print('Relaxing starting candidate {0}'.format(a.info['confid'])) dyn = BFGS(a, trajectory=None, logfile=None) dyn.run(fmax=0.05, steps=100) a.info['key_value_pairs']['raw_score'] = -a.get_potential_energy() da.add_relaxed_step(a) # create the population population = Population(data_connection=da, population_size=population_size, comparator=comp) # test n_to_test new candidates for i in range(n_to_test): print('Now starting configuration number {0}'.format(i)) a1, a2 = population.get_two_candidates() a3, desc = pairing.get_new_individual([a1, a2]) if a3 is None: continue da.add_unrelaxed_candidate(a3, description=desc) # Check if we want to do a mutation if random() < mutation_probability: a3_mut, desc = mutations.get_new_individual([a3]) if a3_mut is not None: da.add_unrelaxed_step(a3_mut, desc) a3 = a3_mut # Relax the new candidate a3.set_calculator(EMT()) dyn = BFGS(a3, trajectory=None, logfile=None) dyn.run(fmax=0.05, steps=100)
def test_cutandsplicepairing(seed): from ase.ga.startgenerator import StartGenerator from ase.ga.utilities import closest_distances_generator, atoms_too_close from ase.ga.cutandsplicepairing import CutAndSplicePairing import numpy as np from ase.build import fcc111 from ase.constraints import FixAtoms # set up the random number generator rng = np.random.RandomState(seed) # first create two random starting candidates slab = fcc111('Au', size=(4, 4, 2), vacuum=10.0, orthogonal=True) slab.set_constraint(FixAtoms(mask=slab.positions[:, 2] <= 10.)) pos = slab.get_positions() cell = slab.get_cell() p0 = np.array([0., 0., max(pos[:, 2]) + 2.]) v1 = cell[0, :] * 0.8 v2 = cell[1, :] * 0.8 v3 = cell[2, :] v3[2] = 3. blmin = closest_distances_generator(atom_numbers=[47, 79], ratio_of_covalent_radii=0.7) atom_numbers = 2 * [47] + 2 * [79] sg = StartGenerator(slab=slab, blocks=atom_numbers, blmin=blmin, box_to_place_in=[p0, [v1, v2, v3]], rng=rng) c1 = sg.get_new_candidate() c1.info['confid'] = 1 c2 = sg.get_new_candidate() c2.info['confid'] = 2 n_top = len(atom_numbers) pairing = CutAndSplicePairing(slab, n_top, blmin, rng=rng) c3, desc = pairing.get_new_individual([c1, c2]) # verify that the stoichiometry is preserved assert np.all(c3.numbers == c1.numbers) top1 = c1[-n_top:] top2 = c2[-n_top:] top3 = c3[-n_top:] # verify that the positions in the new candidate come from c1 or c2 n1 = -1 * np.ones((n_top, )) n2 = -1 * np.ones((n_top, )) for i in range(n_top): for j in range(n_top): if np.allclose(top1.positions[j, :], top3.positions[i, :], 1e-12): n1[i] = j break elif np.allclose(top2.positions[j, :], top3.positions[i, :], 1e-12): n2[i] = j break assert (n1[i] > -1 and n2[i] == -1) or (n1[i] == -1 and n2[i] > -1) # verify that c3 includes atoms from both c1 and c2 assert len(n1[n1 > -1]) > 0 and len(n2[n2 > -1]) > 0 # verify no atoms too close assert not atoms_too_close(top3, blmin)
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) dyn.run(fmax=0.05, steps=100) a.set_raw_score(-a.get_potential_energy()) da.add_relaxed_step(a) # create the population population = Population(data_connection=da, population_size=population_size, comparator=comp) # test n_to_test new candidates for i in xrange(n_to_test): print("Now starting configuration number {0}".format(i)) a1, a2 = population.get_two_candidates() a3, desc = pairing.get_new_individual([a1, a2]) if a3 == None: continue da.add_unrelaxed_candidate(a3, description=desc) # Check if we want to do a mutation if random() < mutation_probability: a3_mut, desc = mutations.get_new_individual([a3]) if a3_mut != None: da.add_unrelaxed_step(a3_mut, desc) a3 = a3_mut # Relax the new candidate a3.set_calculator(EMT()) dyn = BFGS(a3, trajectory=None, logfile=None) dyn.run(fmax=0.05, steps=100)
atom_numbers = 2 * [47] + 2 * [79] sg = StartGenerator( slab=slab, atom_numbers=atom_numbers, closest_allowed_distances=cd, box_to_place_in=[p0, [v1, v2, v3]] ) c1 = sg.get_new_candidate() c1.info["confid"] = 1 c2 = sg.get_new_candidate() c2.info["confid"] = 2 n_top = len(atom_numbers) pairing = CutAndSplicePairing(slab, n_top, cd) c3, desc = pairing.get_new_individual([c1, c2]) # verify that the stoichiometry is preserved assert np.all(c3.numbers == c1.numbers) top1 = c1[-n_top:] top2 = c2[-n_top:] top3 = c3[-n_top:] # verify that the positions in the new candidate come from c1 or c2 n1 = -1 * np.ones((n_top,)) n2 = -1 * np.ones((n_top,)) for i in range(n_top): for j in range(n_top): if np.all(top1.positions[j, :] == top3.positions[i, :]): n1[i] = j
sg = StartGenerator(slab=slab, atom_numbers=atom_numbers, closest_allowed_distances=cd, box_to_place_in=[p0, [v1, v2, v3]]) c1 = sg.get_new_candidate() c1.info['confid'] = 1 c2 = sg.get_new_candidate() c2.info['confid'] = 2 n_top = len(atom_numbers) pairing = CutAndSplicePairing(slab, n_top, cd) c3, desc = pairing.get_new_individual([c1, c2]) # verify that the stoichiometry is preserved assert np.all(c3.numbers == c1.numbers) top1 = c1[-n_top:] top2 = c2[-n_top:] top3 = c3[-n_top:] # verify that the positions in the new candidate come from c1 or c2 n1 = -1 * np.ones((n_top, )) n2 = -1 * np.ones((n_top, )) for i in range(n_top): for j in range(n_top): if np.all(top1.positions[j, :] == top3.positions[i, :]): n1[i] = j break
def run_ga(n_to_test, kptdensity=None): ''' This method specifies how to run the GA once the initial random structures have been stored in godb.db. ''' # Various initializations: population_size = 10 da = DataConnection('godb.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=0.05) # Defining the mix of genetic operators: mutation_probability = 0.3333 pairing = CutAndSplicePairing(slab, n_to_optimize, blmin) rattlemut = RattleMutation(blmin, n_to_optimize, rattle_prop=0.8, rattle_strength=1.5) mirrormut = MirrorMutation(blmin, n_to_optimize) mutations = OperationSelector([1., 1.], [rattlemut, mirrormut]) if True: # Recalculate raw scores of any relaxed candidates # present in the godb.db database (only applies to # iter007). structures = da.get_all_relaxed_candidates() for atoms in structures: atoms = singlepoint(atoms) da.c.delete([atoms.info['relax_id']]) if 'data' not in atoms.info: atoms.info['data'] = {} da.add_relaxed_step(atoms) print('Finished recalculating raw scores') # Relax the randomly generated initial candidates: while da.get_number_of_unrelaxed_candidates() > 0: a = da.get_an_unrelaxed_candidate() a.wrap() a = relax_one(a) da.add_relaxed_step(a) # Create the population population = Population(data_connection=da, population_size=population_size, comparator=comparator, logfile='log.txt') current_pop = population.get_current_population() # Test n_to_test new candidates ga_raw_scores = [] step = 0 for step in range(n_to_test): print('Starting configuration number %d' % step, flush=True) clock = time() a3 = None r = random() if r > mutation_probability: while a3 is None: a1, a2 = population.get_two_candidates() a3, desc = pairing.get_new_individual([a1, a2]) else: while a3 is None: a1 = population.get_one_candidate() a3, desc = mutations.get_new_individual([a1]) dt = time() - clock op = 'pairing' if r > mutation_probability else 'mutating' print('Time for %s candidate(s): %.3f' % (op, dt), flush=True) a3.wrap() da.add_unrelaxed_candidate(a3, description=desc) a3 = relax_one(a3) da.add_relaxed_step(a3) # Various updates: population.update() current_pop = population.get_current_population() write('current_population.traj', current_pop) # Print out information for easy analysis/plotting afterwards: if r > mutation_probability: print('Step %d %s %.3f %.3f %.3f' % (step, desc,\ get_raw_score(a1), get_raw_score(a2), get_raw_score(a3))) else: print('Step %d %s %.3f %.3f' % (step, desc,\ get_raw_score(a1), get_raw_score(a3))) print('Step %d highest raw score in pop: %.3f' % \ (step, get_raw_score(current_pop[0]))) ga_raw_scores.append(get_raw_score(a3)) print('Step %d highest raw score generated by GA: %.3f' % \ (step, max(ga_raw_scores))) emin = population.pop[0].get_potential_energy() print('GA finished after step %d' % step) print('Lowest energy = %8.3f eV' % emin, flush=True) write('all_candidates.traj', da.get_all_relaxed_candidates()) write('current_population.traj', population.get_current_population())
def test_basic_example_main_run(seed, testdir): # set up the random number generator rng = np.random.RandomState(seed) # create the surface slab = fcc111('Au', size=(4, 4, 1), vacuum=10.0, orthogonal=True) slab.set_constraint(FixAtoms(mask=len(slab) * [True])) # define the volume in which the adsorbed cluster is optimized # the volume is defined by a corner position (p0) # and three spanning vectors (v1, v2, v3) pos = slab.get_positions() cell = slab.get_cell() p0 = np.array([0., 0., max(pos[:, 2]) + 2.]) v1 = cell[0, :] * 0.8 v2 = cell[1, :] * 0.8 v3 = cell[2, :] v3[2] = 3. # Define the composition of the atoms to optimize atom_numbers = 2 * [47] + 2 * [79] # define the closest distance two atoms of a given species can be to each other unique_atom_types = get_all_atom_types(slab, atom_numbers) blmin = closest_distances_generator(atom_numbers=unique_atom_types, ratio_of_covalent_radii=0.7) # create the starting population sg = StartGenerator(slab=slab, blocks=atom_numbers, blmin=blmin, box_to_place_in=[p0, [v1, v2, v3]], rng=rng) # generate the starting population population_size = 5 starting_population = [sg.get_new_candidate() for i in range(population_size)] # from ase.visualize import view # uncomment these lines # view(starting_population) # to see the starting population # create the database to store information in d = PrepareDB(db_file_name=db_file, simulation_cell=slab, stoichiometry=atom_numbers) for a in starting_population: d.add_unrelaxed_candidate(a) # XXXXXXXXXX This should be the beginning of a new test, # but we are using some resources from the precious part. # Maybe refactor those things as (module-level?) fixtures. # Change the following three parameters to suit your needs population_size = 5 mutation_probability = 0.3 n_to_test = 5 # 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, rng=rng) mutations = OperationSelector([1., 1., 1.], [MirrorMutation(blmin, n_to_optimize, rng=rng), RattleMutation(blmin, n_to_optimize, rng=rng), PermutationMutation(n_to_optimize, rng=rng)], rng=rng) # Relax all unrelaxed structures (e.g. the starting population) while da.get_number_of_unrelaxed_candidates() > 0: a = da.get_an_unrelaxed_candidate() a.calc = EMT() print('Relaxing starting candidate {0}'.format(a.info['confid'])) dyn = BFGS(a, trajectory=None, logfile=None) dyn.run(fmax=0.05, steps=100) set_raw_score(a, -a.get_potential_energy()) da.add_relaxed_step(a) # create the population population = Population(data_connection=da, population_size=population_size, comparator=comp, rng=rng) # test n_to_test new candidates for i in range(n_to_test): print('Now starting configuration number {0}'.format(i)) a1, a2 = population.get_two_candidates() a3, desc = pairing.get_new_individual([a1, a2]) if a3 is None: continue da.add_unrelaxed_candidate(a3, description=desc) # Check if we want to do a mutation if rng.rand() < mutation_probability: a3_mut, desc = mutations.get_new_individual([a3]) if a3_mut is not None: da.add_unrelaxed_step(a3_mut, desc) a3 = a3_mut # Relax the new candidate a3.calc = EMT() dyn = BFGS(a3, trajectory=None, logfile=None) dyn.run(fmax=0.05, steps=100) set_raw_score(a3, -a3.get_potential_energy()) da.add_relaxed_step(a3) population.update() write('all_candidates.traj', da.get_all_relaxed_candidates())
def test_bulk_operators(seed): # set up the random number generator rng = np.random.RandomState(seed) h2 = Atoms('H2', positions=[[0, 0, 0], [0, 0, 0.75]]) blocks = [('H', 4), ('H2O', 3), (h2, 2)] # the building blocks volume = 40. * sum([x[1] for x in blocks]) # cell volume in angstrom^3 splits = {(2,): 1, (1,): 1} # cell splitting scheme stoichiometry = [] for block, count in blocks: if type(block) == str: stoichiometry += list(Atoms(block).numbers) * count else: stoichiometry += list(block.numbers) * count atom_numbers = list(set(stoichiometry)) blmin = closest_distances_generator(atom_numbers=atom_numbers, ratio_of_covalent_radii=1.3) cellbounds = CellBounds(bounds={'phi': [30, 150], 'chi': [30, 150], 'psi': [30, 150], 'a': [3, 50], 'b': [3, 50], 'c': [3, 50]}) slab = Atoms('', pbc=True) sg = StartGenerator(slab, blocks, blmin, box_volume=volume, number_of_variable_cell_vectors=3, cellbounds=cellbounds, splits=splits, rng=rng) # Generate 2 candidates a1 = sg.get_new_candidate() a1.info['confid'] = 1 a2 = sg.get_new_candidate() a2.info['confid'] = 2 # Define and test genetic operators n_top = len(a1) pairing = CutAndSplicePairing(slab, n_top, blmin, p1=1., p2=0., minfrac=0.15, number_of_variable_cell_vectors=3, cellbounds=cellbounds, use_tags=True, rng=rng) a3, desc = pairing.get_new_individual([a1, a2]) cell = a3.get_cell() assert cellbounds.is_within_bounds(cell) assert not atoms_too_close(a3, blmin, use_tags=True) n_top = len(a1) strainmut = StrainMutation(blmin, stddev=0.7, cellbounds=cellbounds, number_of_variable_cell_vectors=3, use_tags=True, rng=rng) softmut = SoftMutation(blmin, bounds=[2., 5.], used_modes_file=None, use_tags=True) # no rng rotmut = RotationalMutation(blmin, fraction=0.3, min_angle=0.5 * np.pi, rng=rng) rattlemut = RattleMutation(blmin, n_top, rattle_prop=0.3, rattle_strength=0.5, use_tags=True, test_dist_to_slab=False, rng=rng) rattlerotmut = RattleRotationalMutation(rattlemut, rotmut) # no rng permut = PermutationMutation(n_top, probability=0.33, test_dist_to_slab=False, use_tags=True, blmin=blmin, rng=rng) combmut = CombinationMutation(rattlemut, rotmut, verbose=True) # no rng mutations = [strainmut, softmut, rotmut, rattlemut, rattlerotmut, permut, combmut] for i, mut in enumerate(mutations): a = [a1, a2][i % 2] a3 = None while a3 is None: a3, desc = mut.get_new_individual([a]) cell = a3.get_cell() assert cellbounds.is_within_bounds(cell) assert np.all(a3.numbers == a.numbers) assert not atoms_too_close(a3, blmin, use_tags=True) modes_file = 'modes.txt' softmut_with = SoftMutation(blmin, bounds=[2., 5.], use_tags=True, used_modes_file=modes_file) # no rng no_muts = 3 for _ in range(no_muts): softmut_with.get_new_individual([a1]) softmut_with.read_used_modes(modes_file) assert len(list(softmut_with.used_modes.values())[0]) == no_muts os.remove(modes_file) comparator = OFPComparator(recalculate=True) gold = bulk('Au') * (2, 2, 2) assert comparator.looks_like(gold, gold) # This move should not exceed the default threshold gc = gold.copy() gc[0].x += .1 assert comparator.looks_like(gold, gc) # An additional step will exceed the threshold gc[0].x += .2 assert not comparator.looks_like(gold, gc)