General Information

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LAMMPS is a classical molecular dynamics code. It includes potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) 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.

Usage on Vilje

Load the intelcomp, mpt, and lammps modules to use LAMMPS on Vilje, e.g.:

$ module load intelcomp/15.0.1 mpt/2.11 lammps/141209

Sample LAMMPS Job Script

#PBS -l walltime=00:10:00
#PBS -l select=2:ncpus=32:mpiprocs=1:ompthreads=16
#PBS -j oe
#PBS -A nn1234k

# Load program modules
module load intelcomp/15.0.1 mpt/2.11 lammps/141209

# Create and use a temporary work directory
mkdir -p ${WORKDIR}
# Copy sample problem
cp /sw/sdev/Modules/lammps/lammps-141209/examples/kim/* .
# Run simulation
mpiexec_mpt lmp_intel <
# Move temporary work directory to qsub work directory

Replace nn1234k with your project account number in the lammps.pbs job script, and submit the job to the queuing system

$ qsub lammps.pbs

Note that LAMMPS runs in hybrid MPI / OpenMP mode; ‘mpiprocs’ and ‘ompthreads’ in the sample script control the balance between processes and threads. Their values should multiply to 16 to match the number of physical cores on a Vilje node, the optimal balance depends on details of the input case.