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# fmt: off
import numpy as np
import pytest
from ase.build import fcc111
from ase.ga.slab_operators import (
CutSpliceSlabCrossover,
NeighborhoodElementMutation,
RandomCompositionMutation,
RandomElementMutation,
RandomSlabPermutation,
)
@pytest.fixture()
def cu_slab():
a = 1
size = (2, 4, 3)
p1 = fcc111('Cu', size, orthogonal=True, a=a)
p1.info['confid'] = 1
return p1
def test_cut_splice(seed, cu_slab):
# set up the random number generator
rng = np.random.RandomState(seed)
ratio = .4
op = CutSpliceSlabCrossover(min_ratio=ratio, rng=rng)
p1 = cu_slab
natoms = len(p1)
p2 = cu_slab.copy()
p2.symbols = ['Au'] * natoms
p2.info['confid'] = 2
child, desc = op.get_new_individual([p1, p2])
assert desc == 'CutSpliceSlabCrossover: Parents 1 2'
# Check the ratio of elements
syms = child.get_chemical_symbols()
new_ratio = syms.count('Au') / natoms
assert new_ratio > ratio and new_ratio < 1 - ratio
op = CutSpliceSlabCrossover(element_pools=['Cu', 'Au'],
allowed_compositions=[(12, 12)], rng=rng)
child = op.operate(p1, p2)
assert child.get_chemical_symbols().count('Au') == 12
def test_random_composition_mutation(seed, cu_slab):
# set up the random number generator
rng = np.random.RandomState(seed)
p1 = cu_slab
p1.symbols[3] = 'Au'
op = RandomCompositionMutation(element_pools=['Cu', 'Au'],
allowed_compositions=[(12, 12), (18, 6)],
rng=rng)
child, _ = op.get_new_individual([p1])
no_Au = (child.symbols == 'Au').sum()
assert no_Au in [6, 12]
op = RandomCompositionMutation(element_pools=['Cu', 'Au'], rng=rng)
child2 = op.operate(child)
# Make sure we have gotten a new stoichiometry
assert (child2.symbols == 'Au').sum() != no_Au
def test_random_element_mutation(seed, cu_slab):
# set up the random number generator
rng = np.random.RandomState(seed)
op = RandomElementMutation(element_pools=[['Cu', 'Au']], rng=rng)
child, _desc = op.get_new_individual([cu_slab.copy()])
assert (child.symbols == 'Au').sum() == 24
def test_neighborhood_element_mutation(seed, cu_slab):
# set up the random number generator
rng = np.random.RandomState(seed)
op = NeighborhoodElementMutation(element_pools=[['Cu', 'Ni', 'Au']],
rng=rng)
child, _desc = op.get_new_individual([cu_slab])
assert (child.symbols == 'Ni').sum() == 24
def test_random_permutation(seed, cu_slab):
# set up the random number generator
rng = np.random.RandomState(seed)
p1 = cu_slab
p1.symbols[:8] = 'Au'
op = RandomSlabPermutation(rng=rng)
child, _desc = op.get_new_individual([p1])
assert (child.symbols == 'Au').sum() == 8
assert sum(p1.numbers == child.numbers) == 22
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