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from pathlib import Path
import numpy as np
from ase.build import bulk
from ase.io.aims import read_aims as read
from ase.io.aims import parse_geometry_lines
from pytest import approx
parent = Path(__file__).parent
format = "aims"
atoms = bulk("Si")
atoms.positions[0, 0] -= 0.01
file = "geometry.in"
# check cartesian
def test_cartesian(atoms=atoms):
"""write cartesian coords and check if structure was preserved"""
atoms.write(file, format=format)
new_atoms = read((file))
assert np.allclose(atoms.positions, new_atoms.positions)
# check scaled
def test_scaled(atoms=atoms):
"""write fractional coords and check if structure was preserved"""
atoms.write(file, format=format, scaled=True, wrap=False)
new_atoms = read(file)
assert np.allclose(atoms.positions, new_atoms.positions), (
atoms.positions,
new_atoms.positions,
)
# this should fail
def test_scaled_wrapped(atoms=atoms):
"""write fractional coords and check if structure was preserved"""
atoms.write(file, format=format, scaled=True, wrap=True)
new_atoms = read(file)
try:
assert np.allclose(atoms.positions, new_atoms.positions), (
atoms.positions,
new_atoms.positions,
)
except AssertionError:
atoms.wrap()
assert np.allclose(atoms.positions, new_atoms.positions), (
atoms.positions,
new_atoms.positions,
)
sample_geometry_1 = """\
lattice_vector 4.5521460059804628 0.0000000000000000 0.0000000000000000
lattice_vector -2.2760730029902314 3.9422740829149499 0.0000000000000000 # Dummy comment
lattice_vector 0.0000000000000000 0.0000000000000000 7.1603474299999998
atom_frac 0.0000000000000000 0.0000000000000000 0.0000000000000000 Pb # Dummy comment
atom_frac 0.6666666666666666 0.3333333333333333 0.7349025600000001 I
atom_frac 0.3333333333333333 0.6666666666666666 0.2650974399999999 I
#=======================================================
# Parametric constraints
#=======================================================
symmetry_n_params 3 2 1
symmetry_params a c d0_z
symmetry_lv a, 0, 0
symmetry_lv -0.5*a, 0.8660254037844*a, 0
symmetry_lv 0, 0, c
symmetry_frac 0, 0, 0
symmetry_frac 0.6666666666667, 0.3333333333333, 1.0-d0_z
symmetry_frac 0.3333333333333, 0.6666666666667, d0_z
"""
sample_geometry_2 = """\
atom 0.0000000000000000 0.0000000000000000 0.0000000000000000 Pb # Dummy comment
constrain_relaxation .true.
atom 0.6666666666666666 0.3333333333333333 0.7349025600000001 I
initial_moment 1
initial_charge -1
atom 0.3333333333333333 0.6666666666666666 0.2650974399999999 I
constrain_relaxation y
initial_charge -1
initial_moment 1
"""
expected_symbols = ['Pb','I','I']
expected_scaled_positions = np.array([
[0.0000000000000000, 0.0000000000000000, 0.0000000000000000],
[0.6666666666666666, 0.3333333333333333, 0.7349025600000000],
[0.3333333333333333, 0.6666666666666666, 0.2650974400000000],
])
expected_charges = np.array([0, -1, -1])
expected_moments = np.array([0, 1, 1])
expected_lattice_vectors = np.array([
[4.5521460059804628, 0.0000000000000000, 0.0000000000000000],
[-2.2760730029902314, 3.9422740829149499, 0.0000000000000000],
[0.0000000000000000, 0.0000000000000000, 7.1603474299999998],
])
def test_parse_geometry_lines():
lines = sample_geometry_1.splitlines()
atoms = parse_geometry_lines(lines,'sample_geometry_1.in')
assert all(atoms.symbols == expected_symbols)
assert atoms.get_scaled_positions() == approx(expected_scaled_positions)
assert atoms.get_cell()[:] == approx(expected_lattice_vectors)
assert all(atoms.pbc)
lines = sample_geometry_2.splitlines()
atoms = parse_geometry_lines(lines,'sample_geometry_2.in')
assert all(atoms.symbols == expected_symbols)
assert atoms.get_scaled_positions() == approx(expected_scaled_positions)
assert atoms.get_initial_charges() == approx(expected_charges)
assert atoms.get_initial_magnetic_moments() == approx(expected_moments)
assert all(atoms.pbc == [0, 0, 0])
assert len(atoms.constraints) == 2
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