Online LAMMPS

ARCHER, the UK's national supercomputing service offers training in software development and high-performance computing to scientists and researchers across the UK.

ARCHER courses are offered free of charge to all academics.

LAMMPS

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a widely-used classical molecular dynamics (MD) code. This C++ code is easy to use, incredibly versatile, and parallelised to run efficiently on both small-scale personal computers and CPU/GPU/CPU&GPU HPC clusters. As of 2018, LAMMPS has been used, to some degree, in over 14,000 publications in fields as varied as chemistry, physics, material science, granular and lubricated-granular flow, etc.

The course will be run over two 2.5 hour-long sessions. The first session will be an introduction to setting up and running an MD simulation using LAMMPS. We will begin by running a simulation of a Lennard-Jones fluid before delving deeper into how simulations can be set up and run in LAMMPS. In the second session, we will discuss how to download and install LAMMPS, with a more in-depth discussion of the various packages LAMMPS offers and how to use them efficiently.

Trainer

Julien Sindt

Julien is a HPC Applications Developer at EPCC. Before joining EPCC in 2019, he used classical simulation techniques (molecular dynamics, Monte Carlo, discrete-element methods) for various research projects. As part of this work, he has trained a number of M.Sc. and Ph.D. students in these simulation techniques.

 

Format

This online course will run over two sessions on Wednesday afternoons, on 16th and 23rd October 2019 .

We will be using Blackboard Collaborate for the course, which is very simple to use and entirely browser-based.

Collaborate usually works without problems with modern browsers, but Chrome is recommended. Links will appear below each session, further down this page.

Attendees will register for the course in the usual way at www.archer.ac.uk/training/.

Computing requirements

All attendees will need their own desktop or laptop .

If you are logging on to an external system then you will need to have an ssh client installed which comes as default for Linux and Mac systems.

Linux users should open a command-line terminal and use ssh from the command line.

Mac can open the Mac termimal application and use ssh from the command line. However, to display graphics from Cirrus you will also need to install Xquartz. Xquartz provides its own terminal called "Xterm": if you have problems displaying graphics when using the Mac terminal, try logging in using ssh from within this Xterm.

Windows users should install MobaXterm which provides ssh access, a Unix graphics client and a drag-and-drop file browser.

We will provide accounts on ARCHER, for all attendees who register in advance at www.archer.ac.uk/training/.

Course Chat page

Chat page

The Chat page is a live collaborative online document which we will use to share links, information and comments. All course participants are encouraged to contribute.

Timetable

Week 1 (Wed 16th Oct)

Unless otherwise indicated all material is Copyright © EPCC, The University of Edinburgh, and is only made available for private study.

• 14:00 Welcome and overview
• 14:10 Introduction to setting up and running an MD simulation using LAMMPS. We will begin by running a simulation of a Lennard-Jones fluid.
• 15:00 Break
• 15:30 Delving deeper into how simulations can be set up and run in LAMMPS
• 16:30 Close

Materials

Unless otherwise indicated all material is Copyright © EPCC, The University of Edinburgh, and is only made available for private study.

The course materials are available here, and also on ARCHER in /work/y14/shared/LAMMPS_WORKSHOP/

Slides

• Week 1 Slides updated

LAMMPS input scripts

• in.lj
• in.lj_exercise

ARCHER Submission scripts

• lammps_sub.pbs
• lammps_exercise_sub.pbs

Week 1 Video

Week 2 (Wed 23rd Oct)

Unless otherwise indicated all material is Copyright © EPCC, The University of Edinburgh, and is only made available for private study.

• 14:00 Welcome and recap
• 14:10 How to download and install LAMMPS.
• 15:00 Break
• 15:30 LAMMPS packages and how to use them efficiently.
• 16:30 Close

Materials

Unless otherwise indicated all material is Copyright © EPCC, The University of Edinburgh, and is only made available for private study.

The course materials are available here, and also on ARCHER in /work/y14/shared/LAMMPS_WORKSHOP/

Slides

• Week 2 Slides updated

LAMMPS input script

Use this script as a starting point for the course certification exercise.

• in.lj_certification

LAMMPS Makefile for ARCHER

• Makefile.xc30

Week 2 Video

Questions?

If you have any questions please contact the ARCHER Helpdesk.