Merge branch 'main' into h5py_dependency

CederGroupHub · Dec 18, 2023 · 8642e4d · 8642e4d
2 parents f0d5e91 + b419e7d
commit 8642e4d
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/smol/moca/sampler/container.py b/smol/moca/sampler/container.py
@@ -134,9 +134,14 @@ def traced_values(self):
         return self._trace.names
 
     def sampling_efficiency(self, discard=0, flat=True):
-        """Return the sampling efficiency for chains."""
+        """Return the sampling efficiency for chains.
+
+        If the sampling is thinned by > 1, this value becomes only an estimate for the
+        true sampling efficiency, as we do not know the efficiency of the discarded
+        samples.
+        """
         total_accepted = self._trace.accepted[discard:].sum(axis=0)
-        efficiency = total_accepted / (self._total_steps - discard)
+        efficiency = total_accepted / (self._nsamples - discard)
         if flat:
             efficiency = efficiency.mean()
         return efficiency