# 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

```bash
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:

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

On Windows, activate with:
```
.venv\Scripts\activate
```

### 3. Install dependencies

```bash
pip install numpy numba matplotlib jupyter
```

### 4. Run the simulation

Launch Jupyter and open `MDsim.ipynb`:

```bash
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*