MatterViz

matterviz is a toolkit for building interactive web UIs for materials science: periodic tables, 3d crystal structures (and molecules, though needs some improvements!), Bohr atoms, nuclei, heatmaps, scatter plots. It's under active development and not yet ready for production use but we appreciate any feedback from beta testers! 🙏

🔌   MatterViz VSCode Extension

Visualize crystal structures, molecules, and molecular dynamics trajectories directly in VSCode. Features include:

• Native support for common file formats (CIF, POSCAR, XYZ, TRAJ, HDF5, etc.)
• Context menu (right click > "Render with MatterViz") and keyboard shortcuts (ctrl+shift+v on Windows, cmd+shift+v on Mac) for quick access
• Custom viewer for MD trajectories/geometry optimizations
• Extensive customization options via VSCode settings - see Configuration Guide for examples

🗺️   Roadmap

• ✅ MatterViz Web: matterviz.janosh.dev (works but under active development)
• ✅ MatterViz VSCode: marketplace.visualstudio.com/items?itemName=janosh.matterviz (works but under active development)
• ✅ pymatviz: Jupyter/Marimo extension for Python notebooks. Read about widgets in pymatviz readme for details.

📦   Heatmap

This screenshot demonstrates the periodicity of elemental properties (i.e. why it's called periodic table). In this case, you're seeing recurring bumps and valleys in the first ionization energy as a function of atomic number.

⚛️   3D Structure Viewer

⚛️   Element Details Pages

The details page for gold.

https://user-images.githubusercontent.com/30958850/186975855-8e0d94f9-e4e3-47a2-9354-9c012b37307c.mp4

🔨   Installation

npm install --dev matterviz

📙   Usage

Periodic Table

<script>
  import { PeriodicTable } from 'matterviz'

  const heatmap_values = { H: 10, He: 4, Li: 8, Fe: 3, O: 24 }
</script>

<PeriodicTable {heatmap_values} />

Structure

<script>
  import { Structure } from 'matterviz'
  const data_url = '/structures/TiO2.cif'
  // supports .cif, .poscar, .xyz/.extxyz, pymatgen JSON, OPTIMADE JSON, .gz
</script>

<Structure {data_url} style="width: 500px; aspect-ratio: 1" />

Composition

<script>
  import { Composition } from 'matterviz'
  // modes can be 'pie' (default) | 'bubble' | 'bar'
</script>

<Composition composition="LiFePO4" mode="pie" />

Trajectory

<script>
  import { Trajectory } from 'matterviz'
  // supports .xyz/.extxyz, .traj, .hdf5, .npz, .pkl, .dat, .gz, .zip, .bz2, .xz
</script>

<Trajectory data_url="/traj/ase-md.xyz" auto_play fps={10} style="max-height: 700px" />

🧪   Coverage

Statements	Branches	Lines

🙏   Acknowledgements

• Element properties in src/lib/element-data.ts were combined from Bowserinator/Periodic-Table-JSON under Creative Commons license and robertwb/Periodic Table of Elements.csv (unlicensed).
• Thanks to Images of Elements for providing photos of elemental crystals and glowing excited gases.
• Thanks to @kadinzhang and their Periodicity project [code] for the idea to display animated Bohr model atoms and inset a scatter plot into the periodic table to visualize the periodic nature of elemental properties.
• Big thanks to all sources of element images. See fetch-elem-images.ts and static/elements.
• Thanks to @ixxie (shenhav.fyi) for a lot of great suggestions, UX ideas, helping me learn threlte and contributing the Bond.svelte component.

This project would not have been possible as a one-person side project without many fine open-source projects. 🙏 To name just a few: