Type Label Framework for Bonded Force Fields in LAMMPS

Abstract

New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the “type label” framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.

LUNAR: Automated Input Generation and Analysis for Reactive LAMMPS Simulations

“…LUNAR’s design is modularized to simplify complex tasks such as automatic atom typing, assignment of parameters for multibody interactions, compatibility with the LAMMPS type label framework, 33 initialization of molecular systems, and postprocessing. LUNAR supports three traditional run methods: a graphical user interface, a command line interface, and a master script that can be used in an integrated design environment.…”