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import os
import numpy as np
from dynasor.qpoints import get_spherical_qpoints
from dynasor.correlation_functions import compute_dynamic_structure_factors
from dynasor.correlation_functions import compute_static_structure_factors
from dynasor.trajectory import Trajectory
def test_normalization_dynamic_structure_factor():
# traj index files
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')
# input parameters
time_window = 4
dt = 100
q_max = 40
max_points = 500
# setup
traj_format = 'extxyz'
traj = Trajectory(traj_fname, trajectory_format=traj_format)
q_points = get_spherical_qpoints(traj.cell, q_max, max_points)
# run only total
sample1 = compute_dynamic_structure_factors(traj, q_points, dt=dt, window_size=time_window,
calculate_currents=True, calculate_incoherent=True)
# run with partial
traj = Trajectory(traj_fname, trajectory_format=traj_format, atomic_indices=index_fname)
sample2 = compute_dynamic_structure_factors(traj, q_points, dt=dt, window_size=time_window,
calculate_currents=True, calculate_incoherent=True)
# test Fqt
F_tot1 = sample1.Fqt_coh_X_X
F_tot2 = sample2.Fqt_coh
assert np.allclose(F_tot1, F_tot2)
pairs = ['Cs_Cs', 'Br_Br', 'Pb_Pb', 'Cs_Pb', 'Br_Cs', 'Br_Pb']
F_tot_from_partials = np.zeros_like(F_tot1)
for pair in pairs:
F_tot_from_partials += getattr(sample2, f'Fqt_coh_{pair}')
assert np.allclose(F_tot1, F_tot_from_partials)
# test CL
Cl_tot = sample1.Clqt_X_X
Cl_tot_from_partials = np.zeros_like(Cl_tot)
for pair in pairs:
Cl_tot_from_partials += getattr(sample2, f'Clqt_{pair}')
assert np.allclose(Cl_tot, Cl_tot_from_partials), np.max(np.abs(Cl_tot - Cl_tot_from_partials))
# test Ct
Ct_tot = sample1.Ctqt_X_X
Ct_tot_from_partials = np.zeros_like(Ct_tot)
for pair in pairs:
Ct_tot_from_partials += getattr(sample2, f'Ctqt_{pair}')
assert np.allclose(Ct_tot, Ct_tot_from_partials)
# test self-parts
Fs_tot1 = sample1.Fqt_incoh_X
Fs_tot2 = sample2.Fqt_incoh
assert np.allclose(Fs_tot1, Fs_tot2)
Fs_tot_from_partials = np.zeros_like(Fs_tot1)
atom_types = ['Cs', 'Br', 'Pb']
for atom_type in atom_types:
Fs_tot_from_partials += getattr(sample2, f'Fqt_incoh_{atom_type}')
assert np.allclose(Fs_tot1, Fs_tot_from_partials)
def test_normalization_static_structure_factor():
# traj index files
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')
# input parameters
q_max = 40
max_points = 500
# setup
traj_format = 'extxyz'
traj = Trajectory(traj_fname, trajectory_format=traj_format)
q_points = get_spherical_qpoints(traj.cell, q_max, max_points)
# run only total
sample1 = compute_static_structure_factors(traj, q_points)
# run with partial
traj = Trajectory(traj_fname, trajectory_format=traj_format, atomic_indices=index_fname)
sample2 = compute_static_structure_factors(traj, q_points)
# test S(q)
F_tot = sample1.Sq_X_X
pairs = ['Cs_Cs', 'Br_Br', 'Pb_Pb', 'Cs_Pb', 'Br_Cs', 'Br_Pb']
F_tot_from_partials = np.zeros_like(F_tot)
for pair in pairs:
F_tot_from_partials += getattr(sample2, f'Sq_{pair}')
assert np.allclose(F_tot, F_tot_from_partials)
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