From 6bf350fd102ef13414c5167b9adf2c4e7aacc668 Mon Sep 17 00:00:00 2001 From: Eric Date: Wed, 18 Mar 2026 14:26:45 -0600 Subject: [PATCH] Directoins for running locally or on Colab --- README.md | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c54bb6f..3749334 100644 --- a/README.md +++ b/README.md @@ -10,14 +10,38 @@ See the accompanying manual, *Really Simple Molecular Dynamics with Python*, for ## Getting started -### 1. Clone the repository +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) + +[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/emfurst/SimpleMD/blob/main/MDsim.ipynb) + +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: + +```python +!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](https://www.python.org/downloads/) +- **Git** — download from [git-scm.com](https://git-scm.com/downloads) + +#### 1. Clone the repository ```bash git clone https://lem.che.udel.edu/git/furst/SimpleMD.git cd SimpleMD ``` -### 2. Create a Python virtual environment +#### 2. Create a Python virtual environment Create and activate a virtual environment using Python's built-in `venv` module: @@ -31,13 +55,13 @@ On Windows, activate with: .venv\Scripts\activate ``` -### 3. Install dependencies +#### 3. Install dependencies ```bash pip install numpy numba matplotlib jupyter ``` -### 4. Run the simulation +#### 4. Run the simulation Launch Jupyter and open `MDsim.ipynb`: