82 lines
3 KiB
Markdown
82 lines
3 KiB
Markdown
# SimpleMD
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A molecular dynamics code for a Lennard-Jones system.
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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.
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*SimpleMD* is not a high performance simulation. Those seeking modern simulation tools should use LAMMPS or other powerful packages.
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See the accompanying manual, *Really Simple Molecular Dynamics with Python*, for instructions on getting started and exercises to try with the code.
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## Getting started
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There are two ways to run SimpleMD: using Google Colab (no installation required) or running locally on your own machine.
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### Option A: Google Colab (recommended for getting started quickly)
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[](https://colab.research.google.com/github/emfurst/SimpleMD/blob/main/MDsim.ipynb)
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Click the badge above to open `MDsim.ipynb` directly in Google Colab. All required packages (`numpy`, `numba`, `matplotlib`) are pre-installed in Colab.
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You will need to clone the repository in your first notebook cell so that the simulation code is available:
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```python
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!git clone https://github.com/emfurst/SimpleMD.git
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%cd SimpleMD
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```
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Then proceed with the notebook as described in the manual.
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### Option B: Run locally
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You will need the following installed on your computer:
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- **Python 3** (3.10 or later recommended) — download from [python.org](https://www.python.org/downloads/)
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- **Git** (optional) — download from [git-scm.com](https://git-scm.com/downloads)
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#### 1. Get the code
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**Using git:**
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```bash
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git clone https://lem.che.udel.edu/git/furst/SimpleMD.git
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cd SimpleMD
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```
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**Without git:** Download the repository as a zip file from the repository page, extract it, and open a terminal in the extracted folder.
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#### 2. Create a Python virtual environment
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Create and activate a virtual environment using Python's built-in `venv` module:
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```bash
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python3 -m venv .venv
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source .venv/bin/activate
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```
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On Windows, activate with:
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```
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.venv\Scripts\activate
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```
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#### 3. Install dependencies
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```bash
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pip install numpy numba matplotlib jupyter
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```
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#### 4. Run the simulation
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Launch Jupyter and open `MDsim.ipynb`:
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```bash
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jupyter notebook MDsim.ipynb
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```
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The notebook walks through creating a simulation, running it, and analyzing the results. See the manual for detailed instructions and exercises.
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## Contents
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- `CHEG231MD.py` — the molecular dynamics simulation code
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- `MDsim.ipynb` — Jupyter notebook for running and analyzing simulations
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- `maxwell boltzmann/` — Jupyter notebook for calculating the Maxwell-Boltzmann distribution; students can compare simulation results with the distribution
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- `SimpleMD_manual.pdf` — the manual, *Really Simple Molecular Dynamics with Python*
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