LAMMPS
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. The current version of LAMMPS is written in C++.
Licensing Terms and Conditions
LAMMPS is a freely-available open-source code, distributed under the terms of the GNU Public License.
Setup
You should use the module command to load the proper environment as follows:
module load lammps
You can either type this command every time you intend to use LAMMPS within a new session, or you can automate it by including it in your .profile or .login script.
How to Run LAMMPS on the CRAY XT5
Job script using PBS
#!/bin/bash
#PBS -l mppwidth=128
#PBS -l walltime=00:30:00
#PBS -e test128.sterr
#PBS -o test128.stout
#PBS -V
# WORKING directory
export WRK=$PBS_O_WORKDIR
cd $WRK
# set the SCRATCH directory
export SCR=${SCRATCH}/${PBS_JOBNAME}.${PBS_JOBID}
mkdir -p $SCR
# copy all needed file into $SCR, e.g.:
# /bin/cp -f in.file data.file $SCR/.
export NO_STOP_MESSAGE=" "
# run
export LAMMPSEXE=lmp_xt5
#
# Calculate the number of cores to pass to charmrun
cd $SCR
aprun -n 128 LAMMPSEXE -in in.file
# copy back to $WRK needed file
cd $WRK
Further Documentation