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import numpy as np
import pytest
from ase.build import bulk
def get_spos(atoms):
return atoms.get_scaled_positions(wrap=False)
@pytest.fixture()
def atoms():
rng = np.random.RandomState(0)
atoms = bulk('Ti') * (2, 2, 1)
atoms.cell *= 0.9 + 0.2 * rng.random((3, 3))
atoms.rattle(stdev=0.05, rng=rng)
return atoms
@pytest.fixture()
def displacement(atoms):
rng = np.random.RandomState(12345)
return 0.1 * (rng.random((len(atoms), 3)) - 0.5)
@pytest.fixture()
def reference(displacement, atoms):
return displacement + get_spos(atoms)
def test_abc_and_scaled_position(atoms):
scaled = get_spos(atoms)
for i, atom in enumerate(atoms):
assert np.allclose(scaled[i], atom.scaled_position)
assert np.allclose(scaled[i], [atom.a, atom.b, atom.c])
def test_set_scaled_position(atoms, displacement, reference):
for i, atom in enumerate(atoms):
atom.scaled_position += displacement[i]
assert np.allclose(get_spos(atoms), reference)
def test_set_abc(atoms, displacement, reference):
for i, atom in enumerate(atoms):
atom.a += displacement[i, 0]
atom.b += displacement[i, 1]
atom.c += displacement[i, 2]
assert np.allclose(get_spos(atoms), reference)
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