Update core/evolution/evolution.py

core/evolution/evolution.py

@@ -157,6 +157,31 @@ class MolecularEvolution:
             self._log_generation_stats(gen)
             
             survivors = self.population.get_survivors()
+
+            
+            sample_smiles = []
+            if survivors:
+                # best survivor (matches CLI optimisation logic)
+                if self.config.maximize_cn:
+                    best = max(survivors, key=lambda m: m.cn)
+                else:
+                    best = min(survivors, key=lambda m: m.cn_error)
+                sample_smiles.append(best.smiles)
+    
+                # a few random other survivors (small, illustrative)
+                k = min(3, len(survivors))
+                sample_smiles.extend([m.smiles for m in random.sample(survivors, k)])
+
+
+                    # remove duplicates while keeping order
+            sample_smiles = list(dict.fromkeys(sample_smiles))
+    
+            self.history.append({
+                "generation": gen,
+                "smiles": sample_smiles
+            })
+            
+            
             offspring = self._generate_offspring(survivors)
             
             # Create new population