population_size = 20 mutation_probability = 0.3 n_to_test = 20 # Initialize the different components of the GA da = DataConnection('gadb.db') atom_numbers_to_optimize = da.get_atom_numbers_to_optimize() n_to_optimize = len(atom_numbers_to_optimize) slab = da.get_slab() all_atom_types = get_all_atom_types(slab, atom_numbers_to_optimize) blmin = closest_distances_generator(all_atom_types, ratio_of_covalent_radii=0.7) comp = InteratomicDistanceComparator(n_top=n_to_optimize, pair_cor_cum_diff=0.015, pair_cor_max=0.7, dE=0.02, mic=False) pairing = CutAndSplicePairing(slab, n_to_optimize, blmin) mutations = OperationSelector([1., 1., 1.], [MirrorMutation(blmin, n_to_optimize), RattleMutation(blmin, n_to_optimize), PermutationMutation(n_to_optimize)]) # Relax all unrelaxed structures (e.g. the starting population) while da.get_number_of_unrelaxed_candidates() > 0: a = da.get_an_unrelaxed_candidate() a.set_calculator(EMT()) print('Relaxing starting candidate {0}'.format(a.info['confid'])) dyn = BFGS(a, trajectory=None, logfile=None)
from ase.ga.standard_comparators import InteratomicDistanceComparator from ase import Atoms from ase.calculators.singlepoint import SinglePointCalculator a1 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.5, 0, 0], [1.5, 1.5, 0]]) a2 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.4, 0, 0], [1.5, 1.5, 0]]) e1 = 1.0 e2 = 0.8 a1.set_calculator(SinglePointCalculator(e1, None, None, None, a1)) a2.set_calculator(SinglePointCalculator(e2, None, None, None, a2)) comp1 = InteratomicDistanceComparator(n_top=3, pair_cor_cum_diff=0.03, pair_cor_max=0.7, dE=0.3) assert comp1.looks_like(a1, a2) comp2 = InteratomicDistanceComparator(n_top=3, pair_cor_cum_diff=0.03, pair_cor_max=0.7, dE=0.15) assert not comp2.looks_like(a1, a2) comp3 = InteratomicDistanceComparator(n_top=3, pair_cor_cum_diff=0.02, pair_cor_max=0.7, dE=0.3)
SequentialComparator) from ase import Atoms from ase.calculators.singlepoint import SinglePointCalculator from ase.ga import set_raw_score a1 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.5, 0, 0], [1.5, 1.5, 0]]) a2 = Atoms('AgAgAg', positions=[[0, 0, 0], [1.4, 0, 0], [1.5, 1.5, 0]]) e1 = 1.0 e2 = 0.8 a1.set_calculator(SinglePointCalculator(a1, energy=e1)) a2.set_calculator(SinglePointCalculator(a2, energy=e2)) comp1 = InteratomicDistanceComparator(n_top=3, pair_cor_cum_diff=0.03, pair_cor_max=0.7, dE=0.3) assert comp1.looks_like(a1, a2) comp2 = InteratomicDistanceComparator(n_top=3, pair_cor_cum_diff=0.03, pair_cor_max=0.7, dE=0.15) assert not comp2.looks_like(a1, a2) comp3 = InteratomicDistanceComparator(n_top=3, pair_cor_cum_diff=0.02, pair_cor_max=0.7, dE=0.3) assert not comp3.looks_like(a1, a2)