1.8 KiB
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 codeMDsim.ipynb— Jupyter notebook for running and analyzing simulationsmaxwell boltzmann/— Jupyter notebook for calculating the Maxwell-Boltzmann distribution; students can compare simulation results with the distributionSimpleMD_manual.pdf— the manual, Really Simple Molecular Dynamics with Python