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# fmt: off
import numpy as np
import pytest
from ase.io.formats import ioformats, match_magic
# some of the possible bound parameters
bounds_parameters = [
("pp pp pp", (True, True, True)),
("ss mm ff", (False, False, False)),
("fs sm mf", (False, False, False)),
("sf ms ff", (False, False, False)),
("pp ms ff", (True, False, False)),
("ff pp ff", (False, True, False)),
("ff mm pp", (False, False, True)),
("pp ff pp", (True, False, True)),
]
ref_positions = np.array([[0.5, 0.6, 0.7],
[0.6, 0.1, 1.9],
[0.45, 0.32, 0.67]])
@pytest.fixture()
def fmt():
return ioformats['lammps-dump-text']
@pytest.fixture()
def lammpsdump():
def factory(bounds="pp pp pp",
position_cols="x y z",
have_element=True,
have_id=False,
have_type=True,
have_property_atom=False):
_element = "element" if have_element else "unk0"
_id = "id" if have_id else "unk1"
_type = "type" if have_type else "unk2"
_i_property = "i_property" if have_property_atom else "unk3"
_i2_property = "i2_property[1]" if have_property_atom else "unk4"
_d_property = "d_property" if have_property_atom else "unk5"
_d2_property = "d2_property[1]" if have_property_atom else "unk6"
buf = f"""\
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
3
ITEM: BOX BOUNDS {bounds}
0.0e+00 4e+00
0.0e+00 5.0e+00
0.0e+00 2.0e+01
ITEM: ATOMS {_element} {_id} {_type} {position_cols}\
{_i_property} {_i2_property} {_d_property} {_d2_property}
C 1 1 0.5 0.6 0.7 1 2 1.0 2.0
C 3 1 0.6 0.1 1.9 3 4 3.0 4.0
Si 2 2 0.45 0.32 0.67 5 6 5.0 6.0
"""
return buf
return factory
@pytest.fixture()
def lammpsdump_single_atom():
def factory(bounds="pp pp pp",
position_cols="x y z",
have_element=True,
have_id=False,
have_type=True,
have_charge=True):
_element = "element" if have_element else "unk0"
_id = "id" if have_id else "unk1"
_type = "type" if have_type else "unk2"
_charge = "q" if have_charge else "unk3"
buf = f"""\
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
1
ITEM: BOX BOUNDS {bounds}
0.0e+00 4e+00
0.0e+00 5.0e+00
0.0e+00 2.0e+01
ITEM: ATOMS {_element} {_id} {_charge} {_type} {position_cols}
C 1 1 1.0 0.5 0.6 0.7
"""
return buf
return factory
@pytest.fixture()
def lammpsdump_no_element():
def factory(bounds="pp pp pp",
position_cols="x y z",
have_id=True,
have_type=True,
have_mass=True):
_id = "id" if have_id else "unk1"
_type = "type" if have_type else "unk2"
_mass = "mass" if have_mass else "unk3"
buf = f"""\
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
1
ITEM: BOX BOUNDS {bounds}
0.0e+00 4e+00
0.0e+00 5.0e+00
0.0e+00 2.0e+01
ITEM: ATOMS {_id} {_type} {_mass} {position_cols}
1 1 12 0.5 0.6 0.7
"""
return buf
return factory
def lammpsdump_headers():
actual_magic = 'ITEM: TIMESTEP'
yield actual_magic
yield f'anything\n{actual_magic}\nanything'
@pytest.mark.parametrize('header', lammpsdump_headers())
def test_recognize_lammpsdump(header):
fmt_name = 'lammps-dump-text'
fmt = match_magic(header.encode('ascii'))
assert fmt.name == fmt_name
def test_lammpsdump_order(fmt, lammpsdump):
# reordering of atoms by the `id` column
ref_order = np.array([1, 3, 2])
atoms = fmt.parse_atoms(lammpsdump(have_id=True))
assert atoms.cell.orthorhombic
assert pytest.approx(atoms.cell.lengths()) == [4., 5., 20.]
assert pytest.approx(atoms.positions) == ref_positions[ref_order - 1]
def test_lammpsdump_element(fmt, lammpsdump):
# Test lammpsdump with elements column given
atoms = fmt.parse_atoms(lammpsdump())
assert np.all(atoms.get_atomic_numbers() == np.array([6, 6, 14]))
def test_lammpsdump_custom_property(fmt, lammpsdump):
# Test lammpsdump with custom property column given
atoms = fmt.parse_atoms(lammpsdump(have_property_atom=True))
assert np.all(atoms.arrays['i_property'].flatten() ==
np.array([1, 3, 5]))
assert np.all(atoms.arrays['i2_property[1]'].flatten() ==
np.array([2, 4, 6]))
assert np.all(atoms.arrays['d_property'].flatten() ==
np.array([1., 3., 5.]))
assert np.all(atoms.arrays['d2_property[1]'].flatten() ==
np.array([2., 4., 6.]))
def test_lammpsdump_single_atom(fmt, lammpsdump_single_atom):
# Test lammpsdump with a single atom
atoms = fmt.parse_atoms(lammpsdump_single_atom())
assert np.all(atoms.get_atomic_numbers() == np.array([6]))
assert pytest.approx(atoms.get_initial_charges()) == np.array([1.])
def test_lammpsdump_no_element(fmt, lammpsdump_no_element):
# Test lammpsdump with no element column
atoms = fmt.parse_atoms(lammpsdump_no_element())
assert atoms.info['timestep'] == 100
assert np.all(atoms.get_chemical_symbols() == np.array(['C']))
def test_lammpsdump_errors(fmt, lammpsdump):
# elements not given
with pytest.raises(ValueError,
match="Cannot determine atom types.*"):
_ = fmt.parse_atoms(lammpsdump(have_element=False, have_type=False))
# positions not given
with pytest.raises(ValueError,
match="No atomic positions found in LAMMPS output"):
_ = fmt.parse_atoms(lammpsdump(position_cols="unk_x unk_y unk_z"))
@pytest.mark.parametrize("cols,scaled", [
("xs ys zs", True),
("xsu ysu zsu", True),
("x y z", False),
("xu yu zu", False),
])
def test_lammpsdump_position_reading(fmt, lammpsdump, cols, scaled):
# test all 4 kinds of definitions of positions
atoms = fmt.parse_atoms(lammpsdump(position_cols=cols))
assert atoms.cell.orthorhombic
assert pytest.approx(atoms.cell.lengths()) == [4., 5., 20.]
if scaled:
assert pytest.approx(atoms.positions) == ref_positions * np.array(
[4, 5, 20]).T
else:
assert pytest.approx(atoms.positions) == ref_positions
@pytest.mark.parametrize("bounds,expected", bounds_parameters)
def test_lammpsdump_bounds(fmt, lammpsdump, bounds, expected):
# Test lammpsdump with all possible boundaries
atoms = fmt.parse_atoms(lammpsdump(bounds=bounds))
assert pytest.approx(atoms.cell.lengths()) == [4., 5., 20.]
assert np.all(atoms.get_pbc() == expected)
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