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import numpy as np
import pytest
from ase import Atoms
def array_almost_equal(a1, a2, tol=np.finfo(float).eps):
return (np.abs(a1 - a2) < tol).all()
def test_atoms():
print(Atoms())
print(Atoms('H2O'))
# ...
def test_numbers_input():
numbers = np.array([[0, 1], [2, 3]])
with pytest.raises(Exception, match='"numbers" must be 1-dimensional.'):
Atoms(positions=np.zeros((2, 3)), numbers=numbers, cell=np.eye(3))
Atoms(positions=np.zeros((2, 3)), numbers=[0, 1], cell=np.eye(3))
def test_bad_array_shape():
with pytest.raises(ValueError, match='wrong length'):
Atoms().set_masses([1, 2])
with pytest.raises(ValueError, match='wrong length'):
Atoms('H').set_masses([])
with pytest.raises(ValueError, match='wrong shape'):
Atoms('H').set_masses(np.ones((1, 3)))
def test_set_masses():
atoms = Atoms('AgAu')
m0 = atoms.get_masses()
atoms.set_masses([1, None])
assert atoms.get_masses() == pytest.approx([1, m0[1]])
def test_ndof():
a = Atoms('CO')
b = Atoms('H2O')
assert a.get_number_of_degrees_of_freedom() == 6
assert b.get_number_of_degrees_of_freedom() == 9
c = a + b
assert c.get_number_of_degrees_of_freedom() == 15
del c[0]
assert c.get_number_of_degrees_of_freedom() == 12
@pytest.mark.parametrize('zlength', [0, 10])
def test_get_com(zlength):
"""Test that atoms.get_center_of_mass(scaled=True) works"""
d = 1.142
a = Atoms('CO', positions=[(2, 0, 0), (2, -d, 0)], pbc=True)
a.set_cell(np.array(((4, -4, 0), (0, 5.657, 0), (0, 0, zlength))))
scaledref = np.array((0.5, 0.23823622, 0.))
assert array_almost_equal(a.get_center_of_mass(scaled=True),
scaledref, tol=1e-8)
@pytest.mark.parametrize('indices', [[0, 1], slice(0, 2), "0:2"])
def test_get_com_indices(indices):
"""Test get_center_of_mass(indices=...)"""
positions = [
[-0.3, 0.0, +0.3],
[-0.3, 0.0, -0.3],
[+0.3, 0.0, +0.3],
[+0.3, 0.0, -0.3],
]
atoms = Atoms('HHHH', positions=positions)
np.testing.assert_almost_equal(
atoms.get_center_of_mass(indices=indices),
[-0.3, 0.0, 0.0],
)
@pytest.mark.parametrize('scaled', [True, False])
@pytest.mark.parametrize('symbols', ['CO', 'H2'])
def test_set_com(scaled, symbols):
"""Test that atoms.set_center_of_mass() works. """
a = Atoms(symbols, positions=[(0, 0, 0), (0, 0, 1)],
cell=[2, 2, 2], pbc=True)
desired_com = [0.1, 0.5, 0.6]
a.set_center_of_mass(desired_com, scaled=scaled)
assert array_almost_equal(a.get_center_of_mass(scaled=scaled), desired_com)
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