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import os
import pytest
import numpy as np
from ase import Atoms
from dynasor.correlation_functions import compute_spectral_energy_density
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.xyz')
return traj_fname
@pytest.fixture
def traj_fname_xyz_with_velocities():
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 prim():
alat = 6.0
spos_A = np.array([0, 0, 0])
spos_B = np.array([0.5, 0.5, 0.5])
spos_X = np.array([[0.5, 0.5, 0], [0.5, 0, 0.5], [0, 0.5, 0.5]])
scaled_positions = np.vstack((spos_A, spos_B, spos_X))
cell = alat * np.eye(3)
types = ['Cs', 'Pb', 'Br', 'Br', 'Br']
atoms = Atoms(pbc=True, cell=cell, scaled_positions=scaled_positions, symbols=types)
return atoms
def test_sed(traj_fname_xyz_with_velocities, prim):
# setup
size = 6
dt = 2.5
traj = Trajectory(traj_fname_xyz_with_velocities, trajectory_format='extxyz')
atoms_ideal = prim.repeat(size)
q_points = np.array([a * np.array([2 * np.pi / 6.0, 0, 0]) for a in np.linspace(0, 1, size+1)])
# run SED
f, sed = compute_spectral_energy_density(traj, ideal_supercell=atoms_ideal,
primitive_cell=prim, q_points=q_points, dt=dt)
f_target = 1 / dt * 2 * np.pi * np.linspace(0, 1/2, 3)
assert sed.shape == (7, 3)
assert np.allclose(f, f_target)
sed_target = np.array([
[0.10847998, 0.18091865, 0.15408934],
[0.23743116, 0.17269055, 0.29059788],
[0.20541601, 0.21506601, 0.14684155],
[0.12568888, 0.26424448, 0.33979104],
[0.20541601, 0.17761411, 0.14684155],
[0.23743116, 0.19715230, 0.29059788],
[0.10847998, 0.18091865, 0.15408934]])
assert np.allclose(sed, sed_target)
# test with step > 1
step = 2
traj = Trajectory(traj_fname_xyz_with_velocities, trajectory_format='extxyz',
frame_step=step)
f, sed = compute_spectral_energy_density(traj, ideal_supercell=atoms_ideal,
primitive_cell=prim, q_points=q_points, dt=dt)
f_target = 1 / (dt*step) * 2 * np.pi * np.linspace(0, 1/2, 2)
assert sed.shape == (7, 2)
assert np.allclose(f, f_target)
def test_sed_without_velocities(traj_fname_xyz, prim):
size = 6
dt = 2.5
atoms_ideal = prim.repeat(size)
q_points = np.array([a * np.array([2 * np.pi / 6.0, 0, 0]) for a in np.linspace(0, 1, size+1)])
traj = Trajectory(traj_fname_xyz, trajectory_format='extxyz')
with pytest.raises(ValueError):
f, sed = compute_spectral_energy_density(traj, ideal_supercell=atoms_ideal,
primitive_cell=prim, q_points=q_points, dt=dt)
def test_sed_with_incorrect_supercell(traj_fname_xyz, prim):
size = 6
dt = 2.5
atoms_ideal = prim.repeat(size)
del atoms_ideal[0]
q_points = np.array([a * np.array([2 * np.pi / 6.0, 0, 0]) for a in np.linspace(0, 1, size+1)])
traj = Trajectory(traj_fname_xyz, trajectory_format='extxyz')
with pytest.raises(ValueError, match='ideal_supercell must contain the same number of atoms'
' as the trajectory'):
f, sed = compute_spectral_energy_density(traj, ideal_supercell=atoms_ideal,
primitive_cell=prim, q_points=q_points, dt=dt)
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