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import os
import numpy as np
import pytest
from dynasor.correlation_functions import (
compute_dynamic_structure_factors,
compute_static_structure_factors,
)
from dynasor.sample import Sample
from dynasor.trajectory import Trajectory
@pytest.fixture
def traj_fname_xyz():
this_dir = os.path.dirname(__file__)
traj_fname = os.path.join(this_dir,
'trajectory_reader/trajectory_files/dump_with_velocities.xyz')
return traj_fname
@pytest.fixture
def traj_fname_lammps():
this_dir = os.path.dirname(__file__)
traj_fname = os.path.join(
this_dir,
'trajectory_reader/trajectory_files/positions.lammpstrj')
return traj_fname
@pytest.fixture
def q_points():
q_points = np.array([i * np.array([1/2, 2/3, 1.235]) for i in np.linspace(0, 10, 11)])
return q_points
def test_API_dynamic_structure_factor(traj_fname_xyz, q_points):
traj = Trajectory(traj_fname_xyz, 'extxyz')
res = compute_dynamic_structure_factors(traj, q_points=q_points, dt=1.0, window_size=4)
assert isinstance(res, Sample)
def test_API_dynamic_structure_factor_selfpart(traj_fname_xyz, q_points):
traj = Trajectory(traj_fname_xyz, 'extxyz')
res = compute_dynamic_structure_factors(traj, q_points=q_points, dt=1.0, window_size=4,
calculate_incoherent=True)
assert isinstance(res, Sample)
def test_API_static_structure_factor(traj_fname_xyz_long, q_points):
# setup
n_atoms = 320
n_A = 50
atomic_indices = dict()
atomic_indices['A'] = np.arange(0, n_A, 1)
atomic_indices['B'] = np.arange(n_A, n_atoms, 1)
# calculate static
traj = Trajectory(
traj_fname_xyz_long, trajectory_format='extxyz', atomic_indices=atomic_indices)
res1 = compute_static_structure_factors(traj, q_points=q_points)
assert res1.meta_data['number_of_frames'] == 30
# calculate S(q) via compute_dynamic_structure_factors (use dummy dt and window_size)
traj = Trajectory(
traj_fname_xyz_long, trajectory_format='extxyz', atomic_indices=atomic_indices)
res2 = compute_dynamic_structure_factors(traj, q_points=q_points, dt=1.0, window_size=4)
assert res2.meta_data['number_of_frames'] == 30
# compare results
pairs = ['A_A', 'A_B', 'B_B']
for pair in pairs:
Sq1 = getattr(res1, f'Sq_{pair}')
Sq2 = getattr(res2, f'Fqt_coh_{pair}')[:, 0].reshape(-1, 1)
assert np.allclose(Sq1, Sq2)
assert np.allclose(res1.Sq, res2.Fqt_coh[:, 0].reshape(-1, 1))
# Comparing the mdanalysis lammps reader to the internal lammps reader
def test_API_calling_mdanalysis_reader(traj_fname_lammps, q_points):
window = 4
dt = 1.0
traj1 = Trajectory(traj_fname_lammps, 'lammps_internal')
traj2 = Trajectory(traj_fname_lammps, 'lammps_mdanalysis',
length_unit='Angstrom', time_unit='fs')
res1 = compute_dynamic_structure_factors(traj1, q_points=q_points, dt=dt, window_size=window)
res2 = compute_dynamic_structure_factors(traj2, q_points=q_points, dt=dt, window_size=window)
assert isinstance(res1, Sample)
assert isinstance(res2, Sample)
# check that results are the same
assert res1.available_correlation_functions == res2.available_correlation_functions
for key in res1.available_correlation_functions:
np.testing.assert_almost_equal(res1[key], res2[key], decimal=5)
# test of time-sampling parameters
# --------------------------------
def test_API_dynamic_step(traj_fname_xyz_long, q_points):
"""
Ensure that setting step > 1 affects the resulting time
"""
dt = 1.0
time_window = 4
step = 1
for step in [1, 2, 3]:
traj = Trajectory(traj_fname_xyz_long, 'extxyz', frame_step=step)
res = compute_dynamic_structure_factors(
traj, q_points=q_points, dt=dt, window_size=time_window)
assert isinstance(res, Sample)
time = res.time
assert np.allclose(np.diff(time), step * dt), (np.diff(time), step * dt)
# test ValueErrors from bad input arguments
# -----------------------------------------
def test_raises_with_bad_input_args(traj_fname_xyz_long, q_points):
time_window = 4
dt = 1.0
# q-points wrong shape
traj = Trajectory(traj_fname_xyz_long, 'extxyz')
with pytest.raises(ValueError, match=r'q-points array has the wrong shape'):
compute_dynamic_structure_factors(traj, q_points=q_points[:, 1:], dt=dt,
window_size=time_window)
traj = Trajectory(traj_fname_xyz_long, 'extxyz')
with pytest.raises(ValueError, match=r'q-points array has the wrong shape'):
compute_static_structure_factors(traj, q_points=q_points[:, 1:])
# dt not positive
traj = Trajectory(traj_fname_xyz_long, 'extxyz')
with pytest.raises(ValueError, match=r'dt must be positive'):
compute_dynamic_structure_factors(traj, q_points=q_points, dt=-1.0, window_size=time_window)
# bad window_size
traj = Trajectory(traj_fname_xyz_long, 'extxyz')
with pytest.raises(ValueError, match=r'window_size must be larger than 2'):
compute_dynamic_structure_factors(traj, q_points=q_points, dt=dt, window_size=1)
traj = Trajectory(traj_fname_xyz_long, 'extxyz')
with pytest.raises(ValueError, match=r'window_size must be even'):
compute_dynamic_structure_factors(traj, q_points=q_points, dt=dt, window_size=5)
# bad window_step
traj = Trajectory(traj_fname_xyz_long, 'extxyz')
with pytest.raises(ValueError, match=r'window_step must be positive'):
compute_dynamic_structure_factors(traj, q_points=q_points, dt=dt, window_size=time_window,
window_step=-1)
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