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from distutils.version import LooseVersion
import numpy as np
import pytest
from ase import Atoms
from ase.io import read
from ase.build import bulk
from ase.atoms import symbols2numbers
pytestmark = pytest.mark.skipif(LooseVersion(np.__version__) <
LooseVersion("1.14"),
reason="This test requires numpy >= 1.14")
def make_STO_atoms():
atoms = Atoms(['O', 'O', 'O', 'Sr', 'Ti'],
scaled_positions=[[0.5, 0.5, 0],
[0.5, 0, 0.5],
[0, 0.5, 0.5],
[0, 0, 0],
[0.5, 0.5, 0.5]],
cell=[3.905, 3.905, 3.905],
pbc=True)
return atoms
def test_mustem_several_elements():
"""Check writing and reading a xtl mustem file."""
# Reproduce the sto xtl file distributed with muSTEM
atoms = make_STO_atoms()
filename = 'sto_mustem.xtl'
STO_DW_dict = {'Sr': 0.62, 'O': 0.73, 'Ti': 0.43}
STO_DW_dict_Ti_missing = {key: STO_DW_dict[key] for key in ['Sr', 'O']}
with pytest.raises(TypeError):
atoms.write(filename)
with pytest.raises(ValueError):
atoms.write(filename, keV=300)
with pytest.raises(TypeError):
atoms.write(filename,
debye_waller_factors=STO_DW_dict)
atoms.write(filename, keV=300,
debye_waller_factors=STO_DW_dict)
atoms2 = read(filename, format='mustem')
atoms3 = read(filename)
for _atoms in [atoms2, atoms3]:
assert atoms.positions == pytest.approx(_atoms.positions)
np.testing.assert_allclose(atoms.cell, _atoms.cell)
with pytest.raises(ValueError):
# Raise an error if there is a missing key.
atoms.write(filename, keV=300,
debye_waller_factors=STO_DW_dict_Ti_missing)
atoms.write(filename, keV=300,
debye_waller_factors=STO_DW_dict,
occupancies={'Sr': 1.0, 'O': 0.5, 'Ti': 0.9})
with pytest.raises(ValueError):
# Raise an error if there is a missing key.
atoms.write(filename, keV=300,
debye_waller_factors=STO_DW_dict,
occupancies={'O': 0.5, 'Ti': 0.9})
with pytest.raises(ValueError):
# Raise an error if the unit cell is not defined.
atoms4 = Atoms(['Sr', 'Ti', 'O', 'O', 'O'],
positions=[[0, 0, 0],
[0.5, 0.5, 0.5],
[0.5, 0.5, 0],
[0.5, 0, 0.5],
[0, 0.5, 0.5]])
atoms4.write(filename, keV=300,
debye_waller_factors=STO_DW_dict)
atoms5 = make_STO_atoms()
atoms5.set_array('occupancies', np.ones(5))
atoms5.arrays['occupancies'][atoms5.numbers == symbols2numbers('Sr')] = 0.9
# element 0 is Sr and there is onlye one Sr in the cell: this is a valid
# cell to export to xtl file
atoms5.write(filename, keV=300, debye_waller_factors=STO_DW_dict)
atoms6 = read(filename)
condition = atoms6.numbers == symbols2numbers('Sr')
np.testing.assert_allclose(atoms6.arrays['occupancies'][condition], 0.9)
atoms5.arrays['occupancies'][0] = 0.8
with pytest.raises(ValueError):
atoms5.write(filename, keV=300, debye_waller_factors=STO_DW_dict)
atoms7 = make_STO_atoms()
debye_waller_factors = np.array([0.73, 0.73, 0.73, 0.62, 0.43])
atoms7.set_array('debye_waller_factors', debye_waller_factors)
# element 0 is Sr and there is onlye one Sr in the cell: this is a valid
# cell to export to xtl file
atoms7.write(filename, keV=300)
atoms8 = read(filename)
for element in ['Sr', 'Ti', 'O']:
number = symbols2numbers(element)
np.testing.assert_allclose(
atoms7.arrays['debye_waller_factors'][atoms7.numbers == number],
atoms8.arrays['debye_waller_factors'][atoms8.numbers == number],
rtol=1e-2
)
def test_mustem_single_elements():
# Setting Debye-Waller factor as float.
Si_atoms = bulk('Si', cubic=True)
filename = 'Si100.xtl'
DW = 0.62
Si_atoms.write(filename, keV=300, debye_waller_factors=DW)
Si_atoms2 = read(filename)
np.testing.assert_allclose(Si_atoms.positions, Si_atoms2.positions)
np.testing.assert_allclose(Si_atoms.cell, Si_atoms2.cell)
np.testing.assert_allclose(Si_atoms2.arrays['occupancies'], np.ones(8))
np.testing.assert_allclose(Si_atoms2.arrays['debye_waller_factors'],
np.ones(8) * DW, rtol=1e-2)
Si_atoms3 = bulk('Si', cubic=True)
Si_atoms3.set_array('occupancies', np.ones(8) * 0.9)
Si_atoms3.set_array('debye_waller_factors', np.ones(8) * DW)
Si_atoms3.write(filename, keV=300)
Si_atoms4 = read(filename)
np.testing.assert_allclose(Si_atoms3.positions, Si_atoms4.positions)
np.testing.assert_allclose(Si_atoms3.cell, Si_atoms4.cell)
np.testing.assert_allclose(Si_atoms3.arrays['occupancies'],
Si_atoms4.arrays['occupancies'])
np.testing.assert_allclose(Si_atoms3.arrays['debye_waller_factors'],
Si_atoms4.arrays['debye_waller_factors'],
rtol=1e-2)
Si_atoms5 = bulk('Si', cubic=True)
debye_waller_factors = np.ones(8) * DW
debye_waller_factors[0] = debye_waller_factors[0] / 2
Si_atoms5.set_array('debye_waller_factors', debye_waller_factors)
with pytest.raises(ValueError):
# Raise an error if one Debye-Waller factor is different.
Si_atoms5.write(filename, keV=300)
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