weas-widget 0.1.2

A widget to visualize and interact with atomistic structures in Jupyter Notebook.

Welcome to WEAS Widget!

A widget to visualize and edit atomic structures in Jupyter Notebooks. It uses WEAS (Web Environment For Atomistic Structure) in the backend.

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, ...

Installation

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 .

How to use

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.

    pip install weas-widget  --upgrade

If the problem persists, please open a GitHub issue

Features

Select Atoms

• Pick Selection: Click directly on an atom to select it.
• Range Selection: Hold the Shift key and drag the right mouse button to select a group of atoms.

Move, Rotate selected atoms

Press the keyboard shortcut, and move your mouse.

Operation	Shortcut
Move	g
Rotate	r
Duplicate	d

Delete selected atoms

Press the Delete key

Export

• Export the modified atomic structure to ASE or Pymatgen

atoms = viewer.to_ase()

• Save image to a path by:

viewer.save_image("/home/xing/filename.png")

• Download image by:

viewer.download_image("filename.png")

Visualizing crystal structures

For a nice visualization of a crystal, show

• unit cell
• bonded atoms outside the cell
• polyhedra

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

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 = [{"isovalue": 0.0001, "mode": 0}]
viewer

Magnetic moments

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

Phonons

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

import numpy as np
from ase.build import bulk
from weas_widget import WeasWidget
from weas_widget.utils import generate_phonon_trajectory

atoms = bulk("Fe", cubic=True)
eigenvector = np.array([[0, -0.0, 0.5], [0, 0.0, -0.5]])
trajectory = generate_phonon_trajectory(atoms, eigenvector, repeat=[4, 4, 1])
viewer = WeasWidget()
viewer.from_ase(trajectory)
# set a vector field to show the arrow
viewer.avr.vf.settings = [{"origins": "positions", "vectors": "movement", "radius": 0.1}]
viewer.avr.vf.show = True
viewer

Lattice plane

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()

Test

Unit test

pytest

End-to-end test

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

Contact

• Xing Wang [e-mail]

License

MIT