SimpleMD

A molecular dynamics code for a Lennard-Jones system.

The purpose is to provide a basic molecular dynamics code base (CHEG231MD.py) written in fairly plain Python and standard libraries. The code is used as part of a module on molecular thermodynamics in the University of Delaware Chemical Engineering Thermodynamics I course's honors section. Students use it to explore the basic concepts of molecular simulations and molecular processes in thermodynamics.

SimpleMD is not a high performance simulation. Those seeking modern simulation tools should use LAMMPS or other powerful packages.

See the accompanying manual, Really Simple Molecular Dynamics with Python, for instructions on getting started and exercises to try with the code.

Getting started

1. Clone the repository

git clone https://lem.che.udel.edu/git/furst/SimpleMD.git
cd SimpleMD

2. Create a Python virtual environment

Create and activate a virtual environment using Python's built-in venv module:

python3 -m venv .venv
source .venv/bin/activate

On Windows, activate with:

.venv\Scripts\activate

3. Install dependencies

pip install numpy numba matplotlib jupyter

4. Run the simulation

Launch Jupyter and open MDsim.ipynb:

jupyter notebook MDsim.ipynb

The notebook walks through creating a simulation, running it, and analyzing the results. See the manual for detailed instructions and exercises.

Contents

• CHEG231MD.py — the molecular dynamics simulation code
• MDsim.ipynb — Jupyter notebook for running and analyzing simulations
• maxwell boltzmann/ — Jupyter notebook for calculating the Maxwell-Boltzmann distribution; students can compare simulation results with the distribution
• SimpleMD_manual.pdf — the manual, Really Simple Molecular Dynamics with Python