This repository has been archived by the owner on Apr 13, 2024. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 8
/
small_molecule_constants.py
executable file
·88 lines (84 loc) · 3.1 KB
/
small_molecule_constants.py
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
85
86
87
88
TraPPE = {
'O2': {
'pair': {'style': 'lj/cut/coul/long', 'vdW': {'O_O2': (0.0974,3.02), 'O_com': (0.0,0.0)}, 'charges': {'O_O2': -0.113, 'O_com': 0.226}},
'bonds': {('O_O2', 'O_com'): ('harmonic',100.0,0.604)}, # molecule should be kept rigid, force constants don't matter
'angles': {('O_O2', 'O_com', 'O_O2'): ('harmonic',100.0,180.0)}, # molecule should be kept rigid, force constants don't matter
'dihedrals': None,
'impropers': None
},
'N2': {
'pair': {},
'bonds': {},
'angles': {},
'dihedrals': None,
'impropers': None
},
'H2O1': {
'pair': {},
'bonds': {},
'angles': {},
'dihedrals': None,
'impropers': None
}
}
TIP4P_2005_long = {
# this is TIP4P/2005 water, should be used with long-range electrostatics with 8.5 Å cutoff and fix/shake
# keep in mind that using any long pair_style in lammps will include long-range electrostatics FOR ALL ATOMS in the simulation
'H2O1': {
'pair': {'style': 'lj/cut/tip4p/long', 'vdW': {'H_w': (0.0,1.0), 'O_w': (0.1852, 3.1589)}, 'charges': {'H_w': 0.5564, 'O_w': -1.1128}},
'bonds': {('H_w', 'O_w'): ('harmonic', 450.0, 0.9572)},
'angles': {('H_w', 'O_w', 'H_w'): ('harmonic', 55.0, 104.52)},
'dihedrals': None,
'impropers': None
},
'Cl1': {
'pair': {'style': 'lj/cut/tip4p/long', 'vdW': {'Cl_Cl1': (0.22700, 3.51638)}, 'charges': {'Cl_Cl1': -1.0}},
'bonds': None,
'angles': None,
'dihedrals': None,
'impropers': None
}
}
TIP4P_2005_cutoff = {
# this is TIP4P/2005 water but with no long range electrostatics
'H2O1': {
'pair': {'style': 'lj/cut/tip4p/cut', 'vdW': {'H_w': (0.0,0.0), 'O_w': (0.1852, 3.1589)}, 'charges': {'H_w': 0.5564, 'O_w': -1.1128}},
'bonds': {('H_w', 'O_w'): ('harmonic', 450.0, 0.9572)},
'angles': {('H_w', 'O_w', 'H_w'): ('harmonic', 55.0, 104.52)},
'dihedrals': None,
'impropers': None
},
'Cl1': {
'pair': {'style': 'lj/cut/tip4p/long', 'vdW': {'Cl_Cl1': (0.22700, 3.51638)}, 'charges': {'Cl_Cl1': -1.0}},
'bonds': None,
'angles': None,
'dihedrals': None,
'impropers': None
}
}
TIP4P_cutoff = {
# this is the original TIP4P water model
'H2O1': {
'pair': {'style': 'lj/cut/tip4p/cut', 'vdW': {'H_w': (0.0,0.0), 'O_w': (0.1550, 3.1536)}, 'charges': {'H_w': 0.5200, 'O_w': -1.040}},
'bonds': {('H_w', 'O_w'): ('harmonic', 450.0, 0.9572)},
'angles': {('H_w', 'O_w', 'H_w'): ('harmonic', 55.0, 104.52)},
'dihedrals': None,
'impropers': None
},
'Cl1': {
'pair': {'style': 'lj/cut/tip4p/cut', 'vdW': {'Cl_Cl1': (0.22700, 3.51638)}, 'charges': {'Cl_Cl1': -1.0}},
'bonds': None,
'angles': None,
'dihedrals': None,
'impropers': None
}
}
Ions = {
'Cl1': {
'pair': {'style': 'lj/cut/coul/long', 'vdW': {'Cl_Cl1': (0.22700, 3.51638)}, 'charges': {'Cl_Cl1': -1.0}},
'bonds': None,
'angles': None,
'dihedrals': None,
'impropers': None
}
}