Forblaze Mol Documentation

1. System Requirements

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

• 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: Fusion of Visualization and Modeling

In materials science and drug discovery, building high-quality initial structures is as crucial as analyzing the simulation results.

Forblaze Mol has evolved beyond a simple visualization viewer into a platform where you can intuitively build molecular and polymer unit cells in your browser. By integrating high-performance engines, we enable a seamless workflow from modeling to analysis, anywhere and anytime.

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 files and SMILES strings entered into the builder are never uploaded to any server. All data processing, UFF structural relaxation, and rendering take place locally within your browser.

4. Structure Builder

The “Build” tab in the app allows for advanced structure building based on SMILES strings. This feature uses the same core engine as FBTK (Forblaze ToolKit).

• SMILES Parsing: Accurate chemical structure recognition using the purr library.
• Initial Placement: Estimation of chemically valid initial geometries (bond/torsion angles) based on the VSEPR algorithm.
• Structural Relaxation: Fast energy minimization using UFF (Universal Force Field) running directly in your browser.
• Charge Assignment: Electronegativity-based charge calculation for each atom.
• Polymer Building: Build homopolymer unit cells with specific density settings.
• Tacticity Control: Precise control over stereoregularity (isotactic, syndiotactic, etc.) during polymer building.

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

Forblaze Mol supports multiple file loading and exporting.

Import

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

Export

You can save the displayed structures or built models locally in the following formats:

• MOL2: Supports export with bonds, partial charges, and Periodic Boundary Conditions (PBC).
• MOL: Supports export with bond information.
• XYZ: Supports single structures as well as trajectories (animations).
• ExtXYZ: Supports Periodic Boundary Conditions (PBC) and trajectories.
• GLB: Exports the current scene as a 3D object file (.glb) for use in other 3D software.

6. Key Features

• Intuitive 3D Controls: Rotate and zoom models freely using your mouse.
• Animation Playback: Control trajectory animations with keyboard shortcuts.
• Thermodynamic Analysis: Display charts for energy, temperature, and pressure. Analysis is possible with a standalone log file.
• Trajectory Analysis: Calculate Radial Distribution Function (RDF) and Mean Square Displacement (MSD).
• CSV Data Export: Copy thermodynamic data to the clipboard in CSV format.
• Dynamic Bond Display: Real-time visualization of chemical bond changes in reactive MD.

7. 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. It excels in high-load tasks like updating atomic coordinates every frame or running UFF relaxations at high speed.

The Power of WebAssembly (WASM)

WASM runs at near-native speeds in browsers. By compiling our FBTK-based core logic into WASM, we bring sophisticated simulation building capabilities directly to the web.

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.