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