matterviz 0.3.6 → 0.3.7

package/readme.md

@@ -1,219 +1,146 @@
-# [MatterViz VSCode Extension]
+<h1 align="center">
+  <sub><img src="static/favicon.svg" alt="Logo" width="40px"></sub> MatterViz
+</h1>
 
-[matterviz vscode extension]: https://marketplace.visualstudio.com/items?itemName=janosh.matterviz
-
-**MatterViz** offers a VSCode extension for rendering crystal structures and molecular dynamics (MD) or geometry optimization trajectories directly in the editor to speed up typical materials science/computational chemistry workflows.
-
-## ✨ Features
-
-### 🔬 **Structure Visualization**
-
-- **Crystal Structures**: Visualize CIF, POSCAR, VASP, and other crystallographic formats
-- **Molecular Systems**: Display XYZ, JSON, and YAML molecular structures
-- **Interactive 3D Viewer**: Rotate, zoom, and explore structures with intuitive controls
-- **Atomic Properties**: View element information, bonding, and structural details
-
-### 🎬 **Trajectory Analysis**
-
-- **MD Trajectories**: Animate and analyze molecular dynamics simulations
-- **Multi-format Support**: Handle TRAJ, ExtXYZ, HDF5, and compressed formats
-- **Playback Controls**: Navigate through trajectory frames with timeline controls
-- **Frame Analysis**: Extract and analyze individual frames from trajectories
-
-### 🎨 **Customization**
-
-- **Color Schemes**: Multiple built-in color schemes (Jmol, VESTA, Alloy, Pastel, etc.)
-- **Visualization Modes**: Ball-and-stick, space-filling, wireframe representations
-- **Export Options**: Save visualizations to PNG or export structure data to ASE XYZ and pymatgen JSON
+<h4 align="center">
 
-## 🚀 Installation
+[![Tests](https://github.com/janosh/matterviz/actions/workflows/test.yml/badge.svg)](https://github.com/janosh/matterviz/actions/workflows/test.yml)
+[![GH Pages](https://github.com/janosh/matterviz/actions/workflows/gh-pages.yml/badge.svg)](https://github.com/janosh/matterviz/actions/workflows/gh-pages.yml)
+[![VSCode Extension](https://img.shields.io/badge/Install%20VSCode-Extension-blue?logo=typescript&logoColor=white)](https://marketplace.visualstudio.com/items?itemName=janosh.matterviz)
+[![Docs](https://img.shields.io/badge/Read-the%20docs-blue?logo=googledocs&logoColor=white)](https://matterviz.janosh.dev)
+[![Open in StackBlitz](https://img.shields.io/badge/Open%20in-StackBlitz-darkblue?logo=stackblitz&logoColor=white)](https://stackblitz.com/github/janosh/matterviz)
+[![Zenodo DOI](https://zenodo.org/badge/498793280.svg)](https://doi.org/10.5281/zenodo.17094509)
 
-Search for "MatterViz" in the VS Code Extensions marketplace.
+</h4>
 
-## 📋 Usage
+`matterviz` is a toolkit for building interactive web UIs for materials science: 3D crystal structures, molecules, MD/relaxation trajectories, periodic tables, phase diagrams, convex hulls, spectral data (bands, DOS, XRD), heatmaps, and scatter plots.
 
-### Quick Start
+## 🔌 &thinsp; [MatterViz VSCode Extension]
 
-1. **Open a structure file** in VS Code (`.cif`, `.poscar`, `.xyz`, `.json`, etc.)
-2. **Right-click** in the explorer or editor
-3. **Select "MatterViz: Open"** from the context menu
-4. **Or use the keyboard shortcut**: `Ctrl+Shift+V` (Windows/Linux) / `Cmd+Shift+V` (Mac)
+Visualize crystal structures, molecules, and molecular dynamics trajectories [directly in VSCode][MatterViz VSCode Extension]. Features include:
 
-### Supported File Formats
+- Native support for common file formats (CIF, POSCAR, XYZ, TRAJ, HDF5, etc.)
+- Context menu (right click > "Render with MatterViz") and keyboard shortcuts (<kbd>ctrl</kbd>+<kbd>shift</kbd>+<kbd>v</kbd> on Windows, <kbd>cmd</kbd>+<kbd>shift</kbd>+<kbd>v</kbd> on Mac) for quick access
+- Custom viewer for MD trajectories/geometry optimizations
+- **Extensive customization options** via VSCode settings - see [Configuration Guide](extensions/vscode/readme.md#️-configuration--customization) for examples
 
-#### Structure Files
-
-- **CIF** - Crystallographic Information Files
-- **POSCAR/CONTCAR** - VASP structure files
-- **XYZ/ExtXYZ** - Standard molecular coordinate formats
-- **JSON** - JSON-formatted structure data (pymatgen, OPTIMADE)
-- **YAML/YML** - YAML structure definitions
-
-#### Trajectory Files
-
-- **TRAJ** - ASE trajectory files
-- **ExtXYZ** - Extended XYZ trajectories
-- **HDF5/H5** - `flame` HDF5 trajectory formats
-- **JSON** - `pymatgen` JSON trajectory formats
-
-#### Fermi Surface Files
-
-- **BXSF** - XCrySDen band structure format
-- **FRMSF** - FermiSurfer format
-
-#### Volumetric Data Files
-
-- **CUBE** - Gaussian cube files
-- **CHGCAR/ELFCAR/LOCPOT/AECCAR/PARCHG** - VASP volumetric output
-
-#### Compressed Files
+[matterviz vscode extension]: https://marketplace.visualstudio.com/items?itemName=janosh.matterviz
 
-All formats above are also supported with `.gz` compression.
+## 🗺️ &thinsp; Roadmap
 
-#### JSON Files with Multiple Data Types
+- **✅ MatterViz Web**: [matterviz.janosh.dev](https://matterviz.janosh.dev)
+- **✅ MatterViz VSCode/Cursor**: [marketplace.visualstudio.com/items?itemName=janosh.matterviz](https://marketplace.visualstudio.com/items?itemName=janosh.matterviz)
+- **✅ pymatviz**: [Jupyter](https://jupyter.org)/[Marimo](https://marimo.io) widgets for Python notebooks. See [`pymatviz` readme](https://github.com/janosh/pymatviz/blob/main/readme.md#interactive-widgets).
 
-When a `.json` file contains recognized data (structures, band structures, DOS, convex hulls, phase diagrams, Fermi surfaces, Brillouin zones, XRD patterns, or tabular data), MatterViz opens a **JSON browser** with a navigable tree sidebar and visualization canvas. Renderable nodes are marked with colored badges -- click to render, or drag to a canvas edge to create a split view with multiple visualizations side by side. When both band structure and DOS data are found together, they're rendered as a combined Bands+DOS plot.
+![Landing page showing 3D structure viewers](https://github.com/janosh/matterviz/releases/download/v0.2.2/2026-01-23-landing-page.webp)
 
-### Custom Editor Integration
+## ⚛️ &thinsp; 3D Structure Viewer
 
-MatterViz automatically registers as a custom editor for trajectory files such as `.traj`, `.h5`, `.hdf5`, `.xyz.gz`, etc.
+Interactively visualize crystal structures and molecules. Supports drag-and-drop file loading for CIF, POSCAR, XYZ/EXTXYZ, pymatgen JSON, OPTIMADE JSON, and compressed formats.
 
-### Remote SSH Support
+![3D Structure Viewer](https://github.com/janosh/matterviz/releases/download/v0.2.2/2026-01-23-structure-viewer.webp)
 
-MatterViz supports [VSCode](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh)/[Cursor](https://open-vsx.org/extension/jajera/vsx-remote-ssh) remote SSH connections. Connect to your server via Remote SSH extension, and MatterViz should work just like it does locally.
+## 📊 &thinsp; Periodic Table Heatmap
 
-- ✅ **Remote file access**: Visualize structures and trajectories on remote servers (HPC clusters, cloud instances, etc.)
-- ✅ **No manual file transfer**: Files are read directly from the remote filesystem
-- ✅ **File watching**: Changes to remote files are automatically detected and reloaded
-- ⚠️ **File size limit**: Files are currently limited to 1GB to prevent memory issues. Larger files are streamed in chunks which is only supported locally, not via remote SSH.
+Visualize elemental properties across the periodic table. The inset scatter plot shows how properties vary with atomic number - here demonstrating the periodicity of first ionization energy.
 
-## ⚙️ Configuration & Customization
+![Periodic table heatmap](https://github.com/janosh/matterviz/releases/download/v0.2.2/2026-01-23-heatmap.webp)
 
-MatterViz provides extensive customization options through VSCode settings. Access these via:
+## 🔬 &thinsp; Element Details Pages
 
-- **Settings UI**: `File → Preferences → Settings` → Search for "MatterViz"
-- **JSON Settings**: `Ctrl+Shift+P` → "Preferences: Open Settings (JSON)"
+Rich element pages with physical properties, electron configurations, Bohr atom visualizations, and element photos.
 
-### Common Configuration Scenarios
+![Element details page for gold](https://github.com/janosh/matterviz/releases/download/v0.2.2/2026-01-23-details-page.webp)
 
-#### 🎨 **Visual Appearance**
+## 🔨 &thinsp; Installation
 
-```json
-{
-  "matterviz.color_scheme": "Jmol",
-  "matterviz.background_color": "#ffffff",
-  "matterviz.background_opacity": 0.8,
-  "matterviz.structure.show_image_atoms": true,
-  "matterviz.structure.atom_radius": 1.2,
-  "matterviz.structure.bond_thickness": 0.8
-}
+```sh
+npm add -D matterviz
 ```
 
-#### 🎬 **Trajectory Playback**
+## 📙 &thinsp; Usage
 
-```json
-{
-  "matterviz.trajectory.auto_play": true,
-  "matterviz.trajectory.fps": 10,
-  "matterviz.trajectory.display_mode": "structure+scatter",
-  "matterviz.trajectory.show_controls": true
-}
-```
+### Periodic Table
 
-#### 📊 **Plot Customization**
+```svelte
+<script>
+  import { PeriodicTable } from 'matterviz'
 
-```json
-{
-  "matterviz.scatter.point_size": 5,
-  "matterviz.scatter.line_width": 3,
-  "matterviz.plot.grid_lines": true,
-  "matterviz.scatter.show_legend": true
-}
-```
-
-#### 🔧 **Performance Optimization**
+  const heatmap_values = { H: 10, He: 4, Li: 8, Fe: 3, O: 24 }
+</script>
 
-```json
-{
-  "matterviz.trajectory.chunk_size": 500,
-  "matterviz.trajectory.bin_file_threshold": 10485760,
-  "matterviz.structure.sphere_segments": 16
-}
+<PeriodicTable {heatmap_values} />
 ```
 
-### Setting Categories
-
-| Category        | Description                     | Example Settings                                                             |
-| --------------- | ------------------------------- | ---------------------------------------------------------------------------- |
-| **General**     | Global appearance and behavior  | `color_scheme`, `background_color`                                           |
-| **Structure**   | 3D structure visualization      | `atom_radius`, `bond_thickness`, `show_cell`, `lighting`, `show_image_atoms` |
-| **Trajectory**  | Animation and playback controls | `fps`, `auto_play`, `display_mode`, `show_controls`                          |
-| **Plots**       | Scatter plots and histograms    | `scatter_point_size`, `plot_grid_lines`, `auto_fit_range`                    |
-| **Performance** | Memory and processing options   | `chunk_size`, `use_indexing`, `sphere_segments`                              |
+### Structure
 
-### Pro Tips
+```svelte
+<script>
+  import { Structure } from 'matterviz'
+  const data_url = '/structures/TiO2.cif'
+  // supports .cif, .poscar, .xyz/.extxyz, pymatgen JSON, OPTIMADE JSON, .gz
+</script>
 
-- **Reset to defaults**: Remove custom settings from your JSON config
-- **Project-specific settings**: Use workspace settings (`.vscode/settings.json`) for per-project customization
-- **Theme integration**: MatterViz automatically adapts to your VSCode color theme
-- **Performance**: Reduce `sphere_segments` for better performance with large structures
-
-## ⌨️ Keyboard Shortcuts
-
-- `Ctrl+Shift+V` / `Cmd+Shift+V` → Render structure/trajectory with MatterViz
-
-## 🐛 Bug Reporting
+<Structure {data_url} style="width: 500px; aspect-ratio: 1" />
+```
 
-If you encounter any issues with MatterViz, you can use the built-in bug reporting command to collect debug information:
+### Composition
 
-1. Open the Command Palette (`Ctrl+Shift+P` / `Cmd+Shift+P`)
-2. Run **"Report MatterViz Bug"**
-3. The command will open a new document with detailed debug information including:
-   - Your OS and version
-   - VSCode/Cursor version
-   - MatterViz version
-   - Whether you're in a remote session
-   - Files currently being rendered
-   - System resources and memory usage
-   - Extension configuration
-4. Copy the information and include it when [creating a GitHub issue](https://github.com/janosh/matterviz/issues/new)
+```svelte
+<script>
+  import { Composition } from 'matterviz'
+  // modes can be 'pie' (default) | 'bubble' | 'bar'
+</script>
 
-## 📄 License
+<Composition composition="LiFePO4" mode="pie" />
+```
 
-This extension is [MIT-Licensed](./license).
+### Trajectory
 
-## 🔗 Related Projects
+```svelte
+<script>
+  import { Trajectory } from 'matterviz'
+  // supports .xyz/.extxyz, .traj, .hdf5, .npz, .pkl, .dat, .gz, .zip, .bz2, .xz
+</script>
 
-- **✅ MatterViz Web**: [matterviz.janosh.dev](https://matterviz.janosh.dev)
-- **✅ pymatviz**: [Jupyter](https://jupyter.org)/[Marimo](https://marimo.io) extension for Python notebooks. Read about widgets in [`pymatviz` readme](https://github.com/janosh/pymatviz/blob/main/readme.md#interactive-widgets) for details.
+<Trajectory data_url="/traj/ase-md.xyz" auto_play fps={10} style="max-height: 700px" />
+```
 
-## 🤝 Contributing
+## 🧪 &thinsp; Coverage
 
-We welcome contributions! Please see our [Contributing Guide](../../contributing.md) for details.
+| Statements                                                                                 | Branches                                                                          | Lines                                                                            |
+| ------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------- | -------------------------------------------------------------------------------- |
+| ![Statements](https://img.shields.io/badge/statements-99.84%25-brightgreen.svg?style=flat) | ![Branches](https://img.shields.io/badge/branches-82.92%25-yellow.svg?style=flat) | ![Lines](https://img.shields.io/badge/lines-99.84%25-brightgreen.svg?style=flat) |
 
-## 🛠️ Development
+## 🙏 &thinsp; Acknowledgements
 
-```bash
-git clone https://github.com/janosh/matterviz
-cd matterviz/extensions/vscode
-npm install
-npm run build
-vsce package  # creates .vsix for local install
-```
+- Element properties in `src/lib/element/data.ts` were combined from [`Bowserinator/Periodic-Table-JSON`](https://github.com/Bowserinator/Periodic-Table-JSON/blob/master/PeriodicTableJSON.json) under Creative Commons license and [`robertwb/Periodic Table of Elements.csv`](https://gist.github.com/robertwb/22aa4dbfb6bcecd94f2176caa912b952) (unlicensed).
+- Thanks to [Images of Elements](https://images-of-elements.com) for providing photos of elemental crystals and glowing excited gases.
+- Thanks to [@kadinzhang](https://github.com/kadinzhang) and their [Periodicity project](https://ptable.netlify.app) [[code](https://github.com/kadinzhang/Periodicity)] 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`](https://github.com/janosh/matterviz/blob/-/src/scripts/fetch-elem-images.ts) and [`static/elements`](https://github.com/janosh/matterviz/tree/main/static/elements).
+- Thanks to [@ixxie](https://github.com/ixxie) ([shenhav.fyi](https://shenhav.fyi)) for great suggestions.
 
-### Publishing
+This project would not have been possible as a one-person side project without many fine open-source projects. 🙏 To name just a few:
 
-Publish to both [Open VSX](https://open-vsx.org/extension/janosh/matterviz) and [VS Code Marketplace](https://marketplace.visualstudio.com/items?itemName=janosh.matterviz):
+|           3D graphics           |               2D graphics                |                     Docs                     |               Bundler               |               Testing                |
+| :-----------------------------: | :--------------------------------------: | :------------------------------------------: | :---------------------------------: | :----------------------------------: |
+| [three.js](https://threejs.org) |          [d3](https://d3js.org)          |         [mdsvex](https://mdsvex.com)         |     [vite](https://vitejs.dev)      | [playwright](https://playwright.dev) |
+| [threlte](https://threlte.xyz)  | [sharp](https://sharp.pixelplumbing.com) | [rehype](https://github.com/rehypejs/rehype) | [sveltekit](https://kit.svelte.dev) |     [vitest](https://vitest.dev)     |
 
-```bash
-cd extensions/vscode
-npm run package
+## How to cite `matterviz`
 
-# Open VSX (token at ~/.config/matterviz/ovsx-token)
-npx ovsx publish matterviz-*.vsix -p $(cat ~/.config/matterviz/ovsx-token)
+Use [`citation.cff`](citation.cff) or cite the [Zenodo record](https://zenodo.org/badge/latestdoi/498793280) using the following BibTeX entry:
 
-# VS Code Marketplace (requires `brew install azure-cli` for auth)
-az login --allow-no-subscriptions --scope https://app.vssps.visualstudio.com/.default
-TOKEN=$(python3 -c "import json,os;c=json.load(open(os.path.expanduser('~/.azure/msal_token_cache.json')));print(next(t['secret'] for t in c['AccessToken'].values() if 'vssps.visualstudio.com' in t.get('target','')))")
-vsce publish --no-dependencies -p "$TOKEN"
+```bib
+@software{riebesell_matterviz_2022,
+  title = {matterviz: visualization toolkit for materials informatics},
+  author = {Riebesell, Janosh and Evans, Matthew},
+  date = {2026-01-23},
+  year = {2026},
+  doi = {10.5281/zenodo.17094509},
+  url = {https://github.com/janosh/matterviz},
+  note = {10.5281/zenodo.17094509 - https://github.com/janosh/matterviz},
+  urldate = {2026-01-23}, % optional, replace with your date of access
+  version = {0.3.1}, % replace with the version you use
+}
 ```

package/.vscode/launch.json

@@ -1,13 +0,0 @@
-{
-  "version": "0.2.0",
-  "configurations": [
-    {
-      "name": "Run Extension",
-      "type": "extensionHost",
-      "request": "launch",
-      "args": ["--extensionDevelopmentPath=${workspaceFolder}"],
-      "outFiles": ["${workspaceFolder}/dist/**/*.js"],
-      "preLaunchTask": "${workspaceFolder}/npm: build"
-    }
-  ]
-}

package/.vscodeignore

@@ -1,7 +0,0 @@
-# Source files
-src/**
-*.ts
-
-# Build files
-tsconfig.json
-.vscode/**

package/dist/assets/STLExporter-BpTH3YHE.js

@@ -1,8 +0,0 @@
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-`,o+=`		outer loop
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-`}}};export{t as STLExporter};

package/dist/assets/browser-DdDecX_W.js

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package/dist/assets/export-qgn-H9y6.js

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