LAMMPS

Description

From the LAMMPS manual: LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, granular, and coarse-grained systems using a variety of force fields and boundary conditions. LAMMPS stands for Large-scale Atomic / Molecular Massively Parallel Simulator.

Version

16Feb16

Authorized Users

CIRCE account holders

Platforms

CIRCE cluster

Running LAMMPS on CIRCE

Modules

Before running a job, you must first set up your environment properly. Here are the required module files:

apps/lammps/16Feb16

To run LAMMPS on the cluster, ensure that you use module add prior to using any LAMMPS executables. See Modules for more information.

LAMMPS Documentation

The LAMMPS manual is essential to understanding the application and making the most of it. The guide and this page should be all you need to get started with your simulations. Please refer to the Additional Documentation section for a link to the guide.

LAMMPS runs efficiently on single-processor desktop or laptop machines, but is designed for parallel computers. It will run on any parallel machine that compiles C++ and supports the MPI message-passing library. This includes distributed- or shared-memory parallel machines and Beowulf-style clusters. In the most general sense, LAMMPS integrates Newton’s equations of motion for collections of atoms, molecules, or macroscopic particles that interact via short- or long-range forces with a variety of initial and/or boundary conditions. For computational efficiency LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes too large. On parallel machines, LAMMPS uses spatial-decomposition techniques to partition the simulation domain into small 3d sub-domains, one of which is assigned to each processor. Processors communicate and store “ghost” atom information for atoms that border their sub-domain. LAMMPS is most efficient (in a parallel sense) for systems whose particles fill a 3d rectangular box with roughly uniform density.

The following LAMMPS Tools are also installed:

binary2txt - convert a LAMMPS dump file from binary to ASCII text
chain - create a data file of bead-spring chains
createatoms - generate lattices of atoms within a geometry
data2xmovie - convert a data file to a snapshot that xmovie can viz
eam_database - tool to generate EAM alloy potential files
ipp - input pre-processor Perl tool for creating input scripts
lmp2arc - convert LAMMPS output to Accelrys Insight format
lmp2cfg - convert LAMMPS output to CFG files for Atomeye viz
lmp2traj - convert LAMMPS output to contour, density profiles
micelle2d - create a data file of small lipid chains in solvent
msi2lmp - use Accelrys Insight code to setup LAMMPS input
restart2data - convert a binary restart file to an input data file
thermo_extract - C program for extracting thermo info from log file
xmovie - a quick/simple viz package (2d projections of 3d)

Submitting Jobs

You’ll need to create a submission script within the same directory as the input file. A basic submission script would look like:

#!/bin/sh
#SBATCH --ntasks=2
#SBATCH --job-name=lmp_slurm_test
#SBATCH --time=02:00:00

#### Slurm 2 processor LAMMPS test to run for 2 hours.

module load apps/lammps/16Feb16

mpirun lmp_mpi < in.lmptest

This will request 2 processes via MPI, a job name of “lmp_slurm_test”, a 2 hour run-time, and specify the input file as “in.lmptest”.

Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./lmp_slurm_test.sh

You can view the status of your job with the “squeue -u <username>” command

Benchmarks

The following folder contains input parameters for known LAMMMPS tutorials:

/apps/lammps/16Feb16/examples

Additional Information

LAMMPS Guide
- http://lammps.sandia.gov/doc/Manual.html
LAMMPS Tool README files
- /opt/apps/lammps/2Nov10/tools

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with LAMMPS to the IT Help Desk: rc-help@usf.edu