minor changes

gofee/candidates/basic_mutations.py

@@ -179,7 +179,7 @@ class RattleMutation2(OffspringOperation):
         # Perform rattle operations in sequence.
         for i in indices_to_rattle:
             posi_0 = np.copy(a.positions[i])
-            for _ in range(100):
+            for _ in range(10):
                 j = np.random.randint(Nslab,Natoms)
 
                 # Perform rattle
@@ -196,7 +196,8 @@ class RattleMutation2(OffspringOperation):
                 if self.cluster:
                     not_too_close_all = self.check_bondlengths(a, indices=[i], check_isolated=False)
                     if self.n_top > 1:
-                        not_isolated_cluster = self.check_bondlengths(a, indices=np.arange(Nslab,Natoms), indices_placed=np.arange(Nslab,Natoms), check_too_close=False)
+                        #not_isolated_cluster = self.check_bondlengths(a, indices=np.arange(Nslab,Natoms), indices_placed=np.arange(Nslab,Natoms), check_too_close=False)
+                        not_isolated_cluster = self.check_bondlengths(a, indices=[i], indices_placed=np.arange(Nslab,Natoms), check_too_close=False)
                     else:
                         not_isolated_cluster = False
                     valid_bondlengths = not_too_close_all and not_isolated_cluster

gofee/surrogate/gpr.py

@@ -527,7 +527,7 @@ class GPR():
         self.E, self.X, self.prior_energies = self.memory.get_data()
         self.Y = self.E - self.prior_energies - self.bias
 
-        self.update_theta_bounds()
+        #self.update_theta_bounds()
 
         results = []
         for i in range(self.n_restarts_optimizer):