Issues displaying a crystal structure - related to site occupancies?

[ayushsgupta]

I'm having some trouble displaying one particular structure (Fe5GeTe2.zip) in Jupyter Lab using crystal toolkit. Normally I can run a cell with just the pymatgen structure object, and crystal toolkit will automatically render the structure below the cell. However, with this specific structure all I receive is a printout of the structure object and the following error:

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/miniconda3/envs/scan/lib/python3.8/site-packages/IPython/core/formatters.py in __call__(self, obj, include, exclude)
    968 
    969             if method is not None:
--> 970                 return method(include=include, exclude=exclude)
    971             return None
    972         else:

~/miniconda3/envs/scan/lib/python3.8/site-packages/crystal_toolkit/__init__.py in _repr_mimebundle_(self, include, exclude)
     56     if hasattr(self, "get_scene"):
     57         return {
---> 58             "application/vnd.mp.ctk+json": self.get_scene().to_json(),
     59             "text/plain": help_text_ct + self.__repr__(),
     60         }

~/miniconda3/envs/scan/lib/python3.8/site-packages/crystal_toolkit/renderables/structure.py in get_structure_scene(self, origin, legend, draw_image_atoms)
     97             )
     98 
---> 99         site_scene = site.get_scene(legend=legend,)
    100         for scene in site_scene.contents:
    101             primitives[scene.name] += scene.contents

~/miniconda3/envs/scan/lib/python3.8/site-packages/crystal_toolkit/renderables/site.py in get_site_scene(self, connected_sites, connected_sites_not_drawn, hide_incomplete_edges, incomplete_edge_length_scale, connected_sites_colors, connected_sites_not_drawn_colors, origin, draw_polyhedra, explicitly_calculate_polyhedra_hull, bond_radius, legend)
    105             positions=[position],
    106             color="#ffffff",
--> 107             radius=self.properties["display_radius"][0],
    108             phiStart=phiEnd,
    109             phiEnd=np.pi * 2,

KeyError: 'display_radius'

I've tried to trace back the error through the crystal toolkit source code, but unfortunately it's a bit beyond me. The problem appears to be that a site object in crystal toolkit lacks the "display_radius" property, but I'm not sure how this happens. Does it have to do with certain sites having occupancies of less than 1? I can load a different structure in the same notebook and it renders perfectly fine. I'm working with crystal toolkit version 2021.4.2, and JupyterLab version 3.1.0.

Even though other structures were rendering fine, I decided to update crystal toolkit to see if that solved the problem. I updated to version 2021.4.29 fine, but when I went to run jupyter labextension install crystaltoolkit-extension, I got the following error:

An error occured.
ValueError: The extension "crystaltoolkit-extension" does not yet support the current version of JupyterLab.


Conflicting Dependencies:
JupyterLab                        Extension              Package
>=3.1.0-alpha.4 <3.2.0            >=2.0.0 <3.0.0         @jupyterlab/rendermime-interfaces
See the log file for details:  /tmp/jupyterlab-debug-dad5s_b7.log

Any advice would be appreciated!

[mkhorton]

Hi @ayushsgupta. Ok, two separate issues here.

1. The current version of crystal toolkit only explicitly supports JupyterLab 3.x or above -- the extension installation is much simpler now, so you just have to pip install ... and jupyter labextension install ... is not required.

2. It likely is a bug related to the partial occupancies, I will have to investigate.

[ayushsgupta]

@mkhorton Okay, thanks for looking into it!

[mkhorton]

Believe this was closed (see #234) but please re-open if not the case.