Spina

A toy molecular dynamics simulator and visualizer

Introduction

"Simulator" is a toy MD simulator library written in Python. "Visualizer" is a web-based interface that displays the simulation results of Simulator. "Notebooks" is a collection of Jupyter Notebooks for analysis and explanation of concepts.

The visualizer is deployed here

Installation

• Simulator: You need numpy library which can be installed via pip install numpy
• Visualizer: You need a webserver that runs under spina/visualizer folder.
• Jupyter Notebook: You need juypter notebook installed on your system.

Running

• Simulator: You can run simulations by writing your own script that imports the simulation module. An example script, runsimulation.py is provided. python runsimulation.py --help shows explanations of command-line arguments.
  • 3D simulation example: python runsimulation.py --dimensions 3 --max-vel 1.6 --num-per-dim 5 --num-steps 1000 --output sim_3d.json
  • 2D simulation example: python runsimulation.py --dimensions 2 --max-vel 0.2 --num-per-dim 9 --num-steps 1000 --output sim_2d.json
• Visualizer: Python comes with a webserver. In Python 3 run python -m http.server and visit http://localhost:8000 with your browser.
• Notebooks: Open notebooks with Jupyter. They can be previewed (without interaction abilities) on NBViewer or GitHub.