Molecular Dynamics Simulation

ReaxFF Reactive Force Field implementation for Molecular Dynamics Simulations of Hydrocarbon Oxidation in JavaScript.

🌐 Live Demo: https://aryaghan-mutum.github.io/MolecularDynamics/

📖 Documentation: JSDoc API Reference

📊 Coverage Report: Test Coverage

🔧 CI/CD Pipeline: Pipeline Documentation

ReaxFF Potential Functions

Bond Order, Bond Energy, Lone pair, Over/Under Coordination, Valence, Penalty, Coalition, Torsion, Four-body conjugation, Hydrogen bond, C2 Correction, Triple bond correction, Van der Waals, Coulomb interactions, Taper correction.

Quick Start

npm install     # Install dependencies
npm start       # Start dev server at http://localhost:3000
npm run build   # Production build to dist/

Testing & Coverage

npm test              # Run all tests
npm run test:watch    # Watch mode
npm run test:coverage # Coverage report with HTML output

Coverage Report

After running npm run test:coverage, open the HTML report:

# Windows
start coverage/lcov-report/index.html

# Mac/Linux
open coverage/lcov-report/index.html

Documentation

npm run docs          # Generate JSDoc to docs/
npm run docs:watch    # Generate with live reload

View Documentation

# Windows
start docs/index.html

# Mac/Linux  
open docs/index.html

The JSDoc documentation includes:

API reference for all modules
Component documentation
Simulation physics documentation
Utility function documentation

ReaxFF Parameter Files

Located in resources/reaxffparameters/:

File	System
`ffield.reax.cho`	C-H-O
`BaeAiken2013.ff`	Hydrocarbons
`van_duin_zno.ff`	ZnO
`reaxff_aluminum_oxygen_carbon.txt`	Al-O-C
`reaxff_biomolecules_param1.txt`	Biomolecules
`reaxff_glycine_force_field1.txt`	Glycine

Project Structure

src/                    # React app (components, context, hooks, simulation, utils)
tests/                  # Unit tests (mirrors src structure)
app/                    # Legacy vanilla JS
resources/              # ReaxFF parameter files
docs/                   # Generated JSDoc

Controls

Arrow keys: Move player atom
Load Parameters: Select .ff or .txt ReaxFF file

Scripts

Command	Description
`npm start`	Dev server
`npm run build`	Production build
`npm test`	Run tests
`npm run test:coverage`	Coverage report
`npm run docs`	Generate JSDoc
`npm run lint`	ESLint
`npm run format`	Prettier

Tech Stack

React 18, Webpack 5, HTML5 Canvas, Jest, JSDoc