`plot3d` - go beyond NGLview

pyiron / structuretoolkit

build, analyse and visualise atomistic structures for materials science

BSD 3-Clause "New" or "Revised" License

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`plot3d` - go beyond NGLview #124

Open samwaseda opened 8 months ago

samwaseda commented 8 months ago

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 commented 8 months ago

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

samwaseda commented 8 months ago

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

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

superstar54 commented 6 months ago

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