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import os
import pytest
import numpy as np
from tempfile import NamedTemporaryFile
from dynasor.trajectory import Trajectory
from dynasor.qpoints import get_spherical_qpoints
from dynasor.correlation_functions import compute_dynamic_structure_factors
from dynasor.post_processing import get_spherically_averaged_sample_binned
from dynasor.sample import read_sample_from_npz
@pytest.fixture
def filenames():
this_dir = os.path.dirname(__file__)
traj_fname = os.path.join(this_dir,
'trajectory_reader/trajectory_files/dump_long_with_velocities.xyz')
index_fname = os.path.join(this_dir, 'trajectory_reader/trajectory_files/index_file_dump_long')
return traj_fname, index_fname
def test_dynasor_CLI(filenames):
# input parameters
time_window = 8
max_frames = 100000
dt = 100
q_max = 40
q_bins = 20
max_q_points = 10000
traj_fname, index_fname = filenames
tmpfile = NamedTemporaryFile(suffix='.npz', delete=False)
# setup dynasor command
flags = []
flags.append(f'-f {traj_fname} -n {index_fname}')
flags.append('--trajectory-format=extxyz')
flags.append(f'--q-bins={q_bins}')
flags.append(f'--q-max={q_max}')
flags.append(f'--max-q-points={max_q_points}')
flags.append(f'--time-window={time_window}')
flags.append(f'--dt={dt}')
flags.append(f'--max-frames={max_frames}')
flags.append(f'--outfile={tmpfile.name}')
flags.append('--calculate-incoherent')
flags.append('--calculate-currents')
flags_str = ' '.join(flags)
# Run dynasor and read results
command = 'dynasor ' + flags_str
os.system(command)
sample_cli = read_sample_from_npz(tmpfile.name)
# Compute results with dynasor API
traj = Trajectory(traj_fname, trajectory_format='extxyz', atomic_indices=index_fname)
q_points = get_spherical_qpoints(traj.cell, q_max, max_q_points)
sample = compute_dynamic_structure_factors(traj, q_points, dt=dt, window_size=time_window,
calculate_currents=True, calculate_incoherent=True)
sample_api = get_spherically_averaged_sample_binned(sample, num_q_bins=q_bins)
# compare results
assert np.allclose(sample_api.time, sample_cli.time)
assert np.allclose(sample_api.omega, sample_cli.omega)
assert np.allclose(sample_api.q_norms, sample_cli.q_norms)
for key in sample_api.available_correlation_functions:
assert np.allclose(getattr(sample_api, key), getattr(sample_cli, key))
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