MAINT: Update neighbor list before NFF energy calls

Author: xiaochendu

mcmc/calculators/calculators.py

@@ -353,6 +353,10 @@ def calculate(
         if atoms is None:
             atoms = self.atoms
 
+        if hasattr(atoms, "update_nbr_list"):
+            # MCMC may add/remove atoms, so update neighbor list
+            atoms.update_nbr_list(update_atoms=True)
+
         NeuralFF.calculate(self, atoms, properties, system_changes)
 
         if "surface_energy" in properties:
@@ -481,6 +485,10 @@ def calculate(
         if atoms is None:
             atoms = self.atoms
 
+        if hasattr(atoms, "update_nbr_list"):
+            # MCMC may add/remove atoms, so update neighbor list
+            atoms.update_nbr_list(update_atoms=True)
+
         EnsembleNFF.calculate(self, atoms, properties, system_changes)
 
         if "surface_energy" in properties: