LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a molecular-dynamics code The code is designed to be easy to modify or extend with new functionality. LAMMPS can run on a single core but is designed to be highly efficient running on a large number of cores in parallel using message-passing techniques and a spatial decomposition of the simulation domain. It solves systems ranging from single atoms through polymers and proteins to rigid collections of particles. A variety of force fields is supported.
LAMMPS on Rivanna
ARCS builds a version of LAMMPS incorporating the most popular optional packages. To find the available versions and how to load them, run
module spider lammps
This will return a result such as
For detailed information about a specific "lammps" module (including how to load the modules) use the module's full name. For example: $ module spider lammps/2017-08-11
Running this command provides information about the software and shows
This module can be loaded directly: module load lammps/2017-08-11
Users may build their own versions of LAMMPS if they wish to use a different compiler+MPI combination, or to choose individual optional packages. Instructions are available at the LAMMPS "Getting Started" page.
Sample SLURM script
To run the system version of LAMMPS, a script similar to the following can be used. LAMMPS has many options so only the most basic is shown.
#!/bin/bash #SBATCH --account my_acct #SBATCH --nodes=2 #SBATCH --ntasks-per-node=16 #SBATCH --time=3-00:00:00 #SBATCH --output=thermo.out #SBATCH --partition=parallel module load lammps/2017-08-11 srun lmp_intel_openmpi -in run.in.npt