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

There are two ways to run SimpleMD: using Google Colab (no installation required) or running locally on your own machine.

Option A: Google Colab (recommended for getting started quickly)

Click the badge above to open MDsim.ipynb directly in Google Colab. All required packages (numpy, numba, matplotlib) are pre-installed in Colab.

You will need to clone the repository in your first notebook cell so that the simulation code is available:

!git clone https://github.com/emfurst/SimpleMD.git
%cd SimpleMD

Then proceed with the notebook as described in the manual.

Option B: Run locally

You will need the following installed on your computer:

Python 3 (3.10 or later recommended) — download from python.org
Git (optional) — download from git-scm.com

1. Get the code

Using git:

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

Without git: Download the repository as a zip file from the repository page, extract it, and open a terminal in the extracted folder.

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.

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

3 KiB Raw Blame History