The goal of this project is to visualize a sheet of graphene undergoing heating. For this purpose, the method of Molecular Dynamics (MD) was chosen, and the simulation tool was chosen to be LAMMPS- Large-scale Atomic/Molecular Massively Parallel Simulator.
MD is a method where one solves the Newton equations of motion for an N-body system. Knowing the interactioin forces (potential) between particles, we can numerically calculate the trajectory of each particle (mainly atoms). Getting the position of each particle, we can visualize complex systems with a large number of atoms, which would be very difficult otherwise. For a given system, we should choose the right potential acting between the particles (the potential for metal atoms probably won't be correct for a ceramic material), and select initial conditions.
LAMMPS is an open-source code, distributed by Sandia National Laboratories. LAMMPS requires an input script, where the user specifies the commands for the simulation. For simple simulations, the commands refer to the type of the particles, the size of the simulation box, boundary conditions, lattice structure etc. LAMMPS provide some default options (e.g. for different lattices) and also provides the option to specify an input for commands (e.g. custom lattice from input file). For a full manual visit LAMMPS web page
This is a basic LAMMPS script. It has 4 parts- Initialization, Atom creation, Settings and Dynamics. The most important commands are marked with a red arrow and number.1) dimension - this command specifies the dimensions of the simulation.
*All the simulations in this project were run on Tamnun, so the instructions will refer to that.
In order to run a simulation, you will have to prepare a pbs (Portable Batch System) file. When you run a simulation using a batch file, you place it on a queue on Tamnun (some specific queue), and the system will manage it, and run it according to priority on that queue (there is a way of running the file directly or 'interactively' but it is not recommended).
The rectangles highlight the important information that should be in your pbs file.
Second rectangle- shows the name of the queue you are using. Be sure you type it correctly (it is case-sensitive).
Third rectangle- working directory on Tamnun. You only need to change what goes after the forward slash.
Fourth rectangle- specify the script file name you are using. In this case it is "in.script2". Don't change anything else on this line.
When finished creating the script file and pbs file, you will want to run the job using the command:
In order to monitor the progress of your job, you can use: