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[BUG] Show disordered sites without gaps #441

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[BUG] Show disordered sites without gaps #441

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df3cdb2
show disordered sites without gaps
jmmshn-ms Jan 2, 2025
357d6f9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 2, 2025
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8 changes: 6 additions & 2 deletions crystal_toolkit/renderables/site.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,9 @@ def get_site_scene(
radii = [legend.get_radius(sp, site=self) for sp in self.species]
max_radius = float(min(radii))

rscale_factor = 0.996
rscale = 1.0

for sp, occu in self.species.items():
if isinstance(sp, DummySpecie):
cube = Cubes(
Expand Down Expand Up @@ -130,13 +133,14 @@ def get_site_scene(
sphere = Spheres(
positions=[position],
color=color,
radius=radius,
radius=radius * rscale,
phiStart=phiStart,
phiEnd=phiEnd,
clickable=True,
tooltip=name,
)
atoms.append(sphere)
rscale *= rscale_factor

# Add magmoms
if draw_magmoms and (magmom := self.properties.get("magmom")):
Expand All @@ -161,7 +165,7 @@ def get_site_scene(
sphere = Spheres(
positions=[position],
color="#ffffff",
radius=max_radius,
radius=max_radius * rscale_factor,
phiStart=phiEnd,
phiEnd=np.pi * 2,
)
Expand Down
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