Directoins for running locally or on Colab
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README.md
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README.md
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@ -10,14 +10,38 @@ See the accompanying manual, *Really Simple Molecular Dynamics with Python*, for
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## Getting started
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## Getting started
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### 1. Clone the repository
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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** — download from [git-scm.com](https://git-scm.com/downloads)
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#### 1. Clone the repository
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```bash
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```bash
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git clone https://lem.che.udel.edu/git/furst/SimpleMD.git
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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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cd SimpleMD
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```
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```
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### 2. Create a Python virtual environment
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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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Create and activate a virtual environment using Python's built-in `venv` module:
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@ -31,13 +55,13 @@ On Windows, activate with:
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.venv\Scripts\activate
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.venv\Scripts\activate
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```
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```
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### 3. Install dependencies
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#### 3. Install dependencies
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```bash
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```bash
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pip install numpy numba matplotlib jupyter
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pip install numpy numba matplotlib jupyter
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```
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```
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### 4. Run the simulation
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#### 4. Run the simulation
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Launch Jupyter and open `MDsim.ipynb`:
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Launch Jupyter and open `MDsim.ipynb`:
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