Lammps

Overview

LAMMPS (“Large-scale Atomic/Molecular Massively Parallel Simulator”) is a molecular dynamics program from Sandia National Laboratories. LAMMPS can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale which can run on single processors or in parallel using message-passing techniques (MPI). Many of its models have versions that provide accelerated performance on CPUs, GPUs, and Intel Xeon Phis. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems.

Developed at Sandia National Laboratories, LAMMPS is open source code distributed freely under the terms of the GNU General Public License (GPL). For more information on LAMMPS, please checkout LAMMPS home page and LAMMPS Documentation.

Among the available resources through CCC, LAMMPS is installed on the Big Red II research supercomputers at Indiana University and on the Rivanna cluster at University of Virginia.

Using LAMMPS with CCC

From the GUI

1) Browse to /resources/CCC/queues/. Right click on the appropriate queue you want to submit the job and select create job. The Grid Job Tool will pop-up

2) In the Grid Job Tool, select file/open project and open up pre-stored project (.gjp) file or create your own project file by specifying the job name, input, output and other parameters. Some sample project file are attached at the bottom of this page.

3) Once you have created or modified the project file, select submit job from the file menu option and the job will be submitted to the Queue.

4) you can monitor the progress of the job using Queue manager option on the Queue.

Please refer to the CCC Main page for additional tutorial and information.

Using a wrapper script

The grid / fastgrid commands can be used within a bash script to submit a job to the grid-queue through the command-line interface. So you can use a wrapper script (sample wrapper script attached below) to submit your job(s) from the cli. You can also use the script to do some pre-processing like: copying input to the grid, to monitor the job status and then do some post-processing on it like: copying the output file back to the local machine. You can eliminate the copying back and forth from the grid by exporting some directories on your local machine to the grid, however that would require you to have a Genesis II server running on your local machine.

Sample Project Files

Sample JSDL Files

Sample Script to Run the Job

If you have any questions or concerns please feel free to email: mtp5cx@vvirginia.edu