Lennard-Jones Simulator

Computer Modelling Year 3

Lennard-Jones simulator is particle simulator developed by Auro for the Computer Modelling course for Year 3 Physics.

Lennard-Jones simulator is particle simulator that uses velocity-verlet alogrithm to simulate motion of particles in a pbc simluation cube. Different dynamic statistics, namely Mean Squared Displacement and Radial Distribution Function are also output to analyse the motion and state.

**All Parameters are in reduced units.

A. File Structure:

Make sure to run the code from the directory containing all the three folders below.

1. Python:

• main.py: the main python script which is to be run

• Particle3D.py:library to create particles in 3D and manipulate them

• Lennard.py : calculates force and potential under lennard jones potential using provided separation between particles

• Mdutilities.py: generates a simulation box and assigns velocity and position to particles

• PBC.py: contains methods to ensure periodic boundary conditions and minimum image convention

2. input-data:

• The folder contains. Txt files containing information about particles and external conditions. The naming convention of the files are <Type/Element>-.txt e.g argon-solid.txt. The format of the text content discussed below.

• argon-solid.txt and argon-gas.txt:contains initialization information for creating those particles.

3. output-data:

The folder must be preset as the output data files are saved here. Four types of files are saved here.

• trajectory.xyz : contains the trajectory of the particles for VMD visualization.

• energy.dat : contains the time, potential energy, kinetic energy and total energy.

• msd.dat : contains time and mean squared displacement as a function of time.

• rdf.dat : contains radius and radial distribution average as a function of radius.

B. Quick Use:

On calling the python file “main.py” , the source of input data must be provided, argon-solid and argon-gas are provided and saved in input-data folder.

Step 1:
In terminal,

python main.py argon-solid

or if you have created your own particle-state follow the instructions in the next section for the format.

Step 2:

The main.py will run and save the data in the “output-data” folder.

C. How to create input files

The output files must be .txt file.( This has been set for simplicity during command line argument and saving file name)

The input data file must contain:
<Density*>

<Mass of Particle*> < x-velocity> The position and velocities can be random or just 0 as it is set in main.py using mdutilities.py.