weas-widget
Advanced tools
A widget to visualize and interact with atomistic structures in Jupyter Notebook.
A widget to visualize and edit atomic structures in Jupyter Notebooks. It uses 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:
Please try the widget in the following links:
weas-widgetIf your project uses weas-widget, we’d love to showcase it here!
🚀 Let's build a growing community of weas-widget users!
With pip:
pip install weas-widget
To install the latest version from source, first clone the repository and then install using pip:
git clone https://github.com/superstar54/weas-widget
cd weas-widget
npm install
npm run build
pip install -e .
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
If you encounter any problems, please first update the widget to the latest version.
pip install weas-widget --upgrade
If the problem persists, please open a GitHub issue
Shift key and drag to select a group of atoms.Shift + Alt and drag to select a group of atoms.Press the keyboard shortcut, and move your mouse.
| Operation | Shortcut |
|---|---|
| Move | g |
| Rotate | r |
| Duplicate | d |
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).
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.
Press the Delete key
atoms = viewer.to_ase()
viewer.save_image("/home/xing/filename.png")
viewer.download_image("filename.png")
For a nice visualization of a crystal, show
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
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
Requires the optional fermi-surface dependencies (includes seekpath):
pip install "weas-widget[fermi-surface]"
from weas_widget import WeasWidget
viewer = WeasWidget()
viewer.add_fermi_surface_from_bxsf("copper.bxsf", clip_bz=True)
viewer
Show the magnetic moments as a vector field.
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
Animate vibrational (phonon) modes (computed with external software).
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
Draw a plane that is defined by the miller indices and distance from the origin or by selecting the atoms.
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()
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
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")
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.
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
pytest
The e2e test is similar to ipywidgets.
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
FAQs
A widget to visualize and interact with atomistic structures in Jupyter Notebook.
We found that weas-widget demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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