LAMMPS Course for New Users

Description

This lesson is an introduction to molecular dynamics (MD) simulations using the LAMMPS package. It will cover the following topics:

Molecular dynamics simulation fundamentals.
Creating a LAMMPS input file.
Using force-fields and creating independant LAMMPS topology (data) files.
Computing and averaging physical properties during simulation.
Other software related to LAMMPS input creation, data post-processing, and visualization.

For this lesson, we expect attendees to be familiar with HPC environments. We will not be covering the differences between HPC and regular computing environments. This lesson is aimed at anyone who:

has experience using bash (or any other shell).
has an interest in running simulations using LAMMPS.

General Information

Requirements: Participants must have a working laptop or desktop computer with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have access to a terminal (Max and Linux users should have a terminal installed by default; Windows users should get either MobaXterm or, if they are already familiar with it, Windows Subsystems for Linux (WSL). They are also required to abide by the ARCHER2 Training Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody.

Materials will be provided in advance of the lesson. If we can help making learning easier for you (e.g. sign-language interpreters) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email J.Sindt@epcc.ed.ac.uk, R.Apostolo@epcc.ed.ac.uk for more information.

Prerequisites

You should have used remote HPC facilities before. In particular, you should be happy with connecting using SSH, know what a batch scheduling system is and be familiar with using the Linux command line. You should also be happy editing plain text files in a remote terminal (or, alternatively, editing them on your local system and copying them to the remote HPC system using scp).

Schedule

	Setup	Download files required for the lesson
10:00	1. Welcome	What can I expect from this course? How will the course work and how will I get help? How can I give feedback to improve the course?
10:10	2. Connecting to ARCHER2 and transferring data	How can I access ARCHER2 interactively?
10:40	3. An introduction to LAMMPS on ARCHER2	What is LAMMPS? How do I run jobs in ARCHER2?
11:30	4. Break	Break
12:00	5. Setting up a simulation in LAMMPS	What are molecular dynamics simulations? How do we setup a simulation in LAMMPS?
13:00	6. Lunch	Break
14:00	7. Running a simulation and understanding the logfile	What information does LAMMPS print to screen/logfile? What does that information mean?
14:20	8. Advanced input and output commands	How do I calculate a property every N time-steps? How do I write a calculated property to file? How can I use variables to make my input files easier to change?
15:10	9. Break	Break
15:40	10. Additional software	What other software can I use to prepare input files, and topology files? How can I post-process my data?
16:10	11. Next steps	Where can I get further information about LAMMPS? Where can I find out more about ARCHER2?
16:30	12. Creating a topology file	How do I create a topology file for my system?
17:00	Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.