LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a Molecular Dynamics Simulator which can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems.
LAMMPS is developed and maintained at Sandia National Labs. LAMMPS website.
LAMMPS on Biowulf was built as a 32-bit application with MPICH1, Portland Group compilers.
Sample batch script:
#!/bin/bash # This file is lammps.run # #PBS -N lammps #PBS -m be #PBS -k oe export PATH=/usr/local/mpich-pg/bin:$PATH cd /data/susanc/lammps/friction date mpirun -machinefile $PBS_NODEFILE -np $np /usr/local/bin/lammps < in.friction
Submit this job with the command:
qsub -v np=4 -l nodes=2:o2800 lammps.run
nodes=2 represents the number of nodes to run on.
o2800 represents the type of node. See the section Using the Batch System on Biowulf in the User Guide for a discussion of the types of nodes.
This job is being submitted to 4 processors on 2 o2800 (2.8 GHz Opteron) nodes.
A collection of examples is available in /usr/local/src/lammps-29Jan09/examples. You can copy one or more of these examples to your own data space for trial runs.
LAMMPS documentation at the Sandia site.
