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
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
|
from interacticle import Molecule, Atom, Bond, Angle, Torsion
Benzene = Molecule()
Benzene.atoms = [
Atom(-0.0739, 0.1189, -0.000733, 0, 0, 0, 12.011),
Atom( 0.0614, 0.1208, 0.035167, 0, 0, 0, 12.011),
Atom( 0.1353, 0.0019, 0.035867, 0, 0, 0, 12.011),
Atom( 0.0739, -0.1189, 0.000667, 0, 0, 0, 12.011),
Atom(-0.0614, -0.1208, -0.035133, 0, 0, 0, 12.011),
Atom(-0.1353, -0.0019, -0.035833, 0, 0, 0, 12.011),
Atom(-0.1309, 0.2106, -0.001233, 0, 0, 0, 1.008),
Atom( 0.1088, 0.214, 0.062267, 0, 0, 0, 1.008),
Atom( 0.2397, 0.0034, 0.063467, 0, 0, 0, 1.008),
Atom( 0.1309, -0.2106, 0.001267, 0, 0, 0, 1.008),
Atom(-0.1088, -0.214, -0.062233, 0, 0, 0, 1.008),
Atom(-0.2397, -0.0034, -0.063533, 0, 0, 0, 1.008)
]
Benzene.connections = [
Bond(0, 1, 337000, 0.14),
Bond(0, 5, 337000, 0.14),
Bond(1, 2, 337000, 0.14),
Bond(2, 3, 337000, 0.14),
Bond(3, 4, 337000, 0.14),
Bond(4, 5, 337000, 0.14),
Bond(0, 6, 340000, 0.108),
Bond(1, 7, 340000, 0.108),
Bond(2, 8, 340000, 0.108),
Bond(3, 9, 340000, 0.108),
Bond(4,10, 340000, 0.108),
Bond(5,11, 340000, 0.108),
Angle( 0,1,2, 120, 63),
Angle( 1,2,3, 120, 63),
Angle( 2,3,4, 120, 63),
Angle( 3,4,5, 120, 63),
Angle( 4,5,0, 120, 63),
Angle( 5,0,1, 120, 63),
Angle( 6,0,1, 120, 65),
Angle( 7,1,2, 120, 65),
Angle( 8,2,3, 120, 65),
Angle( 9,3,4, 120, 65),
Angle(10,4,5, 120, 65),
Angle(11,5,0, 120, 65),
Torsion( 0,1,2,3, 180, 50),
Torsion( 1,2,3,4, 180, 50),
Torsion( 2,3,4,5, 180, 50),
Torsion( 3,4,5,0, 180, 50),
Torsion( 4,5,0,1, 180, 50),
Torsion( 5,0,1,2, 180, 50),
Torsion( 6,0,1,2, 0, 50),
Torsion( 7,1,2,3, 0, 50),
Torsion( 8,2,3,4, 0, 50),
Torsion( 9,3,4,5, 0, 50),
Torsion(10,4,5,0, 0, 50),
Torsion(11,5,0,1, 0, 50),
]
Water = Molecule()
Water.atoms = [
Atom( 0.0000077, -0.0000421, 0, 0, 0, 0, 15.9992),
Atom(-0.0690251, -0.0760801, 0, 0, 0, 0, 1.0079),
Atom( 0.0979353, -0.0309852, 0, 0, 0, 0, 1.0079)
]
Water.connections = [
Bond(0, 1, 300000, 0.1027),
Bond(0, 2, 300000, 0.1027),
Angle(1,0,2, 114.7, 383)
]
Neon = Molecule()
Neon.atoms = [
Atom(0, 0, 0, 0, 0, 0, 20.18)
]
Argon = Molecule()
Argon.atoms = [
Atom(0, 0, 0, 0, 0, 0, 39.948)
]
|
