LAMMPS

Description

From the LAMMPS manual: 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. LAMMPS stands for Large-scale Atomic / Molecular Massively Parallel Simulator.

Version

  • 12Dec18

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

LAMMPS requires the following module file to run:

  • apps/lammps/12Dec18

Extended Information

LAMMPS runs efficiently on single-processor desktop or laptop machines, but is designed for parallel computers. It will run on any parallel machine that compiles C++ and supports the MPI message-passing library. This includes distributed- or shared-memory parallel machines and Beowulf-style clusters. In the most general sense, LAMMPS integrates Newton’s equations of motion for collections of atoms, molecules, or macroscopic particles that interact via short- or long-range forces with a variety of initial and/or boundary conditions. For computational efficiency LAMMPS uses neighbor lists to keep track of nearby particles. The lists are optimized for systems with particles that are repulsive at short distances, so that the local density of particles never becomes too large. On parallel machines, LAMMPS uses spatial-decomposition techniques to partition the simulation domain into small 3d sub-domains, one of which is assigned to each processor. Processors communicate and store “ghost” atom information for atoms that border their sub-domain. LAMMPS is most efficient (in a parallel sense) for systems whose particles fill a 3d rectangular box with roughly uniform density.

The following LAMMPS Tools are also installed:

  • binary2txt - convert a LAMMPS dump file from binary to ASCII text
  • chain - create a data file of bead-spring chains
  • createatoms - generate lattices of atoms within a geometry
  • data2xmovie - convert a data file to a snapshot that xmovie can viz
  • eam_database - tool to generate EAM alloy potential files
  • ipp - input pre-processor Perl tool for creating input scripts
  • lmp2arc - convert LAMMPS output to Accelrys Insight format
  • lmp2cfg - convert LAMMPS output to CFG files for Atomeye viz
  • lmp2traj - convert LAMMPS output to contour, density profiles
  • micelle2d - create a data file of small lipid chains in solvent
  • msi2lmp - use Accelrys Insight code to setup LAMMPS input
  • restart2data - convert a binary restart file to an input data file
  • thermo_extract - C program for extracting thermo info from log file
  • xmovie - a quick/simple viz package (2d projections of 3d)

Running LAMMPS on CIRCE/SC

The LAMMPS user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting Jobs

You’ll need to create a submission script within the same directory as the input file. A basic submission script would look like:

#!/bin/sh
#
#SBATCH --ntasks=2
#SBATCH --job-name=lmp_slurm_test
#SBATCH --time=02:00:00

#### SLURM 2 processor LAMMPS test to run for 2 hours.

module load apps/lammps/12Dec18

mpirun lmp_mpi < in.lmptest

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./lmp_slurm_test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • LAMMPS Examples
    • /apps/lammps/12Dec18/examples

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with LAMMPS to the IT Help Desk: rc-help@usf.edu