Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/superstar54/weas-widget
A widget to visualize and edit atomic structures in Jupyter Notebook
https://github.com/superstar54/weas-widget
3d crystal editor jupyter-notebook molecule visualization
Last synced: about 1 month ago
JSON representation
A widget to visualize and edit atomic structures in Jupyter Notebook
- Host: GitHub
- URL: https://github.com/superstar54/weas-widget
- Owner: superstar54
- License: mit
- Created: 2024-01-22T23:14:39.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-04-07T07:27:24.000Z (8 months ago)
- Last Synced: 2024-04-14T03:13:05.707Z (7 months ago)
- Topics: 3d, crystal, editor, jupyter-notebook, molecule, visualization
- Language: Python
- Homepage: https://weas-widget.readthedocs.io/en/latest/index.html
- Size: 5.42 MB
- Stars: 16
- Watchers: 1
- Forks: 4
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Welcome to WEAS Widget!
[](https://badge.fury.io/py/weas-widget)
[](http://weas-widget.readthedocs.io/)
[](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.
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`:
```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.
- 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
```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")
```
### 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 = [{"isovalue": 0.0001, "mode": 0}]
viewer
```
### 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
```
### Phonons
Animate vibrational (phonon) modes (computed with external software).
```python
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.
```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()
```
## 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
## License
[MIT](http://opensource.org/licenses/MIT)