show disordered sites without gaps

Author: jmmshn-ms

crystal_toolkit/renderables/site.py

@@ -90,6 +90,9 @@ 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):
@@ -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")):
@@ -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,
         )