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import pytest
import numpy as np
from ase.build import bulk, make_supercell
from ase.lattice import FCC, BCC
from ase.calculators.emt import EMT
a = 4.1
@pytest.fixture
def atoms():
atoms = bulk('Au', a=a)
return atoms
def test_supercell(atoms):
assert atoms.cell.get_bravais_lattice().name == 'FCC'
# Since FCC and BCC are reciprocal, their product is cubic:
P = BCC(2.0).tocell()
assert np.allclose(np.linalg.det(P), 4)
cubatoms = make_supercell(atoms, P)
assert np.allclose(cubatoms.cell, a * np.eye(3))
# Also test some of the Cell object methods now that we are at it:
assert len(cubatoms) == 4
assert cubatoms.cell.orthorhombic
assert np.allclose(cubatoms.cell.lengths(), a)
assert cubatoms.cell.get_bravais_lattice().name == 'CUB'
def test_bcc_to_cub_transformation():
bcc = bulk('Fe', a=a)
P = FCC(2.0).tocell()
assert np.allclose(np.linalg.det(P), 2)
cubatoms = make_supercell(bcc, P)
assert np.allclose(cubatoms.cell, a * np.eye(3))
def getenergy(atoms, eref=None):
atoms.calc = EMT()
e = atoms.get_potential_energy() / len(atoms)
if eref is not None:
err = abs(e - eref)
print('natoms', len(atoms), 'err', err)
assert err < 1e-12, err
return e
def test_random_transformations(atoms):
# Finally we want to check some random transformations.
# This will produce some weird supercells, all of which should have
# the same energy.
rng = np.random.RandomState(44)
e0 = getenergy(atoms)
imgs = []
i = 0
while i < 10:
P = rng.randint(-2, 3, size=(3, 3))
detP = np.linalg.det(P)
if detP == 0:
continue
elif detP < 0:
P[0] *= -1
bigatoms = make_supercell(atoms, P)
imgs.append(bigatoms)
getenergy(bigatoms, eref=e0)
i += 1
# from ase.visualize import view
# view(imgs)
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