[edit] LAMMPS on the ITS HPC Cluster

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics program that has among its capabilities distributed-memory message-passing parallelism (MPI); spatial-decomposition of simulation domain for parallelism; easy to extend with new features and functionality; atomic, polymeric, biological, metallic, granular, or hybrid systems; pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, Yukawa, frictional granular, tabulated, hybrid; molecular potentials: bond, angle, dihedral, improper, class 2 (COMPASS); polymer potentials: all-atom, united-atom, bead-spring; long-range Coulombics: Ewald and PPPM (similar to particle-mesh Ewald); CHARMM and AMBER force-field compatability; constant NVE, NVT, NPT integrators; rRESPA hierarchical timestepping; SHAKE bond and angle constraints; parallel tempering (replica exchange); targeted molecular dynamics (TMD) constraints; and a variety of boundary conditions and constraints.

Currently two version of the lammps is available in the HPC-Cluster. The old 22Jun2007 and new 20May2008 version with the added modification from Prof. Dormidontova group can be used after loading the modules lammps and lammps-20May08. Modules can be loaded in both command line with command

module load .........

and pbs batch script file as follow.

#PBS -l walltime=20:00:00
#PBS -l nodes=4:ppn=2
#PBS -N testjob
#PBS -j oe

cp $PBS_O_WORKDIR/* $TMPDIR
cd $TMPDIR
module load lammps 
#module load lammps-20May08 
mpiexec -comm lam lammps < inputfile
cp -ru $PBS_O_WORKDIR 

To use the lammps-20May08 version uncomment module load lammps-20May08 and comment module load lammps . Instructions to write input file for lammps can be found in project website. LAMMPS web site.

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