def test_list3d(self):
particle_positions = np.array([[9, 6, 4]])
box_space = np.array([8, 6, 4])
cutoff = 2
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.calculate_index(np.array([1, 0, 0])))
lol = s1.cell_neighbour_list_3D()
print(lol)
def test_determine_box_shift(self):
EC = EnergyCalculator(box=np.array([2, 3, 2]),
cutoff_radius=1,
es_sigma=1,
charges=np.array([1]),
lj_sigmas=np.array([1]),
lj_epsilons=np.array([1]),
k_vector=np.array([[1]]))
vector1 = np.array([3, 4, 1])
NL = Neighbourlist(Box=np.array([2, 3, 2]),
particles=np.array([[3, 4, 1]]),
rc=1)
cell_nl = NL.cell_neighbour_list_3D()
EC.cell_neighbour_list = cell_nl
calc_shift = EC._determine_box_shift(0, 2)
reference_shift = np.array([-2, 0, 0])
self.assertTrue(np.array_equal(calc_shift, reference_shift))
def test_cnlist3d_2(self):
particle_positions = np.array([[9, 6, 4], [4, 5, 6], [1, 3, 6]])
box_space = np.array([12, 10, 10])
cutoff = 3
s1 = Neighbourlist(particle_positions, box_space, cutoff)
reference_CnList = np.array(
[[
31, 32, 30, 34, 35, 33, 28, 29, 27, 4, 5, 3, 7, 8, 6, 1, 2, 0,
13, 14, 12, 16, 17, 15, 10, 11, 9, 22, 23, 21, 25, 26, 24, 19,
20, 18
],
[
4, 5, 3, 7, 8, 6, 1, 2,
0, 13, 14, 12, 16, 17, 15, 10, 11,
9, 22, 23, 21, 25, 26, 24, 19, 20, 18, 31, 32, 30, 34, 35, 33,
28, 29, 27
],
[
13, 14, 12, 16, 17, 15,
10, 11, 9, 22, 23, 21, 25, 26, 24, 19, 20, 18, 31, 32, 30, 34,
35, 33, 28, 29, 27, 4, 5, 3, 7, 8, 6, 1, 2, 0
],
[
28, 29, 27, 31, 32,
30, 34, 35, 33, 1, 2, 0, 4, 5, 3, 7, 8, 6, 10, 11,
9, 13, 14, 12, 16, 17, 15, 19, 20, 18, 22, 23, 21, 25, 26, 24
],
[
1, 2, 0, 4, 5, 3, 7, 8,
6, 10, 11, 9, 13, 14, 12, 16, 17, 15, 19, 20, 18, 22, 23, 21,
25, 26, 24, 28, 29, 27,
31, 32, 30, 34, 35, 33
],
[
10, 11, 9, 13, 14, 12, 16, 17, 15, 19, 20, 18, 22, 23, 21, 25,
26, 24, 28, 29, 27, 31,
32, 30, 34, 35, 33, 1, 2, 0, 4, 5, 3, 7, 8, 6
],
[
34, 35, 33, 28, 29,
27, 31, 32, 30, 7, 8, 6, 1, 2, 0, 4, 5, 3, 16, 17, 15, 10, 11,
9, 13, 14, 12, 25, 26, 24, 19, 20, 18, 22, 23, 21
],
[
7, 8, 6, 1, 2, 0, 4, 5, 3, 16, 17, 15, 10, 11, 9, 13, 14, 12,
25, 26, 24, 19, 20, 18, 22, 23, 21, 34, 35, 33, 28, 29, 27,
31, 32, 30
],
[
16, 17, 15, 10, 11, 9, 13, 14, 12, 25, 26, 24, 19, 20, 18, 22,
23, 21, 34, 35, 33, 28, 29, 27, 31, 32, 30, 7, 8, 6, 1, 2, 0,
4, 5, 3
],
[
30, 31, 32, 33, 34, 35, 27, 28, 29, 3, 4, 5, 6, 7, 8, 0, 1, 2,
12, 13, 14, 15, 16, 17, 9, 10, 11, 21, 22, 23, 24, 25, 26, 18,
19, 20
],
[
3, 4, 5, 6, 7, 8, 0, 1, 2, 12, 13, 14, 15, 16, 17, 9, 10, 11,
21, 22, 23, 24, 25, 26, 18, 19, 20, 30, 31, 32, 33, 34, 35,
27, 28, 29
],
[
12, 13, 14, 15, 16, 17, 9, 10, 11, 21, 22, 23, 24, 25, 26, 18,
19, 20, 30, 31, 32, 33, 34, 35, 27, 28, 29, 3, 4, 5, 6, 7, 8,
0, 1, 2
],
[
27, 28, 29, 30, 31, 32, 33, 34, 35, 0, 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
],
[
0, 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
],
[
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, 0, 1, 2, 3, 4, 5,
6, 7, 8
],
[
33, 34, 35, 27, 28, 29, 30, 31, 32, 6, 7, 8, 0, 1, 2, 3, 4, 5,
15, 16, 17, 9, 10, 11, 12, 13, 14, 24, 25, 26, 18, 19, 20, 21,
22, 23
],
[
6, 7, 8, 0, 1, 2, 3, 4, 5, 15, 16, 17, 9, 10, 11, 12, 13, 14,
24, 25, 26, 18, 19, 20, 21, 22, 23, 33, 34, 35, 27, 28, 29,
30, 31, 32
],
[
15, 16, 17, 9, 10, 11, 12, 13, 14, 24, 25, 26, 18, 19, 20, 21,
22, 23, 33, 34, 35, 27, 28, 29, 30, 31, 32, 6, 7, 8, 0, 1, 2,
3, 4, 5
],
[
32, 30, 31, 35, 33, 34, 29, 27, 28, 5, 3, 4, 8, 6, 7, 2, 0, 1,
14, 12, 13, 17, 15, 16, 11, 9, 10, 23, 21, 22, 26, 24, 25, 20,
18, 19
],
[
5, 3, 4, 8, 6, 7, 2, 0, 1, 14, 12, 13, 17, 15, 16, 11, 9, 10,
23, 21, 22, 26, 24, 25, 20, 18, 19, 32, 30, 31, 35, 33, 34,
29, 27, 28
],
[
14, 12, 13, 17, 15, 16, 11, 9, 10, 23, 21, 22, 26, 24, 25, 20,
18, 19, 32, 30, 31, 35, 33, 34, 29, 27, 28, 5, 3, 4, 8, 6, 7,
2, 0, 1
],
[
29, 27, 28, 32, 30, 31, 35, 33, 34, 2, 0, 1, 5, 3, 4, 8, 6, 7,
11, 9, 10, 14, 12, 13, 17, 15, 16, 20, 18, 19, 23, 21, 22, 26,
24, 25
],
[
2, 0, 1, 5, 3, 4, 8, 6, 7, 11, 9, 10, 14, 12, 13, 17, 15, 16,
20, 18, 19, 23, 21, 22, 26, 24, 25, 29, 27, 28, 32, 30, 31,
35, 33, 34
],
[
11, 9, 10, 14, 12, 13, 17, 15, 16, 20, 18, 19, 23, 21, 22, 26,
24, 25, 29, 27, 28, 32, 30, 31, 35, 33, 34, 2, 0, 1, 5, 3, 4,
8, 6, 7
],
[
35, 33, 34, 29, 27, 28, 32, 30, 31, 8, 6, 7, 2, 0, 1, 5, 3, 4,
17, 15, 16, 11, 9, 10, 14, 12, 13, 26, 24, 25, 20, 18, 19, 23,
21, 22
],
[
8, 6, 7, 2, 0, 1, 5, 3, 4, 17, 15, 16, 11, 9, 10, 14, 12, 13,
26, 24, 25, 20, 18, 19, 23, 21, 22, 35, 33, 34, 29, 27, 28,
32, 30, 31
],
[
17, 15, 16, 11, 9, 10, 14, 12, 13, 26, 24, 25, 20, 18, 19, 23,
21, 22, 35, 33, 34, 29, 27, 28, 32, 30, 31, 8, 6, 7, 2, 0, 1,
5, 3, 4
]])
cnlist = s1.cell_neighbour_list_3D()
print(cnlist)
sorted_referenceCnList = np.sort(reference_CnList, axis=0)
sorted_outputCnList = np.sort(cnlist[:, :, 0], axis=0)
npt.assert_equal(sorted_referenceCnList,
sorted_outputCnList,
'Failed',
verbose=True)
