How to save the generated 3d representation of the structure(s) by Viewer3d in Py4vasp?

Question

I used py4vasp to calculate structure from data and then I displayed them in a structure viewer (Viewer3d) by this line: calc.structure[:].plot(). It returns a visualization of the structures as a 3d figure.

How I can save this 3d figure?

Also, If I read the structural information into a dictionary by this: calc.structure[:].read(), how I can plot the structures?

Here is the code which I used in the Jupyter notebook:

from py4vasp import Calculation
calc = Calculation.from_path(".")
calc.structure[:].plot()

Answer 1

Since we do not have all the files specific to your calculation such as the INCAR, POTCAR, POSCAR, KPQINTS and vaspout.h5, I will demonstrate how to save a viewer3d structure to a PNG image using a sample viewer3d structure.

From py4vasp source code, we can see that the viewer is a: NGLWidget

All the following code are written on a Google Colab notebook:

from google.colab import output
output.enable_custom_widget_manager()

import nglview as nv
import ipywidgets as w
import time
import threading
from pathlib import Path
view = nv.demo()
view

type(view)
>> nglview.widget.NGLWidget # This matches with what we get from py4vasp

The viewer3d structure looks like this:

The following code saves the viewer3d as a PNG image.

output_path = "/content/drive/MyDrive/output/img.png"

def save_image(view):
    img = view.render_image()
    
    while not img.value:
        time.sleep(0.1)
    
    with open(output_path, "wb") as f:
        f.write(img.value)

Path(output_path).unlink(missing_ok=True)

thread = threading.Thread(target=save_image, args=(view, ), daemon=False)

thread.start()

The PNG image is now saved at the output path.