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def test_film_operators(seed):
from ase.ga.startgenerator import StartGenerator
from ase.ga.cutandsplicepairing import CutAndSplicePairing
from ase.ga.standardmutations import StrainMutation
from ase.ga.utilities import (closest_distances_generator, atoms_too_close,
CellBounds)
import numpy as np
from ase import Atoms
from ase.build import molecule
# set up the random number generator
rng = np.random.RandomState(seed)
slab = Atoms('', cell=(0, 0, 15), pbc=[True, True, False])
cation, anion = 'Mg', molecule('OH')
d_oh = anion.get_distance(0, 1)
blocks = [(cation, 4), (anion, 8)]
n_top = 4 + 8 * len(anion)
use_tags = True
num_vcv = 2
box_volume = 8. * n_top
blmin = closest_distances_generator(atom_numbers=[1, 8, 12],
ratio_of_covalent_radii=0.6)
cellbounds = CellBounds(bounds={'phi': [0.1 * 180., 0.9 * 180.],
'chi': [0.1 * 180., 0.9 * 180.],
'psi': [0.1 * 180., 0.9 * 180.],
'a': [2, 8], 'b': [2, 8]})
box_to_place_in = [[None, None, 3.], [None, None, [0., 0., 5.]]]
sg = StartGenerator(slab, blocks, blmin, box_volume=box_volume,
splits={(2, 1): 1}, box_to_place_in=box_to_place_in,
number_of_variable_cell_vectors=num_vcv,
cellbounds=cellbounds, test_too_far=True,
test_dist_to_slab=False, rng=rng)
parents = []
for i in range(2):
a = None
while a is None:
a = sg.get_new_candidate()
a.info['confid'] = i
parents.append(a)
assert len(a) == n_top
assert len(np.unique(a.get_tags())) == 4 + 8
assert np.allclose(a.get_pbc(), slab.get_pbc())
p = a.get_positions()
assert np.min(p[:, 2]) > 3. - 0.5 * d_oh
assert np.max(p[:, 2]) < 3. + 5. + 0.5 * d_oh
assert not atoms_too_close(a, blmin, use_tags=use_tags)
c = a.get_cell()
assert np.allclose(c[2], slab.get_cell()[2])
assert cellbounds.is_within_bounds(c)
v = a.get_volume() * 5. / 15.
assert abs(v - box_volume) < 1e-5
# Test cut-and-splice pairing and strain mutation
pairing = CutAndSplicePairing(slab, n_top, blmin,
number_of_variable_cell_vectors=num_vcv,
p1=1., p2=0., minfrac=0.15,
cellbounds=cellbounds, use_tags=use_tags,
rng=rng)
strainmut = StrainMutation(blmin, cellbounds=cellbounds,
number_of_variable_cell_vectors=num_vcv,
use_tags=use_tags, rng=rng)
strainmut.update_scaling_volume(parents)
for operator in [pairing, strainmut]:
child = None
while child is None:
child, desc = operator.get_new_individual(parents)
assert not atoms_too_close(child, blmin, use_tags=use_tags)
cell = child.get_cell()
assert cellbounds.is_within_bounds(cell)
assert np.allclose(cell[2], slab.get_cell()[2])
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