization of the methods, mainly for parallel computing. The main disadvantage is that, due to the complexity of the code, it ha long learning curve. One purpose of these notes is to shorten that curve for researchers are starting to use LAMMPS to simulate soft active matter. In these notes, we first discuss some Molecular Dynamics methods implemented in LAMMPS. We present an hands-on introduction to first-time users and we finish with an advanced hands-on section, where we implement and test Active Brownian particles simulations.