def test_add_candidates():
import pytest
from ase.build import fcc111
from ase.ga.data import PrepareDB
from ase.ga.data import DataConnection
from ase.ga.offspring_creator import OffspringCreator
from ase.ga import set_raw_score
import os
db_file = 'gadb.db'
if os.path.isfile(db_file):
os.remove(db_file)
db = PrepareDB(db_file)
slab1 = fcc111('Ag', size=(2, 2, 2))
db.add_unrelaxed_candidate(slab1)
slab2 = fcc111('Cu', size=(2, 2, 2))
set_raw_score(slab2, 4)
db.add_relaxed_candidate(slab2)
assert slab2.info['confid'] == 3
db = DataConnection(db_file)
assert db.get_number_of_unrelaxed_candidates() == 1
slab3 = db.get_an_unrelaxed_candidate()
old_confid = slab3.info['confid']
slab3[0].symbol = 'Au'
db.add_unrelaxed_candidate(slab3, 'mutated: Parent {0}'.format(old_confid))
new_confid = slab3.info['confid']
# confid should update when using add_unrelaxed_candidate
assert old_confid != new_confid
slab3[1].symbol = 'Au'
db.add_unrelaxed_step(slab3, 'mutated: Parent {0}'.format(new_confid))
# confid should not change when using add_unrelaxed_step
assert slab3.info['confid'] == new_confid
with pytest.raises(AssertionError):
db.add_relaxed_step(slab3)
set_raw_score(slab3, 3)
db.add_relaxed_step(slab3)
slab4 = OffspringCreator.initialize_individual(slab1,
fcc111('Au', size=(2, 2, 2)))
set_raw_score(slab4, 67)
db.add_relaxed_candidate(slab4)
assert slab4.info['confid'] == 7
more_slabs = []
for m in ['Ni', 'Pd', 'Pt']:
slab = fcc111(m, size=(2, 2, 2))
slab = OffspringCreator.initialize_individual(slab1, slab)
set_raw_score(slab, sum(slab.get_masses()))
more_slabs.append(slab)
db.add_more_relaxed_candidates(more_slabs)
assert more_slabs[1].info['confid'] == 9
os.remove(db_file)
pure_slabs.append(slab)
# The population size should be at least the number of different compositions
pop_size = 2 * len(slab)
# We prepare the db and write a few constants that we are going to use later
db = PrepareDB('hull.db',
population_size=pop_size,
reference_energies=refs,
metals=metals,
lattice_constants=lattice_constants)
# We add the pure slabs to the database as relaxed because we have already
# set the raw_score
for slab in pure_slabs:
db.add_relaxed_candidate(slab,
atoms_string=''.join(slab.get_chemical_symbols()))
# Now we create the rest of the candidates for the initial population
for i in range(pop_size - 2):
# How many of each metal is picked at random, making sure that
# we do not pick pure slabs
nA = random.randint(0, len(slab) - 2)
nB = len(slab) - 2 - nA
symbols = [metals[0]] * nA + [metals[1]] * nB + metals
# Making a generic slab with the correct lattice constant
slab = fcc111('X',
size=(2, 4, 3),
a=get_avg_lattice_constant(symbols),
vacuum=5,
orthogonal=True)
from ase.ga import set_raw_score
import os
db_file = 'gadb.db'
if os.path.isfile(db_file):
os.remove(db_file)
db = PrepareDB(db_file)
slab1 = fcc111('Ag', size=(2, 2, 2))
db.add_unrelaxed_candidate(slab1)
slab2 = fcc111('Cu', size=(2, 2, 2))
set_raw_score(slab2, 4)
db.add_relaxed_candidate(slab2)
assert slab2.info['confid'] == 3
db = DataConnection(db_file)
assert db.get_number_of_unrelaxed_candidates() == 1
slab3 = db.get_an_unrelaxed_candidate()
old_confid = slab3.info['confid']
slab3[0].symbol = 'Au'
db.add_unrelaxed_candidate(slab3, 'mutated: Parent {0}'.format(old_confid))
new_confid = slab3.info['confid']
# confid should update when using add_unrelaxed_candidate
assert old_confid != new_confid
slab3[1].symbol = 'Au'
db.add_unrelaxed_step(slab3, 'mutated: Parent {0}'.format(new_confid))
# confid should not change when using add_unrelaxed_step