This page describes a simplification of the files prepared by Koren Schrieber in his 2012/3 Computational Physics class project and corrected by Dan Mordehai. They are adapted for use by all TAMNUN users. The project describes the creation of defects in a graphene sheet using the Molecular Dynamics of LAMMPS and its visualization in AViz.
The explanation of the visualization part is found at Koren's site and the tar file of the codes is mirrored here.
Assuming you are in TAMNUN (or another computer where LAMMPS (later version, not the fortran one, has been compiled) you need three special files input.graphene, Sheet_Input.txt , and lammps_graphene.pbs, as well as the LAMMPS file SiC.tersoff which can be copied on TAMNUN from /usr/local/lammps-130127/potentials/SiC.tersoff - these are contained in the gr_lammps.tar tarball for convenience.
Start by preparing a directory in your TAMNUN account - I called mine dan.
Download or copy the tarball to the correct directory (dan in my example) in your TAMNUN account, then untar it with
tar -xvf gr_lammps.tar
If you have called your directory dan, then you can run a job with
and before you know it all the files will appear in your directory.
This set of files works for the queue all_lp, open to everyone.
To change the number of nodes, you need to edit the files lammps_graphene.pbs
and input.graphene (processors line) in an appropriate manner.
For 20/1/15 Computational Physics class replace all_lp with simphony_q if you are using one of the Computational Physics class accounts, course11-course16 or one of my research group's acoounts. .
If you run into problems with the above on TAMNUN, Dr Adler's class or project students should ask her, other Technion people should ask Julia.