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LAMMPS

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code. LAMMPS can model an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, or granular systems using a variety of force fields and boundary conditions.

If you use LAMMPS results in your published work, please cite:

S. J. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J. Comp. Phys. 117, 1-19 (1995)

and include the URL of the LAMMPS website at http://lammps.sandia.gov.

Installed on blacklight.

Usage

  1. Create a job script which includes commands to
    1. Set up the module command.
    2. Load the module command. You can see which modules are available by typing
      module avail lammps

      and then load the appropriate one with

      module load lammps
    3. Use mpirun to run the executable.
  2. Submit the job script with the qsub command.

Sample Batch Script

#/bin/csh #PBS -l ncpus=16 #PBS -l walltime=30:00 #PBS -j oe #PBS -q batch  cd $PBS_O_WORKDIR source /usr/share/modules/init/csh module load lammps set echo #run my executable mpirun -np 16 lmp_blacklight < in.cb-shear