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LAMMPS

Description

LAMMPS is a large scale classical molecular dynamics code, and stands for Large-scale Atomic/Molecular Massively Parallel Simulator.  LAMMPS has potentials for soft materials (biomolecules, polymers), solid-state materials (metals, semiconductors) 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.

How to Access LAMMPS

NERSC uses modules to manage access to software. To use the default version of LAMMPS, type:

% module load lammps

Using LAMMPS on Edison and Cori

There are two ways of running lAMMPS on Edison and Cori: submitting a batch job, or running interactively in an interactive batch session.

Sample Batch Script to Run LAMMPS on Edison

#!/bin/bash -l
#SBATCH -J test_lammps
#SBATCH -p debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_lammps.o%j

module load lammps

srun -n 48 lmp_edison < test.in # for Edison: 24 cores per node
#srun -n 64 lmp_cori < test.in #for Cori: 32 cores per node

This job script requests two nodes in the debug partition, run for 30 minutes.

Then submit the job script using the sbatch command, e.g., assuming the job script name is test_lammps.slurm:

% sbatch test_lammps.slurm

Running LAMMPS Interactively on Edison and Cori

To request an interactive batch session, issue the command (e.g., requesting 2 nodes):

% salloc -N 2 -p debug

When the batch session is returned to you, issue the following commands:

%  module load lammps 
% srun -n 48 lmp_edison < test.in #for Edison
% #srun -n 64 lmp_cori <test.in #for Cori

 

Documentation

LAMMPS Online Manual

Availability

PackagePlatformCategoryVersionModuleInstall DateDate Made Default
LAMMPS cori applications/ material sciences 20150810 lammps/20150810 2015-11-24 2015-11-24
LAMMPS cori applications/ material sciences 20160514 lammps/20160514 2016-06-29 2016-06-29
LAMMPS edison applications/ material sciences 20130106 lammps/20130106 2013-01-07 2013-01-07
LAMMPS edison applications/ material sciences 20130727 lammps/20130727 2013-07-28
LAMMPS edison applications/ material sciences 20140628 lammps/20140628 2014-09-08
LAMMPS edison applications/ material sciences 20160514 lammps/20160514 2016-07-13