LAMMPS

Large-scale Atomic/Molecular Massively Parallel Simulator

Introduction

LAMMPS or Large-scale Atomic/Molecular Massively Parallel Simulator, is a program intended for materials modeling using molecular dynamics. The program is capable of running simulations for solid-state materials such as metals or semi-conductors, soft matter like biological materials and polymers as well as coarse-grained and mesoscopic systems. LAMMPS is also capable of performing parallel particle simulations at several different scales including the atomic scale, mesoscale and continuum scale. There are two options for running LAMMPS, Serial and Parallel. The Parallel version runs using message-passing and can run with GNU OpenMPI or the GNU MVAPICH2 compilers at the RCC HPC Cluster.

Running LAMMPS Examples on RCC Systems

LAMMPS examples are available only on login nodes. If you would like to run the examples, first copy all or selected examples directories to your home directory with the command,

cp -r /opt/hpc/gnu/lammps/examples .

Example - Serial Job

We will use the body example here and copy it to the home directory first as,

cp -r /opt/hpc/gnu/lammps/examples/body .

Following SLURM submit script will run this example using one CPU core.

#!/bin/bash
#SBATCH -J "lammps"
#SBATCH -n 1
#SBATCH -p genacc_q
#SBATCH -t  00:10:00

lmp < in.body

Example - Parallel Job

We will use the same body example here.

Following submit script will use 4 processes to run this example.

#!/bin/bash
#SBATCH -J "lammps"
#SBATCH -n 4
#SBATCH -p genacc_q
#SBATCH -t  00:10:00

module load gnu-openmpi

srun lmp < in.body

Note that if you want to use the 'SELF' option of jump in a parallel job, you have to change the way you feed the input file to your LAMMPS binary. Therefore, the last line of the above script should be,

srun lmp -in in.body

LAMMPS Modules

There are a number of modules available for LAMMPS which can extend or enhance its capabilities. RCC has a number of these available for use across our three versions of LAMMPS (GNU, Intel and PGI).

Module GNU Intel PGI
ASPHERE Yes Yes Yes
BODY Yes Yes Yes
CLASS2 Yes Yes Yes
COLLOID Yes Yes Yes
COMPRESS No No No
CORESHELL Yes Yes Yes
DIPOLE Yes Yes Yes
GPU No No No
GRANULAR Yes Yes Yes
KIM No No No
KOKKOS No No No
KSPACE Yes Yes Yes
LATTE No No No
MANYBODY Yes Yes Yes
MC Yes Yes Yes
MEAM Yes Yes Yes
MISC Yes Yes Yes
MOLECULE Yes Yes Yes
MPIIO No No No
MSCG No No No
OPT Yes Yes Yes
PERI Yes Yes Yes
POEMS No No No
PYTHON Yes Yes Yes
QEQ Yes Yes Yes
REAX Yes Yes Yes
REPLICA Yes Yes Yes
RIGID Yes Yes Yes
SHOCK Yes Yes Yes
SNAP Yes Yes Yes
SRD Yes Yes Yes
VORONOI Yes Yes Yes
USER-ATC No No No
USER-AWPMD No No No
USER-BOCS Yes Yes Yes
USER-CGDNA Yes Yes Yes
USER-CGSDK Yes Yes Yes
USER-COLVARS No No No
USER-DIFFRACTION Yes Yes Yes
USER-DPD Yes Yes Yes
USER-DRUDE Yes Yes Yes
USER-EFF Yes Yes Yes
USER-FEP Yes Yes Yes
USER-H5MD No No No
USER-INTEL No Yes No
USER-LB No No No
USER-MANIFOLD Yes Yes Yes
USER-MEAMC Yes Yes Yes
USER-MESO Yes Yes Yes
USER-MGPT Yes Yes No
USER-MISC Yes Yes Yes
USER-MOFFF Yes Yes Yes
USER-MOLFILE No No No
USER-NETCDF No No No
USER-OMP Yes Yes Yes
USER-PHONON Yes Yes Yes
USER-QMMM No No No
USER-QTB Yes Yes Yes
USER-QUIP No No No
USER-REAXC Yes Yes Yes
USER-SMD No No No
USER-SMTBQ Yes Yes Yes
USER-SPH Yes Yes Yes
USER-TALLY Yes Yes Yes
USER-UEF Yes Yes Yes
USER-VTK Yes Yes Yes