|
Welcome
|
The course will be flexible to best meet the learning needs of the attendees.
Feedback is an essential part of our training to allow us to continue to improve and make sure the course is as useful as possible to attendees.
|
|
Connecting to ARCHER2 and transferring data
|
|
|
An introduction to LAMMPS on ARCHER2
|
LAMMPS is a versatile software used in a wide range of subjects to run classical molecular dynamics simulations.
Running jobs on ARCHER2 requires a submission to the Slurm batch system using specific account, budget, queue, and qos keywords.
Adding more cores is not always the most effective way of increasing performance.
|
|
Setting up a simulation in LAMMPS
|
Molecular dynamics simulations are a method to analyse the physical movement of a system of many particles that are allowed to interact.
A LAMMPS input file is a an ordered collection of commands with both mandatory and optional arguments.
To successfully run a LAMMPS simulation, an input file needs to cover basic simulation setup, read/create a system topology, force-field, and type/frequency of outputs.
|
|
Understanding the logfile
|
Thermodynamic information outputted by LAMMPS can be used to track whether a simulations is running OK.
Performance data at the end of a logfile can give us insights into how to make a simulation faster.
|
|
Advanced input and output commands
|
Using compute and fix commands, it’s possible to calculate myriad properties during a simulation.
Variables make it easier to script several simulations.
|
|
GPU Acceleration and Additional software
|
LAMMPS has two packages (GPU and KOKKOS) that can make simulations run faster using accelerator cards.
Packmol can be used to pack multiple of the same type of molecules into one topology file.
MDAnalisys is a powerful python library to read, process, and create LAMMPS files.
|
|
Next steps
|
The LAMMPS manual is very easy to understand and provides a number of useful resources for learning about LAMMPS.
You will retain access to ARCHER2 for a while – please make use of it to test LAMMPS more.
You can get access to ARCHER2 resources via a number of different routes.
|
|
Creating a topology file
|
PACKMOL allows the generation of randomly packed systems from single-molecule XYZ files
VMD’s topotools can generate bond, angle, and dihedral information from user-defined properties
|