plot3d - go beyond NGLview

[samwaseda]

Currently we have to rely on NGLview for most of the functionalities, especially if we want to have different colours for a continuous value, or vectors. It's not only extremely slow, but it also doesn't give us the possibility to

• Combine it with continuum plotting
• Save the figure
• Run on machines that do not have NGLview installed

So the functionalities should be extended with plotly

[jan-janssen]

But there is already a plotly part in the visualize module:
https://github.com/pyiron/structuretoolkit/blob/main/structuretoolkit/visualize.py#L146

[samwaseda]

But there is already a plotly part in the visualize module:

I know, but the functionalities are a lot limited than NGLview

[superstar54]

I opened an issue (#156) regarding adding weas-widget, and found it also related to this issue.
weas-widget support coloring atoms by its attributes (charge, force, etc.), and it very fast.

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

atoms = bulk('Au', cubic = True)
atoms *= [8, 8, 8]
charges = np.random.random(len(atoms))
atoms.set_array("charge", charges)

viewer = WeasWidget()
viewer.from_ase(atoms)
viewer.colorBy = "charge"
viewer.colorRamp = ["red", "yellow", "blue"]
viewer