Online LAMMPS training for ARCHER

Author: Julien Sindt
Posted: 31 Oct 2019 | 15:56

In October I ran an online training course teaching current and potential ARCHER users how to run LAMMPS. LAMMPS is a widely-used open-source molecular dynamics (MD) software developed at the National Sandia Laboratories, and is optimised to run well on HPC facilities. It consistently ranks in the top 10 most used programs on ARCHER. Although the course was run on ARCHER and with ARCHER users in mind, I tried to teach users how to use LAMMPS on any platform.

The Online LAMMPS course is split into two sessions. The first covers a lot of the basics of setting up and running an MD simulation using LAMMPS. Attendees are shown how easy it is to run a LAMMPS simulation before delving deeper into what each line of the LAMMPS input script means, how it can be changed, and what some of the options are. In doing so, attendees are also given a whistlestop tour of general molecular dynamics, with subjects like periodic boundary conditions, Verlet neighbour lists, and the velocity-Verlet algorithm being briefly discussed. The second session delves a bit deeper into the complexities that LAMMPS can offer – attendees were shown how to run LAMMPS on ARCHER, how to compile LAMMPS, and how to alter LAMMPS source code safely to allow them to enhance LAMMPS for their needs.

The course was attended by 30-40 people, with a lot of interesting questions being raised by the attendees. The course, and all materials linked to it (practice LAMMPS input scripts; slides; ARCHER submission scripts; etc), are available on the ARCHER training website.

Author

Julien Sindt, EPCC