weas-widget

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A widget to visualize and edit atomic structures in Jupyter Notebook

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# Welcome to WEAS Widget!
[![PyPI version](https://badge.fury.io/py/weas-widget.svg)](https://badge.fury.io/py/weas-widget)
[![Docs status](https://readthedocs.org/projects/weas-widget/badge)](http://weas-widget.readthedocs.io/)
[![Unit test](https://github.com/superstar54/weas-widget/actions/workflows/ci.yml/badge.svg)](https://github.com/superstar54/weas-widget/actions/workflows/ci.yml)

A widget to visualize and edit atomic structures in Jupyter Notebooks. It uses [WEAS](https://github.com/superstar54/weas) (Web Environment For Atomistic Structure) in the backend.
Interact with the widget using LLM agents (e.g., LangChain) to guide edits and analysis from your notebook.

Features:

- Model: space-filling, ball-stick, polyhedral.
- Supports importing data from ASE and Pymatgen.
- Edit structure: move, rotate, delete and replace atoms.
- Supports periodic boundary conditions
- Animations
- Isosurfaces
- Vector fields, e.g., magnetic moments, phonons, ...
- Fermi surface
- Lattice planes
- Integrate with LLMs via LangChain Agent

## Demo
Please try the widget in the following links:
[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/superstar54/weas-widget/blob/main/examples/example.ipynb)

## 🌟 Gallery: projects using `weas-widget`

- **AiiDAlab Plugins:**
    - [aiidalab-qe-vibroscopy](https://github.com/mikibonacci/aiidalab-qe-vibroscopy)
    - [aiidalab-qe-pp](https://github.com/AndresOrtegaGuerrero/aiidalab-qe-pp)
    - [aiidalab-qe-wannier90](https://github.com/superstar54/aiidalab-qe-wannier90)
- [pack-mm](https://ddmms.github.io/pack-mm/tutorials/basic.html)
- [ipyvasp](https://github.com/asaboor-gh/ipyvasp)

### 📢 Want to Feature Your Project?
If your project uses `weas-widget`, we’d love to showcase it here!
- Submit a **pull request (PR)** with a link to your project.
- Need a project removed? Open a PR or issue, and we’ll take care of it.

🚀 Let's build a growing community of `weas-widget` users!

## Installation

With `pip`:

```console
pip install weas-widget
```

To install the latest version from source, first clone the repository and then install using `pip`:

```console
git clone https://github.com/superstar54/weas-widget
cd weas-widget
npm install
npm run build
pip install -e .
```

## How to use

```python
from ase.build import molecule
from weas_widget import WeasWidget
atoms = molecule("C2H6SO")
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer
```

Full documentation at: https://weas-widget.readthedocs.io/en/latest/index.html

## Reporting issues
If you encounter any problems, please first update the widget to the latest version.

```console
    pip install weas-widget  --upgrade
```

If the problem persists, please open a [GitHub issue](https://github.com/superstar54/weas-widget/issues)

## Features

### Select Atoms
- Pick Selection: Click directly on an atom to select it.
- Box Selection: Hold the `Shift` key and drag to select a group of atoms.
- Lasso Selection: Hold `Shift + Alt` and drag to select a group of atoms.

### Shortcuts for editing selected atoms
Press the keyboard shortcut, and move your mouse.

|Operation | Shortcut|
|----------|---------|
| Move     | `g`   |
| Rotate   | `r`   |
| Duplicate| `d`   |

### Rotate selected atoms

To rotate around a custom axis, press ``r`` then ``a`` and click one or two atoms, then press ``a`` again to exit axis picking.
Rotation defaults to the camera axis through the selection center.
One atom sets the rotation center (camera axis), two atoms define the bond axis.
The axis is shown with orange crosses and a long orange line (for two atoms).
Press ``a`` again to exit axis picking and rotate; click an axis atom again to deselect it.
Press ``r`` then ``x``, ``y``, or ``z`` to lock rotation to a world axis (press the same key again to unlock).

### Translate along one axis
To translate along one axis, press ``g`` then ``x``, ``y``, or ``z`` to lock movement.
To translate along an atom-defined axis, press ``g`` then ``a`` and click two atoms, then press ``a`` again to exit axis picking.
To translate in an atom-defined plane, press ``g`` then ``a`` and click three atoms, press ``a`` again to exit axis picking, then press ``p`` for plane or ``n`` for normal.

### Delete selected atoms
Press the ``Delete`` key

### Export
- Export the modified atomic structure to ASE or Pymatgen
```python
atoms = viewer.to_ase()
```
- Save image to a path by:
```python
viewer.save_image("/home/xing/filename.png")
```
- Download image by:
```python
viewer.download_image("filename.png")
```

### Different styles for the atoms.

### Visualizing crystal structures
For a nice visualization of a crystal, show
- unit cell
- bonded atoms outside the cell
- polyhedra

```python
from weas_widget import WeasWidget
viewer1 = WeasWidget()
viewer1.load_example("tio2.cif")
viewer1.avr.model_style = 2
viewer1.avr.boundary = [[-0.1, 1.1], [-0.1, 1.1], [-0.1, 1.1]]
viewer1.avr.show_bonded_atoms = True
viewer1.avr.color_type = "VESTA"
viewer1
```

### Isosurfaces

```python
from ase.build import molecule
from weas_widget import WeasWidget
from ase.io.cube import read_cube_data
volume, atoms = read_cube_data("h2o-homo.cube")
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.avr.iso.volumetric_data = {"values": volume}
viewer.avr.iso.settings = {"positive": {"isovalue": 0.001},
                           "negative": {"isovalue": -0.001, "color": "yellow"}
                           }
viewer
```
<img src="docs/source/_static/images/example-isosurface.png"  width="300px"/>

### Fermi surface

Requires the optional `fermi-surface` dependencies (includes `seekpath`):

```bash
pip install "weas-widget[fermi-surface]"
```

```python
from weas_widget import WeasWidget
viewer = WeasWidget()
viewer.add_fermi_surface_from_bxsf("copper.bxsf", clip_bz=True)
viewer
```
<img src="docs/source/_static/images/fermi-surface.png"  width="300px"/>

### Magnetic moments
Show the magnetic moments as a vector field.

```python
from ase.build import bulk
from weas_widget import WeasWidget
import numpy as np
atoms = bulk("Fe", cubic=True)
atoms*=[2, 2, 1]
atoms.set_array("moment", np.ones(len(atoms)))
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.avr.model_style = 1
viewer
```
<img src="docs/source/_static/images/example-magnetic-moment.png"  width="300px"/>

### Phonons
Animate vibrational (phonon) modes (computed with external software).

```python
import numpy as np
from ase.build import bulk
from weas_widget import WeasWidget
atoms = bulk("Fe", cubic=True)
phonon_setting = {"eigenvectors": np.array([[[0, 0], [0, 0],[0.5, 0]],
                                    [[0, 0], [0, 0], [-0.5, 0]]]
                                    ),
        "kpoint": [0, 0, 0], # optional
        "amplitude": 5, # scale the motion of the atoms
        "factor": 1.5, # scale the length of the arrows
        "nframes": 20,
        "repeat": [4, 4, 1],
        "color": "blue",
        "radius": 0.1,
        }
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.avr.phonon_setting = phonon_setting
viewer
```

### Lattice plane
Draw a plane that is defined by the miller indices and distance from the origin or by selecting the atoms.

```python
viewer.avr.lp.add_plane_from_indices(name = "111",
                                     indices = [1, 1, 1],
                                     distance = 4,
                                     scale = 1.0,
                                     color = [0, 1, 1, 0.5])
viewer.avr.lp.build_plane()
```

### Slice 2D
```python
from ase.build import molecule
from weas_widget import WeasWidget
from ase.io.cube import read_cube_data
volume, atoms = read_cube_data("h2o-homo.cube")
viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.avr.model_style = 1
viewer.avr.volume_slice.volumetric_data = {"values": volume}
viewer.avr.volume_slice.settings = {"Slice 1": {"h": 0, "k": 1, "l": 0, "distance": 5.5, "samplingDistance": 0.1 },
                                    "Slice 2": {"h": 1, "k": 1, "l": 0, "distance": 5.5, "samplingDistance": 0.1 },
                                   }
viewer.camera.setting = {"direction": [0.5, 1, 2], "zoom": 1.5}
viewer
```
<img src="docs/source/_static/images/example-volume-slice.png"  width="300px"/>

### Save and restore state

```python
state = viewer.export_state()
viewer.save_state("snapshot.json")

# later
viewer.load_state("snapshot.json")

# or create a viewer directly from a saved state
viewer = WeasWidget.from_state_file("snapshot.json")
```

### Integrate with LangChain Agent

`WeasToolkit` provides agent-ready tools for inspection and editing (style controls, selection, structure loading, atom edits, camera, measurements, meshes, and more). You can also extend it with your own tools.

```python
from weas_widget import WeasWidget, WeasToolkit
from langchain_openai import ChatOpenAI
from langchain_widget import LangChainWidget
from langchain_openai import ChatOpenAI
from dotenv import load_dotenv
import ipywidgets as ipw

load_dotenv()

viewer = WeasWidget()

chat_model = ChatOpenAI(model="gpt-4o-mini")

chat = LangChainWidget(
    chat_model=chat_model,
    tools=WeasToolkit(viewer=viewer),
    title="WEAS Agent Chat",
    system_prompt=(
        "You are a scientific assistant. "
        "Use the available tools to inspect and manipulate the 3D structure."
    ),
)
ipw.VBox([viewer, chat])
```

See the agent tools reference in the docs: https://weas-widget.readthedocs.io/en/latest/agent_tools.html

## Test

### Unit test

```console
pytest
```

### End-to-end test

The e2e test is similar to [ipywidgets](https://ipywidgets.readthedocs.io/en/latest/dev_testing.html).

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

```
cd tests/notebooks/
yarn install
```

Then run in a terminal:

```
yarn start
```

In another terminal:

```
yarn test
```

If the snapshots need to be updated:

```
yarn test:update
```

## Contact
* Xing Wang  <xingwang1991@gmail.com>

## License
[MIT](http://opensource.org/licenses/MIT)

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