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import numpy as np
import pytest
from ase.build import bulk
from dynasor.tools.acfs import compute_acf, fermi_dirac, smoothing_function
from dynasor.tools.structures import align_structure
@pytest.fixture
def signal_complex():
np.random.seed(42)
N = 1000
x = np.random.random((N, ))
y = np.random.random((N, ))
Z_t = x + 1j * y
return Z_t
def test_numpy_scipy_acf(signal_complex):
delta_t = 0.25
t1, acf1 = compute_acf(signal_complex, delta_t=delta_t, method='numpy')
t2, acf2 = compute_acf(signal_complex, delta_t=delta_t, method='scipy')
assert np.allclose(t1, t2)
assert np.allclose(acf1, acf2)
def test_compute_acf_invalid_arguments(signal_complex):
with pytest.raises(ValueError):
t1, acf1 = compute_acf(signal_complex, method='asd')
def test_fermi_dirac_time_function(signal_complex):
signal = signal_complex.real
time = np.arange(0, 1000, 1)
t_0 = 500
t_width = 20
f = fermi_dirac(time, t_0, t_width)
signal_damped = f * signal
assert np.isclose(signal_damped[0], signal[0])
assert np.isclose(signal_damped[-1], 0.0)
def test_smoothing_function():
data = np.array([1, 2, 2.5, 4, 5.5, 6.5, 7, 8, 7, 2])
res1 = smoothing_function(data, window_size=1, window_type='boxcar')
assert np.allclose(res1, data)
res2 = smoothing_function(data, window_size=2, window_type='boxcar')
assert len(res2) == len(data)
assert np.allclose(res2[0], 1)
assert np.allclose(res2[1], 1.5)
assert np.allclose(res2[2], 2.25)
res3 = smoothing_function(data, window_size=3, window_type='boxcar')
assert len(res3) == len(data)
assert np.allclose(res3[0], 1.5)
assert np.allclose(res3[1], 5.5/3)
assert np.allclose(res3[2], 8.5/3)
assert np.allclose(res3[-1], 4.5)
def test_align_structure():
# randomly rotated Al FCC cubic cell
atoms = bulk('Al', 'fcc', cubic=True).repeat(2)
ref_cell = atoms.cell[:].copy()
atoms.rotate(42, [1, 2, 5], rotate_cell=True)
print(atoms.cell[:])
align_structure(atoms)
assert np.isclose(atoms.cell[0, 1], 0)
assert np.isclose(atoms.cell[0, 2], 0)
assert np.isclose(atoms.cell[1, 2], 0)
assert np.allclose(atoms.cell, ref_cell)
print(atoms.cell[:])
# BCC primtive cell
atoms = bulk('Ti', 'bcc', a=3.3).repeat(2)
print(atoms.cell[:])
align_structure(atoms)
assert np.isclose(atoms.cell[0, 1], 0)
assert np.isclose(atoms.cell[0, 2], 0)
assert np.isclose(atoms.cell[1, 2], 0)
print(atoms.cell[:])
# strange cell which fails with very low tolerance
cell = np.array([[6.66725037e+01, -7.15537500e-02, 3.71540563e-08],
[1.40460691e-01, 6.63955753e+01, 5.54413709e-02],
[5.91136223e-02, -3.04975220e-02, 4.73122339e+01]])
atoms = bulk('Al', 'fcc', cubic=True).repeat(2)
atoms.set_cell(cell, scale_atoms=True)
align_structure(atoms, atol=1e-5)
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