-
Notifications
You must be signed in to change notification settings - Fork 1
/
oxygen_coreshell.lt
86 lines (78 loc) · 3.24 KB
/
oxygen_coreshell.lt
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
#######################################################################
# file "oxygen_coreshell.lt"
# calcite super cell. Core-shell model, using Buckingham potential
#
CaCO3 {
write_once("In Init") {
units real
atom_style full
pair_style buck/coul/long/cs 10.0
bond_style harmonic
#### angle_style harmonic
kspace_style pppm 0.0001
pair_modify tail yes
}
## Atom properties and molecular topology
# "atom_style full" means we use this column format:
# atomID molID atomType charge coordX coordY coordZ
write("Data Atoms") {
$atom:Ca1 $mol:1 @atom:Ca 2.000000 0.00000 0.00000 0.00000
$atom:O1 $mol:3 @atom:O 1.018487 1.28642 -0.00000 4.26538
$atom:Oshell1 $mol:3 @atom:Oshell -2.133000 1.28642 -0.00000 4.26538
$atom:O2 $mol:4 @atom:O 1.018487 -0.64321 1.11407 4.26538
$atom:Oshell2 $mol:4 @atom:Oshell -2.133000 -0.64321 1.11407 4.26538
$atom:O3 $mol:5 @atom:O 1.018487 1.85179 3.20739 4.26538
$atom:Oshell3 $mol:5 @atom:Oshell -2.133000 1.85179 3.20739 4.26538
}
# molID number is unique for each molecule
write_once("Data Masses") {
# atomType mass
# core-mass ratio: 0.1
@atom:Ca 40.078
#### @atom:C 12.0107
@atom:O 14.39946
@atom:Oshell 1.59994
}
write("Data Bonds") {
$bond:OOshell1 @bond:OOshell $atom:O1 $atom:Oshell1
$bond:OOshell2 @bond:OOshell $atom:O2 $atom:Oshell2
$bond:OOshell3 @bond:OOshell $atom:O3 $atom:Oshell3
}
#### write("Data Angles") {
#### $angle:OCO1 @angle:OCO $atom:O1 $atom:C1 $atom:O2
#### $angle:OCO2 @angle:OCO $atom:O1 $atom:C1 $atom:O3
#### }
## Core-shell information, what atoms are split into a core and a shell
# atomID CS-ID
write("Data CS-Info") {
$atom:O1 $mol:1
$atom:Oshell1 $mol:1
$atom:O2 $mol:2
$atom:Oshell2 $mol:2
$atom:O3 $mol:3
$atom:Oshell3 $mol:3
}
# --- Force-field parameters:
write_once("In Settings") {
# Hybrid Buckingham/LJ - Bruneval et.al. J. Phys. Chem. B, Vol. 111, No. 42, 2007
# -- Non-bonded (Pair) interactions --
# Buckingham: pair_coeff atom1 atom2 hybridversion A[Kcal/mol] rho[1/A^6] C[KcalA^6/mol]
pair_coeff @atom:Ca @atom:Ca 19823.81931 2.198 13309.441
#### pair_coeff @atom:C @atom:C 88389.7467 3.6019 581.4312
pair_coeff @atom:O @atom:O 55026.3145 3.9602 268.537
pair_coeff @atom:Ca @atom:O 33027.7416 2.9503 1890.5230
#### pair_coeff @atom:Ca @atom:C 41859.5553 2.8137 2781.821
#### pair_coeff @atom:C @atom:O 69740.6768 3.7768 395.1402
pair_coeff @atom:Oshell @atom:Oshell 1481465.805 0.198913 503.724562
pair_coeff @atom:Ca @atom:Oshell 49673.791 0.289118 0.0
#### pair_coeff @atom:C @atom:Oshell 2304.2385 0.195838 0.0
pair_coeff @atom:O @atom:Oshell 0.0 1.0 0.0 # should be no interaction
# -- Bonded interactions --
bond_coeff @bond:OOshell 1216.214988 0.0
#### special_bonds coul 0.0 1.0 1.0 # cancel coulomb interaction core-shell?
#### angle_coeff @angle:OCO 92 120
# -- Groups:
#### group caco3 type @atom:Ca @atom:C @atom:O @atom:Oshell
group coreandshells type @atom:O @atom:Oshell
}
} # End CaCO3