from wikipedia
LAMMPS ("Large-scale Atomic/Molecular Massively Parallel Simulator") is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of MPI for parallel communication and is a free open-source code, distributed under the terms of the GNU General Public License.

LAMMPS was originally developed under a Cooperative Research and Development Agreement (CRADA) between two laboratories from United States Department of Energy and three other laboratories from private sector firms.[1] It is currently maintained and distributed by researchers at the Sandia National Laboratories.

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 computers, 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 computing sense) for systems whose particles fill a 3D rectangular box with approximately uniform density.

• MPI version

$ module avail lammps

• Potenials files are stored in $LAMMPS_POTENTIALS

LAMMPS_MPI.sge

#!/bin/bash -l
 
#$ -q parallel.q  
 
#$ -N LAMMPS_MPI
 
#$ -pe mpi 32
 
#$ -o $JOB_NAME.$JOB_ID.out
 
 
module load lammps
 
## important : Toujours OMP_NUM_THREADS=1 
 
export OMP_NUM_THREADS=1
 
## lancement de l'application
 
mpirun -np $NSLOTS lmp_mpi -in inputData > output

• http://lammps.sandia.gov/doc/accelerate_intel.html