Web Environment For Atomic Structure (WEAS)

The WEAS package is a JavaScript library designed to visualize and edit atomic structures (molecule, crystal, nanoparticle) in the web environments.

Features:

• Model: space-filling, ball-stick, polyhedral.
• Supported File types: cif, xyz, cube, xsf, POSCAR.
• Edit structure: move, rotate, delete, and replace atoms.
• Atom groups for tagging and selection by group.
• Support periodic boundary conditions.
• Animation (view and edit).
• Volumetric data (isosurface).
• Vector fields, e.g., magnetic moment.
• Import structures and export image/JSON/XYZ/CIF (and animation when available) from the GUI.

Demo

Here are some demo pages:

• Codepen Demo
• ...

How to use

Please visit: WEAS Documentation

Viewer state and history

WEAS separates viewer state changes from operations that record undo/redo.

// Apply state changes without history, with deferred redraws.
viewer.avr.transaction(() => {
  viewer.avr.applyState({ modelStyle: 1, colorBy: "Element" });
});

// Apply state changes with history.
viewer.avr.setState({ colorBy: "Index" }, { record: true, redraw: "full" });

Save and restore state

You can export the full viewer state (atoms, plugins, viewer settings, camera) to JSON and import it later.

const snapshot = viewer.exportState();
// persist snapshot as JSON
const payload = JSON.stringify(snapshot);
// restore later
viewer.importState(JSON.parse(payload));

Import/export structures

The GUI includes import/export buttons for JSON/XYZ/CIF. You can also use the helpers programmatically:

import { parseStructureText, applyStructurePayload, buildExportPayload, downloadText } from "weas";

const parsed = parseStructureText(text, ".cif");
applyStructurePayload(viewer, parsed.data);

const payload = buildExportPayload(viewer, "xyz");
downloadText(payload.text, payload.filename, payload.mimeType);

Examples

Molecule

Crystal structure

Isosurfaces

Volume Slice

Animation

Phonons

How to run a demo locally

Clone the repository,

npm install
npm start

Then go to the demo site.

Test

npm install
npm test

End-to-end test

Use playwright for the e2e test.

For the first time, one needs to install the dependence.

npx playwright install

Then run

npm run build
npx playwright test

Run the test with the title

npx playwright test -g "Animation"

If the snapshots need to be updated:

npx playwright test --update-snapshots

Contact

• Xing Wang [email protected]