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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
|
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.x |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
object potentials;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Subdictionaries specifying types of intermolecular potential.
// Sub-sub dictionaries specify the potentials themselves.
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Removal order
// This is the order in which to remove overlapping pairs if more than one
// type of molecule is present. The most valuable molecule type is at the
// right hand end, the molecule that will be removed 1st is 1st on the list.
// Not all types need to be present, a molecule that is not present is
// automatically less valuable than any on the list. For molecules of the
// same type there is no control over which is removed.
removalOrder ( water );
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Potential Energy Limit
// Maximum permissible pair energy allowed at startup. Used to remove
// overlapping molecules created during preprocessing.
potentialEnergyLimit 1e-18;
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Pair potentials
// If a pair are not present here it is assumed that they do not interact.
// Electrostatic pair interactions are not listed here - they are handled
// separately.
// If there are r different type of molecules, and a pair force is required
// between all combinations, then there are C = r(r+1)/2 combinations,
// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
// Pair potentials are specified by the combinaition of their ids,
// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
// (strictly OR, both or neither will throw an error)
pair
{
O-O
{
pairPotential lennardJones;
rCut 1.0e-9;
rMin 0.1e-9;
dr 1e-13;
lennardJonesCoeffs
{
sigma 3.154e-10;
epsilon 1.07690722e-21;
}
energyScalingFunction noScaling;
writeTables yes;
}
electrostatic
{
pairPotential dampedCoulomb;
rCut 1e-9;
rMin 2e-11;
dr 2e-12;
dampedCoulombCoeffs
{
alpha 2e9;
}
energyScalingFunction shiftedForce;
writeTables yes;
}
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// Tethering Potentials
tether
{
O
{
tetherPotential restrainedHarmonicSpring;
restrainedHarmonicSpringCoeffs
{
springConstant 0.277;
rR 1.2e-9;
}
}
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// External Forces
// Bulk external forces (namely gravity) will be specified as forces rather
// than potentials to allow their direction to be controlled.
external
{
gravity (0 0 0);
}
// ************************************************************************* //
|
