LAMMPS
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers), and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, mesoscopic, or continuum scale.
Useful Links
Using LAMMPS on ARCHER2
LAMMPS is freely available to all ARCHER2 users.
The centrally installed version of LAMMPS is compiled with all the
standard packages included: ASPHERE,
BODY,
CLASS2,
COLLOID,
COMPRESS,
CORESHELL,
DIPOLE,
GRANULAR,
KSPACE,
MANYBODY,
MC, MISC,
MOLECULE,
OPT, PERI,
QEQ,
REPLICA,
RIGID,
SHOCK,
SNAP, SRD.
We do not install any USER packages. If
you are interested in a USER package, we
would encourage you to try to compile your own version and we can help
out if necessary (see below).
Running parallel LAMMPS jobs
LAMMPS can exploit multiple nodes on ARCHER2 and will generally be run in exclusive mode using more than one node.
For example, the following script will run a LAMMPS MD job using 4 nodes (128x4 cores) with MPI only.
#!/bin/bash
#SBATCH --job-name=lammps_test
#SBATCH --nodes=4
#SBATCH --tasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --time=00:20:00
# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]
#SBATCH --partition=standard
#SBATCH --qos=standard
module load lammps
srun --distribution=block:block --hint=nomultithread lmp -i in.test -l out.test
#!/bin/bash
#SBATCH --job-name=lammps_test
#SBATCH --nodes=4
#SBATCH --tasks-per-node=128
#SBATCH --cpus-per-task=1
#SBATCH --time=00:20:00
# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]
#SBATCH --partition=standard
#SBATCH --qos=standard
# Setup the job environment (this module needs to be loaded before any other modules)
module load epcc-job-env
module load lammps
srun --distribution=block:block --hint=nomultithread lmp -i in.test -l out.test
Compiling LAMMPS
The large range of optional packages available for LAMMPS, and opportunity for extensibility, may mean that it is convenient for users to compile their own copy. In practice, LAMMPS is relatively easy to compile, so we encourage users to have a go.
Compilation instructions for LAMMPS on ARCHER2 can be found on GitHub: