LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
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, meso, or continuum scale.
To access the default version of LAMMPS on the HEC, simply type the command:
module add lammps
To see what other versions of LAMMPS are currently available, type:
module avail lammps
For more details on the module command, see Using environment modules on the HEC.
LAMMPS batch jobs may be run by creating a batch job control script (for example, called LAMMPS_job.com) like the following, which will submit the in.chain benchmark model to run on a single 16-core compute node:
#$ -S /bin/bash #$ -q parallel #$ -l node_type=10Geth* #$ -l nodes=1 source /etc/profile module add lammps mpirun lmp-mpi < in.chain
The script is then submitted for running by typing:
The above is an MPI-based parallel job script.