1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
# fmt: off
from ase.atoms import Atoms
from ase.md.analysis import DiffusionCoefficient
from ase.units import fs as fs_conversion
eps = 1e-10
timestep = 1 * fs_conversion # fs
# Answer in \AA^2/<ASE time unit>
ans_orig = 5.0e-01 / fs_conversion
def test_atom():
# Creating simple trajectories
# Textbook case. The displacement coefficient should
# be 0.5 A^2 / fs except for the final molecule
# He atom
he = Atoms('He', positions=[(0, 0, 0)])
traj_he = [he.copy() for _ in range(2)]
traj_he[1].set_positions([(1, 1, 1)])
dc_he = DiffusionCoefficient(traj_he, timestep)
dc_he.calculate(ignore_n_images=0, number_of_segments=1)
ans = dc_he.get_diffusion_coefficients()[0][0]
assert abs(ans - ans_orig) < eps
def test_co_molecule():
co = Atoms('CO', positions=[(0, 0, 0), (0, 0, 1)])
traj_co = [co.copy() for _ in range(2)]
traj_co[1].set_positions([(-1, -1, -1), (-1, -1, 0)])
dc_co = DiffusionCoefficient(traj_co, timestep, molecule=False)
dc_co.calculate(ignore_n_images=0, number_of_segments=1)
ans = dc_co.get_diffusion_coefficients()[0][0]
assert abs(ans - ans_orig) < eps
for index in range(2):
dc_co = DiffusionCoefficient(traj_co, timestep, atom_indices=[index],
molecule=False)
dc_co.calculate()
ans = dc_co.get_diffusion_coefficients()[0][0]
assert abs(ans - ans_orig) < eps
dc_co = DiffusionCoefficient(traj_co, timestep, molecule=True)
dc_co.calculate(ignore_n_images=0, number_of_segments=1)
ans = dc_co.get_diffusion_coefficients()[0][0]
assert abs(ans - ans_orig) < eps
|
