We develop and use molecular dynamics and related simulation methodologies, especially those encompassed in our LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular simulation package (https://www.lammps.org). LAMMPS is a freely available, widely used software package that runs in serial or on high performance computing platforms, and includes potentials for sold-state materials, soft matter, and coarse-grained or mesoscopic systems.