Issue with Bond Formation between Two Atoms in a Molecular Template

Hi everyone,

I’m currently working on constructing a molecular template and I’m having trouble with bond formation between two of the atoms. The output file shows that the reaction is taking place, however, the final structure does not seem to have formed the expected new bond.

Can anyone provide insight into why this might be happening? Any suggestions for troubleshooting would be greatly appreciated.

Thank you!
Here is my input file:
input:
velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template

thermo 50

dump 1 all atom 50 dump.deposit.atom

fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 5 mol1 mol2 rxn1_stp1_map

fix 1 statted_grp_REACT nvt temp 300 300 100
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density f_myrxns[1] #f_myrxns[2]

run 100000
write_data out.data

Pre-reaction template:
7 atoms
5 bonds
4 angles
1 impropers

Types

1 3
2 4
3 6
4 6
5 3
6 9
7 5

Charges

1 0.0000
2 0.0000
3 0.0000
4 0.0000
5 0.0000
6 0.0000
7 0.0000

Coords

1 4.7600 -3.2700 0.0300
2 3.4900 -3.6000 -0.2000
3 5.5500 -4.0000 -0.0300
4 5.0300 -2.2600 0.2800
5 6.0100 -6.5900 0.1500
6 6.8500 -5.5600 0.0600
7 8.2400 -5.5400 0.6100

Bonds

1 3 1 2
2 4 1 3
3 4 1 4
4 12 5 6
5 13 6 7

Angles

1 3 2 1 3
2 3 2 1 4
3 4 3 1 4
4 19 5 6 7

Impropers

1 1 2 3 1 4

Post-reaction template:
7 atoms
6 bonds
4 angles
1 impropers

Types

1 3
2 4
3 6
4 6
5 3
6 9
7 5

Charges

1 0.0000
2 0.0000
3 0.0000
4 0.0000
5 0.0000
6 0.0000
7 0.0000

Coords

1 4.7600 -3.2700 0.0300
2 3.4900 -3.6000 -0.2000
3 5.5500 -4.0000 -0.0300
4 5.0300 -2.2600 0.2800
5 6.0100 -6.5900 0.1500
6 6.8500 -5.5600 0.0600
7 8.2400 -5.5400 0.6100

Bonds

1 3 1 2
2 4 1 3
3 4 1 4
4 12 5 6
5 13 6 7
6 14 1 6

Angles

1 3 2 1 3
2 3 2 1 4
3 4 3 1 4
4 19 5 6 7

Impropers

1 1 2 3 1 4

Map:
3 edgeIDs
7 equivalences

BondingIDs

1
6

EdgeIDs

2
5
7

Equivalences

1 1
2 2
3 3
4 4
5 5
6 6
7 7

Output file:
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:940)
Per MPI rank memory allocation (min/avg/max) = 21.94 | 23.03 | 23.94 Mbytes
Step Temp Press Density f_myrxns[1]
40000 300 7696.5495 1.3166147 0
40050 282.15512 -692.57079 1.3166147 1
40100 283.10287 6613.0668 1.3166147 1
40150 305.3794 -9385.778 1.3166147 1
40200 311.95165 -1525.2818 1.3166147 1
40250 269.13037 7636.6255 1.3166147 1
40300 298.5939 3434.2697 1.3166147 1

For future reference, please include the full input script and other required files required to test your system, such as the data file. Also, it is easier for us if you attach the files, rather than pasting them into the post.

The problem here is that you don’t have enough atoms in your reaction templates. Because your system includes dihedrals/impropers, you should include atoms at least three bonds away from reacting atoms. Typically these types of templates would throw an error, but you are slipping through the error checks because none of your atom types are changing between the pre- and post reaction template.

I tried to upload a file but was notified that I am unable to do so as a new user. Here are my input and output files.

in.gro2lam:

units real
boundary p p p
atom_style full

atom_modify map array
pair_style lj/cut/coul/cut 8.5 10
bond_style harmonic
angle_style harmonic
dihedral_style fourier
improper_style cvff

read_data data.gro2lam

neighbor 1.9 bin
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.8333
pair_modify shift no tail yes mix arithmetic
neigh_modify every 1 delay 1 check yes

timestep 1
dump myDump all atom 100 dump.lammpstrj

thermo 10
thermo_style custom step temp press vol epair emol etotal enthalpy

velocity all create 300 1234567 rot yes dist gaussian

fix npt_name1 all npt temp 300 300 100 iso 50 50 1000
thermo_style custom step temp etotal ke pe
thermo_modify format float %20.10g
run 40000
unfix npt_name1

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template

thermo 50

dump 1 all atom 50 dump.deposit.atom

dump 1 all xyz 1 test_vis.xyz

fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 5 mol1 mol2 rxn1_stp1_map

fix 1 statted_grp_REACT nvt temp 300 300 100

optionally, you can customize behavior of reacting atoms,

by using the internally-created ‘bond_react_MASTER_group’, like so:

fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density f_myrxns[1] #f_myrxns[2]

restart 100 restart1 restart2

run 100000
write_data 123

write_restart restart_longrun

write_data restart_longrun.data

data.gro2lam:
#Lammps data file. Generated with GRO2LAM converter.

75 atoms
79 bonds
136 angles
177 dihedrals
7 impropers

9 atom types
13 bond types
20 angle types
17 dihedral types
3 improper types

-4.5800 15.4200 xlo xhi
-7.5100 12.4900 ylo yhi
-5.5000 14.5000 zlo zhi

Masses

1 15.999405 # os
2 65.377783 # UF_Zn
3 12.010736 # c2
4 12.010736 # ce
5 12.010736 # c3
6 1.007941 # ha
7 1.007941 # hc
8 18.998403 # f
9 12.010736 # c1

Pair Coeffs #

1 0.16992 3.00001
2 0.12394 2.46155
3 0.08596 3.39967
4 0.08596 3.39967
5 0.10935 3.39967
6 0.01499 2.59964
7 0.01569 2.64953
8 0.06097 3.11815
9 0.20990 3.39967

Bond Coeffs #harmonic

1 298.6144 1.8240
2 298.6144 1.8515
3 547.0385 1.3461
4 342.9361 1.0879
5 320.5468 1.5159
6 382.6171 1.4574
7 330.4421 1.0969
8 374.7209 1.3710
9 326.6438 1.5095
10 356.7295 1.3497
11 389.0141 1.3596
12 624.7014 1.3070
13 371.4225 1.4671

Angle Coeffs #harmonic

1 59.72289 108.54600
2 59.72289 115.16200
3 49.47635 120.45000
4 38.08180 116.90000
5 63.96942 122.53000
6 65.36875 123.26000
7 63.36971 117.12000
8 46.77764 110.59000
9 39.38118 107.58000
10 69.16694 115.19000
11 59.72289 124.32600
12 59.72289 128.03100
13 66.36828 110.76000
14 70.86613 107.36000
15 68.66718 112.80000
16 74.26450 115.05000
17 59.72289 127.55900
18 50.57582 120.42000
19 59.72289 124.82700
20 48.37688 109.41000

Dihedral Coeffs #fourier

1 1 0.00000 1 0
2 1 0.00000 1 0
3 1 0.00000 1 0
4 1 0.00000 1 0
5 1 0.00000 1 0
6 1 1.04950 2 180
7 1 1.04950 2 180
8 1 0.00000 1 0
9 1 0.99952 2 180
10 1 6.64682 2 180
11 1 0.99952 2 180
12 1 6.64682 2 180
13 1 0.00000 1 0
14 1 0.00000 1 0
15 1 0.00000 2 0
16 1 0.00000 2 180
17 1 0.00000 2 180

Improper Coeffs #cvff

1 1.09947 -1 2
2 1.09947 -1 2
3 1.09947 -1 2

Atoms #full

1 1 1 0.0000 -0.0300 -0.1000 0.1200 # os
2 1 2 0.0000 -0.5800 0.8400 -1.3500 # UF_Zn
3 1 2 0.0000 1.7700 0.1800 0.3600 # UF_Zn
4 1 2 0.0000 -0.3100 -1.8900 -0.2200 # UF_Zn
5 1 2 0.0000 -0.9000 0.3300 1.6600 # UF_Zn
6 1 3 0.0000 -3.8500 -2.5600 3.6300 # c2
7 1 4 0.0000 -3.1000 -3.0600 2.6600 # ce
8 1 5 0.0000 -3.1600 -4.4800 2.1700 # c3
9 1 4 0.0000 -2.1100 -2.1900 1.9600 # ce
10 1 1 0.0000 -2.0300 -0.9800 2.3200 # os
11 1 1 0.0000 -1.4200 -2.7000 1.0400 # os
12 1 6 0.0000 -4.5800 -3.1600 4.1500 # ha
13 1 6 0.0000 -3.7500 -1.5300 3.9200 # ha
14 1 7 0.0000 -3.3800 -4.5000 1.1100 # hc
15 1 7 0.0000 -2.1900 -4.9600 2.3100 # hc
16 1 7 0.0000 -3.9200 -5.0400 2.7100 # hc
17 1 3 0.0000 -2.7300 -3.2200 -3.8700 # c2
18 1 4 0.0000 -2.5300 -1.9100 -3.7700 # ce
19 1 5 0.0000 -3.0800 -0.8900 -4.7100 # c3
20 1 4 0.0000 -1.7100 -1.3700 -2.6400 # ce
21 1 1 0.0000 -1.5500 -0.1300 -2.5900 # os
22 1 1 0.0000 -1.2200 -2.1900 -1.8200 # os
23 1 6 0.0000 -3.3200 -3.6400 -4.6700 # ha
24 1 6 0.0000 -2.3000 -3.9000 -3.1500 # ha
25 1 7 0.0000 -3.7100 -0.1900 -4.1700 # hc
26 1 7 0.0000 -2.2700 -0.3200 -5.1500 # hc
27 1 7 0.0000 -3.6600 -1.3700 -5.5000 # hc
28 1 3 0.0000 1.3500 1.8700 5.3300 # c2
29 1 4 0.0000 2.1000 1.5900 4.2700 # ce
30 1 5 0.0000 3.5800 1.7800 4.2100 # c3
31 1 4 0.0000 1.4600 1.0700 3.0300 # ce
32 1 1 0.0000 2.2000 0.8500 2.0400 # os
33 1 1 0.0000 0.2200 0.8700 3.0400 # os
34 1 6 0.0000 1.7800 2.2500 6.2400 # ha
35 1 6 0.0000 0.2900 1.7200 5.3100 # ha
36 1 7 0.0000 4.0600 0.8300 3.9700 # hc
37 1 7 0.0000 3.8400 2.4700 3.4100 # hc
38 1 7 0.0000 3.9700 2.1600 5.1500 # hc
39 1 3 0.0000 4.0800 3.0100 -2.4000 # c2
40 1 4 0.0000 2.8200 2.7900 -2.7500 # ce
41 1 5 0.0000 2.1400 3.3700 -3.9400 # c3
42 1 4 0.0000 1.9700 1.9000 -1.8900 # ce
43 1 1 0.0000 2.4900 1.3700 -0.8800 # os
44 1 1 0.0000 0.7700 1.7300 -2.2400 # os
45 1 6 0.0000 4.7200 3.6400 -2.9900 # ha
46 1 6 0.0000 4.5000 2.5500 -1.5200 # ha
47 1 7 0.0000 1.8100 2.5700 -4.6000 # hc
48 1 7 0.0000 1.2600 3.9200 -3.6400 # hc
49 1 7 0.0000 2.8200 4.0300 -4.4800 # hc
50 1 3 0.0000 4.7600 -3.2700 0.0300 # c2
51 1 4 0.0000 3.4900 -3.6000 -0.2000 # ce
52 1 5 0.0000 3.0200 -4.9700 -0.5500 # c3
53 1 4 0.0000 2.4300 -2.5500 -0.1000 # ce
54 1 1 0.0000 2.7800 -1.3800 0.1800 # os
55 1 1 0.0000 1.2400 -2.9200 -0.2900 # os
56 1 6 0.0000 5.5500 -4.0000 -0.0300 # ha
57 1 6 0.0000 5.0300 -2.2600 0.2800 # ha
58 1 7 0.0000 2.2800 -5.3100 0.1700 # hc
59 1 7 0.0000 2.5300 -4.9500 -1.5200 # hc
60 1 7 0.0000 3.8500 -5.6700 -0.5800 # hc
61 1 5 0.0000 -3.2100 3.7000 0.4300 # c3
62 1 3 0.0000 -2.2300 2.4700 0.3300 # c2
63 1 8 0.0000 -4.4400 3.3500 0.0300 # f
64 1 8 0.0000 -3.3100 4.1600 1.6800 # f
65 1 8 0.0000 -2.8100 4.7100 -0.3400 # f
66 1 1 0.0000 -1.7700 2.2600 -0.8000 # os
67 1 1 0.0000 -2.0300 1.8600 1.3800 # os
68 1 3 0.0000 6.0100 -6.5900 0.1500 # c2
69 1 9 0.0000 6.8500 -5.5600 0.0600 # c1
70 1 5 0.0000 8.2400 -5.5400 0.6100 # c3
71 1 6 0.0000 6.2900 -7.5100 0.6400 # ha
72 1 6 0.0000 5.0200 -6.5300 -0.2700 # ha
73 1 7 0.0000 8.9500 -5.3400 -0.1800 # hc
74 1 7 0.0000 8.3300 -4.7300 1.3400 # hc
75 1 7 0.0000 8.4700 -6.4900 1.0900 # hc

Bonds

1 2 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 21
6 2 2 44
7 2 2 66
8 2 3 32
9 2 3 43
10 2 3 54
11 2 4 11
12 2 4 22
13 2 4 55
14 2 5 10
15 2 5 33
16 2 5 67
17 3 6 7
18 4 6 12
19 4 6 13
20 5 7 8
21 6 7 9
22 7 8 14
23 7 8 15
24 7 8 16
25 8 9 10
26 8 9 11
27 3 17 18
28 4 17 23
29 4 17 24
30 5 18 19
31 6 18 20
32 7 19 25
33 7 19 26
34 7 19 27
35 8 20 21
36 8 20 22
37 3 28 29
38 4 28 34
39 4 28 35
40 5 29 30
41 6 29 31
42 7 30 36
43 7 30 37
44 7 30 38
45 8 31 32
46 8 31 33
47 3 39 40
48 4 39 45
49 4 39 46
50 5 40 41
51 6 40 42
52 7 41 47
53 7 41 48
54 7 41 49
55 8 42 43
56 8 42 44
57 3 50 51
58 4 50 56
59 4 50 57
60 5 51 52
61 6 51 53
62 7 52 58
63 7 52 59
64 7 52 60
65 8 53 54
66 8 53 55
67 9 61 62
68 10 61 63
69 10 61 64
70 10 61 65
71 11 62 66
72 11 62 67
73 12 68 69
74 4 68 71
75 4 68 72
76 13 69 70
77 7 70 73
78 7 70 74
79 7 70 75

Angles

1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 1 3 1 4
5 1 3 1 5
6 1 4 1 5
7 2 1 2 21
8 2 1 2 44
9 2 1 2 66
10 2 21 2 44
11 2 21 2 66
12 2 44 2 66
13 2 1 3 32
14 2 1 3 43
15 2 1 3 54
16 2 32 3 43
17 2 32 3 54
18 2 43 3 54
19 2 1 4 11
20 2 1 4 22
21 2 1 4 55
22 2 11 4 22
23 2 11 4 55
24 2 22 4 55
25 2 1 5 10
26 2 1 5 33
27 2 1 5 67
28 2 10 5 33
29 2 10 5 67
30 2 33 5 67
31 3 7 6 12
32 3 7 6 13
33 4 12 6 13
34 5 6 7 8
35 6 6 7 9
36 7 8 7 9
37 8 7 8 14
38 8 7 8 15
39 8 7 8 16
40 9 14 8 15
41 9 14 8 16
42 9 15 8 16
43 10 7 9 10
44 10 7 9 11
45 11 10 9 11
46 12 5 10 9
47 12 4 11 9
48 3 18 17 23
49 3 18 17 24
50 4 23 17 24
51 5 17 18 19
52 6 17 18 20
53 7 19 18 20
54 8 18 19 25
55 8 18 19 26
56 8 18 19 27
57 9 25 19 26
58 9 25 19 27
59 9 26 19 27
60 10 18 20 21
61 10 18 20 22
62 11 21 20 22
63 12 2 21 20
64 12 4 22 20
65 3 29 28 34
66 3 29 28 35
67 4 34 28 35
68 5 28 29 30
69 6 28 29 31
70 7 30 29 31
71 8 29 30 36
72 8 29 30 37
73 8 29 30 38
74 9 36 30 37
75 9 36 30 38
76 9 37 30 38
77 10 29 31 32
78 10 29 31 33
79 11 32 31 33
80 12 3 32 31
81 12 5 33 31
82 3 40 39 45
83 3 40 39 46
84 4 45 39 46
85 5 39 40 41
86 6 39 40 42
87 7 41 40 42
88 8 40 41 47
89 8 40 41 48
90 8 40 41 49
91 9 47 41 48
92 9 47 41 49
93 9 48 41 49
94 10 40 42 43
95 10 40 42 44
96 11 43 42 44
97 12 3 43 42
98 12 2 44 42
99 3 51 50 56
100 3 51 50 57
101 4 56 50 57
102 5 50 51 52
103 6 50 51 53
104 7 52 51 53
105 8 51 52 58
106 8 51 52 59
107 8 51 52 60
108 9 58 52 59
109 9 58 52 60
110 9 59 52 60
111 10 51 53 54
112 10 51 53 55
113 11 54 53 55
114 12 3 54 53
115 12 4 55 53
116 13 62 61 63
117 13 62 61 64
118 13 62 61 65
119 14 63 61 64
120 14 63 61 65
121 14 64 61 65
122 15 61 62 66
123 15 61 62 67
124 16 66 62 67
125 17 2 66 62
126 17 5 67 62
127 18 69 68 71
128 18 69 68 72
129 4 71 68 72
130 19 68 69 70
131 20 69 70 73
132 20 69 70 74
133 20 69 70 75
134 9 73 70 74
135 9 73 70 75
136 9 74 70 75

Dihedrals

1 14 1 2 21 20
2 14 1 2 44 42
3 2 1 2 66 62
4 14 1 3 32 31
5 14 1 3 43 42
6 14 1 3 54 53
7 14 1 4 11 9
8 14 1 4 22 20
9 14 1 4 55 53
10 14 1 5 10 9
11 14 1 5 33 31
12 2 1 5 67 62
13 3 2 1 3 32
14 3 2 1 3 43
15 3 2 1 3 54
16 3 2 1 4 11
17 3 2 1 4 22
18 3 2 1 4 55
19 3 2 1 5 10
20 3 2 1 5 33
21 3 2 1 5 67
22 4 2 21 20 18
23 5 2 21 20 22
24 4 2 44 42 40
25 5 2 44 42 43
26 6 2 66 62 61
27 7 2 66 62 67
28 3 3 1 2 21
29 3 3 1 2 44
30 3 3 1 2 66
31 3 3 1 4 11
32 3 3 1 4 22
33 3 3 1 4 55
34 3 3 1 5 10
35 3 3 1 5 33
36 3 3 1 5 67
37 4 3 32 31 29
38 5 3 32 31 33
39 4 3 43 42 40
40 5 3 43 42 44
41 4 3 54 53 51
42 5 3 54 53 55
43 3 4 1 2 21
44 3 4 1 2 44
45 3 4 1 2 66
46 3 4 1 3 32
47 3 4 1 3 43
48 3 4 1 3 54
49 3 4 1 5 10
50 3 4 1 5 33
51 3 4 1 5 67
52 4 4 11 9 7
53 5 4 11 9 10
54 4 4 22 20 18
55 5 4 22 20 21
56 4 4 55 53 51
57 5 4 55 53 54
58 3 5 1 2 21
59 3 5 1 2 44
60 3 5 1 2 66
61 3 5 1 3 32
62 3 5 1 3 43
63 3 5 1 3 54
64 3 5 1 4 11
65 3 5 1 4 22
66 3 5 1 4 55
67 4 5 10 9 7
68 5 5 10 9 11
69 4 5 33 31 29
70 5 5 33 31 32
71 6 5 67 62 61
72 7 5 67 62 66
73 8 6 7 8 14
74 8 6 7 8 15
75 8 6 7 8 16
76 9 6 7 9 10
77 9 6 7 9 11
78 10 8 7 6 12
79 10 8 7 6 13
80 11 8 7 9 10
81 11 8 7 9 11
82 12 9 7 6 12
83 12 9 7 6 13
84 13 9 7 8 14
85 13 9 7 8 15
86 13 9 7 8 16
87 14 9 10 5 33
88 14 9 10 5 67
89 14 9 11 4 22
90 14 9 11 4 55
91 14 10 5 33 31
92 2 10 5 67 62
93 14 11 4 22 20
94 14 11 4 55 53
95 8 17 18 19 25
96 8 17 18 19 26
97 8 17 18 19 27
98 9 17 18 20 21
99 9 17 18 20 22
100 10 19 18 17 23
101 10 19 18 17 24
102 11 19 18 20 21
103 11 19 18 20 22
104 12 20 18 17 23
105 12 20 18 17 24
106 13 20 18 19 25
107 13 20 18 19 26
108 13 20 18 19 27
109 14 20 21 2 44
110 14 20 21 2 66
111 14 20 22 4 55
112 14 21 2 44 42
113 2 21 2 66 62
114 14 22 4 55 53
115 8 28 29 30 36
116 8 28 29 30 37
117 8 28 29 30 38
118 9 28 29 31 32
119 9 28 29 31 33
120 10 30 29 28 34
121 10 30 29 28 35
122 11 30 29 31 32
123 11 30 29 31 33
124 12 31 29 28 34
125 12 31 29 28 35
126 13 31 29 30 36
127 13 31 29 30 37
128 13 31 29 30 38
129 14 31 32 3 43
130 14 31 32 3 54
131 14 31 33 5 67
132 14 32 3 43 42
133 14 32 3 54 53
134 2 33 5 67 62
135 8 39 40 41 47
136 8 39 40 41 48
137 8 39 40 41 49
138 9 39 40 42 43
139 9 39 40 42 44
140 10 41 40 39 45
141 10 41 40 39 46
142 11 41 40 42 43
143 11 41 40 42 44
144 12 42 40 39 45
145 12 42 40 39 46
146 13 42 40 41 47
147 13 42 40 41 48
148 13 42 40 41 49
149 14 42 43 3 54
150 14 42 44 2 66
151 14 43 3 54 53
152 2 44 2 66 62
153 8 50 51 52 58
154 8 50 51 52 59
155 8 50 51 52 60
156 9 50 51 53 54
157 9 50 51 53 55
158 10 52 51 50 56
159 10 52 51 50 57
160 11 52 51 53 54
161 11 52 51 53 55
162 12 53 51 50 56
163 12 53 51 50 57
164 13 53 51 52 58
165 13 53 51 52 59
166 13 53 51 52 60
167 15 63 61 62 66
168 15 63 61 62 67
169 15 64 61 62 66
170 15 64 61 62 67
171 15 65 61 62 66
172 15 65 61 62 67
173 16 68 69 70 73
174 16 68 69 70 74
175 16 68 69 70 75
176 17 70 69 68 71
177 17 70 69 68 72

Impropers

1 1 7 12 6 13
2 1 18 23 17 24
3 1 29 34 28 35
4 1 40 45 39 46
5 1 51 56 50 57
6 2 61 66 62 67
7 3 69 71 68 72

template:
unreacted-template:
7 atoms
5 bonds
4 angles
1 impropers

Types

1 3
2 4
3 6
4 6
5 3
6 9
7 5

Charges

1 0.0000
2 0.0000
3 0.0000
4 0.0000
5 0.0000
6 0.0000
7 0.0000

Coords

1 4.7600 -3.2700 0.0300
2 3.4900 -3.6000 -0.2000
3 5.5500 -4.0000 -0.0300
4 5.0300 -2.2600 0.2800
5 6.0100 -6.5900 0.1500
6 6.8500 -5.5600 0.0600
7 8.2400 -5.5400 0.6100

Bonds

1 3 1 2
2 4 1 3
3 4 1 4
4 12 5 6
5 13 6 7

Angles

1 3 2 1 3
2 3 2 1 4
3 4 3 1 4
4 19 5 6 7

Impropers

1 1 2 3 1 4

reacted-template:

7 atoms
6 bonds
4 angles
1 impropers

Types

1 3
2 4
3 6
4 6
5 3
6 9
7 5

Charges

1 0.0000
2 0.0000
3 0.0000
4 0.0000
5 0.0000
6 0.0000
7 0.0000

Coords

1 4.7600 -3.2700 0.0300
2 3.4900 -3.6000 -0.2000
3 5.5500 -4.0000 -0.0300
4 5.0300 -2.2600 0.2800
5 6.0100 -6.5900 0.1500
6 6.8500 -5.5600 0.0600
7 8.2400 -5.5400 0.6100

Bonds

1 3 1 2
2 4 1 3
3 4 1 4
4 12 5 6
5 13 6 7
6 6 1 6

Angles

1 3 2 1 3
2 3 2 1 4
3 4 3 1 4
4 19 5 6 7

Impropers

1 1 2 3 1 4

map:

3 edgeIDs
7 equivalences

BondingIDs

1
6

EdgeIDs

2
5
7

Equivalences

1 1
2 2
3 3
4 4
5 5
6 6
7 7

output files:
data.output:
LAMMPS data file via write_data, version 23 Jun 2022, timestep = 140000

75 atoms
9 atom types
79 bonds
13 bond types
136 angles
20 angle types
177 dihedrals
17 dihedral types
7 impropers
3 improper types

0.28869358790650423 10.551306412093451 xlo xhi
-2.6413064120934955 7.621306412093486 ylo yhi
-0.6313064120934957 9.63130641209345 zlo zhi

Masses

1 15.999405
2 65.37778299999999
3 12.010736
4 12.010736
5 12.010736
6 1.007941
7 1.007941
8 18.998403
9 12.010736

Pair Coeffs # lj/cut/coul/cut

1 0.16992 3.00001
2 0.12394 2.46155
3 0.08596 3.39967
4 0.08596 3.39967
5 0.10935 3.39967
6 0.01499 2.59964
7 0.01569 2.64953
8 0.06097 3.11815
9 0.2099 3.39967

Bond Coeffs # harmonic

1 298.614 1.824
2 298.614 1.8515
3 547.038 1.3461
4 342.936 1.0879
5 320.547 1.5159
6 382.617 1.4574
7 330.442 1.0969
8 374.721 1.371
9 326.644 1.5095
10 356.729 1.3497
11 389.014 1.3596
12 624.701 1.307
13 371.423 1.4671

Angle Coeffs # harmonic

1 59.7229 108.546
2 59.7229 115.162
3 49.4763 120.45
4 38.0818 116.9
5 63.9694 122.53
6 65.3688 123.26
7 63.3697 117.12
8 46.7776 110.59
9 39.3812 107.58
10 69.1669 115.19
11 59.7229 124.326
12 59.7229 128.031
13 66.3683 110.76
14 70.8661 107.36
15 68.6672 112.8
16 74.2645 115.05
17 59.7229 127.559
18 50.5758 120.42
19 59.7229 124.827
20 48.3769 109.41

Dihedral Coeffs # fourier

1 1 0 1 0
2 1 0 1 0
3 1 0 1 0
4 1 0 1 0
5 1 0 1 0
6 1 1.0495 2 180
7 1 1.0495 2 180
8 1 0 1 0
9 1 0.99952 2 180
10 1 6.64682 2 180
11 1 0.99952 2 180
12 1 6.64682 2 180
13 1 0 1 0
14 1 0 1 0
15 1 0 2 0
16 1 0 2 180
17 1 0 2 180

Improper Coeffs # cvff

1 1.09947 -1 2
2 1.09947 -1 2
3 1.09947 -1 2

Atoms # full

23 1 6 0 3.732585111655578 -1.9978871975766939 6.206060077727041 -2 -1 -1
17 1 3 0 4.374985367507047 -1.0899060582191058 6.476777366468168 -2 -1 -1
24 1 6 0 5.126445173202733 -0.915909289750158 5.629233629294396 -2 -1 -1
73 1 7 0 1.3466028266430345 -0.18802775991556228 5.596875066383086 0 -1 0
27 1 7 0 2.7314811382951882 -1.6309191000349963 8.39079111122763 -2 -1 -1
19 1 5 0 3.3871458900817646 -0.8603219653388519 8.748018491280769 -2 -1 -1
18 1 4 0 4.282563932113073 -0.3707573647205841 7.62546161738183 -2 -1 -1
25 1 7 0 3.960237365751685 -1.2354536891815133 9.59710739565234 -2 -1 -1
56 1 6 0 2.4167572972162197 1.9860455893468023 0.09104060722813105 -1 -1 0
60 1 7 0 0.6876507967405521 0.23359656729249184 1.5015376624589134 -1 -1 0
50 1 3 0 1.387730106300539 2.3056393808541693 -0.35026375917516095 -1 -1 0
14 1 7 0 3.3324204847099406 1.252570593642279 2.842711168108783 -2 -1 0
8 1 5 0 3.7331541755854545 1.972999366150918 3.5169078962238016 -2 -1 0
58 1 7 0 0.48070262294916233 1.8853564668038665 2.3110581995153407 -1 -1 0
15 1 7 0 4.755845280126039 1.7104796798122022 3.863245234419861 -2 -1 0
16 1 7 0 3.118829815237362 1.9856181829335573 4.368871384853932 -2 -1 0
75 1 7 0 1.6233644347011869 1.0590369914067816 6.736684366611766 0 -1 0
70 1 5 0 0.8768003897449098 0.744615891751565 6.025366297603765 0 -1 0
74 1 7 0 0.8723863271803495 1.4967720781981824 5.170157394136615 0 -1 0
21 1 1 0 5.404651508355133 1.6904922803234137 7.01258026340973 -2 -1 -1
20 1 4 0 5.264952609352194 0.6418877806194203 7.985850857828059 -2 -1 -1
26 1 7 0 2.799973185863831 -0.023846329156707275 9.180561160195301 -2 -1 -1
9 1 4 0 4.4786927587084815 3.707599503439506 1.7330905232623468 -2 -1 0
11 1 1 0 5.383832863249738 2.746285676200918 1.438548096655134 -2 -1 0
10 1 1 0 4.025988419868056 4.679169593898549 0.8950900830191565 -2 -1 0
6 1 3 0 2.6887177133520272 4.329271596983812 3.3639537695304673 -2 -1 0
7 1 4 0 3.614767034426607 3.4012941536529153 2.9134539728358066 -2 -1 0
12 1 6 0 2.073114963863531 4.152165222580076 4.2216562319360875 -2 -1 0
65 1 8 0 0.8610105349117774 4.683383113676562 6.820518166016818 -2 -1 -1
66 1 1 0 3.523490513390004 4.00397445514408 7.465910905398128 -2 -1 -1
2 1 2 0 5.290802454677275 3.465085451681248 7.348139013857245 -2 -1 -1
57 1 6 0 1.408090966477763 2.8191995268940415 8.9947281276148 -1 -1 -1
5 1 2 0 4.986100777080367 5.332067376640526 -0.5260865878740703 -2 -1 0
13 1 6 0 2.5442631379894287 5.235782533195587 2.8398103823370424 -2 -1 0
63 1 8 0 1.0111762160658626 5.429555472986436 8.7716424325201 -2 -1 -1
67 1 1 0 3.8122501821783477 6.016293575195773 8.507560444587106 -2 -1 -1
62 1 3 0 3.083493575678463 5.2050674352451765 7.690899081320716 -2 -1 -1
61 1 5 0 1.6424614516305736 5.603915279586709 7.538636626598162 -2 -1 -1
64 1 8 0 1.3751952972809414 6.881770591900359 7.066375062489732 -2 -1 -1
35 1 6 0 6.020263114667842 -1.3618200864655274 1.6031121180176124 -2 0 0
28 1 3 0 7.132603105916446 -1.3822354348604602 1.613498780167498 -2 0 0
29 1 4 0 7.865673216369606 -2.3080024127099685 0.9814793627231372 -2 0 0
30 1 5 0 9.348160457436247 -2.322549636909316 1.1927059781924865 -2 0 0
38 1 7 0 9.929376985183623 -2.022504128840793 0.33000140145111523 -2 0 0
36 1 7 0 9.635979111057363 -1.55787993421153 1.9055824863900486 -2 0 0
34 1 6 0 7.636797015799999 -0.504434560118585 2.2228691564834278 -2 0 0
46 1 6 0 7.936078201045218 -2.5187787690974597 6.2446418446580765 -2 0 -1
45 1 6 0 7.545764651604794 -1.895603818347306 4.62874750644503 -2 0 -1
51 1 4 0 10.391435768435937 1.897834839925223 0.1710534978326284 -2 -1 0
55 1 1 0 7.887747429299509 1.8781015993497026 0.05719179459012326 -2 -1 0
53 1 4 0 9.072572954230951 2.402386366341582 -0.3888600924488495 -2 -1 0
52 1 5 0 10.393736807266263 1.207675792212695 1.5427816383247037 -2 -1 0
59 1 7 0 9.344856379514656 1.0047441941384019 1.9227543465442942 -2 -1 0
68 1 3 0 8.750083488040971 1.0671989595497944 6.273076621855525 -1 -1 0
69 1 9 0 9.841891637259412 0.51476449592448 6.646693793906649 -1 -1 0
72 1 6 0 8.661434994215085 1.3985407870316358 5.2385567380520675 -1 -1 0
71 1 6 0 8.217144417818453 1.618088560429116 7.022652163938443 -1 -1 0
22 1 1 0 5.4746812178848305 0.9430403494432745 9.322513041011115 -2 -1 -1
4 1 2 0 6.2132259053446655 2.51033573663044 -0.23030317934305997 -2 -1 0
44 1 1 0 5.973055464278582 4.367991620916433 5.909917362030553 -2 -1 -1
1 1 1 0 6.077948471015853 4.002600621848966 8.936785394028142 -2 -1 -1
54 1 1 0 9.02766947921288 3.3777423283206134 8.865982815799242 -2 -1 -1
3 1 2 0 7.80735750641798 4.670703965016909 8.6229273372779 -2 -1 -1
32 1 1 0 8.231905923985243 5.986491951416841 -0.43404321242420213 -2 -1 0
31 1 4 0 7.310575634109043 6.791215735524267 0.25276218580809007 -2 -1 0
33 1 1 0 5.9965739241687555 6.721378121806836 0.020775518196037082 -2 -1 0
37 1 7 0 9.736090541057678 6.987219719673445 1.4940900937765074 -2 -1 0
48 1 7 0 5.5554714977164315 7.238548844921094 3.48896915316651 -2 -1 -1
49 1 7 0 6.804038248093443 6.17348607757042 2.7252841488189437 -2 -1 -1
41 1 5 0 6.216540915919993 6.326907063169234 3.592807341104453 -2 -1 -1
47 1 7 0 5.603755882383607 5.528662716431591 3.7473147188126115 -2 -1 -1
42 1 4 0 7.062920509364718 5.208448176487678 5.903575920503032 -2 -1 -1
40 1 4 0 6.935580840480813 6.3380679198166545 4.947163654320942 -2 -1 -1
43 1 1 0 7.902471470644311 5.4090395899934425 6.972562099285635 -2 -1 -1
39 1 3 0 7.512465910837384 7.498806227880801 5.299027455311732 -2 -1 -1

Velocities

23 -0.010654883154058494 -0.026897028742423983 -0.013652548748494042
17 0.0010818976062666307 -0.003266177585682986 0.0044954181622369775
24 0.0018064724812868699 0.029819837947999053 -0.0037331658298610927
73 0.038971870941149386 0.01678056223402893 -0.012858985410218193
27 0.012707589863164075 0.027318580958844808 0.008604212912725189
19 0.007741548069307954 0.000586120884534651 -0.00836022133116406
18 -0.002268927195917619 0.0020799847872238026 0.0014661403260975935
25 -0.028563738590447446 0.0048816205837973825 -0.0010325595551069205
56 0.000864171529808038 0.010782506135282883 0.014766168721596477
60 0.009613759840280298 -0.01116119883598892 -0.009690756597685283
50 -0.004562285272431948 -0.0033315928455596925 -0.0014316582598061266
14 0.004481978373338267 -0.031177007063052126 -0.019522004010153512
8 -0.003567960625660588 0.002830209396514492 0.008324931980662765
58 -0.005225097846649362 -0.0021840845408985852 -0.010585042554941063
15 0.05135245976871512 -0.0023714876091472203 0.004228177787678175
16 0.002586861513254382 0.006159327264363038 -0.006574248066182968
75 -0.026562649299532042 -0.020061314402785656 0.027863941932577272
70 0.0029238751442082368 -0.0003398382461673869 0.0006892089482401563
74 -0.02946483156249466 0.022637673483074296 0.006662259948189864
21 -0.0013496534966735726 0.002556274174537212 -0.005501994743184737
20 -0.007834066292677033 0.003942539352606048 -0.002843245650138028
26 0.00853749286343677 0.010861846584064114 0.023335278201828426
9 -0.0010905061148011993 0.001739358622473361 0.004344759426500918
11 0.004364998206610881 -2.9644050858429673e-05 -0.0018194138474064642
10 0.006673844678409054 -0.002366064931119935 0.004535289369192881
6 -0.008123807812362067 -0.0020567555314772276 0.0019182667582903685
7 -0.00506914428067115 -0.0016277786364948942 -0.0060772237983401775
12 0.005282781771544514 0.019593298295356127 -0.0007823008280609914
65 -0.0014559492158749097 0.002478515281879076 0.001606397954358885
66 -0.0014390839530019042 0.0055441791736432705 -0.006029349426961233
2 -0.00029466740323199177 -0.001088281593074629 -0.00020840942077646803
57 0.0059188153642401155 0.030765473124695197 -0.024777078699016568
5 0.0028359885363880306 -0.0038059457212268645 -0.001265803663857065
13 0.004259177231895094 0.0167865170238558 0.01845480320220382
63 -0.0010459461297840872 -0.0015692423256810602 -5.798458569170816e-05
67 0.003427022401645458 0.0005917165540523307 0.001768843661151186
62 0.0027849116281136546 0.001746902724566446 0.0013817002400219808
61 -0.0006495732109603768 -0.004304387417044288 -5.3083952899138664e-05
64 -0.0013510232836927395 -0.0005841102676765167 -0.001246656028741911
35 -0.02547626674581084 0.012610181754602216 -0.0028192455252634054
28 -0.004962343087422446 0.004084163375182711 7.973694424307977e-06
29 -0.0007098993343464564 0.0019000076034183168 -0.0010520655827269301
30 -0.005349074650632641 0.00393587478472166 -0.0038929383143972906
38 0.013521251456741917 0.011132242308898475 0.006264226622629051
36 -0.009466360650263718 -0.011264096505464255 -0.012201386182156111
34 -0.00048130778588229434 0.013450173999756643 0.010411662777385068
46 -0.010737140847359005 0.027147856008055266 0.011608874366845563
45 0.010302897787220459 0.010266957101894734 0.02190122277855361
51 -0.0081244352621841 -0.00834334229113559 0.0033333609667929127
55 0.0003993046338300058 0.0017460392512764682 -0.006163915718091438
53 -0.008903260178730839 -0.004595841698423335 0.0015849022776332333
52 0.010021936222174316 0.002227856380163249 -0.0005982817380845737
59 -0.007566249151100588 -0.011998491089351299 -0.010904413723373819
68 -0.0018413124985606382 0.0008175425384529019 0.0026604327635411126
69 -0.0008308731381683777 0.002184538341546311 0.003466854383974293
72 0.032430781604932554 0.00018830847152264288 -0.004896057449185395
71 0.018971022223088385 0.004281821784003941 0.0024486209773398764
22 -0.0016225463394756192 0.0016265279993913882 0.004827411517893988
4 0.0002295641408359953 -0.001654407687028919 -0.0006576117688339094
44 0.002916150300380562 -0.005713680957693969 -0.004977869045610538
1 -0.0039347790780531 -0.00044943661593048137 0.0013028441271478786
54 0.005222024464967573 -0.0030428483418376887 0.0035639265407402337
3 -0.0012547307145791885 0.0021260555656283948 0.0004020093391320838
32 -0.005852265442466247 0.0032491353751109594 0.001033842795973379
31 -0.000864853434354827 -0.000182781478127642 0.0059724008994809594
33 0.003158253744180014 0.0013644180737803857 0.00018416228345413083
37 0.02094881873916317 0.005963971630267264 -0.00906365101232195
48 -0.0035611661299739896 -0.029189255534090755 0.01734095557508358
49 -0.002079692533845814 -0.010474153008250725 0.0051479274758719626
41 0.0009966106022291634 -0.0016191636175834376 -0.004203690474898797
47 0.0056720291000045935 0.012368232312116511 -0.007867526075931313
42 0.0029763127784060137 0.005212692521857026 0.008152492255192833
40 -0.004914486349654764 -0.002562688964215275 -0.005021026007934324
43 -0.0031299348491656835 -0.002866783461562377 -0.001370409704003504
39 0.0074649227542734516 0.002615340356151165 0.0015146007640637305

Bonds

1 3 17 18
2 4 17 23
3 4 17 24
4 7 19 25
5 7 19 26
6 7 19 27
7 5 18 19
8 6 18 20
9 3 50 51
10 4 50 56
11 4 50 57
12 7 8 14
13 7 8 15
14 7 8 16
15 7 70 73
16 7 70 74
17 7 70 75
18 8 20 21
19 8 20 22
20 8 9 10
21 8 9 11
22 3 6 7
23 4 6 12
24 4 6 13
25 5 7 8
26 6 7 9
27 2 2 21
28 2 2 44
29 2 2 66
30 2 5 10
31 2 5 33
32 2 5 67
33 11 62 66
34 11 62 67
35 9 61 62
36 10 61 63
37 10 61 64
38 10 61 65
39 3 28 29
40 4 28 34
41 4 28 35
42 5 29 30
43 6 29 31
44 7 30 36
45 7 30 37
46 7 30 38
47 5 51 52
48 6 51 53
49 8 53 54
50 8 53 55
51 7 52 58
52 7 52 59
53 7 52 60
54 12 68 69
55 4 68 71
56 4 68 72
57 13 69 70
58 2 4 11
59 2 4 22
60 2 4 55
61 2 1 2
62 2 1 3
63 2 1 4
64 2 1 5
65 2 3 32
66 2 3 43
67 2 3 54
68 8 31 32
69 8 31 33
70 7 41 47
71 7 41 48
72 7 41 49
73 8 42 43
74 8 42 44
75 5 40 41
76 6 40 42
77 3 39 40
78 4 39 45
79 4 39 46

Angles

1 3 18 17 23
2 3 18 17 24
3 4 23 17 24
4 8 18 19 25
5 8 18 19 26
6 8 18 19 27
7 9 25 19 26
8 9 25 19 27
9 9 26 19 27
10 5 17 18 19
11 6 17 18 20
12 7 19 18 20
13 3 51 50 56
14 3 51 50 57
15 4 56 50 57
16 8 7 8 14
17 8 7 8 15
18 8 7 8 16
19 9 14 8 15
20 9 14 8 16
21 9 15 8 16
22 20 69 70 73
23 20 69 70 74
24 20 69 70 75
25 9 73 70 74
26 9 73 70 75
27 9 74 70 75
28 12 2 21 20
29 10 18 20 21
30 10 18 20 22
31 11 21 20 22
32 10 7 9 10
33 10 7 9 11
34 11 10 9 11
35 12 4 11 9
36 12 5 10 9
37 3 7 6 12
38 3 7 6 13
39 4 12 6 13
40 5 6 7 8
41 6 6 7 9
42 7 8 7 9
43 17 2 66 62
44 2 1 2 21
45 2 1 2 44
46 2 1 2 66
47 2 21 2 44
48 2 21 2 66
49 2 44 2 66
50 2 1 5 10
51 2 1 5 33
52 2 1 5 67
53 2 10 5 33
54 2 10 5 67
55 2 33 5 67
56 17 5 67 62
57 15 61 62 66
58 15 61 62 67
59 16 66 62 67
60 13 62 61 63
61 13 62 61 64
62 13 62 61 65
63 14 63 61 64
64 14 63 61 65
65 14 64 61 65
66 3 29 28 34
67 3 29 28 35
68 4 34 28 35
69 5 28 29 30
70 6 28 29 31
71 7 30 29 31
72 8 29 30 36
73 8 29 30 37
74 8 29 30 38
75 9 36 30 37
76 9 36 30 38
77 9 37 30 38
78 5 50 51 52
79 6 50 51 53
80 7 52 51 53
81 12 4 55 53
82 10 51 53 54
83 10 51 53 55
84 11 54 53 55
85 8 51 52 58
86 8 51 52 59
87 8 51 52 60
88 9 58 52 59
89 9 58 52 60
90 9 59 52 60
91 18 69 68 71
92 18 69 68 72
93 4 71 68 72
94 19 68 69 70
95 12 4 22 20
96 2 1 4 11
97 2 1 4 22
98 2 1 4 55
99 2 11 4 22
100 2 11 4 55
101 2 22 4 55
102 12 2 44 42
103 1 2 1 3
104 1 2 1 4
105 1 2 1 5
106 1 3 1 4
107 1 3 1 5
108 1 4 1 5
109 12 3 54 53
110 2 1 3 32
111 2 1 3 43
112 2 1 3 54
113 2 32 3 43
114 2 32 3 54
115 2 43 3 54
116 12 3 32 31
117 10 29 31 32
118 10 29 31 33
119 11 32 31 33
120 12 5 33 31
121 8 40 41 47
122 8 40 41 48
123 8 40 41 49
124 9 47 41 48
125 9 47 41 49
126 9 48 41 49
127 10 40 42 43
128 10 40 42 44
129 11 43 42 44
130 5 39 40 41
131 6 39 40 42
132 7 41 40 42
133 12 3 43 42
134 3 40 39 45
135 3 40 39 46
136 4 45 39 46

Dihedrals

1 8 17 18 19 25
2 8 17 18 19 26
3 8 17 18 19 27
4 9 17 18 20 21
5 9 17 18 20 22
6 10 19 18 17 23
7 10 19 18 17 24
8 11 19 18 20 21
9 11 19 18 20 22
10 12 20 18 17 23
11 12 20 18 17 24
12 13 20 18 19 25
13 13 20 18 19 26
14 13 20 18 19 27
15 4 2 21 20 18
16 5 2 21 20 22
17 14 20 21 2 44
18 14 20 21 2 66
19 4 4 11 9 7
20 5 4 11 9 10
21 14 9 11 4 22
22 14 9 11 4 55
23 4 5 10 9 7
24 5 5 10 9 11
25 14 9 10 5 33
26 14 9 10 5 67
27 8 6 7 8 14
28 8 6 7 8 15
29 8 6 7 8 16
30 9 6 7 9 10
31 9 6 7 9 11
32 10 8 7 6 12
33 10 8 7 6 13
34 11 8 7 9 10
35 11 8 7 9 11
36 12 9 7 6 12
37 12 9 7 6 13
38 13 9 7 8 14
39 13 9 7 8 15
40 13 9 7 8 16
41 6 2 66 62 61
42 7 2 66 62 67
43 14 1 2 21 20
44 14 1 2 44 42
45 2 1 2 66 62
46 14 21 2 44 42
47 2 21 2 66 62
48 2 44 2 66 62
49 14 1 5 10 9
50 14 1 5 33 31
51 2 1 5 67 62
52 14 10 5 33 31
53 2 10 5 67 62
54 2 33 5 67 62
55 6 5 67 62 61
56 7 5 67 62 66
57 15 63 61 62 66
58 15 63 61 62 67
59 15 64 61 62 66
60 15 64 61 62 67
61 15 65 61 62 66
62 15 65 61 62 67
63 8 28 29 30 36
64 8 28 29 30 37
65 8 28 29 30 38
66 9 28 29 31 32
67 9 28 29 31 33
68 10 30 29 28 34
69 10 30 29 28 35
70 11 30 29 31 32
71 11 30 29 31 33
72 12 31 29 28 34
73 12 31 29 28 35
74 13 31 29 30 36
75 13 31 29 30 37
76 13 31 29 30 38
77 8 50 51 52 58
78 8 50 51 52 59
79 8 50 51 52 60
80 9 50 51 53 54
81 9 50 51 53 55
82 10 52 51 50 56
83 10 52 51 50 57
84 11 52 51 53 54
85 11 52 51 53 55
86 12 53 51 50 56
87 12 53 51 50 57
88 13 53 51 52 58
89 13 53 51 52 59
90 13 53 51 52 60
91 4 4 55 53 51
92 5 4 55 53 54
93 16 68 69 70 73
94 16 68 69 70 74
95 16 68 69 70 75
96 17 70 69 68 71
97 17 70 69 68 72
98 4 4 22 20 18
99 5 4 22 20 21
100 14 20 22 4 55
101 14 1 4 11 9
102 14 1 4 22 20
103 14 1 4 55 53
104 14 11 4 22 20
105 14 11 4 55 53
106 14 22 4 55 53
107 4 2 44 42 40
108 5 2 44 42 43
109 14 42 44 2 66
110 3 2 1 3 32
111 3 2 1 3 43
112 3 2 1 3 54
113 3 2 1 4 11
114 3 2 1 4 22
115 3 2 1 4 55
116 3 2 1 5 10
117 3 2 1 5 33
118 3 2 1 5 67
119 3 3 1 2 21
120 3 3 1 2 44
121 3 3 1 2 66
122 3 3 1 4 11
123 3 3 1 4 22
124 3 3 1 4 55
125 3 3 1 5 10
126 3 3 1 5 33
127 3 3 1 5 67
128 3 4 1 2 21
129 3 4 1 2 44
130 3 4 1 2 66
131 3 4 1 3 32
132 3 4 1 3 43
133 3 4 1 3 54
134 3 4 1 5 10
135 3 4 1 5 33
136 3 4 1 5 67
137 3 5 1 2 21
138 3 5 1 2 44
139 3 5 1 2 66
140 3 5 1 3 32
141 3 5 1 3 43
142 3 5 1 3 54
143 3 5 1 4 11
144 3 5 1 4 22
145 3 5 1 4 55
146 4 3 54 53 51
147 5 3 54 53 55
148 14 1 3 32 31
149 14 1 3 43 42
150 14 1 3 54 53
151 14 32 3 43 42
152 14 32 3 54 53
153 14 43 3 54 53
154 4 3 32 31 29
155 5 3 32 31 33
156 14 31 32 3 43
157 14 31 32 3 54
158 4 5 33 31 29
159 5 5 33 31 32
160 14 31 33 5 67
161 8 39 40 41 47
162 8 39 40 41 48
163 8 39 40 41 49
164 9 39 40 42 43
165 9 39 40 42 44
166 10 41 40 39 45
167 10 41 40 39 46
168 11 41 40 42 43
169 11 41 40 42 44
170 12 42 40 39 45
171 12 42 40 39 46
172 13 42 40 41 47
173 13 42 40 41 48
174 13 42 40 41 49
175 4 3 43 42 40
176 5 3 43 42 44
177 14 42 43 3 54

Impropers

1 1 18 23 17 24
2 1 51 56 50 57
3 1 7 12 6 13
4 2 61 66 62 67
5 1 29 34 28 35
6 1 40 45 39 46
7 3 69 71 68 72

bond_react_props_internal # i_limit_tags i_react_tags

23 0 0
17 0 0
24 0 0
73 0 0
27 0 0
19 0 0
18 0 0
25 0 0
56 0 0
60 0 0
50 0 0
14 0 0
8 0 0
58 0 0
15 0 0
16 0 0
75 0 0
70 0 0
74 0 0
21 0 0
20 0 0
26 0 0
9 0 0
11 0 0
10 0 0
6 0 0
7 0 0
12 0 0
65 0 0
66 0 0
2 0 0
57 0 0
5 0 0
13 0 0
63 0 0
67 0 0
62 0 0
61 0 0
64 0 0
35 0 0
28 0 0
29 0 0
30 0 0
38 0 0
36 0 0
34 0 0
46 0 0
45 0 0
51 0 0
55 0 0
53 0 0
52 0 0
59 0 0
68 0 0
69 0 0
72 0 0
71 0 0
22 0 0
4 0 0
44 0 0
1 0 0
54 0 0
3 0 0
32 0 0
31 0 0
33 0 0
37 0 0
48 0 0
49 0 0
41 0 0
47 0 0
42 0 0
40 0 0
43 0 0
39 0 0

bond_react_stabilization_internal # i_statted_tags

23 1
17 1
24 1
73 1
27 1
19 1
18 1
25 1
56 1
60 1
50 1
14 1
8 1
58 1
15 1
16 1
75 1
70 1
74 1
21 1
20 1
26 1
9 1
11 1
10 1
6 1
7 1
12 1
65 1
66 1
2 1
57 1
5 1
13 1
63 1
67 1
62 1
61 1
64 1
35 1
28 1
29 1
30 1
38 1
36 1
34 1
46 1
45 1
51 1
55 1
53 1
52 1
59 1
68 1
69 1
72 1
71 1
22 1
4 1
44 1
1 1
54 1
3 1
32 1
31 1
33 1
37 1
48 1
49 1
41 1
47 1
42 1
40 1
43 1
39 1

log.lammps:
LAMMPS (23 Jun 2022 - Update 3)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task

units real
boundary p p p
atom_style full

atom_modify map array
pair_style lj/cut/coul/cut 8.5 10
bond_style harmonic
angle_style harmonic
dihedral_style fourier
improper_style cvff

read_data data.gro2lam
Reading data file …
orthogonal box = (-4.58 -7.51 -5.5) to (15.42 12.49 14.5)
2 by 4 by 4 MPI processor grid
reading atoms …
75 atoms
scanning bonds …
4 = max bonds/atom
scanning angles …
6 = max angles/atom
scanning dihedrals …
36 = max dihedrals/atom
scanning impropers …
1 = max impropers/atom
reading bonds …
79 bonds
reading angles …
136 angles
reading dihedrals …
177 dihedrals
reading impropers …
7 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
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.014 seconds
read_data CPU = 0.056 seconds

neighbor 1.9 bin
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.8333
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.8333
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000 seconds
pair_modify shift no tail yes mix arithmetic
neigh_modify every 1 delay 1 check yes

timestep 1
dump myDump all atom 100 dump.lammpstrj

thermo 10
thermo_style custom step temp press vol epair emol etotal enthalpy

velocity all create 300 1234567 rot yes dist gaussian

fix npt_name1 all npt temp 300 300 100 iso 50 50 1000
thermo_style custom step temp etotal ke pe
thermo_modify format float %20.10g
run 40000
Generated 36 of 36 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info …
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.9
ghost atom cutoff = 11.9
binsize = 5.95, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 20.79 | 21.16 | 22.44 Mbytes

Step Temp TotEng KinEng PotEng
0 300 257.4885488 66.17398311 191.3145657
10 587.0476327 248.589683 129.4909338 119.0987492
20 404.2032229 247.3704523 89.15912416 158.2113282
30 480.6327679 243.2818203 106.0179489 137.2638714
40 483.9552419 235.9027239 106.75082 129.1519039
50 539.4045846 229.5945863 118.9818329 110.6127534
60 436.0499876 226.5883561 96.18388171 130.4044743
70 471.4938141 223.2883798 104.002079 119.2863008
80 445.8341473 218.8831568 98.34207111 120.5410857
90 476.7719817 214.6047902 105.1663369 109.4384533
100 488.0179769 210.7196375 107.6469779 103.0726596
110 407.7998291 207.2860207 89.95246335 117.3335574
120 403.1443277 203.2226572 88.9255531 114.2971041
130 494.6951082 198.4393246 109.1198191 89.31950545
140 455.7639709 193.8758148 100.532391 93.34342376
150 436.50696 190.1832754 96.28468067 93.89859472
160 394.074861 186.4829402 86.92501065 99.55792951
170 367.68199 182.8260504 81.10327266 101.7227777
180 332.3074986 178.8778071 73.30036934 105.5774377
190 380.9282138 175.4573017 84.02512395 91.43217776
200 363.8167926 172.229184 80.25068764 91.97849638
210 369.9013924 169.3799379 81.59282831 87.78710957
220 364.2933912 166.2240707 80.35581571 85.86825499
230 335.9176543 163.1005165 74.09669728 89.00381919
240 338.8070648 160.139655 74.73404329 85.40561175
250 312.9260036 157.7059649 69.02520026 88.68076466
260 285.4166515 155.3490397 62.95718892 92.39185081
270 296.533986 153.0947997 65.40944994 87.68534978
280 322.3264884 150.6816557 71.09875867 79.58289708
290 292.9906542 148.5472869 64.62786201 83.9194249
300 293.7309614 146.8538667 64.79115893 82.06270781
310 270.2411802 145.4756636 59.60978431 85.86587932
320 275.64499 143.8030216 60.80175638 83.0012652
330 306.5484296 142.1104479 67.61843534 74.4920126
340 314.3787594 140.9189437 69.34564905 71.57329465
350 260.447575 140.0907144 57.44951142 82.64120295
360 296.086659 139.1342842 65.31077856 73.82350561
370 259.6378313 138.2071839 57.27089821 80.93628567
380 294.2779012 137.2241948 64.91180287 72.31239191
390 299.7717537 136.4315817 66.12363655 70.30794511
400 272.8558127 136.2142507 60.18651981 76.02773087
410 220.0153343 136.047505 48.53097005 87.51653496
420 237.5973779 135.6350453 52.40921625 83.22582903
430 282.1072127 135.4105611 62.2271931 73.18336798
440 255.178966 135.6306574 56.28736196 79.34329543
450 271.7666305 135.8252928 59.94626805 75.87902475
460 266.2303604 135.9374259 58.72507791 77.21234796
470 246.060014 136.4446823 54.27590404 82.16877823
480 231.07555 137.213886 50.9706318 86.2432542
490 255.3483326 138.0383427 56.32472082 81.71362185
500 270.874163 138.9546474 59.74940762 79.20523977
510 295.6500762 139.9194123 65.21447716 74.70493514
520 323.2187772 140.8576972 71.29557968 69.56211753
530 308.9360242 141.9551688 68.14509083 73.81007797
540 309.955221 143.2294956 68.36990519 74.85959045
550 293.9009645 144.5393229 64.82865821 79.71066468
560 284.3549408 145.6822349 62.72299684 82.95923806
570 320.5926862 146.5979734 70.71631667 75.88165674
580 315.1786591 147.5705157 69.52209088 78.04842481
590 306.4027244 148.7751252 67.58629571 81.18882954
600 326.8525586 150.0073374 72.09711896 77.91021843
610 336.7285301 151.1427413 74.2755602 76.86718113
620 288.6404835 152.0648239 63.66830161 88.39652228
630 317.6381259 152.7890787 70.06459992 82.72447878
640 318.0942457 153.7142577 70.1652108 83.5490469
650 295.4705724 154.8699329 65.17488223 89.6950507
660 296.8067538 155.9846165 65.46961705 90.51499946
670 306.6425528 156.6814945 67.63919703 89.04229744
680 337.2950742 157.0632602 74.40052847 82.66273175
690 326.0168746 157.6790486 71.91278384 85.76626481
700 315.5106034 158.4235232 69.59531114 88.82821203
710 279.1703054 158.7671776 61.57937025 97.18780734
720 320.8878913 158.7253742 70.78143301 87.94394121
730 345.6071134 158.6887802 76.23399761 82.45478263
740 326.0984453 158.8299284 71.93077671 86.89915166
750 341.8399259 158.8025034 75.40303161 83.39947175
760 324.9659547 158.508943 71.68097199 86.82797098
770 317.6961396 157.6161919 70.07739659 87.53879531
780 376.0260407 156.4764505 82.94380288 73.53264762
790 353.9784885 155.7592496 78.08055506 77.6786945
800 313.1151883 155.2499422 69.0669306 86.18301161
810 326.2304966 154.1447836 71.95990457 82.18487902
820 324.4645157 152.5978988 71.57036461 81.02753419
830 280.0608094 151.4641575 61.77579757 89.68835993
840 312.7213389 150.5086685 68.98005533 81.52861316
850 328.0000965 149.1986003 72.35024281 76.84835753
860 300.0785067 147.564439 66.19130011 81.37313888
870 305.442226 146.0013441 67.37442902 78.62691505
880 321.6941928 144.8370815 70.95928693 73.87779457
890 291.5153111 144.1217842 64.3024309 79.81935326
900 223.7445015 143.4659131 49.35354955 94.1123635
910 259.0903139 142.4270539 57.15012686 85.27692703
920 312.8615143 141.2974681 69.01097522 72.28649292
930 306.2638128 140.5731427 67.55565458 73.01748809
940 264.9810616 139.8999542 58.44950765 81.45044659
950 294.4586474 138.9172454 64.95167187 73.96557353
960 320.32536 138.1168257 70.65734986 67.45947584
970 292.2929246 137.808945 64.47395684 73.33498819
980 256.225213 137.7173184 56.51814306 81.19917533
990 266.8062122 137.4521984 58.85209927 78.60009914
1000 263.7891365 137.0786116 58.18659287 78.89201871

 39000           291.4021848          121.7598978          64.27747751          57.48242033
 39010           271.2619361          122.3273971          59.83494259          62.49245451
 39020           291.3544536          122.8397242          64.26694898          58.57277523
 39030           283.1802205          123.3952495          62.46387709           60.9313724
 39040           292.2692179          124.1610406          64.46872763          59.69231297
 39050           288.9289589          125.3892078          63.73193348          61.65727429
 39060           251.2184237          126.6507365          55.41374575          71.23699075
 39070           319.9336269           127.542795          70.57094141          56.97185359
 39080            314.884674          128.5249788          69.45724366          59.06773509
 39090           302.6781128          129.2800365          66.76472108           62.5153154
 39100           287.7762975          129.9086091          63.47767951          66.43092963
 39110           336.3344267          130.7377581          74.18862891           56.5491292
 39120           301.6288142          132.3719263          66.53326686          65.83865942
 39130           320.3817952          133.8296042          70.66979835          63.15980588
 39140           313.5231586          135.2610906          69.15692066           66.1041699
 39150           321.1577138          136.2872245          70.84095043          65.44627411
 39160           347.0996226           137.339502          76.56321522          60.77628682
 39170           330.2630226          138.1775727          72.84939894          65.32817375
 39180           306.3562112          139.2889845          67.57603583          71.71294864
 39190           317.5258983          140.4579026          70.03984477          70.41805779
 39200           323.2323111          141.3508566          71.29856497          70.05229162
 39210           338.9120207          141.6397894          74.75719444            66.882595
 39220           344.2148648          141.8870997          75.92689549          65.96020419
 39230           304.2062082          142.3713248          67.10178828          75.26953654
 39240           299.5474675          142.9245943          66.07416351          76.85043081
 39250           352.0105639          142.9860941          77.64647036          65.33962377
 39260           331.9949992          142.6225796          73.23143823          69.39114138
 39270           304.2176852          142.0485194          67.10431987          74.94419956
 39280           310.9071276          141.6703212          68.57987671          73.09044449
 39290           345.9649373          141.1809507          76.31292639          64.86802435
 39300           310.8275699           140.557777          68.56232787           71.9954491
 39310           332.4628919          139.7101274          73.33464597          66.37548148
 39320           328.0949661          138.3501397          72.37116915           65.9789706
 39330           353.7245747          136.7140979          78.02454677          58.68955116
 39340           308.4352853          134.6976145          68.03463786          66.66297667
 39350           310.5442056          132.1199091          68.49982339          63.62008572
 39360           258.0366343          129.7517214          56.91770627          72.83401513
 39370           291.9014883          127.7438724          64.38761387          63.35625856
 39380           287.6422766          125.7029044          63.44811718          62.25478719
 39390           322.7785868          123.5727228          71.19848251          52.37424031
 39400           269.5609548          122.0093153          59.45974024          62.54957508
 39410           273.2509673          121.0418655          60.27368299          60.76818249
 39420           259.1189525          120.1610108          57.15644395          63.00456686
 39430           289.0864176          119.1872693          63.76666571          55.42060357
 39440           239.3968708          118.4458831          52.80614828          65.63973486
 39450           276.9319058           118.114815          61.08562419          57.02919076
 39460           276.5793437          118.0929388          61.00785606          57.08508275
 39470           284.0936023          118.0072997           62.6653508          55.34194892
 39480            266.240242          117.7714947          58.72725759           59.0442371
 39490           296.7632829          117.6234863          65.46002823          52.16345806
 39500           283.9220645           117.743428            62.627513          55.11591499
 39510           296.8086547          118.1406086          65.47003635          52.67057222
 39520           261.5325529          118.7385678          57.68883579          61.04973198
 39530           269.6483554          119.1410452          59.47901904          59.66202616
 39540           279.2423222          119.4991732          61.59525571          57.90391749
 39550           307.1041942          120.0223728          67.74102586          52.28134694
 39560           274.1444953            120.71204          60.47077733          60.24126271
 39570           295.9325142          121.0907158          65.27677733          55.81393842
 39580           263.7537639          121.7857094           58.1787904          63.60691903
 39590            296.796329          122.7224026          65.46731754          57.25508503
 39600           297.8968626           123.922448          65.71007319          58.21237481
 39610           282.8113838          124.5001657          62.38251912          62.11764662
 39620           276.4756162          125.0188391          60.98497587          64.03386327
 39630           299.2940099          126.2657043          66.01825586           60.2474484
 39640            290.570952          127.9484522          64.09412423          63.85432795
 39650            309.279922          129.0071524          68.22094779          60.78620464
 39660           282.9548565          129.8484843          62.41416631          67.43431804
 39670            326.699592           130.811731          72.06337762          58.74835337
 39680            341.453745          131.7934442          75.31784785          56.47559631
 39690           366.7284718            132.68385          80.89294566          51.79090438
 39700            325.282515          133.6368208          71.75079885          61.88602196
 39710           278.2068658          134.6733447           61.3668548          73.30648994
 39720           338.8135726          135.0820775          74.73547877          60.34659874
 39730           336.4773699          135.3205677           74.2201593          61.10040845
 39740           330.1124643          135.7422121          72.81618878          62.92602327
 39750           305.1742756          136.5207761          67.31532453          69.20545152
 39760            318.446065          137.0682591          70.24281509          66.82544403
 39770           357.8391755          137.4617156          78.93214518          58.52957045
 39780           345.4931612          137.7647855          76.20886204          61.55592346
 39790           338.3190761          137.9224585          74.62640276          63.29605575
 39800           307.7249359          137.7357863          67.87794903           69.8578373
 39810            329.934539          137.1805536          72.77694205           64.4036115
 39820           342.1036298          136.3120962           75.4611994          60.85089685
 39830           326.3287599           135.188724          71.98157948          63.20714451
 39840            332.869888          133.4214313          73.42442115          59.99701016
 39850           317.9911688          130.8013533           70.1424741          60.65887919
 39860           303.8790439          127.1219716          67.02962241          60.09234916
 39870           303.7220692          123.4567426          66.99499693           56.4617457
 39880           288.8557745          120.8162745          63.71579047          57.10048406
 39890           278.7674499          118.6952944           61.4905084          57.20478596
 39900           282.6919781          116.7055255          62.35618062          54.34934491
 39910           292.0735649          115.3067303           64.4255705          50.88115976
 39920           289.2052207          114.3326796           63.7928713          50.53980826
 39930           287.5361488          113.7346829          63.42470752          50.30997543
 39940           280.9970853           112.845935          61.98232126          50.86361378
 39950           280.2495019          111.9818066          61.81741934          50.16438728
 39960           252.4821013          111.4606638          55.69248768          55.76817614
 39970           281.4325464          111.2811732          62.07837524            49.202798
 39980           285.6292735          110.7396872          63.00408907          47.73559816
 39990           249.3602515          109.8332437          55.00387023          54.82937352
 40000            282.367039          109.9628661          62.28450556          47.67836052

WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:940)
Loop time of 7.26253 on 32 procs for 40000 steps with 75 atoms

Performance: 475.868 ns/day, 0.050 hours/ns, 5507.726 timesteps/s
92.7% CPU use with 32 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

Pair | 0.28644 | 0.38998 | 0.47708 | 8.9 | 5.37
Bond | 0.0099461 | 0.038009 | 0.14331 | 16.0 | 0.52
Neigh | 0.21358 | 0.25818 | 0.27462 | 4.0 | 3.55
Comm | 3.3668 | 3.7612 | 4.2268 | 11.4 | 51.79
Output | 0.1094 | 0.11599 | 0.29738 | 9.6 | 1.60
Modify | 2.08 | 2.5333 | 2.9811 | 13.3 | 34.88
Other | | 0.1659 | | | 2.28

Nlocal: 2.34375 ave 5 max 0 min
Histogram: 4 0 10 0 4 0 4 0 5 5
Nghost: 1422.47 ave 1505 max 1341 min
Histogram: 2 2 3 4 4 8 3 2 3 1
Neighs: 563 ave 1518 max 0 min
Histogram: 6 7 3 3 3 1 3 4 1 1

Total # of neighbors = 18016
Ave neighs/atom = 240.21333
Ave special neighs/atom = 9.9733333
Neighbor list builds = 941
Dangerous builds = 0
unfix npt_name1

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule template mol1:
1 molecules
0 fragments
7 atoms with max type 9
5 bonds with max type 13
4 angles with max type 19
0 dihedrals with max type 0
1 impropers with max type 1
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule template mol2:
1 molecules
0 fragments
7 atoms with max type 9
6 bonds with max type 13
4 angles with max type 19
0 dihedrals with max type 0
1 impropers with max type 1

thermo 50

dump 1 all atom 50 dump.deposit.atom

dump 1 all xyz 1 test_vis.xyz

fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 5 mol1 mol2 rxn1_stp1_map
WARNING: Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead. (src/REACTION/fix_bond_react.cpp:3852)
WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2490)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp 300 300 100

optionally, you can customize behavior of reacting atoms,

by using the internally-created ‘bond_react_MASTER_group’, like so:

fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density f_myrxns[1] #f_myrxns[2]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)

restart 100 restart1 restart2

run 100000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

@Article{Gissinger17,
author = {J. R. Gissinger, B. D. Jensen, 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,
pages = {9953–9961}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 36 of 36 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info …
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11.9
ghost atom cutoff = 11.9
binsize = 5.95, bins = 2 2 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/cut/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
WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:940)

Per MPI rank memory allocation (min/avg/max) = 21.94 | 23.03 | 23.94 Mbytes
Step Temp Press Density f_myrxns[1]
40000 300 7696.5495 1.3166147 0
40050 282.15512 -692.57079 1.3166147 1
40100 283.10287 6613.0668 1.3166147 1
40150 305.3794 -9385.778 1.3166147 1
40200 311.95165 -1525.2818 1.3166147 1
40250 269.13037 7636.6255 1.3166147 1
40300 298.5939 3434.2697 1.3166147 1
40350 302.91412 -422.28393 1.3166147 1
40400 293.48027 -79.059475 1.3166147 1
40450 290.15227 421.45681 1.3166147 1
40500 282.98163 -6158.2893 1.3166147 1
40550 277.2044 3426.3402 1.3166147 1
40600 224.35545 4627.8004 1.3166147 1
40650 269.11876 -2005.2626 1.3166147 1
40700 266.08827 1747.9416 1.3166147 1
40750 270.83102 2643.6349 1.3166147 1
40800 318.672 13722.563 1.3166147 1
40850 318.05729 -3562.5421 1.3166147 1
40900 329.88257 2278.8441 1.3166147 1
40950 290.92389 -9560.5814 1.3166147 1
41000 295.41398 -945.57715 1.3166147 1
41050 321.8624 823.8906 1.3166147 1
41100 292.32079 2757.0195 1.3166147 1
41150 260.84043 -381.03497 1.3166147 1
41200 263.40161 8122.0495 1.3166147 1
41250 278.32936 4861.3972 1.3166147 1
41300 301.5835 302.09914 1.3166147 1
41350 330.68068 6971.068 1.3166147 1
41400 350.12147 -1072.7255 1.3166147 1
41450 325.28167 -4183.2464 1.3166147 1
41500 314.69749 -4186.736 1.3166147 1
41550 301.92338 4146.4373 1.3166147 1
41600 237.99432 767.56567 1.3166147 1
41650 267.44834 1753.519 1.3166147 1
41700 314.94005 1925.7718 1.3166147 1
41750 306.866 441.42134 1.3166147 1
41800 330.18596 6973.121 1.3166147 1
41850 310.57295 8401.1113 1.3166147 1
41900 356.46596 8539.847 1.3166147 1
41950 408.90665 -9874.1144 1.3166147 1
42000 431.08453 8061.9701 1.3166147 1

138400   273.19541     -5007.5646      1.3166147      1            
138450   252.07701      1534.1472      1.3166147      1            
138500   298.91898      551.05382      1.3166147      1            
138550   319.88787     -4520.2939      1.3166147      1            
138600   320.11254      5975.0125      1.3166147      1            
138650   315.77353     -4858.6965      1.3166147      1            
138700   314.67698      6176.3678      1.3166147      1            
138750   304.72166     -16183.746      1.3166147      1            
138800   325.7765       5440.4228      1.3166147      1            
138850   295.47849      3094.4365      1.3166147      1            
138900   246.25343     -1241.5222      1.3166147      1            
138950   269.38481     -557.23339      1.3166147      1            
139000   265.32197     -6423.5196      1.3166147      1            
139050   240.04582     -8311.8814      1.3166147      1            
139100   283.80395     -6303.125       1.3166147      1            
139150   298.42108      645.26683      1.3166147      1            
139200   293.01524      1965.7648      1.3166147      1            
139250   293.64768     -3810.0893      1.3166147      1            
139300   305.30315     -7095.9866      1.3166147      1            
139350   313.45896      7013.1202      1.3166147      1            
139400   355.18828     -4983.2216      1.3166147      1            
139450   292.58989     -7847.4803      1.3166147      1            
139500   281.3609       13162.833      1.3166147      1            
139550   258.65401     -8968.595       1.3166147      1            
139600   265.41648      1450.9412      1.3166147      1            
139650   277.19405      2441.2891      1.3166147      1            
139700   259.29155     -1570.9474      1.3166147      1            
139750   292.26881      120.39865      1.3166147      1            
139800   302.84862     -1456.4963      1.3166147      1            
139850   308.91877      1800.9206      1.3166147      1            
139900   300.8811      -7871.9171      1.3166147      1            
139950   312.58522     -276.47514      1.3166147      1            
140000   280.43833     -5384.4351      1.3166147      1            

WARNING: Bond/angle/dihedral extent > half of periodic box length (src/domain.cpp:940)
Loop time of 31.0372 on 32 procs for 100000 steps with 75 atoms

Performance: 278.376 ns/day, 0.086 hours/ns, 3221.939 timesteps/s
97.2% CPU use with 32 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

Pair | 0.26418 | 0.56588 | 0.90603 | 21.5 | 1.82
Bond | 0.036462 | 0.080727 | 0.17024 | 10.1 | 0.26
Neigh | 0.28749 | 0.30136 | 0.30641 | 1.0 | 0.97
Comm | 5.7331 | 6.09 | 6.4721 | 7.1 | 19.62
Output | 0.25093 | 0.25459 | 0.36006 | 3.8 | 0.82
Modify | 21.99 | 22.159 | 22.353 | 2.1 | 71.39
Other | | 1.586 | | | 5.11

Nlocal: 2.34375 ave 6 max 0 min
Histogram: 7 5 0 3 0 10 3 0 2 2
Nghost: 1378.28 ave 1432 max 1328 min
Histogram: 2 4 4 4 3 5 3 0 4 3
Neighs: 567.188 ave 1646 max 0 min
Histogram: 8 4 1 4 4 4 5 1 0 1

Total # of neighbors = 18150
Ave neighs/atom = 242
Ave special neighs/atom = 10.293333
Neighbor list builds = 2146
Dangerous builds = 0
write_data data.output
System init for write_data …
Generated 36 of 36 mixed pair_coeff terms from arithmetic mixing rule

write_restart restart_longrun

write_data restart_longrun.data

Total wall time: 0:00:38

@osaki what you are doing is useless. Nobody can make sense from all these repeated “number dumps” without being able to detect some commentary and discussion.

I have upgraded your status to “basic user” so you can attach files and will close this topic because it has become unreadable to almost anybody.

Thus please create a new topic with a proper and concise discussion of your problem and attach your combined files as a compressed tar archive with the suitable information what file contains what, unless it is self-explanatory, because the file names follow the typical LAMMPS conventions.