Demonstrates a complete structural analysis workflow for atomistic oxide glass structures using amorphouspy.
# Install amorphouspy (from the amorphouspy repo)cd /path/to/amorphouspy
pixi install
# Or with pip
pip install amorphouspyjupyter lab
# open example.ipynb and run all cells| Step | Description |
|---|---|
| 1 | Load a glass structure from .extxyz |
| 2 | Compute partial radial distribution functions g(r) |
| 3 | Compute coordination number distributions |
| 4 | Compute Q0–Q4 species distribution and network connectivity |
| 5 | Compute bond angle distributions (O-Si-O, Si-O-Si) |
| 6 | Compute total and partial structure factor S(q) — neutron or X-ray |
| 7 | Compute Guttman primitive ring-size distribution |
| 8 | Compute cavity volumes, surface areas, and shape statistics |
| 9 | Visualise cavities in 3D (Plotly) |
| 10 | Run full analysis with analyze_structure |
| 11 | Interactive dashboard with plot_analysis_results_plotly |
Example structure:data/SiONa_25.extxyz — 25 mol% Na₂O · 75 mol% SiO₂ sodium silicate glass, ~10 000 atoms.
amorphouspy
See the documentation for more detail.