NB: you need to search for http://localhost:3000 to use Interactive MD, otherwise fetching is not corret

Molecular Dynamics Simulation with Real-time Data Analysis

Overview

This project combines a client-side molecular dynamics simulation with a server-side data collection and analysis system. The simulation runs in a web browser and sends real-time data to a Node.js server, which then processes and analyzes the data using Python scripts.

Architecture

The system consists of three main components:

1. Client: HTML/JavaScript molecular dynamics simulation
2. Server: Node.js/Express server for data collection
3. Analysis: Python scripts for real-time data visualization

Component Details

1. Client (Molecular Dynamics Simulation)

Original Source: Based on Daniel V. Schroeder's "Interactive Molecular Dynamics" simulation Modifications: Extended with server communication capabilities

Key Features:

• 2D molecular dynamics simulation using Lennard-Jones potential
• Real-time physics calculations with Verlet integration
• Interactive controls for manipulating atoms
• Multiple data collection modes
• Real-time server communication

Server Communication Extensions:

• Mode Selection: Sends current data collection mode to server
• System Data: Sends macroscopic properties (energy, temperature, pressure)
• Distribution Data: Sends velocity distributions of all atoms

Key Modified Functions:

// Mode selection handler
async function SendMode(mode) {
    const data = { mode: mode };
    // Sends current data collection mode to server
}

// System data transmission
async function writeStatsToJson() {
    // Sends energy, volume, particle count, temperature, pressure
}

// Distribution data transmission  
async function writeAllToJson() {
    // Sends velocity components (vx, vy) for all atoms
}

2. Server (Node.js/Express)

The server handles two main operational modes:

Mode 1: System Data Collection (mode = 'system')

• Creates/updates Data.csv with macroscopic properties
• Runs system.py for data analysis
• Listens on /system endpoint for incoming data

Mode 2: Distribution Data Collection (mode = 'all')

• Creates/updates distribution.csv with velocity distributions
• Runs distribution.py for velocity analysis
• Listens on /all endpoint for incoming data

Server Configuration:

const mode = 'all'; // or 'system' - controls operational mode
const N = 20; // Configuration parameter

3. Analysis Scripts (Python)

system.py - Macroscopic Properties Analysis

• Reads Data.csv containing system-wide properties
• Real-time plotting of energy evolution
• Uses matplotlib animation for live updates

distribution.py - Velocity Distribution Analysis

• Reads distribution.csv with atom velocity data
• Creates histograms for:
  • vx (x-component velocity)
  • vy (y-component velocity)
  • v (total velocity magnitude)
• Real-time updates of velocity distributions

Installation and Setup

Prerequisites

• Node.js and npm
• Python 3.x with packages: numpy, pandas, matplotlib

Installation Steps:

1. Install Node.js dependencies:

npm install express path python-shell csv-writer

2. Install Python dependencies:

pip install numpy pandas matplotlib

3. Directory structure:

project/
├── server.js
├── index.html
├── system.py
├── distribution.py
├── Data.csv (generated)
└── distribution.csv (generated)

Usage Instructions

Starting the System:

1. Start the Node.js server:

node server.js

2. Open the client in a web browser:

http://localhost:3000

3. Start the simulation using the "Start" button

4. Choose data collection mode in the "Data type" dropdown:

   • System totals: Collects macroscopic properties
   • All atoms: Collects velocity distributions

5. Start Python analysis scripts in separate terminals:

python system.py
python distribution.py

Operational Modes:

System Mode (mode = 'system')

• Collects: Energy, Temperature, Pressure, Volume, Particle count
• Output: Data.csv
• Analysis: Real-time energy evolution plot

Distribution Mode (mode = 'all')

• Collects: Velocity components (vx, vy) for all atoms
• Output: distribution.csv
• Analysis: Real-time velocity distribution histograms

API Endpoints

POST /system

Body: JSON with system properties

{
  "E": "Energy",
  "V": "Volume", 
  "N": "Num",
  "T": "Temp",
  "P": "Press"
}

POST /all

Body: JSON with velocity data

{
  "data": [
    {"vx": 0.123, "vy": -0.456},
    {"vx": -0.789, "vy": 0.321}
  ]
}

POST /mode

Body: JSON with operational mode

{
  "mode": "system"  // or "all"
}

Extending the System

Adding New Data Collection Modes:

1. Extend server.js:

else if (mode == 'new_mode') {
    // Add new CSV writer configuration
    // Add new Python script execution
    // Add new endpoint handler
}

2. Extend client data transmission:

// Add new data collection function
async function collectNewData() {
    const newData = { /* new data structure */ };
    const response = await fetch('/new_endpoint', options);
}

3. Create new analysis script:

# new_analysis.py
# Implement real-time analysis for new data type

Adding New Analysis Visualizations:

1. Modify existing Python scripts to add new plot types
2. Create new Python scripts for specialized analysis
3. Extend data collection to include additional parameters

Customizing Physics Parameters:

Modify the client-side simulation constants:

• forceCutoff: Interaction range
• wallStiffness: Container wall strength
• bondStrength: Molecular bond strength
• g: Gravitational constant

Configuration Options

Server Configuration:

const mode = 'all'; // Operational mode
const N = 20; // System parameter
const port = 3000; // Server port

Client Configuration:

• Number of atoms (1-2500)
• Box size and volume
• Time step and simulation speed
• Gravity strength
• Data collection intervals

File Descriptions

• server.js: Node.js server with data collection endpoints
• index.html: Client-side molecular dynamics simulation
• system.py: Real-time energy evolution analysis
• distribution.py: Real-time velocity distribution analysis
• Data.csv: Generated system property data (mode='system')
• distribution.csv: Generated velocity distribution data (mode='all')

Troubleshooting

Common Issues:

1. Port already in use: Change port variable in server.js
2. Missing dependencies: Run npm install and pip install commands
3. CSV file errors: Ensure write permissions in project directory
4. Python script errors: Verify matplotlib backend compatibility

Performance Considerations:

• Large atom counts (>1000) may impact browser performance
• High data collection frequency may slow down simulation
• Consider increasing stepsPerFrame for better performance

Acknowledgments

Original Simulation: Daniel V. Schroeder, "Interactive Molecular Dynamics"
Client Modifications: Extended with server communication capabilities
Server & Analysis: Custom implementation for real-time data processing

This system provides a complete pipeline from molecular dynamics simulation to real-time data analysis, making it ideal for educational demonstrations and computational physics experiments.