Forblaze Mol Documentation

1. System Requirements

Forblaze Mol utilizes WebGPU, a modern web technology, to achieve high-speed rendering. We recommend the following environment for the best experience:

• Recommended Browser: Google Chrome / Microsoft Edge (Latest version)
• Required Features: WebGPU and WebAssembly (WASM) must be enabled.
• Hardware: For models with tens of thousands of atoms, a PC with a dedicated GPU (NVIDIA, AMD, etc.) is recommended.

2. Introduction: A New Way to Visualize MD

Molecular Dynamics (MD) simulations are increasingly vital in materials science and drug discovery. Traditional visualization tools often rely on complex installations, making it difficult to handle data easily while traveling or at home.

“Can we complete our analysis entirely within a browser, without compromising performance?” This question led to the birth of the Forblaze Mol project.

Please note that while Forblaze Mol is designed with the highest priority on safety through local processing, it is a beta service. Users are responsible for judging the accuracy of results and using the tool at their own risk.

3. Data Security

Forblaze Mol is designed with privacy and security as top priorities. Your simulation files are never uploaded to any server. All data processing and rendering take place locally within your web browser. This ensures that even sensitive research data can be visualized safely.

4. Supported Formats (LAMMPS, VASP, Gaussian, CP2K, etc.)

Forblaze Mol allows you to select and load multiple files simultaneously. The app automatically extracts necessary information from the selected files.

• LAMMPS: data, dump, in, log
• Quantum ESPRESSO: out
• VASP: XDATCAR, POSCAR, OUTCAR
• MXDORTO: file07.dat, file09p.dat, file09v.dat, file05.dat
• CP2K: out, xyz
• Others: PDB, XYZ, MOL2, MOL, SDF

5. Key Features

• Intuitive 3D Controls: Rotate and zoom models freely using your mouse.
• Animation Playback: Use keyboard shortcuts to play and pause trajectory animations.
• Thermodynamic Analysis: Display charts for energy, temperature, and pressure. Analysis is possible with a standalone log file even without loading a trajectory.
• Trajectory Analysis: Calculate Radial Distribution Function (RDF) and Mean Square Displacement (MSD) from loaded MD results.
• CSV Data Export: Copy loaded thermodynamic data to the clipboard in CSV format.
• GLB Export: Export the current snapshot as a 3D object file (.glb) that can be inserted into applications like PowerPoint.
• Dynamic Bond Display: Real-time visualization of chemical bond formation and dissociation.

6. Technical Background: Rust, Bevy, and WASM

To achieve large-scale computation and rendering in a web browser, we adopted Rust, the Bevy engine, and WebAssembly (WASM).

Why Rust?

Rust offers execution speeds comparable to C++ while ensuring memory safety. Its performance enables rendering tens of thousands of atoms smoothly.

The Power of WebAssembly (WASM)

WASM runs at near-native speeds in browsers. By compiling our core logic into WASM, we enable smooth interactive manipulation of large atomic systems.

7. Basic Usage

• Step 1: Launch the App
  Click the “App” link in the header to navigate to the application page.
• Step 2: Load Data
  Select your files from the designated area. The app scans the beginning of the file to recognize the format.
• Step 3: Visualize & Interact
  Interact with the 3D model using your mouse and control animations with keyboard shortcuts.

8. Contact & Bug Reports

Forblaze Mol is currently in beta. If you encounter any bugs or have feature requests, please let us know via our dedicated Google Form.