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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 Hopper

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

Sample Batch Script to Run LAMMPS on Hopper

#PBS -N myjob
#PBS -q debug
#PBS -l mppwidth=16
#PBS -l walltime=00:30:00
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR
module load lammps

aprun -n 16 lmp_hopper < test.in

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

% qsub test_lammps pbs

Sample Interactive Batch Script to Run LAMMPS on Hopper

To request an interactive batch session, issue the command (e.g., requesting 16 PEs):

% qsub -I -V -q interactive -l mppwidth=16

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

%  cd $PBS_O_WORKDIR 
% module load lammps
% aprun -n 16 lmp_hopper < test.in

Using LAMMPS on Carver

A sample batch script for Carver is as follows:

#PBS -l nodes=2:ppn=8,walltime=0:30:00
#PBS -N test_lammps
#PBS -q debug
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR

module load lammps
mpirun -np 16 lmp_carver < infile        

Documentation

LAMMPS Online Manual

Availability

PackagePlatformCategoryVersionModuleInstall DateDate Made Default
lammps carver applications/ material sciences 2010-07-04 lammps/2009.09 2010-07-08 2010-07-08
LAMMPS carver applications/ material sciences 2010.07.04 lammps/2010.07.04 2012-01-13
LAMMPS carver applications/ material sciences 2011.08 lammps/2011.08 2012-01-13
LAMMPS carver applications/ material sciences 2012.04 lammps/2012.04 2012-04-18
LAMMPS carver applications/ material sciences 2013.08.30 lammps/2013.08.30 2013-09-02
LAMMPS carver applications/ material sciences 2014.02.01 lammps-gpu/2014.02.01 2014-03-19 2014-03-19
LAMMPS carver applications/ material sciences 2014.02.01 lammps/2014.02.01 2014-04-02
LAMMPS carver applications/ material sciences 2014.09.05 lammps/2014.09.05 2014-10-27
LAMMPS carver_sl6 applications/ material sciences 2014.02.01 lammps/2014.02.01 2014-09-09 2014-09-09
LAMMPS carver_sl6 applications/ material sciences 2014.09.05 lammps/2014.09.05 2014-10-27
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 hopper applications/ material sciences 2011.02 lammps/2011.02 2011-02-23 2011-02-23
LAMMPS hopper applications/ material sciences 2011.08 lammps/2011.08 2012-01-13
LAMMPS hopper applications/ material sciences 2011.11.09.js lammps/2011.11.09.js 2012-01-13
LAMMPS hopper applications/ material sciences 2012.02 lammps/2012.02 2012-02-15 2012-03-08
LAMMPS hopper applications/ material sciences 2012.06 lammps/2012.06 2012-06-05
LAMMPS hopper applications/ material sciences 2012.08 lammps/2012.08 2012-08-23
LAMMPS hopper applications/ material sciences 2013.03 lammps/2013.03 2013-05-13
LAMMPS hopper applications/ material sciences 2013.06 lammps/2013.06 2013-06-11
LAMMPS hopper applications/ material sciences 2013.07 lammps/2013.07 2013-07-10
LAMMPS hopper applications/ material sciences 20140628 lammps/20140628 2014-09-08