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type labels for create_atoms_polystyrene example

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This commit is contained in:
Jacob Gissinger
2022-12-20 13:15:59 -05:00
parent 21b14cd7e4
commit 84d97a9ef7
10 changed files with 1870 additions and 1905 deletions
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456
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template
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molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
81 angles
121 dihedrals
35 impropers
1 fragments
Fragments
create_fit 34 44
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 1
32 2
33 1
34 5
35 1
36 2
37 1
38 2
39 1
40 2
41 1
42 2
43 2
44 6
45 2
46 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Coords
1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 11 3 4
5 2 3 5
6 12 13 4
7 13 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 10 15 14
16 10 16 14
17 9 14 34
18 1 17 18
19 2 17 19
20 2 17 27
21 7 19 20
22 2 19 21
23 8 29 20
24 9 30 20
25 9 44 20
26 1 21 22
27 2 21 23
28 1 23 24
29 2 23 25
30 1 25 26
31 2 25 27
32 1 27 28
33 1 31 32
34 2 31 33
35 2 31 41
36 7 33 34
37 2 33 35
38 8 43 34
39 9 44 34
40 1 35 36
41 2 35 37
42 1 37 38
43 2 37 39
44 1 39 40
45 2 39 41
46 1 41 42
47 10 45 44
48 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 17 1 3 4
5 2 1 3 5
6 17 5 3 4
7 18 3 4 13
8 19 3 4 14
9 20 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 21 15 14 4
23 21 16 14 4
24 22 4 14 34
25 15 15 14 16
26 14 15 14 34
27 14 16 14 34
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 44
37 12 29 20 30
38 12 29 20 44
39 13 30 20 44
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
52 1 33 31 32
53 1 41 31 32
54 2 33 31 41
55 9 31 33 34
56 2 31 33 35
57 9 35 33 34
58 11 33 34 14
59 12 43 34 14
60 13 14 34 44
61 10 33 34 43
62 11 33 34 44
63 12 43 34 44
64 1 33 35 36
65 2 33 35 37
66 1 37 35 36
67 1 35 37 38
68 2 35 37 39
69 1 39 37 38
70 1 37 39 40
71 2 37 39 41
72 1 41 39 40
73 2 31 41 39
74 1 31 41 42
75 1 39 41 42
76 16 20 44 34
77 14 45 44 20
78 14 46 44 20
79 14 45 44 34
80 14 46 44 34
81 15 45 44 46
Dihedrals
1 20 2 1 3 4
2 2 5 3 1 2
3 21 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 22 1 3 4 13
10 23 1 3 4 14
11 22 5 3 4 13
12 23 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 20 6 5 3 4
16 21 7 5 3 4
17 24 3 4 14 15
18 24 3 4 14 16
19 25 3 4 14 34
20 26 13 4 14 15
21 26 13 4 14 16
22 27 13 4 14 34
23 2 3 5 7 8
24 4 3 5 7 9
25 5 6 5 7 8
26 2 9 7 5 6
27 2 5 7 9 10
28 4 5 7 9 11
29 5 8 7 9 10
30 2 11 9 7 8
31 4 7 9 11 1
32 2 7 9 11 12
33 2 1 11 9 10
34 5 10 9 11 12
35 28 4 14 34 33
36 29 4 14 34 43
37 30 4 14 34 44
38 31 15 14 34 33
39 32 15 14 34 43
40 33 15 14 34 44
41 31 16 14 34 33
42 32 16 14 34 43
43 33 16 14 34 44
44 10 18 17 19 20
45 2 21 19 17 18
46 11 27 17 19 20
47 4 27 17 19 21
48 2 25 27 17 18
49 5 18 17 27 28
50 4 19 17 27 25
51 2 19 17 27 28
52 12 17 19 20 29
53 13 17 19 20 30
54 13 17 19 20 44
55 12 21 19 20 29
56 13 21 19 20 30
57 13 21 19 20 44
58 2 17 19 21 22
59 4 17 19 21 23
60 10 22 21 19 20
61 11 23 21 19 20
62 34 34 44 20 19
63 31 45 44 20 19
64 31 46 44 20 19
65 35 34 44 20 29
66 32 45 44 20 29
67 32 46 44 20 29
68 36 34 44 20 30
69 33 45 44 20 30
70 33 46 44 20 30
71 2 19 21 23 24
72 4 19 21 23 25
73 5 22 21 23 24
74 2 25 23 21 22
75 2 21 23 25 26
76 4 21 23 25 27
77 5 24 23 25 26
78 2 27 25 23 24
79 4 23 25 27 17
80 2 23 25 27 28
81 2 17 27 25 26
82 5 26 25 27 28
83 10 32 31 33 34
84 2 35 33 31 32
85 11 41 31 33 34
86 4 41 31 33 35
87 2 39 41 31 32
88 5 32 31 41 42
89 4 33 31 41 39
90 2 33 31 41 42
91 13 31 33 34 14
92 12 31 33 34 43
93 13 31 33 34 44
94 13 35 33 34 14
95 12 35 33 34 43
96 13 35 33 34 44
97 2 31 33 35 36
98 4 31 33 35 37
99 10 36 35 33 34
100 11 37 35 33 34
101 36 20 44 34 14
102 33 45 44 34 14
103 33 46 44 34 14
104 34 20 44 34 33
105 31 45 44 34 33
106 31 46 44 34 33
107 35 20 44 34 43
108 32 45 44 34 43
109 32 46 44 34 43
110 2 33 35 37 38
111 4 33 35 37 39
112 5 36 35 37 38
113 2 39 37 35 36
114 2 35 37 39 40
115 4 35 37 39 41
116 5 38 37 39 40
117 2 41 39 37 38
118 4 37 39 41 31
119 2 37 39 41 42
120 2 31 41 39 40
121 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 8 1 3 5 4
3 9 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 1 19 17 27 18
9 5 17 19 21 20
10 1 19 21 23 22
11 1 21 23 25 24
12 1 23 25 27 26
13 1 17 27 25 28
14 1 33 31 41 32
15 5 31 33 35 34
16 1 33 35 37 36
17 1 35 37 39 38
18 1 37 39 41 40
19 1 31 41 39 42
20 1 15 14 16 4
21 1 15 14 4 34
22 1 16 14 4 34
23 1 15 14 16 34
24 1 19 20 29 30
25 1 19 20 29 44
26 1 19 20 30 44
27 1 29 20 30 44
28 1 33 34 43 14
29 1 33 34 14 44
30 1 43 34 14 44
31 1 33 34 43 44
32 1 45 44 34 20
33 1 46 44 34 20
34 1 45 44 46 20
35 1 45 44 46 34

489
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.molecule_template Normal file
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molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
81 angles
121 dihedrals
19 impropers
1 fragments
Fragments
create_fit 34 44
Coords
1 24.130699158 1.043900013 -1.309299946
2 25.062700272 1.582900047 -1.309299946
3 22.900699615 1.753900051 -1.309299946
4 22.900699615 3.253900051 -1.309299946
5 21.670700073 1.043900013 -1.309299946
6 20.738700867 1.582900047 -1.309299946
7 21.670700073 -0.376100004 -1.309299946
8 20.738700867 -0.915099978 -1.309299946
9 22.900699615 -1.086099982 -1.309299946
10 22.900699615 -2.163100004 -1.309299946
11 24.130699158 -0.376100004 -1.309299946
12 25.062700272 -0.915099978 -1.309299946
13 23.766700745 3.658900023 -0.952300012
14 21.622699738 3.802900076 -1.871299982
15 21.672700882 4.544899940 -1.970299959
16 20.979700089 2.979899883 -2.165299892
17 13.465800285 0.682500005 -1.658900023
18 14.397800446 1.221500039 -1.658900023
19 12.235799789 1.392500043 -1.658900023
20 12.235799789 2.892499924 -1.658900023
21 11.005800247 0.682500005 -1.658900023
22 10.073800087 1.221500039 -1.658900023
23 11.005800247 -0.737500012 -1.658900023
24 10.073800087 -1.276499987 -1.658900023
25 12.235799789 -1.447499990 -1.658900023
26 12.235799789 -2.524499893 -1.658900023
27 13.465800285 -0.737500012 -1.658900023
28 14.397800446 -1.276499987 -1.658900023
29 13.101799965 3.297499895 -1.301900029
30 10.957799911 3.441499949 -2.220900059
31 18.663499832 0.855499983 -1.372099996
32 19.595500946 1.394500017 -1.372099996
33 17.433500290 1.565500021 -1.372099996
34 17.433500290 3.065500021 -1.372099996
35 16.203500748 0.855499983 -1.372099996
36 15.271499634 1.394500017 -1.372099996
37 16.203500748 -0.564499974 -1.372099996
38 15.271499634 -1.103500009 -1.372099996
39 17.433500290 -1.274500012 -1.372099996
40 17.433500290 -2.351500034 -1.372099996
41 18.663499832 -0.564499974 -1.372099996
42 19.595500946 -1.103500009 -1.372099996
43 18.299499512 3.470499992 -1.015100002
44 16.155500412 3.614500046 -1.934100032
45 16.205499649 4.356500149 -2.033099890
46 15.512499809 2.791500092 -2.228100061
Types
1 cp
2 hc
3 cp
4 c1
5 cp
6 hc
7 cp
8 hc
9 cp
10 hc
11 cp
12 hc
13 hc
14 c2
15 hc
16 hc
17 cp
18 hc
19 cp
20 c1
21 cp
22 hc
23 cp
24 hc
25 cp
26 hc
27 cp
28 hc
29 hc
30 c2
31 cp
32 hc
33 cp
34 c1
35 cp
36 hc
37 cp
38 hc
39 cp
40 hc
41 cp
42 hc
43 hc
44 c2
45 hc
46 hc
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
31 1
32 1
33 1
34 1
35 1
36 1
37 1
38 1
39 1
40 1
41 1
42 1
43 1
44 1
45 1
46 1
Bonds
1 hc-cp 1 2
2 cp-cp 1 3
3 cp-cp 1 11
4 cp-c1 3 4
5 cp-cp 3 5
6 hc-c1 13 4
7 c1-c2 4 14
8 hc-cp 5 6
9 cp-cp 5 7
10 hc-cp 7 8
11 cp-cp 7 9
12 hc-cp 9 10
13 cp-cp 9 11
14 hc-cp 11 12
15 hc-c2 15 14
16 hc-c2 16 14
17 c1-c2 34 14
18 hc-cp 17 18
19 cp-cp 17 19
20 cp-cp 17 27
21 cp-c1 19 20
22 cp-cp 19 21
23 hc-c1 29 20
24 c1-c2 20 30
25 c1-c2 20 44
26 hc-cp 21 22
27 cp-cp 21 23
28 hc-cp 23 24
29 cp-cp 23 25
30 hc-cp 25 26
31 cp-cp 25 27
32 hc-cp 27 28
33 hc-cp 31 32
34 cp-cp 31 33
35 cp-cp 31 41
36 cp-c1 33 34
37 cp-cp 33 35
38 hc-c1 43 34
39 c1-c2 34 44
40 hc-cp 35 36
41 cp-cp 35 37
42 hc-cp 37 38
43 cp-cp 37 39
44 hc-cp 39 40
45 cp-cp 39 41
46 hc-cp 41 42
47 hc-c2 45 44
48 hc-c2 46 44
Angles
1 hc-cp-cp 3 1 2
2 hc-cp-cp 11 1 2
3 cp-cp-cp 3 1 11
4 cp-cp-c1 1 3 4
5 cp-cp-cp 1 3 5
6 cp-cp-c1 5 3 4
7 hc-c1-cp 3 4 13
8 cp-c1-c2 3 4 14
9 hc-c1-c2 13 4 14
10 hc-cp-cp 3 5 6
11 cp-cp-cp 3 5 7
12 hc-cp-cp 7 5 6
13 hc-cp-cp 5 7 8
14 cp-cp-cp 5 7 9
15 hc-cp-cp 9 7 8
16 hc-cp-cp 7 9 10
17 cp-cp-cp 7 9 11
18 hc-cp-cp 11 9 10
19 cp-cp-cp 1 11 9
20 hc-cp-cp 1 11 12
21 hc-cp-cp 9 11 12
22 hc-c2-c1 15 14 4
23 hc-c2-c1 16 14 4
24 c1-c2-c1 4 14 34
25 hc-c2-hc 15 14 16
26 hc-c2-c1 15 14 34
27 hc-c2-c1 16 14 34
28 hc-cp-cp 19 17 18
29 hc-cp-cp 27 17 18
30 cp-cp-cp 19 17 27
31 cp-cp-c1 17 19 20
32 cp-cp-cp 17 19 21
33 cp-cp-c1 21 19 20
34 hc-c1-cp 19 20 29
35 cp-c1-c2 19 20 30
36 cp-c1-c2 19 20 44
37 hc-c1-c2 29 20 30
38 hc-c1-c2 29 20 44
39 c2-c1-c2 30 20 44
40 hc-cp-cp 19 21 22
41 cp-cp-cp 19 21 23
42 hc-cp-cp 23 21 22
43 hc-cp-cp 21 23 24
44 cp-cp-cp 21 23 25
45 hc-cp-cp 25 23 24
46 hc-cp-cp 23 25 26
47 cp-cp-cp 23 25 27
48 hc-cp-cp 27 25 26
49 cp-cp-cp 17 27 25
50 hc-cp-cp 17 27 28
51 hc-cp-cp 25 27 28
52 hc-cp-cp 33 31 32
53 hc-cp-cp 41 31 32
54 cp-cp-cp 33 31 41
55 cp-cp-c1 31 33 34
56 cp-cp-cp 31 33 35
57 cp-cp-c1 35 33 34
58 cp-c1-c2 33 34 14
59 hc-c1-c2 43 34 14
60 c2-c1-c2 14 34 44
61 hc-c1-cp 33 34 43
62 cp-c1-c2 33 34 44
63 hc-c1-c2 43 34 44
64 hc-cp-cp 33 35 36
65 cp-cp-cp 33 35 37
66 hc-cp-cp 37 35 36
67 hc-cp-cp 35 37 38
68 cp-cp-cp 35 37 39
69 hc-cp-cp 39 37 38
70 hc-cp-cp 37 39 40
71 cp-cp-cp 37 39 41
72 hc-cp-cp 41 39 40
73 cp-cp-cp 31 41 39
74 hc-cp-cp 31 41 42
75 hc-cp-cp 39 41 42
76 c1-c2-c1 20 44 34
77 hc-c2-c1 45 44 20
78 hc-c2-c1 46 44 20
79 hc-c2-c1 45 44 34
80 hc-c2-c1 46 44 34
81 hc-c2-hc 45 44 46
Dihedrals
1 hc-cp-cp-c1 2 1 3 4
2 hc-cp-cp-cp 5 3 1 2
3 cp-cp-cp-c1 11 1 3 4
4 cp-cp-cp-cp 11 1 3 5
5 hc-cp-cp-cp 9 11 1 2
6 hc-cp-cp-hc 2 1 11 12
7 cp-cp-cp-cp 3 1 11 9
8 hc-cp-cp-cp 3 1 11 12
9 cp-cp-c1-hc 1 3 4 13
10 cp-cp-c1-c2 1 3 4 14
11 cp-cp-c1-hc 5 3 4 13
12 cp-cp-c1-c2 5 3 4 14
13 hc-cp-cp-cp 1 3 5 6
14 cp-cp-cp-cp 1 3 5 7
15 hc-cp-cp-c1 6 5 3 4
16 cp-cp-cp-c1 7 5 3 4
17 cp-c1-c2-hc 3 4 14 15
18 cp-c1-c2-hc 3 4 14 16
19 cp-c1-c2-c1 3 4 14 34
20 hc-c1-c2-hc 13 4 14 15
21 hc-c1-c2-hc 13 4 14 16
22 hc-c1-c2-c1 13 4 14 34
23 hc-cp-cp-cp 3 5 7 8
24 cp-cp-cp-cp 3 5 7 9
25 hc-cp-cp-hc 6 5 7 8
26 hc-cp-cp-cp 9 7 5 6
27 hc-cp-cp-cp 5 7 9 10
28 cp-cp-cp-cp 5 7 9 11
29 hc-cp-cp-hc 8 7 9 10
30 hc-cp-cp-cp 11 9 7 8
31 cp-cp-cp-cp 7 9 11 1
32 hc-cp-cp-cp 7 9 11 12
33 hc-cp-cp-cp 1 11 9 10
34 hc-cp-cp-hc 10 9 11 12
35 cp-c1-c2-c1 33 34 14 4
36 hc-c1-c2-c1 43 34 14 4
37 c2-c1-c2-c1 44 34 14 4
38 cp-c1-c2-hc 33 34 14 15
39 hc-c1-c2-hc 43 34 14 15
40 c2-c1-c2-hc 44 34 14 15
41 cp-c1-c2-hc 33 34 14 16
42 hc-c1-c2-hc 43 34 14 16
43 c2-c1-c2-hc 44 34 14 16
44 hc-cp-cp-c1 18 17 19 20
45 hc-cp-cp-cp 21 19 17 18
46 cp-cp-cp-c1 27 17 19 20
47 cp-cp-cp-cp 27 17 19 21
48 hc-cp-cp-cp 25 27 17 18
49 hc-cp-cp-hc 18 17 27 28
50 cp-cp-cp-cp 19 17 27 25
51 hc-cp-cp-cp 19 17 27 28
52 cp-cp-c1-hc 17 19 20 29
53 cp-cp-c1-c2 17 19 20 30
54 cp-cp-c1-c2 17 19 20 44
55 cp-cp-c1-hc 21 19 20 29
56 cp-cp-c1-c2 21 19 20 30
57 cp-cp-c1-c2 21 19 20 44
58 hc-cp-cp-cp 17 19 21 22
59 cp-cp-cp-cp 17 19 21 23
60 hc-cp-cp-c1 22 21 19 20
61 cp-cp-cp-c1 23 21 19 20
62 cp-c1-c2-c1 19 20 44 34
63 cp-c1-c2-hc 19 20 44 45
64 cp-c1-c2-hc 19 20 44 46
65 hc-c1-c2-c1 29 20 44 34
66 hc-c1-c2-hc 29 20 44 45
67 hc-c1-c2-hc 29 20 44 46
68 c2-c1-c2-c1 30 20 44 34
69 c2-c1-c2-hc 30 20 44 45
70 c2-c1-c2-hc 30 20 44 46
71 hc-cp-cp-cp 19 21 23 24
72 cp-cp-cp-cp 19 21 23 25
73 hc-cp-cp-hc 22 21 23 24
74 hc-cp-cp-cp 25 23 21 22
75 hc-cp-cp-cp 21 23 25 26
76 cp-cp-cp-cp 21 23 25 27
77 hc-cp-cp-hc 24 23 25 26
78 hc-cp-cp-cp 27 25 23 24
79 cp-cp-cp-cp 23 25 27 17
80 hc-cp-cp-cp 23 25 27 28
81 hc-cp-cp-cp 17 27 25 26
82 hc-cp-cp-hc 26 25 27 28
83 hc-cp-cp-c1 32 31 33 34
84 hc-cp-cp-cp 35 33 31 32
85 cp-cp-cp-c1 41 31 33 34
86 cp-cp-cp-cp 41 31 33 35
87 hc-cp-cp-cp 39 41 31 32
88 hc-cp-cp-hc 32 31 41 42
89 cp-cp-cp-cp 33 31 41 39
90 hc-cp-cp-cp 33 31 41 42
91 cp-cp-c1-c2 31 33 34 14
92 cp-cp-c1-hc 31 33 34 43
93 cp-cp-c1-c2 31 33 34 44
94 cp-cp-c1-c2 35 33 34 14
95 cp-cp-c1-hc 35 33 34 43
96 cp-cp-c1-c2 35 33 34 44
97 hc-cp-cp-cp 31 33 35 36
98 cp-cp-cp-cp 31 33 35 37
99 hc-cp-cp-c1 36 35 33 34
100 cp-cp-cp-c1 37 35 33 34
101 c2-c1-c2-c1 14 34 44 20
102 c2-c1-c2-hc 14 34 44 45
103 c2-c1-c2-hc 14 34 44 46
104 cp-c1-c2-c1 33 34 44 20
105 cp-c1-c2-hc 33 34 44 45
106 cp-c1-c2-hc 33 34 44 46
107 hc-c1-c2-c1 43 34 44 20
108 hc-c1-c2-hc 43 34 44 45
109 hc-c1-c2-hc 43 34 44 46
110 hc-cp-cp-cp 33 35 37 38
111 cp-cp-cp-cp 33 35 37 39
112 hc-cp-cp-hc 36 35 37 38
113 hc-cp-cp-cp 39 37 35 36
114 hc-cp-cp-cp 35 37 39 40
115 cp-cp-cp-cp 35 37 39 41
116 hc-cp-cp-hc 38 37 39 40
117 hc-cp-cp-cp 41 39 37 38
118 cp-cp-cp-cp 37 39 41 31
119 hc-cp-cp-cp 37 39 41 42
120 hc-cp-cp-cp 31 41 39 40
121 hc-cp-cp-hc 40 39 41 42
Impropers
1 hc-cp-cp-cp 3 1 11 2
2 cp-cp-cp-c1 1 3 5 4
3 hc-c1-cp-c2 3 4 13 14
4 hc-cp-cp-cp 3 5 7 6
5 hc-cp-cp-cp 5 7 9 8
6 hc-cp-cp-cp 7 9 11 10
7 hc-cp-cp-cp 1 11 9 12
8 hc-cp-cp-cp 19 17 27 18
9 cp-cp-cp-c1 17 19 21 20
10 hc-cp-cp-cp 19 21 23 22
11 hc-cp-cp-cp 21 23 25 24
12 hc-cp-cp-cp 23 25 27 26
13 hc-cp-cp-cp 17 27 25 28
14 hc-cp-cp-cp 33 31 41 32
15 cp-cp-cp-c1 31 33 35 34
16 hc-cp-cp-cp 33 35 37 36
17 hc-cp-cp-cp 35 37 39 38
18 hc-cp-cp-cp 37 39 41 40
19 hc-cp-cp-cp 31 41 39 42

294
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template
View File

@ -1,294 +0,0 @@
molecule template: end of styrene chain
30 atoms
31 bonds
51 angles
73 dihedrals
21 impropers
Types
1 2
2 2
3 6
4 2
5 2
6 1
7 2
8 1
9 2
10 1
11 2
12 1
13 5
14 1
15 2
16 1
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
Coords
1 59.89981112372972 62.733697275315585 59.09884284578856
2 61.41970248324232 63.42116581894993 59.52874545893742
3 60.864754970096406 62.91724243011892 59.559720865992695
4 62.139819000186826 61.41011937002877 60.81065044071466
5 60.036455711425084 57.160029629288026 60.31958663310848
6 59.734195751174056 58.18706337912225 60.20562410798949
7 57.64574781117771 57.712432799329 59.860109977091554
8 58.37408644866664 58.50134169314242 59.94422053768215
9 56.94300092269842 60.093170109004795 59.5955638127831
10 57.974275786582744 59.85577775892068 59.793714995577716
11 58.63231375134033 61.922969938852454 59.79065033121885
12 58.934573711591355 60.89593618901822 59.904612856337835
13 61.30908151524225 61.68041745837013 60.28316188676589
14 60.29468229868386 60.58165855333751 60.16601625920239
15 61.725768540066994 58.98982945913568 60.51467315154424
16 60.69449367618267 59.2272218092198 60.31652196874961
17 56.90935800040509 62.609851248143706 59.150831390216375
18 57.940632148874506 62.37245957639904 59.3489824055682
19 56.509546622906285 63.96428799226142 59.00032568066915
20 57.52394583946467 65.06304689729403 59.11747130823266
21 55.14943732039887 64.27856630628159 58.738922110361806
22 54.84717807556275 65.30559937777636 58.62495975268562
23 54.18913939539026 63.23840787618404 58.62802424960169
24 53.15786524692084 63.4757995479287 58.42987323424986
25 54.58895077288906 61.88397113206633 58.77852995914891
26 53.86061213540014 61.09506223825291 58.69441939855832
27 55.94906007539648 61.56969281804616 59.039933529456256
28 56.2513193202326 60.54265974655139 59.15389588713244
29 58.35468332440925 64.79274880895268 59.64495986218142
30 57.07961929431883 66.29987186904283 58.394030287459465
Charges
1 0.0354
2 0.0354
3 -0.0696
4 0.0516
5 0.1403
6 -0.1734
7 0.1288
8 -0.1134
9 0.1403
10 -0.1734
11 0.1237
12 -0.129
13 -0.0182
14 0.0266
15 0.1237
16 -0.129
17 -0.129
18 0.1237
19 0.0266
20 -0.0182
21 -0.129
22 0.1237
23 -0.1734
24 0.1403
25 -0.1134
26 0.1288
27 -0.1734
28 0.1403
29 0.0516
30 -0.0696
Bonds
1 10 1 3
2 10 2 3
3 8 4 13
4 1 6 5
5 1 8 7
6 2 8 6
7 1 10 9
8 2 10 8
9 1 12 11
10 2 12 10
11 9 13 3
12 7 14 13
13 2 14 12
14 1 16 15
15 2 16 14
16 2 16 6
17 1 17 18
18 2 17 19
19 2 17 27
20 7 19 20
21 2 19 21
22 9 20 30
23 9 20 3
24 1 21 22
25 2 21 23
26 1 23 24
27 2 23 25
28 1 25 26
29 2 25 27
30 1 27 28
31 8 29 20
Angles
1 16 20 3 13
2 14 2 3 20
3 14 1 3 20
4 14 2 3 13
5 14 1 3 13
6 15 2 3 1
7 2 16 6 8
8 1 16 6 5
9 1 8 6 5
10 1 10 8 7
11 2 10 8 6
12 1 6 8 7
13 1 12 10 9
14 2 12 10 8
15 1 8 10 9
16 1 14 12 11
17 2 14 12 10
18 1 10 12 11
19 10 14 13 4
20 11 14 13 3
21 12 4 13 3
22 9 16 14 13
23 2 16 14 12
24 9 12 14 13
25 1 14 16 15
26 1 6 16 15
27 2 14 16 6
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 3
37 12 29 20 30
38 12 29 20 3
39 13 30 20 3
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
Dihedrals
1 2 8 6 16 15
2 2 16 6 8 7
3 2 6 8 10 9
4 4 10 8 6 16
5 2 10 8 6 5
6 5 7 8 6 5
7 2 8 10 12 11
8 2 12 10 8 7
9 4 12 10 8 6
10 5 9 10 8 7
11 10 11 12 14 13
12 11 10 12 14 13
13 2 14 12 10 9
14 4 14 12 10 8
15 5 11 12 10 9
16 17 14 13 3 20
17 14 14 13 3 2
18 14 14 13 3 1
19 18 4 13 3 20
20 15 4 13 3 2
21 15 4 13 3 1
22 2 12 14 16 15
23 12 16 14 13 4
24 13 16 14 13 3
25 12 12 14 13 4
26 13 12 14 13 3
27 2 16 14 12 11
28 4 16 14 12 10
29 10 15 16 14 13
30 11 6 16 14 13
31 4 6 16 14 12
32 5 15 16 6 5
33 4 14 16 6 8
34 2 14 16 6 5
35 10 18 17 19 20
36 11 27 17 19 20
37 4 27 17 19 21
38 5 18 17 27 28
39 4 19 17 27 25
40 2 19 17 27 28
41 2 21 19 17 18
42 12 17 19 20 29
43 13 17 19 20 30
44 13 17 19 20 3
45 12 21 19 20 29
46 13 21 19 20 30
47 13 21 19 20 3
48 2 17 19 21 22
49 4 17 19 21 23
50 17 19 20 3 13
51 14 19 20 3 2
52 14 19 20 3 1
53 18 29 20 3 13
54 15 29 20 3 2
55 15 29 20 3 1
56 19 30 20 3 13
57 16 30 20 3 2
58 16 30 20 3 1
59 10 22 21 19 20
60 11 23 21 19 20
61 2 19 21 23 24
62 4 19 21 23 25
63 5 22 21 23 24
64 2 25 23 21 22
65 2 21 23 25 26
66 4 21 23 25 27
67 5 24 23 25 26
68 2 27 25 23 24
69 4 23 25 27 17
70 2 23 25 27 28
71 5 26 25 27 28
72 2 25 27 17 18
73 2 17 27 25 26
Impropers
1 1 2 3 13 20
2 1 1 3 13 20
3 1 2 3 1 20
4 1 2 3 1 13
5 1 16 6 8 5
6 1 10 8 6 7
7 1 12 10 8 9
8 1 14 12 10 11
9 7 14 13 4 3
10 5 16 14 12 13
11 1 14 16 6 15
12 1 19 17 27 18
13 5 17 19 21 20
14 1 19 20 29 30
15 1 19 20 29 3
16 1 19 20 30 3
17 1 29 20 30 3
18 1 19 21 23 22
19 1 21 23 25 24
20 1 23 25 27 26
21 1 17 27 25 28

319
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_pre.molecule_template Normal file
View File

@ -0,0 +1,319 @@
molecule template: end of styrene chain
30 atoms
31 bonds
51 angles
73 dihedrals
13 impropers
Coords
1 59.899810791 62.733695984 59.098842621
2 61.419700623 63.421165466 59.528743744
3 60.864753723 62.917243958 59.559719086
4 62.139820099 61.410118103 60.810649872
5 60.036457062 57.160030365 60.319587708
6 59.734195709 58.187065125 60.205623627
7 57.645748138 57.712432861 59.860111237
8 58.374088287 58.501342773 59.944221497
9 56.943000793 60.093170166 59.595561981
10 57.974277496 59.855777740 59.793716431
11 58.632312775 61.922969818 59.790649414
12 58.934574127 60.895935059 59.904613495
13 61.309082031 61.680416107 60.283161163
14 60.294681549 60.581657410 60.166015625
15 61.725769043 58.989830017 60.514671326
16 60.694492340 59.227222443 60.316520691
17 56.909358978 62.609851837 59.150833130
18 57.940631866 62.372459412 59.348983765
19 56.509548187 63.964286804 59.000324249
20 57.523944855 65.063049316 59.117469788
21 55.149436951 64.278564453 58.738922119
22 54.847179413 65.305603027 58.624958038
23 54.189140320 63.238407135 58.628025055
24 53.157863617 63.475799561 58.429874420
25 54.588951111 61.883972168 58.778530121
26 53.860610962 61.095062256 58.694419861
27 55.949058533 61.569694519 59.039932251
28 56.251319885 60.542659760 59.153896332
29 58.354682922 64.792747498 59.644958496
30 57.079620361 66.299873352 58.394031525
Types
1 hc
2 hc
3 c2
4 hc
5 hc
6 cp
7 hc
8 cp
9 hc
10 cp
11 hc
12 cp
13 c1
14 cp
15 hc
16 cp
17 cp
18 hc
19 cp
20 c1
21 cp
22 hc
23 cp
24 hc
25 cp
26 hc
27 cp
28 hc
29 hc
30 c2
Charges
1 0.035400
2 0.035400
3 -0.069600
4 0.051600
5 0.140300
6 -0.173400
7 0.128800
8 -0.113400
9 0.140300
10 -0.173400
11 0.123700
12 -0.129000
13 -0.018200
14 0.026600
15 0.123700
16 -0.129000
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
Molecules
1 1
2 1
3 1
4 1
5 1
6 1
7 1
8 1
9 1
10 1
11 1
12 1
13 1
14 1
15 1
16 1
17 1
18 1
19 1
20 1
21 1
22 1
23 1
24 1
25 1
26 1
27 1
28 1
29 1
30 1
Bonds
1 hc-c2 1 3
2 hc-c2 2 3
3 c1-c2 3 13
4 c1-c2 3 20
5 hc-c1 4 13
6 hc-cp 5 6
7 cp-cp 6 8
8 cp-cp 6 16
9 hc-cp 7 8
10 cp-cp 8 10
11 hc-cp 9 10
12 cp-cp 10 12
13 hc-cp 11 12
14 cp-cp 12 14
15 cp-c1 14 13
16 cp-cp 14 16
17 hc-cp 15 16
18 hc-cp 18 17
19 cp-cp 17 19
20 cp-cp 17 27
21 cp-c1 19 20
22 cp-cp 19 21
23 c1-c2 30 20
24 hc-c1 29 20
25 hc-cp 22 21
26 cp-cp 21 23
27 hc-cp 24 23
28 cp-cp 23 25
29 hc-cp 26 25
30 cp-cp 25 27
31 hc-cp 28 27
Angles
1 hc-c2-hc 1 3 2
2 hc-c2-c1 1 3 13
3 hc-c2-c1 1 3 20
4 hc-c2-c1 2 3 13
5 hc-c2-c1 2 3 20
6 c1-c2-c1 13 3 20
7 hc-cp-cp 5 6 8
8 hc-cp-cp 5 6 16
9 cp-cp-cp 8 6 16
10 hc-cp-cp 7 8 6
11 cp-cp-cp 6 8 10
12 hc-cp-cp 7 8 10
13 hc-cp-cp 9 10 8
14 cp-cp-cp 8 10 12
15 hc-cp-cp 9 10 12
16 hc-cp-cp 11 12 10
17 cp-cp-cp 10 12 14
18 hc-cp-cp 11 12 14
19 hc-c1-c2 4 13 3
20 cp-c1-c2 3 13 14
21 hc-c1-cp 4 13 14
22 cp-cp-c1 12 14 13
23 cp-cp-cp 12 14 16
24 cp-cp-c1 16 14 13
25 cp-cp-cp 6 16 14
26 hc-cp-cp 15 16 6
27 hc-cp-cp 15 16 14
28 hc-cp-cp 18 17 19
29 hc-cp-cp 18 17 27
30 cp-cp-cp 19 17 27
31 cp-cp-c1 17 19 20
32 cp-cp-cp 17 19 21
33 cp-cp-c1 21 19 20
34 cp-c1-c2 3 20 19
35 c2-c1-c2 3 20 30
36 hc-c1-c2 29 20 3
37 cp-c1-c2 30 20 19
38 hc-c1-cp 29 20 19
39 hc-c1-c2 29 20 30
40 hc-cp-cp 22 21 19
41 cp-cp-cp 19 21 23
42 hc-cp-cp 22 21 23
43 hc-cp-cp 24 23 21
44 cp-cp-cp 21 23 25
45 hc-cp-cp 24 23 25
46 hc-cp-cp 26 25 23
47 cp-cp-cp 23 25 27
48 hc-cp-cp 26 25 27
49 cp-cp-cp 17 27 25
50 hc-cp-cp 28 27 17
51 hc-cp-cp 28 27 25
Dihedrals
1 hc-c1-c2-hc 1 3 13 4
2 cp-c1-c2-hc 1 3 13 14
3 hc-c1-c2-hc 2 3 13 4
4 cp-c1-c2-hc 2 3 13 14
5 hc-c1-c2-c1 20 3 13 4
6 cp-c1-c2-c1 20 3 13 14
7 cp-c1-c2-hc 1 3 20 19
8 c2-c1-c2-hc 1 3 20 30
9 hc-c1-c2-hc 1 3 20 29
10 cp-c1-c2-hc 2 3 20 19
11 c2-c1-c2-hc 2 3 20 30
12 hc-c1-c2-hc 2 3 20 29
13 cp-c1-c2-c1 13 3 20 19
14 c2-c1-c2-c1 13 3 20 30
15 hc-c1-c2-c1 13 3 20 29
16 hc-cp-cp-hc 5 6 8 7
17 hc-cp-cp-cp 5 6 8 10
18 hc-cp-cp-cp 7 8 6 16
19 cp-cp-cp-cp 16 6 8 10
20 hc-cp-cp-cp 5 6 16 14
21 hc-cp-cp-hc 5 6 16 15
22 cp-cp-cp-cp 8 6 16 14
23 hc-cp-cp-cp 15 16 6 8
24 hc-cp-cp-cp 9 10 8 6
25 cp-cp-cp-cp 6 8 10 12
26 hc-cp-cp-hc 7 8 10 9
27 hc-cp-cp-cp 7 8 10 12
28 hc-cp-cp-cp 11 12 10 8
29 cp-cp-cp-cp 8 10 12 14
30 hc-cp-cp-hc 9 10 12 11
31 hc-cp-cp-cp 9 10 12 14
32 cp-cp-cp-c1 10 12 14 13
33 cp-cp-cp-cp 10 12 14 16
34 hc-cp-cp-c1 11 12 14 13
35 hc-cp-cp-cp 11 12 14 16
36 cp-cp-c1-c2 12 14 13 3
37 cp-cp-c1-c2 16 14 13 3
38 cp-cp-c1-hc 12 14 13 4
39 cp-cp-c1-hc 16 14 13 4
40 cp-cp-cp-cp 12 14 16 6
41 hc-cp-cp-cp 15 16 14 12
42 cp-cp-cp-c1 6 16 14 13
43 hc-cp-cp-c1 15 16 14 13
44 hc-cp-cp-c1 18 17 19 20
45 hc-cp-cp-cp 18 17 19 21
46 cp-cp-cp-c1 27 17 19 20
47 cp-cp-cp-cp 27 17 19 21
48 hc-cp-cp-cp 18 17 27 25
49 hc-cp-cp-hc 18 17 27 28
50 cp-cp-cp-cp 19 17 27 25
51 hc-cp-cp-cp 28 27 17 19
52 cp-cp-c1-c2 17 19 20 3
53 cp-cp-c1-c2 17 19 20 30
54 cp-cp-c1-hc 17 19 20 29
55 cp-cp-c1-c2 21 19 20 3
56 cp-cp-c1-c2 21 19 20 30
57 cp-cp-c1-hc 21 19 20 29
58 hc-cp-cp-cp 22 21 19 17
59 cp-cp-cp-cp 17 19 21 23
60 hc-cp-cp-c1 22 21 19 20
61 cp-cp-cp-c1 23 21 19 20
62 hc-cp-cp-cp 24 23 21 19
63 cp-cp-cp-cp 19 21 23 25
64 hc-cp-cp-hc 22 21 23 24
65 hc-cp-cp-cp 22 21 23 25
66 hc-cp-cp-cp 26 25 23 21
67 cp-cp-cp-cp 21 23 25 27
68 hc-cp-cp-hc 24 23 25 26
69 hc-cp-cp-cp 24 23 25 27
70 cp-cp-cp-cp 23 25 27 17
71 hc-cp-cp-cp 28 27 25 23
72 hc-cp-cp-cp 26 25 27 17
73 hc-cp-cp-hc 26 25 27 28
Impropers
1 hc-cp-cp-cp 5 6 8 16
2 hc-cp-cp-cp 7 8 6 10
3 hc-cp-cp-cp 9 10 8 12
4 hc-cp-cp-cp 11 12 10 14
5 hc-c1-cp-c2 4 13 3 14
6 cp-cp-cp-c1 12 14 16 13
7 hc-cp-cp-cp 15 16 14 6
8 hc-cp-cp-cp 18 17 19 27
9 cp-cp-cp-c1 17 19 21 20
10 hc-cp-cp-cp 22 21 19 23
11 hc-cp-cp-cp 24 23 21 25
12 hc-cp-cp-cp 26 25 23 27
13 hc-cp-cp-cp 28 27 25 17

10
examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene
View File

@ -6,9 +6,7 @@ boundary p p p
atom_style full atom_style full
kspace_style pppm 1.0e-4 pair_style lj/class2/coul/cut 8.5
pair_style lj/class2/coul/long 8.5
angle_style class2 angle_style class2
@ -27,13 +25,13 @@ read_data trimer.data &
extra/improper/per/atom 25 & extra/improper/per/atom 25 &
extra/special/per/atom 25 extra/special/per/atom 25
molecule mol1 grow_styrene_pre.data_template molecule mol1 grow_styrene_pre.molecule_template
molecule mol2 grow_styrene_post.data_template molecule mol2 grow_styrene_post.molecule_template
fix myrxns all bond/react stabilization yes statted_grp .03 & fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map & react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 & modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 30 stabilize_steps 200 max_rxn 30
fix 1 statted_grp_REACT nvt temp $T $T 100 fix 1 statted_grp_REACT nvt temp $T $T 100

196
examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1
View File

@ -1,196 +0,0 @@
LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.077 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 125000 91125
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 39 39 39
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 48.02 | 48.02 | 48.02 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.9852 -52.954497 0.00034590142 13
4100 3021.3611 -65.03731 0.00036752025 14
4200 3002.7136 1.5750081 0.00036752025 14
4300 3218.6248 -120.74039 0.00038913909 15
4400 3345.1482 -0.96545269 0.00038913909 15
4500 3603.2429 1.2438833 0.00038913909 15
4600 3129.8814 -249.91806 0.00041075793 16
4700 3769.052 -289.24351 0.00043237677 17
4800 3560.4714 -3.1655406 0.00043237677 17
4900 3452.2717 -2.1270765 0.00043237677 17
5000 3594.3247 -523.48506 0.00045399561 18
5100 3578.4199 1.0009097 0.00045399561 18
5200 3822.1566 1.0526914 0.00047561445 19
5300 3901.8883 -0.14607602 0.00047561445 19
5400 4059.3644 -1.7789927 0.00049723329 20
5500 4163.6847 1.0240127 0.00049723329 20
5600 4109.1649 0.80199787 0.00049723329 20
5700 4391.2091 2.8730036 0.00049723329 20
5800 4279.6579 -0.36499822 0.00051885212 21
5900 4296.2695 -1.3064528 0.00051885212 21
6000 4065.3758 -2.0483224 0.00051885212 21
6100 4772.5362 -2.6814694 0.00054047096 22
6200 4627.029 2.999215 0.0005620898 23
6300 5120.7881 0.65372968 0.00058370864 24
6400 4588.9559 3.7570705 0.00058370864 24
6500 5008.7814 2.3595833 0.00060532748 25
6600 5195.0053 1.4641612 0.00060532748 25
6700 5622.293 -0.33396047 0.00062694632 26
6800 5515.1957 -4.234874 0.00062694632 26
6900 5156.7455 0.40171954 0.00064856516 27
7000 5120.1639 -1.6065245 0.00064856516 27
7100 5650.0327 0.94436323 0.00067018399 28
7200 5985.1115 -3.8940347 0.00069180283 29
7300 5983.197 0.5293568 0.00069180283 29
7400 6001.1559 -0.13712834 0.00071342167 30
7500 5889.2134 0.17230892 0.00071342167 30
7600 5797.31 2.0920058 0.00071342167 30
7700 5865.2783 -0.18556395 0.00071342167 30
7800 6207.0659 -5.6237083 0.00071342167 30
7900 5627.5108 -2.3718942 0.00071342167 30
8000 5823.9502 -0.85418578 0.00071342167 30
Loop time of 184.87 on 1 procs for 8000 steps with 528 atoms
Performance: 3.739 ns/day, 6.419 hours/ns, 43.274 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3043 | 3.3043 | 3.3043 | 0.0 | 1.79
Bond | 8.0003 | 8.0003 | 8.0003 | 0.0 | 4.33
Kspace | 168.33 | 168.33 | 168.33 | 0.0 | 91.05
Neigh | 4.6322 | 4.6322 | 4.6322 | 0.0 | 2.51
Comm | 0.077927 | 0.077927 | 0.077927 | 0.0 | 0.04
Output | 0.0020548 | 0.0020548 | 0.0020548 | 0.0 | 0.00
Modify | 0.5005 | 0.5005 | 0.5005 | 0.0 | 0.27
Other | | 0.02483 | | | 0.01
Nlocal: 528.000 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 341.000 ave 341 max 341 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35111.0 ave 35111 max 35111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35111
Ave neighs/atom = 66.498106
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:03:05

196
examples/PACKAGES/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4
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@ -1,196 +0,0 @@
LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 2 by 2 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 39200 24300
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 39 39 39
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 38.70 | 38.92 | 39.43 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.2204 -53.187892 0.00034590142 13
4100 3024.6375 -65.068146 0.00036752025 14
4200 3004.6784 1.4155214 0.00036752025 14
4300 3033.1895 1.8572273 0.00036752025 14
4400 3157.2542 -0.92462977 0.00036752025 14
4500 3557.7137 -194.46498 0.00038913909 15
4600 3096.485 -1.830492 0.00038913909 15
4700 3488.088 -286.81055 0.00041075793 16
4800 3390.5493 -372.77818 0.00043237677 17
4900 3773.7226 -446.58574 0.00045399561 18
5000 3703.0159 -0.81188551 0.00045399561 18
5100 4051.3067 1.2567439 0.00045399561 18
5200 3813.3682 0.92945737 0.00047561445 19
5300 4036.0078 -2.5336258 0.00049723329 20
5400 4219.803 -0.96928261 0.00049723329 20
5500 4433.7447 -0.026762463 0.00051885212 21
5600 4477.4505 -1.417316 0.00054047096 22
5700 4500.0306 -1.0551443 0.00054047096 22
5800 4600.3507 -4.9580056 0.00054047096 22
5900 4765.4978 -2.2546941 0.0005620898 23
6000 5442.6193 0.91161284 0.00058370864 24
6100 5086.8047 -0.9875332 0.00060532748 25
6200 5485.3437 -2.8296626 0.00062694632 26
6300 4988.0396 -0.15179023 0.00064856516 27
6400 5597.3703 4.2941885 0.00067018399 28
6500 5677.0263 -2.8611595 0.00069180283 29
6600 6058.0009 1.4111778 0.00071342167 30
6700 5859.0817 -2.5782466 0.00071342167 30
6800 5879.3941 -4.5681807 0.00071342167 30
6900 6398.288 2.5259412 0.00071342167 30
7000 6250.1096 -2.6049627 0.00071342167 30
7100 5849.651 -0.44062578 0.00071342167 30
7200 5778.6532 -0.27299118 0.00071342167 30
7300 5977.6661 4.2483639 0.00071342167 30
7400 5862.4231 1.0289519 0.00071342167 30
7500 6482.376 7.5412373 0.00071342167 30
7600 5810.4325 1.0343075 0.00071342167 30
7700 5916.7304 2.304302 0.00071342167 30
7800 5869.9504 -0.5946555 0.00071342167 30
7900 5804.0522 -4.1207689 0.00071342167 30
8000 6077.1704 0.52211243 0.00071342167 30
Loop time of 60.5603 on 4 procs for 8000 steps with 528 atoms
Performance: 11.413 ns/day, 2.103 hours/ns, 132.100 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0041695 | 0.90113 | 2.3423 | 102.8 | 1.49
Bond | 0.011606 | 2.1188 | 5.8107 | 163.9 | 3.50
Kspace | 47.987 | 52.817 | 55.679 | 43.7 | 87.21
Neigh | 3.5961 | 3.6262 | 3.6496 | 1.2 | 5.99
Comm | 0.11097 | 0.16569 | 0.26369 | 15.3 | 0.27
Output | 0.0020366 | 0.0023427 | 0.0032469 | 1.1 | 0.00
Modify | 0.62302 | 0.91659 | 1.1227 | 21.5 | 1.51
Other | | 0.0126 | | | 0.02
Nlocal: 132.000 ave 295 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 133.000 ave 349 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 8383.50 ave 20143 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 33534
Ave neighs/atom = 63.511364
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:00

256
examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.1 Normal file
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@ -0,0 +1,256 @@
LAMMPS (4 Nov 2022)
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
boundary p p p
atom_style full
pair_style lj/class2/coul/cut 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data trimer.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-200 -200 -200) to (200 200 200)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
48 atoms
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
20 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
molecule mol1 grow_styrene_pre.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
30 atoms with max type 4
31 bonds with max type 6
51 angles with max type 10
73 dihedrals with max type 13
13 impropers with max type 3
molecule mol2 grow_styrene_post.molecule_template
Read molecule template mol2:
1 molecules
1 fragments
46 atoms with max type 4
48 bonds with max type 6
81 angles with max type 10
121 dihedrals with max type 13
19 impropers with max type 3
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map modify_create fit create_fit overlap 2.0 stabilize_steps 200 max_rxn 30
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo 100
dump 1 all xyz 1 test_vis.xyz
run 8000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 6 of 6 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 77 77 77
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 36.99 | 36.99 | 36.99 Mbytes
Step Temp Press Density f_myrxns[1]
0 0 0.076588866 8.1070333e-06 0
100 598.41967 -0.1670029 1.0809378e-05 1
200 696.77845 0.11857422 1.0809378e-05 1
300 932.97222 -0.058615676 1.3511722e-05 2
400 1016.3732 0.062233715 1.3511722e-05 2
500 1006.451 -0.17987841 1.6214067e-05 3
600 1143.8859 0.33297898 1.6214067e-05 3
700 1209.6144 -0.22743773 1.8916411e-05 4
800 1429.1639 0.14048255 1.8916411e-05 4
900 1375.0968 -0.04016551 2.1618755e-05 5
1000 1583.6696 -0.23364852 2.1618755e-05 5
1100 1811.0697 -0.054436797 2.43211e-05 6
1200 1928.4658 0.012242837 2.43211e-05 6
1300 1666.6176 0.057157656 2.43211e-05 6
1400 1686.18 -28.442814 2.7023444e-05 7
1500 1704.6248 -0.16861218 2.7023444e-05 7
1600 2171.7628 -33.6156 2.9725789e-05 8
1700 1991.2922 -0.11813381 2.9725789e-05 8
1800 2037.4991 -40.015612 3.2428133e-05 9
1900 2143.9447 -0.090964375 3.2428133e-05 9
2000 1927.9564 0.29856007 3.2428133e-05 9
2100 2255.5877 -4.9166327 3.5130478e-05 10
2200 2512.5193 0.00044804842 3.5130478e-05 10
2300 2336.1503 -45.094726 3.7832822e-05 11
2400 2508.9655 -0.1024684 3.7832822e-05 11
2500 2747.7344 -53.939212 4.0535167e-05 12
2600 2790.5736 0.07042181 4.0535167e-05 12
2700 3014.7092 -0.0025387793 4.0535167e-05 12
2800 2745.0295 -0.099361314 4.3237511e-05 13
2900 2952.1281 -0.13667582 4.3237511e-05 13
3000 3032.5298 0.28882784 4.5939855e-05 14
3100 3149.992 0.55269076 4.5939855e-05 14
3200 3422.5233 -0.11794908 4.86422e-05 15
3300 3040.2691 -0.067532834 4.86422e-05 15
3400 3323.3263 0.049969149 5.1344544e-05 16
3500 3539.0877 -0.065546641 5.1344544e-05 16
3600 3894.6897 -0.24222461 5.4046889e-05 17
3700 3689.3513 0.21366533 5.4046889e-05 17
3800 3924.799 -0.60817646 5.6749233e-05 18
3900 3713.1947 -0.024834682 5.6749233e-05 18
4000 3887.6151 0.052787631 5.9451578e-05 19
4100 3868.2877 0.42532898 5.9451578e-05 19
4200 3784.9874 -0.12018512 5.9451578e-05 19
4300 4169.9997 0.19652089 6.2153922e-05 20
4400 4112.291 -0.084839982 6.2153922e-05 20
4500 3974.2226 -0.13641761 6.2153922e-05 20
4600 4064.3852 0.16435039 6.2153922e-05 20
4700 3880.0044 -0.42874552 6.2153922e-05 20
4800 4508.2324 0.20208091 6.2153922e-05 20
4900 4364.033 -0.56300441 6.2153922e-05 20
5000 4030.4642 -0.29006515 6.2153922e-05 20
5100 4010.9518 0.32060145 6.2153922e-05 20
5200 4058.5072 0.088924924 6.2153922e-05 20
5300 4529.9866 -0.38882748 6.4856266e-05 21
5400 4305.9161 0.24046553 6.4856266e-05 21
5500 4556.8628 -0.014044879 6.4856266e-05 21
5600 4730.2206 0.1526293 6.4856266e-05 21
5700 4810.9968 -17.600253 6.7558611e-05 22
5800 4655.651 -0.25941928 6.7558611e-05 22
5900 4507.1045 -0.084691005 6.7558611e-05 22
6000 4516.0965 0.092662842 7.0260955e-05 23
6100 4592.4068 0.10403004 7.0260955e-05 23
6200 4583.9491 0.1692786 7.29633e-05 24
6300 4512.226 0.32590723 7.29633e-05 24
6400 4885.9205 -0.24208842 7.5665644e-05 25
6500 5250.5008 0.4135064 7.5665644e-05 25
6600 5216.9452 0.00059199905 7.8367989e-05 26
6700 5302.2925 0.50452368 7.8367989e-05 26
6800 4931.7328 -0.064719953 8.1070333e-05 27
6900 5549.8746 0.55101191 8.1070333e-05 27
7000 5472.9107 0.31358281 8.3772677e-05 28
7100 5559.9339 0.14034743 8.3772677e-05 28
7200 5726.4492 -0.39732059 8.6475022e-05 29
7300 5869.324 0.18989804 8.6475022e-05 29
7400 6109.5519 0.11206572 8.9177366e-05 30
7500 5966.7085 0.2059557 8.9177366e-05 30
7600 6051.2064 0.025316679 8.9177366e-05 30
7700 5719.6669 0.16548544 8.9177366e-05 30
7800 6118.8183 -0.20036999 8.9177366e-05 30
7900 6477.1901 0.10308473 8.9177366e-05 30
8000 6241.9498 0.090165102 8.9177366e-05 30
Loop time of 17.4848 on 1 procs for 8000 steps with 528 atoms
Performance: 39.531 ns/day, 0.607 hours/ns, 457.540 timesteps/s, 241.581 katom-step/s
97.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0991 | 3.0991 | 3.0991 | 0.0 | 17.72
Bond | 7.6807 | 7.6807 | 7.6807 | 0.0 | 43.93
Neigh | 1.6906 | 1.6906 | 1.6906 | 0.0 | 9.67
Comm | 0.019091 | 0.019091 | 0.019091 | 0.0 | 0.11
Output | 4.5095 | 4.5095 | 4.5095 | 0.0 | 25.79
Modify | 0.46277 | 0.46277 | 0.46277 | 0.0 | 2.65
Other | | 0.02296 | | | 0.13
Nlocal: 528 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35904 ave 35904 max 35904 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35904
Ave neighs/atom = 68
Ave special neighs/atom = 11.409091
Neighbor list builds = 1836
Dangerous builds = 0
# write_data final.data nofix
Total wall time: 0:00:17

256
examples/PACKAGES/reaction/create_atoms_polystyrene/log.4Nov2022.grow_styrene.g++.4 Normal file
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@ -0,0 +1,256 @@
LAMMPS (4 Nov 2022)
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
boundary p p p
atom_style full
pair_style lj/class2/coul/cut 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data trimer.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-200 -200 -200) to (200 200 200)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
48 atoms
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
20 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
molecule mol1 grow_styrene_pre.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
30 atoms with max type 4
31 bonds with max type 6
51 angles with max type 10
73 dihedrals with max type 13
13 impropers with max type 3
molecule mol2 grow_styrene_post.molecule_template
Read molecule template mol2:
1 molecules
1 fragments
46 atoms with max type 4
48 bonds with max type 6
81 angles with max type 10
121 dihedrals with max type 13
19 impropers with max type 3
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map modify_create fit create_fit overlap 2.0 stabilize_steps 200 max_rxn 30
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo 100
dump 1 all xyz 1 test_vis.xyz
run 8000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 6 of 6 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 77 77 77
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 35.37 | 35.56 | 36.15 Mbytes
Step Temp Press Density f_myrxns[1]
0 0 0.076588866 8.1070333e-06 0
100 598.29879 -0.17888669 1.0809378e-05 1
200 699.08337 0.11172183 1.0809378e-05 1
300 931.85797 -0.13923465 1.3511722e-05 2
400 893.78126 0.14680427 1.3511722e-05 2
500 1001.0848 -0.021703999 1.6214067e-05 3
600 989.24943 0.04641672 1.6214067e-05 3
700 1244.794 -0.19464667 1.8916411e-05 4
800 1210.997 -0.06710628 1.8916411e-05 4
900 1310.0005 0.099408095 2.1618755e-05 5
1000 1640.5956 -0.05975911 2.1618755e-05 5
1100 1380.7273 -0.025206389 2.1618755e-05 5
1200 1637.6542 0.057149266 2.43211e-05 6
1300 1757.3409 0.3232123 2.43211e-05 6
1400 1664.5048 -0.29656858 2.7023444e-05 7
1500 1578.9691 0.21997047 2.7023444e-05 7
1600 1848.9227 -0.11783672 2.9725789e-05 8
1700 1981.1695 0.28374154 2.9725789e-05 8
1800 2330.8852 -0.082109894 3.2428133e-05 9
1900 2177.4096 0.23853778 3.2428133e-05 9
2000 2095.1618 -1.5405667 3.5130478e-05 10
2100 2272.2653 0.05572226 3.5130478e-05 10
2200 2599.5994 -2.2307507 3.7832822e-05 11
2300 2457.7904 0.40228312 3.7832822e-05 11
2400 2372.9736 -3.3415973 4.0535167e-05 12
2500 2427.4613 -0.16211888 4.0535167e-05 12
2600 3022.2608 -4.3278098 4.3237511e-05 13
2700 3115.6526 0.013828954 4.3237511e-05 13
2800 2841.7091 -6.4163443 4.5939855e-05 14
2900 3047.8436 0.16052429 4.5939855e-05 14
3000 3373.7997 -7.7904706 4.86422e-05 15
3100 3381.6653 0.35152687 4.86422e-05 15
3200 3589.5561 -10.754027 5.1344544e-05 16
3300 3473.4415 -0.13274479 5.1344544e-05 16
3400 3696.3283 -13.75504 5.4046889e-05 17
3500 3486.5442 -0.31091832 5.4046889e-05 17
3600 3647.0818 0.34662993 5.4046889e-05 17
3700 3636.7138 -0.041981737 5.4046889e-05 17
3800 3427.6532 0.42008936 5.6749233e-05 18
3900 3574.0094 -0.05475272 5.6749233e-05 18
4000 4158.9339 0.14426361 5.9451578e-05 19
4100 3862.5026 0.094232438 5.9451578e-05 19
4200 3969.4378 -0.10602108 6.2153922e-05 20
4300 3840.0126 0.29190336 6.2153922e-05 20
4400 4365.9912 -36.954812 6.4856266e-05 21
4500 4565.3708 0.061879092 6.4856266e-05 21
4600 4565.491 -70.588435 6.7558611e-05 22
4700 4570.2702 -0.56661378 6.7558611e-05 22
4800 4445.786 0.20534323 6.7558611e-05 22
4900 4782.6436 0.012783481 7.0260955e-05 23
5000 4777.2132 0.092416308 7.0260955e-05 23
5100 4944.0402 0.11614993 7.29633e-05 24
5200 5139.165 -0.23180938 7.29633e-05 24
5300 4647.2328 0.13570142 7.5665644e-05 25
5400 4982.7355 -0.25477884 7.5665644e-05 25
5500 5400.5924 0.19902824 7.8367989e-05 26
5600 5761.3552 0.083102065 7.8367989e-05 26
5700 5723.8581 0.039332796 8.1070333e-05 27
5800 5548.0789 -0.14511631 8.1070333e-05 27
5900 5358.5431 -0.099694264 8.3772677e-05 28
6000 5591.2678 9.9924655e-05 8.3772677e-05 28
6100 6101.8008 0.26538732 8.6475022e-05 29
6200 5848.9979 0.091137862 8.6475022e-05 29
6300 5582.1828 -0.039900602 8.9177366e-05 30
6400 6077.0548 0.3191104 8.9177366e-05 30
6500 5794.6827 0.69322336 8.9177366e-05 30
6600 5610.4331 0.080420058 8.9177366e-05 30
6700 5615.3492 0.12810868 8.9177366e-05 30
6800 5900.9749 -0.31704866 8.9177366e-05 30
6900 6233.9524 0.010288514 8.9177366e-05 30
7000 5972.7488 -1.0442089 8.9177366e-05 30
7100 6258.1332 0.56270399 8.9177366e-05 30
7200 6172.5919 -0.19595153 8.9177366e-05 30
7300 5898.7547 0.020862491 8.9177366e-05 30
7400 5815.1659 -0.0020680171 8.9177366e-05 30
7500 6003.867 -0.12288131 8.9177366e-05 30
7600 5966.0609 -0.1504333 8.9177366e-05 30
7700 6274.3331 -0.62752757 8.9177366e-05 30
7800 6051.0914 0.22821201 8.9177366e-05 30
7900 5981.5209 -0.19623554 8.9177366e-05 30
8000 5835.4657 0.3602475 8.9177366e-05 30
Loop time of 13.936 on 4 procs for 8000 steps with 528 atoms
Performance: 49.598 ns/day, 0.484 hours/ns, 574.051 timesteps/s, 303.099 katom-step/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.001058 | 0.78388 | 3.1317 | 153.1 | 5.62
Bond | 0.0031874 | 2.0525 | 8.1984 | 247.7 | 14.73
Neigh | 0.53495 | 0.53527 | 0.53551 | 0.0 | 3.84
Comm | 0.01177 | 0.012451 | 0.013306 | 0.5 | 0.09
Output | 1.3336 | 1.4735 | 1.7322 | 13.2 | 10.57
Modify | 0.55142 | 9.0568 | 12.031 | 163.3 | 64.99
Other | | 0.02159 | | | 0.15
Nlocal: 132 ave 528 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 9115.75 ave 36463 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 36463
Ave neighs/atom = 69.058712
Ave special neighs/atom = 11.409091
Neighbor list builds = 771
Dangerous builds = 0
# write_data final.data nofix
Total wall time: 0:00:13

1303
examples/PACKAGES/reaction/create_atoms_polystyrene/trimer.data
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