Bug in crystaltoolkit_relax_viewer.ipynb in examples

[exenGT]

Hi,

I tried to run crystaltoolkit_relax_viewer.ipynb in the "examples" folder, but running the last cell gives this error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[11], line 17
     11 if "struct_layout" not in vars():
     12     # don't create layout twice because it causes duplicate
     13     # ID errors when restarting Dash app in Jupyter notebook
     14     struct_comp = ctc.StructureMoleculeComponent(
     15         id="structure", struct_or_mol=structure
     16     )
---> 17     struct_layout = struct_comp.layout()
     20 step_size = max(1, len(trajectory) // 20)  # ensure slider has max 20 steps
     21 slider = dcc.Slider(
     22     id="slider", min=0, max=len(trajectory) - 1, step=step_size, updatemode="drag"
     23 )

File ~/miniconda3/envs/chem/lib/python3.9/site-packages/crystal_toolkit/components/structure.py:896, in StructureMoleculeComponent.layout(self, size)
    886 def layout(self, size: str = "500px") -> html.Div:
    887     """Get the layout for this component.
    888 
    889     Args:
   (...)
    893         html.Div: A html.Div containing the 3D structure or molecule
    894     """
    895     return html.Div(
--> 896         self._sub_layouts["struct"], style={"width": size, "height": size}
    897     )

File ~/miniconda3/envs/chem/lib/python3.9/site-packages/crystal_toolkit/components/structure.py:851, in StructureMoleculeComponent._sub_layouts(self)
    847     options_layout = None
    849 if self.show_legend:
    850     legend_layout = html.Div(
--> 851         self._make_legend(self._initial_data["legend_data"]),
    852         id=self.id("legend_container"),
    853     )
    854 else:
    855     legend_layout = None

File ~/miniconda3/envs/chem/lib/python3.9/site-packages/crystal_toolkit/components/structure.py:592, in StructureMoleculeComponent._make_legend(self, legend)
    585     c = tuple(int(hex_code[1:][i : i + 2], 16) for i in (0, 2, 4))
    586     return (
    587         "black"
    588         if 1 - (c[0] * 0.299 + c[1] * 0.587 + c[2] * 0.114) / 255 < 0.5
    589         else "white"
    590     )
--> 592 legend_colors = {
    593     k: self._legend.get_color(Species(k))
    594     for k, v in legend["composition"].items()
    595 }
    597 legend_elements = [
    598     html.Span(
    599         html.Span(
   (...)
    605     for name, color in legend_colors.items()
    606 ]
    608 return html.Div(
    609     legend_elements,
    610     id=self.id("legend"),
    611     style={"display": "flex"},
    612     className="buttons",
    613 )

File ~/miniconda3/envs/chem/lib/python3.9/site-packages/crystal_toolkit/components/structure.py:593, in <dictcomp>(.0)
    585     c = tuple(int(hex_code[1:][i : i + 2], 16) for i in (0, 2, 4))
    586     return (
    587         "black"
    588         if 1 - (c[0] * 0.299 + c[1] * 0.587 + c[2] * 0.114) / 255 < 0.5
    589         else "white"
    590     )
    592 legend_colors = {
--> 593     k: self._legend.get_color(Species(k))
    594     for k, v in legend["composition"].items()
    595 }
    597 legend_elements = [
    598     html.Span(
    599         html.Span(
   (...)
    605     for name, color in legend_colors.items()
    606 ]
    608 return html.Div(
    609     legend_elements,
    610     id=self.id("legend"),
    611     style={"display": "flex"},
    612     className="buttons",
    613 )

File ~/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/core/periodic_table.py:1077, in Species.__init__(self, symbol, oxidation_state, properties)
   1049 def __init__(
   1050     self,
   1051     symbol: str,
   1052     oxidation_state: float | None = 0.0,
   1053     properties: dict | None = None,
   1054 ):
   1055     """
   1056     Initializes a Species.
   1057 
   (...)
   1075         Properties are now checked when comparing two Species for equality.
   1076     """
-> 1077     self._el = Element(symbol)
   1078     self._oxi_state = oxidation_state
   1079     self._properties = properties or {}

File ~/miniconda3/envs/chem/lib/python3.9/enum.py:384, in EnumMeta.__call__(cls, value, names, module, qualname, type, start)
    359 """
    360 Either returns an existing member, or creates a new enum class.
    361 
   (...)
    381 `type`, if set, will be mixed in as the first base class.
    382 """
    383 if names is None:  # simple value lookup
--> 384     return cls.__new__(cls, value)
    385 # otherwise, functional API: we're creating a new Enum type
    386 return cls._create_(
    387         value,
    388         names,
   (...)
    392         start=start,
    393         )

File ~/miniconda3/envs/chem/lib/python3.9/enum.py:702, in Enum.__new__(cls, value)
    700 ve_exc = ValueError("%r is not a valid %s" % (value, cls.__qualname__))
    701 if result is None and exc is None:
--> 702     raise ve_exc
    703 elif exc is None:
    704     exc = TypeError(
    705             'error in %s._missing_: returned %r instead of None or a valid member'
    706             % (cls.__name__, result)
    707             )

ValueError: 'Li+' is not a valid Element

I think it is related to the presence of oxidation state in the cif file. Is this the expected behavior? If not, how should it be fixed?

Thanks, JW

[janosh]

I can't repro. Maybe try

pip install -U pymatgen crystal-toolkit

[exenGT]

After updating, everything works as expected! Closing this issue now.