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# fmt: off
"""Check that reading and writing .con files is consistent."""
import numpy as np
import numpy.testing as npt
import pytest
import ase
import ase.io
import ase.symbols
# Error tolerance.
TOL = 1e-6
# The corresponding data as an ASE Atoms object.
DATA = ase.Atoms(
"Cu3",
cell=np.array([[7.22, 0, 0], [1, 10.83, 0], [1, 1, 14.44]]),
positions=np.array(
[
[1.04833333, 0.965, 0.9025],
[3.02, 2.77, 0.9025],
[6.36666667, 10.865, 13.5375],
]
),
pbc=(True, True, True),
)
def test_eon_read_single(datadir):
box = ase.io.read(f"{datadir}/io/eon/single.con", format="eon")
npt.assert_allclose(box.cell, DATA.cell, rtol=TOL, atol=0)
assert (box.symbols == ase.symbols.string2symbols("Cu3")).all()
npt.assert_allclose(box.get_masses(), np.array([63.5459999] * 3), rtol=TOL)
npt.assert_allclose(box.positions, DATA.positions, rtol=TOL)
def test_eon_write_single(datadir):
out_file = "out.con"
ase.io.write(out_file, DATA, format="eon")
data2 = ase.io.read(out_file, format="eon")
npt.assert_allclose(data2.cell, DATA.cell, rtol=TOL, atol=0)
npt.assert_allclose(data2.positions, DATA.positions, rtol=TOL)
def test_eon_roundtrip_multi(datadir):
out_file = "out.con"
images = ase.io.read(f"{datadir}/io/eon/multi.con", format="eon", index=":")
ase.io.write(out_file, images, format="eon")
data = ase.io.read(out_file, format="eon", index=":")
assert len(data) == 10
npt.assert_allclose(
data[0].constraints[0].get_indices(),
np.array([0, 1]), rtol=1e-5, atol=0
)
npt.assert_allclose(
data[1].constraints[0].get_indices(),
np.array([]), rtol=1e-5, atol=0
)
def test_eon_read_multi(datadir):
images = ase.io.read(f"{datadir}/io/eon/multi.con", format="eon", index=":")
assert len(images) == 10
npt.assert_allclose(
images[0].constraints[0].get_indices(),
np.array([0, 1]), rtol=1e-5, atol=0
)
npt.assert_allclose(
images[1].constraints[0].get_indices(),
np.array([]), rtol=1e-5, atol=0
)
def test_eon_isotope_fail():
out_file = "out.con"
DATA.set_masses([33, 31, 22])
with pytest.raises(RuntimeError):
ase.io.write(out_file, DATA, format="eon")
def test_eon_masses():
# Error tolerance.
TOL = 1e-8
data = ase.lattice.compounds.B2(['Cs', 'Cl'], latticeconstant=4.123,
size=(3, 3, 3))
m_Cs = ase.data.atomic_masses[ase.data.atomic_numbers['Cs']]
m_Cl = ase.data.atomic_masses[ase.data.atomic_numbers['Cl']]
con_file = 'pos.con'
# Write and read the .con file.
ase.io.write(con_file, data, format='eon')
data2 = ase.io.read(con_file, format='eon')
# Check masses.
symbols = np.asarray(data2.get_chemical_symbols())
masses = np.asarray(data2.get_masses())
assert (abs(masses[symbols == 'Cs'] - m_Cs)).sum() < TOL
assert (abs(masses[symbols == 'Cl'] - m_Cl)).sum() < TOL
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