From df3cdb268dba3e007bd04f1cf24cee34ee64a11a Mon Sep 17 00:00:00 2001
From: Jimmy Shen <v-jimshen@microsoft.com>
Date: Thu, 2 Jan 2025 06:55:45 -0800
Subject: [PATCH] show disordered sites without gaps

---
 crystal_toolkit/renderables/site.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/crystal_toolkit/renderables/site.py b/crystal_toolkit/renderables/site.py
index ef43be57..a5e52e09 100644
--- a/crystal_toolkit/renderables/site.py
+++ b/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,
         )