modified logfile

gofee.py

@@ -335,11 +335,13 @@ class GOFEE():
         relaxed_candidates = self.certainty_filter(relaxed_candidates)
         relaxed_candidates = self.population.pop_MLrelaxed + relaxed_candidates
         
+        """
         if self.master:
             Epred = np.array([a.info['key_value_pairs']['Epred'] for a in relaxed_candidates])
             Epred_std = np.array([a.info['key_value_pairs']['Epred_std'] for a in relaxed_candidates])
             fitness = Epred - self.kappa*Epred_std
             print(np.c_[Epred, Epred_std, fitness])
+        """
         return relaxed_candidates
 
     def generate_candidate(self):

surrogate/gpr.py

@@ -240,9 +240,6 @@ class GPR():
             fmin_l_bfgs_b(self.neg_log_marginal_likelihood,
                           theta_initial,
                           bounds=self.kernel.theta_bounds)
-        if convergence_dict["warnflag"] != 0:
-            warnings.warn("fmin_l_bfgs_b terminated abnormally with the "
-                          " state: %s" % convergence_dict)
         return theta_opt, func_min
 
     def numerical_neg_lml(self, dx=1e-4):

test_systems/TiO2/run_search.py

 import numpy as np
 
 from ase.calculators.dftb import Dftb
+from ase.io import read
 
-from surrogate.gpr import GPR
-
-from ase.io import read, write
 from candidate_operations.candidate_generation import CandidateGenerator, StartGenerator, OperationConstraint
 from candidate_operations.basic_mutations import RattleMutation, RattleMutation2, PermutationMutation
+from gofee import GOFEE
 
 import sys
 
-from gofee import GOFEE
-
 ### Set up StartGenerator and mutations ###
 # read slab
 slab = read('slab.traj', index='0')
@@ -33,14 +30,10 @@ sg = StartGenerator(slab, stoichiometry, box)
 
 # initialize rattle mutation
 n_to_optimize = len(stoichiometry)
-
-# Add position constraint to mutations
-z_constraint = OperationConstraint(zlim=[6.5, 15])
-
 candidate_generator = CandidateGenerator([0.2, 0.2, 0.6],
-                                         [sg,
-                                          PermutationMutation(n_to_optimize, Npermute=2),
-                                          RattleMutation(n_to_optimize, Nrattle=3, rattle_range=4)])
+                                        [sg,
+                                         PermutationMutation(n_to_optimize, Npermute=2),
+                                         RattleMutation(n_to_optimize, Nrattle=3, rattle_range=4)])
 
 ### Define calculator ###
 calc = Dftb(label='TiO2_surface',
@@ -54,16 +47,14 @@ calc = Dftb(label='TiO2_surface',
             kpts=(2,1,1))
 
 ### Initialize and run search ###
-search = GOFEE(structures=None,
-               calc=calc,
-               gpr=None,
+search = GOFEE(calc=calc,
                startgenerator=sg,
                candidate_generator=candidate_generator,
                max_steps=200,
-               dmax_cov=1.5,
+               max_relax_dist=4,
                population_size=5,
                kappa=1,
                dualpoint=True,
                restart='restart')
 
-search.run()
+search.run()
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