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bond/react: repackage examples

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jrgissing
2020-01-01 12:58:10 -05:00
parent 293e5c3242
commit 1dc8d4acaa
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52
examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
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# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
# stable at 800K
fix 1 statted_grp_REACT nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
# write_restart restart_longrun
# write_data restart_longrun.data

BIN
examples/USER/misc/bond_react/nylon,6-6_melt/large_nylon_melt.data.gz
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175
examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
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LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
1 by 1 by 1 MPI processor grid
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 11
25 angles with max type 23
30 dihedrals with max type 30
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 13
19 angles with max type 25
16 dihedrals with max type 29
10 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.20765
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0333156
estimated relative force accuracy = 0.000100329
using double precision FFTs
3d grid and FFT values/proc = 12167 5832
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 = 15 15 15
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
Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
100 697.22819 -4624.0512 0.80366765 57 22
150 723.60507 -17175.571 0.80366765 76 48
200 736.71277 -12961.963 0.80366765 84 64
Loop time of 102.825 on 1 procs for 200 steps with 35200 atoms
Performance: 0.168 ns/day, 142.812 hours/ns, 1.945 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 27.193 | 27.193 | 27.193 | 0.0 | 26.45
Bond | 11.324 | 11.324 | 11.324 | 0.0 | 11.01
Kspace | 4.1878 | 4.1878 | 4.1878 | 0.0 | 4.07
Neigh | 54.724 | 54.724 | 54.724 | 0.0 | 53.22
Comm | 0.40662 | 0.40662 | 0.40662 | 0.0 | 0.40
Output | 0.0011101 | 0.0011101 | 0.0011101 | 0.0 | 0.00
Modify | 4.9422 | 4.9422 | 4.9422 | 0.0 | 4.81
Other | | 0.04545 | | | 0.04
Nlocal: 35200 ave 35200 max 35200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 38403 ave 38403 max 38403 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.9281e+06 ave 6.9281e+06 max 6.9281e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6928101
Ave neighs/atom = 196.821
Ave special neighs/atom = 9.83727
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:43

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examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
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LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz
orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
2 by 1 by 2 MPI processor grid
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 11
25 angles with max type 23
30 dihedrals with max type 30
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 13
19 angles with max type 25
16 dihedrals with max type 29
10 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.20765
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0333156
estimated relative force accuracy = 0.000100329
using double precision FFTs
3d grid and FFT values/proc = 4508 1620
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 = 15 15 15
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
Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
100 697.22819 -4624.0512 0.80366765 57 22
150 724.40407 -17166.729 0.80366765 76 49
200 737.28582 -12968.224 0.80366765 84 65
Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms
Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.926 | 13.247 | 13.493 | 6.7 | 25.89
Bond | 5.2132 | 5.2733 | 5.3367 | 1.9 | 10.31
Kspace | 2.3601 | 2.6534 | 3.0067 | 16.0 | 5.19
Neigh | 25.93 | 25.934 | 25.937 | 0.1 | 50.68
Comm | 0.73273 | 0.75464 | 0.78505 | 2.3 | 1.47
Output | 0.00045228 | 0.00067407 | 0.0013323 | 0.0 | 0.00
Modify | 3.2682 | 3.2686 | 3.2692 | 0.0 | 6.39
Other | | 0.03995 | | | 0.08
Nlocal: 8800 ave 8913 max 8652 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 18366 ave 18461 max 18190 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 6928132
Ave neighs/atom = 196.822
Ave special neighs/atom = 9.83608
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:52

35
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_map
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this is a nominal superimpose file
2 edgeIDs
18 equivalences
BondingIDs
10
1
EdgeIDs
16
8
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18

189
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_reacted.data_template
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@ -1,189 +0,0 @@
this is a molecule template for: initial nylon crosslink, post-reacting
18 atoms
17 bonds
31 angles
39 dihedrals
20 impropers
Types
1 9
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
16 1
17 3
18 3
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -5.522237 -0.752722 1.631158
2 -5.170398 -0.545733 0.178130
3 -6.469695 -0.553072 -0.648889
4 -6.052076 -1.721152 1.744648
5 -6.183059 0.071387 1.971497
6 -4.489340 -1.389197 -0.173156
7 -4.637591 0.453703 0.051252
8 -5.618658 0.138919 4.386107
9 -4.669492 -0.989819 3.943591
10 -4.270194 -0.766405 2.474102
11 -3.348470 -1.875393 2.024289
12 -3.569794 0.564183 2.345995
13 -5.201079 -1.993301 4.044219
14 -3.736682 -0.984819 4.598305
15 -4.255402 1.370923 2.679069
16 -6.136394 -0.339866 -2.136775
17 -6.996331 -1.555519 -0.517408
18 -7.153308 0.284949 -0.289930
Bonds
1 9 1 2
2 10 1 4
3 10 1 5
4 11 1 10
5 1 2 3
6 2 2 6
7 2 2 7
8 1 3 16
9 2 3 17
10 2 3 18
11 1 8 9
12 6 9 10
13 2 9 13
14 2 9 14
15 7 10 11
16 5 10 12
17 8 12 15
Angles
1 14 2 1 4
2 14 2 1 5
3 15 2 1 10
4 16 4 1 5
5 17 4 1 10
6 17 5 1 10
7 18 1 2 3
8 19 1 2 6
9 19 1 2 7
10 1 3 2 6
11 1 3 2 7
12 3 6 2 7
13 2 2 3 16
14 1 2 3 17
15 1 2 3 18
16 1 16 3 17
17 1 16 3 18
18 3 17 3 18
19 12 8 9 10
20 1 8 9 13
21 1 8 9 14
22 13 13 9 10
23 13 14 9 10
24 3 13 9 14
25 10 9 10 11
26 8 9 10 12
27 20 1 10 9
28 21 11 10 12
29 22 1 10 11
30 23 1 10 12
31 11 10 12 15
Dihedrals
1 16 4 1 2 3
2 17 4 1 2 6
3 17 4 1 2 7
4 16 5 1 2 3
5 17 5 1 2 6
6 17 5 1 2 7
7 18 10 1 2 3
8 19 10 1 2 6
9 19 10 1 2 7
10 20 2 1 10 9
11 21 2 1 10 11
12 22 2 1 10 12
13 23 4 1 10 9
14 24 4 1 10 11
15 25 4 1 10 12
16 23 5 1 10 9
17 24 5 1 10 11
18 25 5 1 10 12
19 26 1 2 3 16
20 27 1 2 3 17
21 27 1 2 3 18
22 4 16 3 2 6
23 2 6 2 3 17
24 2 6 2 3 18
25 4 16 3 2 7
26 2 7 2 3 17
27 2 7 2 3 18
28 14 8 9 10 11
29 12 8 9 10 12
30 28 8 9 10 1
31 15 13 9 10 11
32 13 13 9 10 12
33 29 13 9 10 1
34 15 14 9 10 11
35 13 14 9 10 12
36 29 14 9 10 1
37 10 9 10 12 15
38 11 11 10 12 15
39 30 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 2 3 16 17
10 1 2 3 16 18
11 1 2 3 17 18
12 1 16 3 17 18
13 1 8 9 13 10
14 1 8 9 14 10
15 1 8 9 13 14
16 1 13 9 14 10
17 1 9 10 11 12
18 1 1 10 9 11
19 1 1 10 9 12
20 1 1 10 11 12

160
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp1_unreacted.data_template
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@ -1,160 +0,0 @@
this is a molecule template for: initial nylon crosslink, pre-reacting
18 atoms
16 bonds
25 angles
23 dihedrals
14 impropers
Types
1 2
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
16 1
17 3
18 3
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
16 -3.964987 2.900602 -1.551341
17 -4.460694 2.836102 0.668882
18 -4.828494 3.219656 -0.122111
Bonds
1 12 1 2
2 4 1 4
3 4 1 5
4 1 2 3
5 2 2 6
6 2 2 7
7 1 3 16
8 2 3 17
9 2 3 18
10 1 8 9
11 6 9 10
12 2 9 13
13 2 9 14
14 7 10 11
15 5 10 12
16 8 12 15
Angles
1 6 2 1 4
2 6 2 1 5
3 7 4 1 5
4 24 1 2 3
5 5 1 2 6
6 5 1 2 7
7 1 3 2 6
8 1 3 2 7
9 3 6 2 7
10 2 2 3 16
11 1 2 3 17
12 1 2 3 18
13 1 16 3 17
14 1 16 3 18
15 3 17 3 18
16 12 8 9 10
17 1 8 9 13
18 1 8 9 14
19 13 13 9 10
20 13 14 9 10
21 3 13 9 14
22 10 9 10 11
23 8 9 10 12
24 21 11 10 12
25 11 10 12 15
Dihedrals
1 31 4 1 2 3
2 32 4 1 2 6
3 32 4 1 2 7
4 31 5 1 2 3
5 32 5 1 2 6
6 32 5 1 2 7
7 33 1 2 3 16
8 1 1 2 3 17
9 1 1 2 3 18
10 4 16 3 2 6
11 2 6 2 3 17
12 2 6 2 3 18
13 4 16 3 2 7
14 2 7 2 3 17
15 2 7 2 3 18
16 14 8 9 10 11
17 12 8 9 10 12
18 15 13 9 10 11
19 13 13 9 10 12
20 15 14 9 10 11
21 13 14 9 10 12
22 10 9 10 12 15
23 11 11 10 12 15
Impropers
1 1 2 1 4 5
2 9 9 10 11 12
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 2 3 16 17
8 1 2 3 16 18
9 1 2 3 17 18
10 1 16 3 17 18
11 1 8 9 13 10
12 1 8 9 14 10
13 1 8 9 13 14
14 1 13 9 14 10

32
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_map
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@ -1,32 +0,0 @@
this is a nominal superimpose file
2 edgeIDs
15 equivalences
BondingIDs
4
12
EdgeIDs
8
3
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15

131
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_reacted.data_template
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@ -1,131 +0,0 @@
this is a molecule template for: water condensation, post-reacting
15 atoms
13 bonds
19 angles
16 dihedrals
10 impropers
Types
1 9
2 1
3 1
4 10
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 11
13 3
14 3
15 10
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
Coords
1 -4.856280 -1.050468 1.432625
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 9 1 2
2 10 1 5
3 11 1 10
4 1 2 3
5 2 2 6
6 2 2 7
7 13 4 12
8 1 8 9
9 6 9 10
10 2 9 13
11 2 9 14
12 7 10 11
13 13 15 12
Angles
1 14 2 1 5
2 15 2 1 10
3 17 5 1 10
4 18 1 2 3
5 19 1 2 6
6 19 1 2 7
7 1 3 2 6
8 1 3 2 7
9 3 6 2 7
10 12 8 9 10
11 1 8 9 13
12 1 8 9 14
13 13 13 9 10
14 13 14 9 10
15 3 13 9 14
16 10 9 10 11
17 20 1 10 9
18 22 1 10 11
19 25 15 12 4
Dihedrals
1 16 5 1 2 3
2 17 5 1 2 6
3 17 5 1 2 7
4 18 10 1 2 3
5 19 10 1 2 6
6 19 10 1 2 7
7 20 2 1 10 9
8 21 2 1 10 11
9 23 5 1 10 9
10 24 5 1 10 11
11 14 8 9 10 11
12 28 8 9 10 1
13 15 13 9 10 11
14 29 13 9 10 1
15 15 14 9 10 11
16 29 14 9 10 1
Impropers
1 10 2 1 5 10
2 11 1 10 9 11
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 8 9 13 10
8 1 8 9 14 10
9 1 8 9 13 14
10 1 13 9 14 10

158
examples/USER/misc/bond_react/nylon,6-6_melt/rxn1_stp2_unreacted.data_template
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@ -1,158 +0,0 @@
this is a molecule template for: water condensation, pre-reacting
15 atoms
14 bonds
25 angles
30 dihedrals
16 impropers
Types
1 9
2 1
3 1
4 4
5 4
6 3
7 3
8 1
9 1
10 5
11 8
12 6
13 3
14 3
15 7
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 9 1 2
2 10 1 4
3 10 1 5
4 11 1 10
5 1 2 3
6 2 2 6
7 2 2 7
8 1 8 9
9 6 9 10
10 2 9 13
11 2 9 14
12 7 10 11
13 5 10 12
14 8 12 15
Angles
1 14 2 1 4
2 14 2 1 5
3 15 2 1 10
4 16 4 1 5
5 17 4 1 10
6 17 5 1 10
7 18 1 2 3
8 19 1 2 6
9 19 1 2 7
10 1 3 2 6
11 1 3 2 7
12 3 6 2 7
13 12 8 9 10
14 1 8 9 13
15 1 8 9 14
16 13 13 9 10
17 13 14 9 10
18 3 13 9 14
19 10 9 10 11
20 8 9 10 12
21 20 1 10 9
22 21 11 10 12
23 22 1 10 11
24 23 1 10 12
25 11 10 12 15
Dihedrals
1 16 4 1 2 3
2 17 4 1 2 6
3 17 4 1 2 7
4 16 5 1 2 3
5 17 5 1 2 6
6 17 5 1 2 7
7 18 10 1 2 3
8 19 10 1 2 6
9 19 10 1 2 7
10 20 2 1 10 9
11 21 2 1 10 11
12 22 2 1 10 12
13 23 4 1 10 9
14 24 4 1 10 11
15 25 4 1 10 12
16 23 5 1 10 9
17 24 5 1 10 11
18 25 5 1 10 12
19 14 8 9 10 11
20 12 8 9 10 12
21 28 8 9 10 1
22 15 13 9 10 11
23 13 13 9 10 12
24 29 13 9 10 1
25 15 14 9 10 11
26 13 14 9 10 12
27 29 14 9 10 1
28 10 9 10 12 15
29 11 11 10 12 15
30 30 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 8 9 13 10
10 1 8 9 14 10
11 1 8 9 13 14
12 1 13 9 14 10
13 1 9 10 11 12
14 1 1 10 9 11
15 1 1 10 9 12
16 1 1 10 11 12

49
examples/USER/misc/bond_react/tiny_epoxy/in.tiny_epoxy.stabilized
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@ -1,49 +0,0 @@
# two molecules DGEBA (diepoxy) and one DETA (linker)
# two crosslinking reactions
units real
boundary p p p
atom_style full
pair_style lj/class2 8
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_epoxy.data
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_pre.data_template
molecule mol2 rxn1_stp1_post.data_template
molecule mol3 rxn1_stp2_post.data_template
molecule mol4 rxn2_stp1_pre.data_template
molecule mol5 rxn2_stp1_post.data_template
molecule mol6 rxn2_stp2_post.data_template
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix rxns all bond/react stabilization yes statted_grp .03 &
react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map &
react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map &
react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map &
react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
fix 1 statted_grp_REACT nvt temp 300 300 100
thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
run 2000
# write_restart restart_longrun
# write_data restart_longrun.data nofix

172
examples/USER/misc/bond_react/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.1
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@ -1,172 +0,0 @@
LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (10 -10 -15) to (30 20 10)
1 by 1 by 1 MPI processor grid
reading atoms ...
118 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
123 bonds
reading angles ...
221 angles
reading dihedrals ...
302 dihedrals
reading impropers ...
115 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
10 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000286808 secs
read_data CPU = 0.00724107 secs
Read molecule mol1:
31 atoms with max type 10
30 bonds with max type 15
53 angles with max type 29
66 dihedrals with max type 39
31 impropers with max type 5
Read molecule mol2:
31 atoms with max type 10
30 bonds with max type 17
55 angles with max type 36
75 dihedrals with max type 51
34 impropers with max type 5
Read molecule mol3:
31 atoms with max type 11
30 bonds with max type 18
53 angles with max type 37
72 dihedrals with max type 53
31 impropers with max type 5
Read molecule mol4:
42 atoms with max type 11
41 bonds with max type 18
73 angles with max type 41
96 dihedrals with max type 54
43 impropers with max type 5
Read molecule mol5:
42 atoms with max type 11
41 bonds with max type 18
75 angles with max type 37
108 dihedrals with max type 53
46 impropers with max type 5
Read molecule mol6:
42 atoms with max type 11
41 bonds with max type 19
73 angles with max type 50
102 dihedrals with max type 66
43 impropers with max type 22
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 4 6 5
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2, 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) = 17.28 | 17.28 | 17.28 Mbytes
Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
0 300 0 0 0 0
50 391.52956 1 0 0 0
100 475.26826 1 1 0 0
150 605.26215 1 1 1 0
200 545.7485 1 1 1 0
250 461.64929 1 1 1 1
300 452.10611 1 1 1 1
350 379.61671 1 1 1 1
400 331.22444 1 1 1 1
450 275.63969 1 1 1 1
500 316.63407 1 1 1 1
550 261.39841 1 1 1 1
600 313.70928 1 1 1 1
650 294.24011 1 1 1 1
700 285.81736 1 1 1 1
750 340.37496 1 1 1 1
800 333.2496 1 1 1 1
850 307.40826 1 1 1 1
900 304.68718 1 1 1 1
950 328.0289 1 1 1 1
1000 290.22808 1 1 1 1
1050 272.78518 1 1 1 1
1100 291.30546 1 1 1 1
1150 320.33992 1 1 1 1
1200 330.57057 1 1 1 1
1250 300.51008 1 1 1 1
1300 293.6209 1 1 1 1
1350 324.36604 1 1 1 1
1400 331.15408 1 1 1 1
1450 302.23396 1 1 1 1
1500 297.55562 1 1 1 1
1550 277.3187 1 1 1 1
1600 289.66052 1 1 1 1
1650 281.85404 1 1 1 1
1700 293.4999 1 1 1 1
1750 306.21866 1 1 1 1
1800 283.22696 1 1 1 1
1850 295.10473 1 1 1 1
1900 317.3843 1 1 1 1
1950 305.14825 1 1 1 1
2000 289.00911 1 1 1 1
Loop time of 1.87066 on 1 procs for 2000 steps with 118 atoms
Performance: 92.374 ns/day, 0.260 hours/ns, 1069.141 timesteps/s
98.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12832 | 0.12832 | 0.12832 | 0.0 | 6.86
Bond | 0.77458 | 0.77458 | 0.77458 | 0.0 | 41.41
Neigh | 0.45068 | 0.45068 | 0.45068 | 0.0 | 24.09
Comm | 0.029785 | 0.029785 | 0.029785 | 0.0 | 1.59
Output | 0.31635 | 0.31635 | 0.31635 | 0.0 | 16.91
Modify | 0.16657 | 0.16657 | 0.16657 | 0.0 | 8.90
Other | | 0.004368 | | | 0.23
Nlocal: 118 ave 118 max 118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 332 ave 332 max 332 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4338 ave 4338 max 4338 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4338
Ave neighs/atom = 36.7627
Ave special neighs/atom = 10.5763
Neighbor list builds = 2000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

172
examples/USER/misc/bond_react/tiny_epoxy/log.20Nov19.tiny_epoxy.stabilized.g++.4
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@ -1,172 +0,0 @@
LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (10 -10 -15) to (30 20 10)
1 by 2 by 2 MPI processor grid
reading atoms ...
118 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
4 = max impropers/atom
reading bonds ...
123 bonds
reading angles ...
221 angles
reading dihedrals ...
302 dihedrals
reading impropers ...
115 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
10 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
22 = max # of special neighbors
special bonds CPU = 0.000239905 secs
read_data CPU = 0.0080783 secs
Read molecule mol1:
31 atoms with max type 10
30 bonds with max type 15
53 angles with max type 29
66 dihedrals with max type 39
31 impropers with max type 5
Read molecule mol2:
31 atoms with max type 10
30 bonds with max type 17
55 angles with max type 36
75 dihedrals with max type 51
34 impropers with max type 5
Read molecule mol3:
31 atoms with max type 11
30 bonds with max type 18
53 angles with max type 37
72 dihedrals with max type 53
31 impropers with max type 5
Read molecule mol4:
42 atoms with max type 11
41 bonds with max type 18
73 angles with max type 41
96 dihedrals with max type 54
43 impropers with max type 5
Read molecule mol5:
42 atoms with max type 11
41 bonds with max type 18
75 angles with max type 37
108 dihedrals with max type 53
46 impropers with max type 5
Read molecule mol6:
42 atoms with max type 11
41 bonds with max type 19
73 angles with max type 50
102 dihedrals with max type 66
43 impropers with max type 22
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 4 6 5
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2, 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) = 16.26 | 16.45 | 16.63 Mbytes
Step Temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
0 300 0 0 0 0
50 391.52956 1 0 0 0
100 475.26826 1 1 0 0
150 605.26215 1 1 1 0
200 545.7485 1 1 1 0
250 461.64929 1 1 1 1
300 452.10611 1 1 1 1
350 379.61671 1 1 1 1
400 331.22444 1 1 1 1
450 275.63969 1 1 1 1
500 316.63407 1 1 1 1
550 261.39841 1 1 1 1
600 313.70928 1 1 1 1
650 294.24011 1 1 1 1
700 285.81736 1 1 1 1
750 340.37496 1 1 1 1
800 333.2496 1 1 1 1
850 307.40826 1 1 1 1
900 304.68718 1 1 1 1
950 328.0289 1 1 1 1
1000 290.22808 1 1 1 1
1050 272.78518 1 1 1 1
1100 291.30546 1 1 1 1
1150 320.33992 1 1 1 1
1200 330.57057 1 1 1 1
1250 300.51008 1 1 1 1
1300 293.6209 1 1 1 1
1350 324.36604 1 1 1 1
1400 331.15408 1 1 1 1
1450 302.23396 1 1 1 1
1500 297.55562 1 1 1 1
1550 277.3187 1 1 1 1
1600 289.66052 1 1 1 1
1650 281.85404 1 1 1 1
1700 293.4999 1 1 1 1
1750 306.21866 1 1 1 1
1800 283.22695 1 1 1 1
1850 295.10472 1 1 1 1
1900 317.38431 1 1 1 1
1950 305.14824 1 1 1 1
2000 289.00909 1 1 1 1
Loop time of 0.689125 on 4 procs for 2000 steps with 118 atoms
Performance: 250.753 ns/day, 0.096 hours/ns, 2902.231 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.02002 | 0.030617 | 0.053133 | 7.7 | 4.44
Bond | 0.10356 | 0.18908 | 0.22691 | 11.6 | 27.44
Neigh | 0.16721 | 0.17002 | 0.17247 | 0.5 | 24.67
Comm | 0.057286 | 0.12002 | 0.21612 | 17.0 | 17.42
Output | 0.00028991 | 0.00034121 | 0.00049323 | 0.0 | 0.05
Modify | 0.17626 | 0.17675 | 0.17721 | 0.1 | 25.65
Other | | 0.002287 | | | 0.33
Nlocal: 29.5 ave 41 max 18 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 306 ave 349 max 269 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 1084.5 ave 2154 max 397 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 4338
Ave neighs/atom = 36.7627
Ave special neighs/atom = 10.5763
Neighbor list builds = 2000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

47
examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp1.map
View File

@ -1,47 +0,0 @@
this is a map file
1 edgeIDs
31 equivalences
BondingIDs
15
1
EdgeIDs
5
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31

315
examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp1_post.data_template
View File

@ -1,315 +0,0 @@
rxn1_stp1_post
31 atoms
30 bonds
55 angles
75 dihedrals
34 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 10
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 22.582573 10.988183 -5.014054
2 23.904713 10.750493 -4.202215
3 23.989172 9.487042 -3.323374
4 24.067001 11.723383 -4.037435
5 24.627851 7.325302 -3.319944
6 24.554632 8.418972 -4.080365
7 22.667763 11.445703 -5.999605
8 21.787441 10.247643 -4.916974
9 24.964962 10.712683 -4.449374
10 24.616703 9.689913 -2.456034
11 22.989313 9.208153 -2.991455
12 18.808882 13.758042 -3.958724
13 19.293213 12.549683 -3.196594
14 20.810543 12.417832 -3.417504
15 21.090193 12.251203 -4.891234
16 17.657042 16.437199 -3.985224
17 19.126713 16.210239 -4.245154
18 19.589151 14.957593 -3.479565
19 19.000433 13.609432 -5.041715
20 18.761223 11.614392 -3.573184
21 19.082903 12.688992 -2.085145
22 21.202852 11.511562 -2.848624
23 21.328482 13.360252 -3.038924
24 19.949852 12.199403 -5.680355
25 21.477343 13.247442 -5.445915
26 17.080341 15.555528 -4.334374
27 17.319832 17.341927 -4.532204
28 19.720472 17.115158 -3.887564
29 19.298622 16.058659 -5.361685
30 19.410772 15.105113 -2.363724
31 20.700163 14.782252 -3.666344
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 8 6 5
12 13 13 12
13 13 18 12
14 14 12 19
15 15 13 14
16 1 13 20
17 1 13 21
18 13 14 15
19 1 14 22
20 1 14 23
21 14 15 24
22 14 15 25
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 22 3 6 5
20 23 13 12 18
21 24 13 12 19
22 24 18 12 19
23 25 14 13 12
24 26 20 13 12
25 26 21 13 12
26 27 14 13 20
27 27 14 13 21
28 2 20 13 21
29 25 13 14 15
30 27 13 14 22
31 27 13 14 23
32 26 22 14 15
33 26 23 14 15
34 2 22 14 23
35 23 1 15 14
36 24 1 15 24
37 24 1 15 25
38 24 14 15 24
39 24 14 15 25
40 28 24 15 25
41 24 17 16 26
42 24 17 16 27
43 28 26 16 27
44 25 18 17 16
45 26 28 17 16
46 26 29 17 16
47 27 18 17 28
48 27 18 17 29
49 2 28 17 29
50 25 17 18 12
51 26 30 18 12
52 26 31 18 12
53 27 17 18 30
54 27 17 18 31
55 2 30 18 31
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 30 8 1 15 25
13 46 2 1 15 14
14 47 2 1 15 24
15 47 2 1 15 25
16 28 7 1 15 14
17 30 7 1 15 24
18 30 7 1 15 25
19 48 6 3 2 1
20 40 10 3 2 1
21 40 11 3 2 1
22 49 6 3 2 9
23 41 10 3 2 9
24 41 11 3 2 9
25 50 6 3 2 4
26 42 10 3 2 4
27 42 11 3 2 4
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 29 13 14 15 25
55 28 22 14 15 1
56 30 22 14 15 24
57 30 22 14 15 25
58 28 23 14 15 1
59 30 23 14 15 24
60 30 23 14 15 25
61 29 18 17 16 26
62 30 28 17 16 26
63 30 29 17 16 26
64 29 18 17 16 27
65 30 28 17 16 27
66 30 29 17 16 27
67 31 16 17 18 12
68 32 30 18 17 16
69 32 31 18 17 16
70 32 28 17 18 12
71 33 28 17 18 30
72 33 28 17 18 31
73 32 29 17 18 12
74 33 29 17 18 30
75 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 5 17 16 26 27
3 1 2 1 8 7
4 1 2 1 8 15
5 1 8 1 7 15
6 1 2 1 7 15
7 1 1 2 3 9
8 1 1 2 3 4
9 1 1 2 4 9
10 1 3 2 4 9
11 1 2 3 6 10
12 1 2 3 6 11
13 1 2 3 10 11
14 1 6 3 10 11
15 1 14 13 20 12
16 1 14 13 21 12
17 1 20 13 21 12
18 1 14 13 20 21
19 1 13 14 22 15
20 1 13 14 23 15
21 1 13 14 22 23
22 1 22 14 23 15
23 1 1 15 14 24
24 1 1 15 14 25
25 1 1 15 24 25
26 1 14 15 24 25
27 1 18 17 28 16
28 1 18 17 29 16
29 1 28 17 29 16
30 1 18 17 28 29
31 1 17 18 30 12
32 1 17 18 31 12
33 1 30 18 31 12
34 1 17 18 30 31

301
examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp1_pre.data_template
View File

@ -1,301 +0,0 @@
rxn1_stp1_pre
31 atoms
30 bonds
53 angles
66 dihedrals
31 impropers
Types
1 2
2 2
3 1
4 3
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 10
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 19.846882 9.569666 -1.229588
2 21.168802 9.331466 -0.418038
3 21.253012 8.067936 0.460722
4 20.170443 10.460656 0.020692
5 21.891691 5.906196 0.464152
6 21.818472 6.999866 -0.296268
7 19.932211 10.027435 -2.215008
8 19.051722 8.829116 -1.132808
9 22.229073 9.293536 -0.665088
10 21.880442 8.270676 1.328162
11 20.253073 7.789126 0.792482
12 16.072590 12.338870 -0.174330
13 16.557261 11.130320 0.587290
14 18.074570 10.998810 0.366080
15 18.353970 10.832370 -1.107720
16 14.920720 15.017820 -0.200530
17 16.390430 14.791100 -0.460440
18 16.852980 13.538320 0.304870
19 16.263750 12.190560 -1.257430
20 16.025360 10.195070 0.210470
21 16.347120 11.269210 1.698830
22 18.467180 10.092570 0.934800
23 18.592390 11.941300 0.744640
24 17.843861 9.919930 -1.479780
25 19.448191 10.736480 -1.267520
26 14.344120 14.136250 -0.550130
27 14.583470 15.922760 -0.747140
28 16.984060 15.696010 -0.102600
29 16.562420 14.639820 -1.577000
30 16.674820 13.685670 1.420760
31 17.963949 13.362980 0.117850
Bonds
1 6 1 8
2 4 1 4
3 5 1 2
4 6 1 7
5 4 2 4
6 2 2 3
7 6 2 9
8 3 3 6
9 1 3 10
10 1 3 11
11 8 5 6
12 13 13 12
13 13 18 12
14 14 12 19
15 15 13 14
16 1 13 20
17 1 13 21
18 13 14 15
19 1 14 22
20 1 14 23
21 14 15 24
22 14 15 25
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 9 4 1 8
2 10 2 1 8
3 11 8 1 7
4 8 2 1 4
5 9 4 1 7
6 10 2 1 7
7 8 1 2 4
8 29 1 2 3
9 10 1 2 9
10 5 3 2 4
11 9 4 2 9
12 7 3 2 9
13 4 2 3 6
14 1 2 3 10
15 1 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 12 1 4 2
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 24 14 15 24
37 24 14 15 25
38 28 24 15 25
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
Dihedrals
1 10 8 1 4 2
2 10 7 1 4 2
3 13 4 2 1 8
4 12 3 2 1 8
5 14 8 1 2 9
6 11 3 2 1 4
7 13 4 1 2 9
8 13 4 2 1 7
9 12 3 2 1 7
10 14 7 1 2 9
11 9 3 2 4 1
12 10 9 2 4 1
13 34 1 2 3 6
14 35 1 2 3 10
15 35 1 2 3 11
16 36 4 2 3 6
17 37 4 2 3 10
18 37 4 2 3 11
19 38 9 2 3 6
20 39 9 2 3 10
21 39 9 2 3 11
22 8 2 3 6 5
23 7 10 3 6 5
24 7 11 3 6 5
25 27 14 13 12 18
26 28 20 13 12 18
27 28 21 13 12 18
28 29 14 13 12 19
29 30 20 13 12 19
30 30 21 13 12 19
31 27 17 18 12 13
32 28 30 18 12 13
33 28 31 18 12 13
34 29 17 18 12 19
35 30 30 18 12 19
36 30 31 18 12 19
37 31 12 13 14 15
38 32 22 14 13 12
39 32 23 14 13 12
40 32 20 13 14 15
41 33 20 13 14 22
42 33 20 13 14 23
43 32 21 13 14 15
44 33 21 13 14 22
45 33 21 13 14 23
46 29 13 14 15 24
47 29 13 14 15 25
48 30 22 14 15 24
49 30 22 14 15 25
50 30 23 14 15 24
51 30 23 14 15 25
52 29 18 17 16 26
53 30 28 17 16 26
54 30 29 17 16 26
55 29 18 17 16 27
56 30 28 17 16 27
57 30 29 17 16 27
58 31 16 17 18 12
59 32 30 18 17 16
60 32 31 18 17 16
61 32 28 17 18 12
62 33 28 17 18 30
63 33 28 17 18 31
64 32 29 17 18 12
65 33 29 17 18 30
66 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 5 14 15 24 25
3 5 17 16 26 27
4 1 2 1 4 8
5 1 4 1 8 7
6 1 2 1 8 7
7 1 2 1 4 7
8 1 1 2 3 4
9 1 1 2 4 9
10 1 1 2 3 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31

47
examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp2.map
View File

@ -1,47 +0,0 @@
this is a map file
1 edgeIDs
31 equivalences
BondingIDs
4
25
EdgeIDs
5
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31

307
examples/USER/misc/bond_react/tiny_epoxy/rxn1_stp2_post.data_template
View File

@ -1,307 +0,0 @@
rxn1_stp2_post
31 atoms
30 bonds
53 angles
72 dihedrals
31 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 24 14 15 24
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 46 2 1 15 14
13 47 2 1 15 24
14 28 7 1 15 14
15 30 7 1 15 24
16 48 6 3 2 1
17 40 10 3 2 1
18 40 11 3 2 1
19 49 6 3 2 9
20 41 10 3 2 9
21 41 11 3 2 9
22 50 6 3 2 4
23 42 10 3 2 4
24 42 11 3 2 4
25 52 1 2 4 25
26 52 3 2 4 25
27 53 9 2 4 25
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 28 22 14 15 1
55 30 22 14 15 24
56 28 23 14 15 1
57 30 23 14 15 24
58 29 18 17 16 26
59 30 28 17 16 26
60 30 29 17 16 26
61 29 18 17 16 27
62 30 28 17 16 27
63 30 29 17 16 27
64 31 16 17 18 12
65 32 30 18 17 16
66 32 31 18 17 16
67 32 28 17 18 12
68 33 28 17 18 30
69 33 28 17 18 31
70 32 29 17 18 12
71 33 29 17 18 30
72 33 29 17 18 31
Impropers
1 4 13 12 18 19
2 4 1 15 14 24
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31

59
examples/USER/misc/bond_react/tiny_epoxy/rxn2_stp1.map
View File

@ -1,59 +0,0 @@
this is a map file
2 edgeIDs
42 equivalences
BondingIDs
15
32
EdgeIDs
5
36
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31
32 32
33 33
34 34
35 35
36 36
37 37
38 38
39 39
40 40
41 41
42 42

424
examples/USER/misc/bond_react/tiny_epoxy/rxn2_stp1_post.data_template
View File

@ -1,424 +0,0 @@
rxn2_stp1_post
42 atoms
41 bonds
75 angles
108 dihedrals
46 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 1
33 6
34 1
35 7
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.680189 9.134390 -4.183100
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 32 15
24 13 17 16
25 14 16 26
26 14 16 27
27 15 17 18
28 1 17 28
29 1 17 29
30 1 18 30
31 1 18 31
32 1 32 39
33 16 32 33
34 1 32 38
35 17 33 35
36 16 34 33
37 12 33 40
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 23 1 15 32
39 24 14 15 24
40 23 14 15 32
41 24 32 15 24
42 24 17 16 26
43 24 17 16 27
44 28 26 16 27
45 25 18 17 16
46 26 28 17 16
47 26 29 17 16
48 27 18 17 28
49 27 18 17 29
50 2 28 17 29
51 25 17 18 12
52 26 30 18 12
53 26 31 18 12
54 27 17 18 30
55 27 17 18 31
56 2 30 18 31
57 26 39 32 15
58 31 33 32 15
59 26 38 32 15
60 30 33 32 39
61 2 39 32 38
62 30 33 32 38
63 34 32 33 35
64 32 32 33 34
65 33 32 33 40
66 34 34 33 35
67 35 35 33 40
68 33 34 33 40
69 36 33 34 37
70 30 33 34 41
71 30 33 34 42
72 3 37 34 41
73 3 37 34 42
74 2 41 34 42
75 22 34 37 36
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 28 8 1 15 32
13 46 2 1 15 14
14 47 2 1 15 24
15 46 2 1 15 32
16 28 7 1 15 14
17 30 7 1 15 24
18 28 7 1 15 32
19 48 6 3 2 1
20 40 10 3 2 1
21 40 11 3 2 1
22 49 6 3 2 9
23 41 10 3 2 9
24 41 11 3 2 9
25 50 6 3 2 4
26 42 10 3 2 4
27 42 11 3 2 4
28 52 1 2 4 25
29 52 3 2 4 25
30 53 9 2 4 25
31 51 2 3 6 5
32 7 10 3 6 5
33 7 11 3 6 5
34 27 14 13 12 18
35 28 20 13 12 18
36 28 21 13 12 18
37 29 14 13 12 19
38 30 20 13 12 19
39 30 21 13 12 19
40 27 17 18 12 13
41 28 30 18 12 13
42 28 31 18 12 13
43 29 17 18 12 19
44 30 30 18 12 19
45 30 31 18 12 19
46 31 12 13 14 15
47 32 22 14 13 12
48 32 23 14 13 12
49 32 20 13 14 15
50 33 20 13 14 22
51 33 20 13 14 23
52 32 21 13 14 15
53 33 21 13 14 22
54 33 21 13 14 23
55 27 13 14 15 1
56 29 13 14 15 24
57 27 13 14 15 32
58 28 22 14 15 1
59 30 22 14 15 24
60 28 22 14 15 32
61 28 23 14 15 1
62 30 23 14 15 24
63 28 23 14 15 32
64 28 39 32 15 1
65 46 33 32 15 1
66 28 38 32 15 1
67 28 39 32 15 14
68 46 33 32 15 14
69 28 38 32 15 14
70 30 39 32 15 24
71 47 33 32 15 24
72 30 38 32 15 24
73 29 18 17 16 26
74 30 28 17 16 26
75 30 29 17 16 26
76 29 18 17 16 27
77 30 28 17 16 27
78 30 29 17 16 27
79 31 16 17 18 12
80 32 30 18 17 16
81 32 31 18 17 16
82 32 28 17 18 12
83 33 28 17 18 30
84 33 28 17 18 31
85 32 29 17 18 12
86 33 29 17 18 30
87 33 29 17 18 31
88 45 15 32 33 35
89 43 15 32 33 34
90 44 15 32 33 40
91 42 39 32 33 35
92 40 39 32 33 34
93 41 39 32 33 40
94 42 38 32 33 35
95 40 38 32 33 34
96 41 38 32 33 40
97 48 37 34 33 32
98 40 41 34 33 32
99 40 42 34 33 32
100 50 37 34 33 35
101 42 41 34 33 35
102 42 42 34 33 35
103 49 37 34 33 40
104 41 41 34 33 40
105 41 42 34 33 40
106 51 33 34 37 36
107 7 41 34 37 36
108 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 5 17 16 26 27
3 1 2 1 8 7
4 1 2 1 8 15
5 1 8 1 7 15
6 1 2 1 7 15
7 1 1 2 3 9
8 1 1 2 3 4
9 1 1 2 4 9
10 1 3 2 4 9
11 1 2 3 6 10
12 1 2 3 6 11
13 1 2 3 10 11
14 1 6 3 10 11
15 1 14 13 20 12
16 1 14 13 21 12
17 1 20 13 21 12
18 1 14 13 20 21
19 1 13 14 22 15
20 1 13 14 23 15
21 1 13 14 22 23
22 1 22 14 23 15
23 1 1 15 14 24
24 1 1 15 14 32
25 1 1 15 32 24
26 1 14 15 32 24
27 1 18 17 28 16
28 1 18 17 29 16
29 1 28 17 29 16
30 1 18 17 28 29
31 1 17 18 30 12
32 1 17 18 31 12
33 1 30 18 31 12
34 1 17 18 30 31
35 1 33 32 39 15
36 1 39 32 38 15
37 1 33 32 38 15
38 1 33 32 39 38
39 1 32 33 34 35
40 1 32 33 35 40
41 1 32 33 34 40
42 1 34 33 35 40
43 1 33 34 37 41
44 1 33 34 37 42
45 1 33 34 41 42
46 1 37 34 41 42

407
examples/USER/misc/bond_react/tiny_epoxy/rxn2_stp1_pre.data_template
View File

@ -1,407 +0,0 @@
rxn2_stp1_pre
42 atoms
41 bonds
73 angles
96 dihedrals
43 impropers
Types
1 1
2 6
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 10
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 2
33 2
34 1
35 3
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 17.213690 10.780300 -1.896260
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.703360 9.118830 -4.174240
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 16 1 2
3 1 1 7
4 13 1 15
5 16 3 2
6 12 2 9
7 17 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 14 15 24
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
31 6 39 32
32 4 32 35
33 5 32 33
34 6 38 32
35 4 33 35
36 2 34 33
37 6 40 33
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 30 2 1 8
2 2 8 1 7
3 26 8 1 15
4 30 2 1 7
5 31 2 1 15
6 26 7 1 15
7 32 1 2 3
8 33 1 2 9
9 34 1 2 4
10 33 3 2 9
11 34 3 2 4
12 35 4 2 9
13 36 2 3 6
14 30 2 3 10
15 30 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 37 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 24 1 15 24
38 24 14 15 24
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
54 38 39 32 35
55 39 39 32 33
56 11 39 32 38
57 8 33 32 35
58 38 38 32 35
59 39 38 32 33
60 8 32 33 35
61 6 34 33 32
62 39 40 33 32
63 5 34 33 35
64 38 40 33 35
65 7 34 33 40
66 40 37 34 33
67 41 41 34 33
68 41 42 34 33
69 3 37 34 41
70 3 37 34 42
71 2 41 34 42
72 12 32 35 33
73 22 34 37 36
Dihedrals
1 40 8 1 2 3
2 41 8 1 2 9
3 42 8 1 2 4
4 40 7 1 2 3
5 41 7 1 2 9
6 42 7 1 2 4
7 43 15 1 2 3
8 44 15 1 2 9
9 45 15 1 2 4
10 28 8 1 15 14
11 30 8 1 15 24
12 46 2 1 15 14
13 47 2 1 15 24
14 28 7 1 15 14
15 30 7 1 15 24
16 48 6 3 2 1
17 40 10 3 2 1
18 40 11 3 2 1
19 49 6 3 2 9
20 41 10 3 2 9
21 41 11 3 2 9
22 50 6 3 2 4
23 42 10 3 2 4
24 42 11 3 2 4
25 52 1 2 4 25
26 52 3 2 4 25
27 53 9 2 4 25
28 51 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 29 13 14 15 24
54 28 22 14 15 1
55 30 22 14 15 24
56 28 23 14 15 1
57 30 23 14 15 24
58 29 18 17 16 26
59 30 28 17 16 26
60 30 29 17 16 26
61 29 18 17 16 27
62 30 28 17 16 27
63 30 29 17 16 27
64 31 16 17 18 12
65 32 30 18 17 16
66 32 31 18 17 16
67 32 28 17 18 12
68 33 28 17 18 30
69 33 28 17 18 31
70 32 29 17 18 12
71 33 29 17 18 30
72 33 29 17 18 31
73 10 39 32 35 33
74 10 38 32 35 33
75 54 39 32 33 35
76 12 34 33 32 39
77 14 39 32 33 40
78 11 34 33 32 35
79 54 40 33 32 35
80 54 38 32 33 35
81 12 34 33 32 38
82 14 38 32 33 40
83 9 34 33 35 32
84 10 40 33 35 32
85 5 37 34 33 32
86 2 41 34 33 32
87 2 42 34 33 32
88 4 37 34 33 35
89 1 41 34 33 35
90 1 42 34 33 35
91 6 37 34 33 40
92 3 41 34 33 40
93 3 42 34 33 40
94 8 33 34 37 36
95 7 41 34 37 36
96 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 4 1 15 14 24
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31
32 1 39 32 33 35
33 1 39 32 38 35
34 1 39 32 38 33
35 1 38 32 33 35
36 1 34 33 32 35
37 1 40 33 32 35
38 1 34 33 40 32
39 1 34 33 40 35
40 1 37 34 41 33
41 1 37 34 42 33
42 1 41 34 42 33
43 1 37 34 41 42

59
examples/USER/misc/bond_react/tiny_epoxy/rxn2_stp2.map
View File

@ -1,59 +0,0 @@
this is a map file
2 edgeIDs
42 equivalences
BondingIDs
35
24
EdgeIDs
5
36
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31
32 32
33 33
34 34
35 35
36 36
37 37
38 38
39 39
40 40
41 41
42 42

413
examples/USER/misc/bond_react/tiny_epoxy/rxn2_stp2_post.data_template
View File

@ -1,413 +0,0 @@
rxn2_stp2_post
42 atoms
41 bonds
73 angles
102 dihedrals
43 impropers
Types
1 1
2 2
3 1
4 7
5 4
6 7
7 8
8 8
9 8
10 8
11 8
12 9
13 1
14 1
15 9
16 9
17 1
18 1
19 10
20 8
21 8
22 8
23 8
24 11
25 11
26 10
27 10
28 8
29 8
30 8
31 8
32 1
33 6
34 1
35 7
36 4
37 7
38 8
39 8
40 8
41 8
42 8
Charges
1 0.000000
2 0.000000
3 0.000000
4 0.100000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.000000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 -0.025000
16 -0.025000
17 0.000000
18 0.000000
19 0.000000
20 0.000000
21 0.000000
22 0.000000
23 0.000000
24 0.000000
25 0.000000
26 0.000000
27 0.000000
28 0.000000
29 0.000000
30 0.000000
31 0.000000
32 0.000000
33 0.000000
34 0.000000
35 0.100000
36 0.000000
37 0.000000
38 0.000000
39 0.000000
40 0.000000
41 0.000000
42 0.000000
Coords
1 19.846411 9.569080 -1.229960
2 21.168550 9.331390 -0.418120
3 21.253010 8.067940 0.460720
4 21.330839 10.304280 -0.253340
5 21.891689 5.906200 0.464150
6 21.818470 6.999870 -0.296270
7 19.931601 10.026600 -2.215510
8 19.051279 8.828540 -1.132880
9 22.228800 9.293580 -0.665280
10 21.880541 8.270810 1.328060
11 20.253151 7.789050 0.792640
12 16.072720 12.338940 -0.174630
13 16.557051 11.130580 0.587500
14 18.074381 10.998730 0.366590
15 18.354031 10.832100 -1.107140
16 14.920880 15.018100 -0.201130
17 16.390551 14.791140 -0.461060
18 16.852989 13.538490 0.304530
19 16.264271 12.190330 -1.257620
20 16.025061 10.195290 0.210910
21 16.346741 11.269890 1.698950
22 18.466690 10.092460 0.935470
23 18.592319 11.941150 0.745170
24 16.017490 9.805710 -4.329880
25 20.881861 11.302060 -0.773030
26 14.344180 14.136430 -0.550280
27 14.583670 15.922830 -0.748110
28 16.984310 15.696060 -0.103470
29 16.562460 14.639560 -1.577590
30 16.674610 13.686010 1.420370
31 17.964001 13.363150 0.117750
32 18.680189 9.134390 -4.183100
33 18.099751 8.263650 -5.343000
34 19.081829 7.609610 -6.334180
35 17.971729 9.827680 -5.367080
36 20.263880 5.733600 -6.736780
37 19.414030 6.299980 -5.878960
38 18.194740 9.091640 -3.210950
39 19.788940 9.208560 -4.119640
40 17.399309 7.432220 -5.407800
41 18.616249 7.545570 -7.316910
42 19.987049 8.212500 -6.399400
Bonds
1 1 1 8
2 2 1 2
3 1 1 7
4 13 1 15
5 2 3 2
6 6 2 9
7 19 2 4
8 3 3 6
9 1 3 10
10 1 3 11
11 18 4 25
12 8 6 5
13 13 13 12
14 13 18 12
15 14 12 19
16 15 13 14
17 1 13 20
18 1 13 21
19 13 14 15
20 1 14 22
21 1 14 23
22 13 32 15
23 13 17 16
24 14 16 26
25 14 16 27
26 15 17 18
27 1 17 28
28 1 17 29
29 1 18 30
30 1 18 31
31 18 35 24
32 1 32 39
33 16 32 33
34 1 32 38
35 17 35 33
36 16 34 33
37 12 40 33
38 3 34 37
39 1 34 41
40 1 34 42
41 8 37 36
Angles
1 1 2 1 8
2 2 8 1 7
3 26 8 1 15
4 1 2 1 7
5 42 2 1 15
6 26 7 1 15
7 43 1 2 3
8 7 1 2 9
9 44 1 2 4
10 7 3 2 9
11 44 3 2 4
12 45 4 2 9
13 4 2 3 6
14 1 2 3 10
15 1 2 3 11
16 3 6 3 10
17 3 6 3 11
18 2 10 3 11
19 46 2 4 25
20 22 3 6 5
21 23 13 12 18
22 24 13 12 19
23 24 18 12 19
24 25 14 13 12
25 26 20 13 12
26 26 21 13 12
27 27 14 13 20
28 27 14 13 21
29 2 20 13 21
30 25 13 14 15
31 27 13 14 22
32 27 13 14 23
33 26 22 14 15
34 26 23 14 15
35 2 22 14 23
36 23 1 15 14
37 23 1 15 32
38 23 14 15 32
39 24 17 16 26
40 24 17 16 27
41 28 26 16 27
42 25 18 17 16
43 26 28 17 16
44 26 29 17 16
45 27 18 17 28
46 27 18 17 29
47 2 28 17 29
48 25 17 18 12
49 26 30 18 12
50 26 31 18 12
51 27 17 18 30
52 27 17 18 31
53 2 30 18 31
54 26 39 32 15
55 47 15 32 33
56 26 38 32 15
57 48 39 32 33
58 2 39 32 38
59 48 38 32 33
60 34 32 33 35
61 32 32 33 34
62 33 32 33 40
63 34 34 33 35
64 35 35 33 40
65 33 34 33 40
66 49 37 34 33
67 48 41 34 33
68 48 42 34 33
69 3 37 34 41
70 3 37 34 42
71 2 41 34 42
72 50 24 35 33
73 22 34 37 36
Dihedrals
1 55 8 1 2 3
2 3 8 1 2 9
3 56 8 1 2 4
4 55 7 1 2 3
5 3 7 1 2 9
6 56 7 1 2 4
7 57 15 1 2 3
8 58 15 1 2 9
9 59 15 1 2 4
10 28 8 1 15 14
11 28 8 1 15 32
12 60 2 1 15 14
13 60 2 1 15 32
14 28 7 1 15 14
15 28 7 1 15 32
16 61 6 3 2 1
17 55 10 3 2 1
18 55 11 3 2 1
19 6 6 3 2 9
20 3 10 3 2 9
21 3 11 3 2 9
22 62 6 3 2 4
23 56 10 3 2 4
24 56 11 3 2 4
25 63 1 2 4 25
26 63 3 2 4 25
27 64 9 2 4 25
28 8 2 3 6 5
29 7 10 3 6 5
30 7 11 3 6 5
31 27 14 13 12 18
32 28 20 13 12 18
33 28 21 13 12 18
34 29 14 13 12 19
35 30 20 13 12 19
36 30 21 13 12 19
37 27 17 18 12 13
38 28 30 18 12 13
39 28 31 18 12 13
40 29 17 18 12 19
41 30 30 18 12 19
42 30 31 18 12 19
43 31 12 13 14 15
44 32 22 14 13 12
45 32 23 14 13 12
46 32 20 13 14 15
47 33 20 13 14 22
48 33 20 13 14 23
49 32 21 13 14 15
50 33 21 13 14 22
51 33 21 13 14 23
52 27 13 14 15 1
53 27 13 14 15 32
54 28 22 14 15 1
55 28 22 14 15 32
56 28 23 14 15 1
57 28 23 14 15 32
58 28 39 32 15 1
59 46 33 32 15 1
60 28 38 32 15 1
61 28 39 32 15 14
62 46 33 32 15 14
63 28 38 32 15 14
64 29 18 17 16 26
65 30 28 17 16 26
66 30 29 17 16 26
67 29 18 17 16 27
68 30 28 17 16 27
69 30 29 17 16 27
70 31 16 17 18 12
71 32 30 18 17 16
72 32 31 18 17 16
73 32 28 17 18 12
74 33 28 17 18 30
75 33 28 17 18 31
76 32 29 17 18 12
77 33 29 17 18 30
78 33 29 17 18 31
79 45 15 32 33 35
80 43 15 32 33 34
81 44 15 32 33 40
82 42 39 32 33 35
83 40 39 32 33 34
84 41 39 32 33 40
85 42 38 32 33 35
86 40 38 32 33 34
87 41 38 32 33 40
88 65 24 35 33 32
89 65 24 35 33 34
90 66 24 35 33 40
91 48 37 34 33 32
92 40 41 34 33 32
93 40 42 34 33 32
94 50 37 34 33 35
95 42 41 34 33 35
96 42 42 34 33 35
97 49 37 34 33 40
98 41 41 34 33 40
99 41 42 34 33 40
100 51 33 34 37 36
101 7 41 34 37 36
102 7 42 34 37 36
Impropers
1 4 13 12 18 19
2 22 1 15 14 32
3 5 17 16 26 27
4 1 2 1 8 7
5 1 2 1 8 15
6 1 8 1 7 15
7 1 2 1 7 15
8 1 1 2 3 9
9 1 1 2 3 4
10 1 1 2 4 9
11 1 3 2 4 9
12 1 2 3 6 10
13 1 2 3 6 11
14 1 2 3 10 11
15 1 6 3 10 11
16 1 14 13 20 12
17 1 14 13 21 12
18 1 20 13 21 12
19 1 14 13 20 21
20 1 13 14 22 15
21 1 13 14 23 15
22 1 13 14 22 23
23 1 22 14 23 15
24 1 18 17 28 16
25 1 18 17 29 16
26 1 28 17 29 16
27 1 18 17 28 29
28 1 17 18 30 12
29 1 17 18 31 12
30 1 30 18 31 12
31 1 17 18 30 31
32 1 39 32 15 33
33 1 39 32 38 15
34 1 38 32 15 33
35 1 39 32 38 33
36 1 32 33 34 35
37 1 32 33 35 40
38 1 32 33 34 40
39 1 34 33 35 40
40 1 37 34 41 33
41 1 37 34 42 33
42 1 41 34 42 33
43 1 37 34 41 42

1582
examples/USER/misc/bond_react/tiny_epoxy/tiny_epoxy.data
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File diff suppressed because it is too large Load Diff

52
examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized
View File

@ -1,52 +0,0 @@
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_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 10000
# write_restart restart_longrun
# write_data restart_longrun.data

48
examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized
View File

@ -1,48 +0,0 @@
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization no &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 1000
# write_restart restart_longrun
# write_data restart_longrun.data

148
examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.1
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@ -1,148 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 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
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000181113 secs
read_data CPU = 0.0251833 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
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 = 10 10 10
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
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
87.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13
Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01
Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70
Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60
Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74
Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80
Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64
Other | | 0.001306 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 740 ave 740 max 740 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

148
examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.stabilized.g++.4
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@ -1,148 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 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
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000178751 secs
read_data CPU = 0.0385782 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
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 = 10 10 10
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
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
98.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85
Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84
Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16
Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78
Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03
Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93
Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10
Other | | 0.0008281 | | | 0.31
Nlocal: 11 ave 21 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 32.5 ave 43 max 23 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 185 ave 376 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.1
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@ -1,147 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 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
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000217102 secs
read_data CPU = 0.00630778 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
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 = 10 10 10
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
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
91.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17
Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42
Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78
Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61
Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74
Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98
Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91
Other | | 0.001336 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 818 ave 818 max 818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
examples/USER/misc/bond_react/tiny_nylon/log.5Jun19.tiny_nylon.unstabilized.g++.4
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@ -1,147 +0,0 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 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
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000163256 secs
read_data CPU = 0.0244579 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
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 = 10 10 10
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
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56
Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62
Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04
Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16
Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31
Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13
Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91
Other | | 0.0007123 | | | 0.28
Nlocal: 11 ave 29 max 0 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 25 ave 31 max 12 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 204.5 ave 443 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

35
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_map
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@ -1,35 +0,0 @@
this is a nominal superimpose file
2 edgeIDs
18 equivalences
BondingIDs
10
1
EdgeIDs
16
8
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18

189
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_reacted.data_template
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@ -1,189 +0,0 @@
this is a molecule template for: initial nylon crosslink, post-reacting
18 atoms
17 bonds
31 angles
39 dihedrals
20 impropers
Types
1 9
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
16 1
17 4
18 4
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -5.522237 -0.752722 1.631158
2 -5.170398 -0.545733 0.178130
3 -6.469695 -0.553072 -0.648889
4 -6.052076 -1.721152 1.744648
5 -6.183059 0.071387 1.971497
6 -4.489340 -1.389197 -0.173156
7 -4.637591 0.453703 0.051252
8 -5.618658 0.138919 4.386107
9 -4.669492 -0.989819 3.943591
10 -4.270194 -0.766405 2.474102
11 -3.348470 -1.875393 2.024289
12 -3.569794 0.564183 2.345995
13 -5.201079 -1.993301 4.044219
14 -3.736682 -0.984819 4.598305
15 -4.255402 1.370923 2.679069
16 -6.136394 -0.339866 -2.136775
17 -6.996331 -1.555519 -0.517408
18 -7.153308 0.284949 -0.289930
Bonds
1 11 1 2
2 12 1 4
3 12 1 5
4 13 1 10
5 2 2 3
6 1 2 6
7 1 2 7
8 2 3 16
9 1 3 17
10 1 3 18
11 2 8 9
12 4 9 10
13 1 9 13
14 1 9 14
15 5 10 11
16 3 10 12
17 6 12 15
Angles
1 17 2 1 4
2 17 2 1 5
3 18 2 1 10
4 19 4 1 5
5 20 4 1 10
6 20 5 1 10
7 21 1 2 3
8 22 1 2 6
9 22 1 2 7
10 2 3 2 6
11 2 3 2 7
12 1 6 2 7
13 3 2 3 16
14 2 2 3 17
15 2 2 3 18
16 2 16 3 17
17 2 16 3 18
18 1 17 3 18
19 8 8 9 10
20 2 8 9 13
21 2 8 9 14
22 23 13 9 10
23 23 14 9 10
24 1 13 9 14
25 6 9 10 11
26 4 9 10 12
27 24 1 10 9
28 25 11 10 12
29 26 1 10 11
30 27 1 10 12
31 7 10 12 15
Dihedrals
1 19 4 1 2 3
2 20 4 1 2 6
3 20 4 1 2 7
4 19 5 1 2 3
5 20 5 1 2 6
6 20 5 1 2 7
7 21 10 1 2 3
8 22 10 1 2 6
9 22 10 1 2 7
10 23 2 1 10 9
11 24 2 1 10 11
12 25 2 1 10 12
13 26 4 1 10 9
14 27 4 1 10 11
15 28 4 1 10 12
16 26 5 1 10 9
17 27 5 1 10 11
18 28 5 1 10 12
19 29 1 2 3 16
20 30 1 2 3 17
21 30 1 2 3 18
22 4 16 3 2 6
23 2 6 2 3 17
24 2 6 2 3 18
25 4 16 3 2 7
26 2 7 2 3 17
27 2 7 2 3 18
28 10 8 9 10 11
29 8 8 9 10 12
30 31 8 9 10 1
31 11 13 9 10 11
32 9 13 9 10 12
33 32 13 9 10 1
34 11 14 9 10 11
35 9 14 9 10 12
36 32 14 9 10 1
37 6 9 10 12 15
38 7 11 10 12 15
39 33 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 2 3 16 17
10 1 2 3 16 18
11 1 2 3 17 18
12 1 16 3 17 18
13 1 8 9 13 10
14 1 8 9 14 10
15 1 8 9 13 14
16 1 13 9 14 10
17 1 9 10 11 12
18 1 1 10 9 11
19 1 1 10 9 12
20 1 1 10 11 12

160
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp1_unreacted.data_template
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@ -1,160 +0,0 @@
this is a molecule template for: initial nylon crosslink, pre-reacting
18 atoms
16 bonds
25 angles
23 dihedrals
14 impropers
Types
1 7
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
16 1
17 4
18 4
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
16 0.000000
17 0.000000
18 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
16 -3.964987 2.900602 -1.551341
17 -4.460694 2.836102 0.668882
18 -4.828494 3.219656 -0.122111
Bonds
1 14 1 2
2 10 1 4
3 10 1 5
4 2 2 3
5 1 2 6
6 1 2 7
7 2 3 16
8 1 3 17
9 1 3 18
10 2 8 9
11 4 9 10
12 1 9 13
13 1 9 14
14 5 10 11
15 3 10 12
16 6 12 15
Angles
1 15 2 1 4
2 15 2 1 5
3 16 4 1 5
4 28 1 2 3
5 14 1 2 6
6 14 1 2 7
7 2 3 2 6
8 2 3 2 7
9 1 6 2 7
10 3 2 3 16
11 2 2 3 17
12 2 2 3 18
13 2 16 3 17
14 2 16 3 18
15 1 17 3 18
16 8 8 9 10
17 2 8 9 13
18 2 8 9 14
19 23 13 9 10
20 23 14 9 10
21 1 13 9 14
22 6 9 10 11
23 4 9 10 12
24 25 11 10 12
25 7 10 12 15
Dihedrals
1 34 4 1 2 3
2 35 4 1 2 6
3 35 4 1 2 7
4 34 5 1 2 3
5 35 5 1 2 6
6 35 5 1 2 7
7 36 1 2 3 16
8 12 1 2 3 17
9 12 1 2 3 18
10 4 16 3 2 6
11 2 6 2 3 17
12 2 6 2 3 18
13 4 16 3 2 7
14 2 7 2 3 17
15 2 7 2 3 18
16 10 8 9 10 11
17 8 8 9 10 12
18 11 13 9 10 11
19 9 13 9 10 12
20 11 14 9 10 11
21 9 14 9 10 12
22 6 9 10 12 15
23 7 11 10 12 15
Impropers
1 6 2 1 4 5
2 11 9 10 11 12
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 2 3 16 17
8 1 2 3 16 18
9 1 2 3 17 18
10 1 16 3 17 18
11 1 8 9 13 10
12 1 8 9 14 10
13 1 8 9 13 14
14 1 13 9 14 10

32
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_map
View File

@ -1,32 +0,0 @@
this is a nominal superimpose file
2 edgeIDs
15 equivalences
BondingIDs
4
12
EdgeIDs
8
3
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15

131
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_reacted.data_template
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@ -1,131 +0,0 @@
this is a molecule template for: water condensation, post-reacting
15 atoms
13 bonds
19 angles
16 dihedrals
10 impropers
Types
1 9
2 1
3 1
4 10
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 11
13 4
14 4
15 10
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.410000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 -0.820000
13 0.000000
14 0.000000
15 0.410000
Coords
1 -4.856280 -1.050468 1.432625
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 11 1 2
2 12 1 5
3 13 1 10
4 2 2 3
5 1 2 6
6 1 2 7
7 15 4 12
8 2 8 9
9 4 9 10
10 1 9 13
11 1 9 14
12 5 10 11
13 15 15 12
Angles
1 17 2 1 5
2 18 2 1 10
3 20 5 1 10
4 21 1 2 3
5 22 1 2 6
6 22 1 2 7
7 2 3 2 6
8 2 3 2 7
9 1 6 2 7
10 8 8 9 10
11 2 8 9 13
12 2 8 9 14
13 23 13 9 10
14 23 14 9 10
15 1 13 9 14
16 6 9 10 11
17 24 1 10 9
18 26 1 10 11
19 29 15 12 4
Dihedrals
1 19 5 1 2 3
2 20 5 1 2 6
3 20 5 1 2 7
4 21 10 1 2 3
5 22 10 1 2 6
6 22 10 1 2 7
7 23 2 1 10 9
8 24 2 1 10 11
9 26 5 1 10 9
10 27 5 1 10 11
11 10 8 9 10 11
12 31 8 9 10 1
13 11 13 9 10 11
14 32 13 9 10 1
15 11 14 9 10 11
16 32 14 9 10 1
Impropers
1 12 2 1 5 10
2 13 1 10 9 11
3 1 1 2 3 6
4 1 1 2 3 7
5 1 1 2 6 7
6 1 3 2 6 7
7 1 8 9 13 10
8 1 8 9 14 10
9 1 8 9 13 14
10 1 13 9 14 10

158
examples/USER/misc/bond_react/tiny_nylon/rxn1_stp2_unreacted.data_template
View File

@ -1,158 +0,0 @@
this is a molecule template for: water condensation, pre-reacting
15 atoms
14 bonds
25 angles
30 dihedrals
16 impropers
Types
1 9
2 1
3 1
4 8
5 8
6 4
7 4
8 1
9 1
10 2
11 6
12 3
13 4
14 4
15 5
Charges
1 -0.300000
2 0.000000
3 0.000000
4 0.000000
5 0.000000
6 0.000000
7 0.000000
8 0.000000
9 0.000000
10 0.300000
11 0.000000
12 0.000000
13 0.000000
14 0.000000
15 0.000000
Coords
1 -4.922858 -0.946982 1.146055
2 -5.047195 -0.935267 -0.358173
3 -6.526281 -0.755366 -0.743523
4 -5.282604 0.020447 1.552710
5 -3.860697 -1.095850 1.428305
6 -4.662382 -1.920900 -0.781524
7 -4.433977 -0.072765 -0.784071
8 -5.506279 0.202610 4.825816
9 -4.449177 -0.844592 4.423366
10 -4.103916 -0.749629 2.925195
11 -3.376249 -1.886171 2.245643
12 -4.493235 0.477214 2.137199
13 -4.849053 -1.888877 4.663994
14 -3.491823 -0.662913 5.018510
15 -5.020777 1.189745 2.805427
Bonds
1 11 1 2
2 12 1 4
3 12 1 5
4 13 1 10
5 2 2 3
6 1 2 6
7 1 2 7
8 2 8 9
9 4 9 10
10 1 9 13
11 1 9 14
12 5 10 11
13 3 10 12
14 6 12 15
Angles
1 17 2 1 4
2 17 2 1 5
3 18 2 1 10
4 19 4 1 5
5 20 4 1 10
6 20 5 1 10
7 21 1 2 3
8 22 1 2 6
9 22 1 2 7
10 2 3 2 6
11 2 3 2 7
12 1 6 2 7
13 8 8 9 10
14 2 8 9 13
15 2 8 9 14
16 23 13 9 10
17 23 14 9 10
18 1 13 9 14
19 6 9 10 11
20 4 9 10 12
21 24 1 10 9
22 25 11 10 12
23 26 1 10 11
24 27 1 10 12
25 7 10 12 15
Dihedrals
1 19 4 1 2 3
2 20 4 1 2 6
3 20 4 1 2 7
4 19 5 1 2 3
5 20 5 1 2 6
6 20 5 1 2 7
7 21 10 1 2 3
8 22 10 1 2 6
9 22 10 1 2 7
10 23 2 1 10 9
11 24 2 1 10 11
12 25 2 1 10 12
13 26 4 1 10 9
14 27 4 1 10 11
15 28 4 1 10 12
16 26 5 1 10 9
17 27 5 1 10 11
18 28 5 1 10 12
19 10 8 9 10 11
20 8 8 9 10 12
21 31 8 9 10 1
22 11 13 9 10 11
23 9 13 9 10 12
24 32 13 9 10 1
25 11 14 9 10 11
26 9 14 9 10 12
27 32 14 9 10 1
28 6 9 10 12 15
29 7 11 10 12 15
30 33 1 10 12 15
Impropers
1 1 2 1 4 5
2 1 2 1 4 10
3 1 2 1 5 10
4 1 4 1 5 10
5 1 1 2 3 6
6 1 1 2 3 7
7 1 1 2 6 7
8 1 3 2 6 7
9 1 8 9 13 10
10 1 8 9 14 10
11 1 8 9 13 14
12 1 13 9 14 10
13 1 9 10 11 12
14 1 1 10 9 11
15 1 1 10 9 12
16 1 1 10 11 12

795
examples/USER/misc/bond_react/tiny_nylon/tiny_nylon.data
View File

@ -1,795 +0,0 @@
this is LAMMPS data file containing two nylon monomers
44 atoms
11 atom types
42 bonds
15 bond types
74 angles
29 angle types
100 dihedrals
36 dihedral types
44 impropers
13 improper types
5 extra bond per atom
15 extra angle per atom
15 extra dihedral per atom
25 extra improper per atom
25 extra special per atom
-25 25 xlo xhi
-25 25 ylo yhi
-25 25 zlo zhi
Masses
1 12.0112
2 12.0112
3 15.9994
4 1.00797
5 1.00797
6 15.9994
7 14.0067
8 1.00797
9 14.0067
10 1.00797
11 15.9994
Pair Coeffs # lj/class2/coul/cut
1 0.054 4.01
2 0.12 3.81
3 0.24 3.535
4 0.02 2.7
5 0.013 1.098
6 0.267 3.3
7 0.065 4.07
8 0.013 1.098
9 0.106 4.07
10 0.013 1.098
11 0.26 3.61
Bond Coeffs # class2
1 1.101 345 -691.89 844.6
2 1.53 299.67 -501.77 679.81
3 1.3649 368.731 -832.478 1274.02
4 1.5202 253.707 -423.037 396.9
5 1.202 851.14 -1918.49 2160.77
6 0.965 532.506 -1282.9 2004.77
7 1.53 299.67 -501.77 679.81
8 1.101 345 -691.89 844.6
9 1.457 365.805 -699.637 998.484
10 1.006 466.74 -1073.6 1251.11
11 1.452 327.166 -547.899 526.5
12 1.01 462.75 -1053.63 1545.76
13 1.416 359.159 -558.473 1146.38
14 1.457 365.805 -699.637 998.484
15 0.97 563.28 -1428.22 1902.12
Angle Coeffs # class2
1 107.66 39.641 -12.921 -2.4318
2 110.77 41.453 -10.604 5.129
3 112.67 39.516 -7.443 -9.5583
4 123.145 55.5431 -17.2123 0.1348
5 118.986 98.6813 -22.2485 10.3673
6 123.145 55.5431 -17.2123 0.1348
7 111.254 53.5303 -11.8454 -11.5405
8 108.53 51.9747 -9.4851 -10.9985
9 107.734 40.6099 -28.8121 0
10 110.77 41.453 -10.604 5.129
11 112.67 39.516 -7.443 -9.5583
12 107.66 39.641 -12.921 -2.4318
13 111.91 60.7147 -13.3366 -13.0785
14 110.62 51.3137 -6.7198 -2.6003
15 110.954 50.8652 -4.4522 -10.0298
16 107.067 45.252 -7.5558 -9.512
17 113.868 45.9271 -20.0824 0
18 111.037 31.8958 -6.6942 -6.837
19 116.94 37.5749 -8.6676 0
20 117.961 37.4964 -8.1837 0
21 114.302 42.6589 -10.5464 -9.3243
22 108.937 57.401 2.9374 0
23 107.734 40.6099 -28.8121 0
24 116.926 39.4193 -10.9945 -8.7733
25 118.986 98.6813 -22.2485 10.3673
26 125.542 92.572 -34.48 -11.1871
27 0 0 0 0
28 111.91 60.7147 -13.3366 -13.0785
29 103.7 49.84 -11.6 -8
BondBond Coeffs
1 5.3316 1.101 1.101
2 3.3872 1.53 1.101
3 0 1.53 1.53
4 0 1.5202 1.3649
5 0 1.3649 1.202
6 46.0685 1.5202 1.202
7 0 1.3649 0.965
8 5.4199 1.53 1.5202
9 0.7115 1.5202 1.101
10 3.3872 1.53 1.101
11 0 1.53 1.53
12 5.3316 1.101 1.101
13 4.6217 1.53 1.457
14 12.426 1.457 1.101
15 -6.4168 1.457 1.006
16 -1.8749 1.006 1.006
17 -3.471 1.452 1.01
18 12.1186 1.452 1.416
19 -0.5655 1.01 1.01
20 -4.3126 1.01 1.416
21 3.5446 1.452 1.53
22 15.2994 1.452 1.101
23 0.7115 1.101 1.5202
24 0 1.416 1.5202
25 0 1.202 1.3649
26 138.495 1.416 1.202
27 0 1.416 1.3649
28 4.6217 1.457 1.53
29 -9.5 0.97 0.97
BondAngle Coeffs
1 18.103 18.103 1.101 1.101
2 20.754 11.421 1.53 1.101
3 8.016 8.016 1.53 1.53
4 0 0 1.5202 1.3649
5 0 0 1.3649 1.202
6 34.9982 37.1298 1.5202 1.202
7 0 0 1.3649 0.965
8 18.1678 15.8758 1.53 1.5202
9 12.4632 9.1765 1.5202 1.101
10 20.754 11.421 1.53 1.101
11 8.016 8.016 1.53 1.53
12 18.103 18.103 1.101 1.101
13 6.0876 16.5702 1.53 1.457
14 42.4332 13.4582 1.457 1.101
15 31.8096 20.5799 1.457 1.006
16 28.0322 28.0322 1.006 1.006
17 11.8828 5.9339 1.452 1.01
18 3.7812 14.8633 1.452 1.416
19 19.8125 19.8125 1.01 1.01
20 10.8422 29.5743 1.01 1.416
21 4.6031 -5.479 1.452 1.53
22 34.8907 10.6917 1.452 1.101
23 9.1765 12.4632 1.101 1.5202
24 0 0 1.416 1.5202
25 0 0 1.202 1.3649
26 62.7124 52.4045 1.416 1.202
27 0 0 1.416 1.3649
28 16.5702 6.0876 1.457 1.53
29 22.35 22.35 0.97 0.97
Dihedral Coeffs # class2
1 -0.0228 0 0.028 0 -0.1863 0
2 -0.1432 0 0.0617 0 -0.1083 0
3 0.0972 0 0.0722 0 -0.2581 0
4 0 0 0.0316 0 -0.1681 0
5 0 0 0.0514 0 -0.143 0
6 0 0 0 0 0 0
7 -2.7332 0 2.9646 0 -0.0155 0
8 0 0 0 0 0 0
9 0 0 0 0 0 0
10 0.0442 0 0.0292 0 0.0562 0
11 -0.1804 0 0.0012 0 0.0371 0
12 -0.2428 0 0.4065 0 -0.3079 0
13 -0.1432 0 0.0617 0 -0.1083 0
14 0.1764 0 0.1766 0 -0.5206 0
15 0 0 0.0316 0 -0.1681 0
16 0 0 0.0514 0 -0.143 0
17 -1.1506 0 -0.6344 0 -0.1845 0
18 -0.5187 0 -0.4837 0 -0.1692 0
19 -0.0483 0 -0.0077 0 -0.0014 0
20 -0.0148 0 -0.0791 0 -0.0148 0
21 0.0143 0 -0.0132 0 0.0091 0
22 0.0219 0 -0.026 0 0.0714 0
23 -0.7532 0 2.7392 0 0.0907 0
24 0.8297 0 3.7234 0 -0.0495 0
25 0 0 0 0 0 0
26 0 0 0 0 0 0
27 -1.6938 0 2.7386 0 -0.336 0
28 0 0 0 0 0 0
29 0.0972 0 0.0722 0 -0.2581 0
30 -0.0228 0 0.028 0 -0.1863 0
31 0.1693 0 -0.009 0 -0.0687 0
32 0.1693 0 -0.009 0 -0.0687 0
33 0 0 0 0 0 0
34 -1.1506 0 -0.6344 0 -0.1845 0
35 -0.5187 0 -0.4837 0 -0.1692 0
36 0.1764 0 0.1766 0 -0.5206 0
AngleAngleTorsion Coeffs
1 -5.3624 108.53 110.77
2 -12.564 110.77 110.77
3 -0.3801 112.67 108.53
4 -16.164 112.67 110.77
5 -22.045 112.67 112.67
6 0 0 111.254
7 0 118.985 111.254
8 0 108.53 0
9 0 107.734 0
10 -8.019 108.53 123.145
11 -15.3496 107.734 123.145
12 -15.7572 111.91 110.77
13 -12.564 110.77 110.77
14 -27.3953 112.67 111.91
15 -16.164 112.67 110.77
16 -22.045 112.67 112.67
17 -7.5499 111.91 110.954
18 -10.4258 110.62 110.954
19 -4.6337 113.868 114.302
20 -6.659 113.868 108.937
21 -7.4314 111.037 114.302
22 -8.1335 111.037 108.937
23 -6.5335 111.037 116.926
24 -15.5547 111.037 125.542
25 0 111.037 0
26 -1.3234 117.961 116.926
27 -7.3186 117.961 125.542
28 0 117.961 0
29 -1.0631 114.302 112.67
30 -12.7974 114.302 110.77
31 -5.4514 108.53 116.926
32 -12.2417 107.734 116.926
33 0 0 111.254
34 -7.5499 110.954 111.91
35 -10.4258 110.954 110.62
36 -27.3953 111.91 112.67
EndBondTorsion Coeffs
1 -0.0204 0.3628 -0.4426 -0.0097 -0.0315 -0.0755 1.5202 1.101
2 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
3 0.0062 -0.0002 0.0036 0.0055 0.006 -0.0009 1.53 1.5202
4 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
5 -0.0732 0 0 -0.0732 0 0 1.53 1.53
6 0 0 0 0 0 0 1.5202 0.965
7 0 0 0 0 0 0 1.202 0.965
8 0 0 0 0 0 0 1.53 1.3649
9 0 0 0 0 0 0 1.101 1.3649
10 0.2654 0.0503 0.1046 -0.281 0.0816 -0.1522 1.53 1.202
11 1.2143 0.2831 0.3916 -0.2298 0.0354 0.3853 1.101 1.202
12 0.1022 0.209 0.6433 0.196 0.7056 0.112 1.457 1.101
13 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
14 0.1032 0.5896 -0.4836 0.0579 -0.0043 -0.1906 1.53 1.457
15 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
16 -0.0732 0 0 -0.0732 0 0 1.53 1.53
17 -0.9466 0.9356 -0.5542 0.057 0.0625 0.4112 1.53 1.006
18 -1.1685 0.9266 -0.0993 0.085 0.3061 0.2104 1.101 1.006
19 -0.0992 -0.0727 -0.4139 0.132 0.0015 0.1324 1.01 1.53
20 -0.4894 0.1644 0.3105 -0.8983 0.2826 0.0881 1.01 1.101
21 -0.1245 -0.9369 0.7781 -0.2033 0.0035 0.056 1.416 1.53
22 0.2292 1.1732 -0.058 -0.3667 0.8197 0.1335 1.416 1.101
23 0.2299 -0.1141 -0.1424 0.0933 -0.4631 0.2883 1.452 1.5202
24 0.1598 0.7253 -0.1007 0.1226 -2.1326 0.5581 1.452 1.202
25 0 0 0 0 0 0 1.452 1.3649
26 0.6413 0.1676 0.144 -0.6979 0.5619 0.4212 1.01 1.5202
27 0.1214 0.1936 0.0816 -0.7604 -2.6431 1.2467 1.01 1.202
28 0 0 0 0 0 0 1.01 1.3649
29 -0.0797 -0.0406 0.0255 0.0742 0.0105 0.0518 1.452 1.53
30 0.3022 0.2513 0.4641 -0.0601 -0.3763 -0.1876 1.452 1.101
31 -0.2631 -0.0076 -0.1145 -0.2751 -0.3058 -0.1767 1.53 1.416
32 -0.0268 0.7836 0.0035 0.3552 -0.2685 0.5834 1.101 1.416
33 0 0 0 0 0 0 1.416 0.965
34 0.057 0.0625 0.4112 -0.9466 0.9356 -0.5542 1.006 1.53
35 0.085 0.3061 0.2104 -1.1685 0.9266 -0.0993 1.006 1.101
36 0.0579 -0.0043 -0.1906 0.1032 0.5896 -0.4836 1.457 1.53
MiddleBondTorsion Coeffs
1 -3.5039 1.2458 -0.761 1.53
2 -14.261 -0.5322 -0.4864 1.53
3 -1.5945 0.2267 -0.6911 1.53
4 -14.879 -3.6581 -0.3138 1.53
5 -17.787 -7.1877 0 1.53
6 0 0 0 1.3649
7 0 0 0 1.3649
8 0 0 0 1.5202
9 0 0 0 1.5202
10 0.3388 -0.1096 0.1219 1.5202
11 0.2359 0.9139 0.9594 1.5202
12 -10.4959 -0.7647 -0.0545 1.53
13 -14.261 -0.5322 -0.4864 1.53
14 -15.4174 -7.3055 -1.0749 1.53
15 -14.879 -3.6581 -0.3138 1.53
16 -17.787 -7.1877 0 1.53
17 -2.2208 0.5479 -0.3527 1.457
18 -3.4611 1.6996 -0.6007 1.457
19 -3.5406 -3.3866 0.0352 1.452
20 -1.1752 2.8058 0.8083 1.452
21 -3.9501 -0.4002 -0.6798 1.452
22 -0.6899 -2.2646 1.1579 1.452
23 0 0 0 1.416
24 -8.8301 14.3079 -1.7716 1.416
25 0 0 0 1.416
26 0 0 0 1.416
27 -0.9084 6.1447 -0.4852 1.416
28 0 0 0 1.416
29 -4.2324 -3.3023 -1.3244 1.53
30 -4.1028 -0.5941 -0.047 1.53
31 0 0 0 1.5202
32 0 0 0 1.5202
33 0 0 0 1.3649
34 -2.2208 0.5479 -0.3527 1.457
35 -3.4611 1.6996 -0.6007 1.457
36 -15.4174 -7.3055 -1.0749 1.53
BondBond13 Coeffs
1 0 1.5202 1.101
2 0 1.101 1.101
3 0 1.53 1.5202
4 0 1.53 1.101
5 0 1.53 1.53
6 0 1.5202 0.965
7 0 1.202 0.965
8 0 1.53 1.3649
9 0 1.101 1.3649
10 0 1.53 1.202
11 0 1.101 1.202
12 0 1.457 1.101
13 0 1.101 1.101
14 0 1.53 1.457
15 0 1.53 1.101
16 0 1.53 1.53
17 0 1.53 1.006
18 0 1.101 1.006
19 0 1.01 1.53
20 0 1.01 1.101
21 0 1.416 1.53
22 0 1.416 1.101
23 0 1.452 1.5202
24 0 1.452 1.202
25 0 1.452 1.3649
26 0 1.01 1.5202
27 0 1.01 1.202
28 0 1.01 1.3649
29 0 1.452 1.53
30 0 1.452 1.101
31 0 1.53 1.416
32 0 1.101 1.416
33 0 1.416 0.965
34 0 1.006 1.53
35 0 1.006 1.101
36 0 1.457 1.53
AngleTorsion Coeffs
1 -0.7466 -0.9448 -0.6321 0.0162 1.4211 -1.4092 108.53 110.77
2 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
3 -0.2607 0.3203 -0.2283 0.0515 -0.0674 -0.0474 112.67 108.53
4 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
5 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
6 0 0 0 0 0 0 0 111.254
7 0 0 0 0 0 0 118.985 111.254
8 0 0 0 0 0 0 108.53 0
9 0 0 0 0 0 0 107.734 0
10 0.0885 -1.3703 -0.5452 0.675 0.5965 0.6725 108.53 123.145
11 9.1299 -0.4847 0.3582 -1.4946 0.7308 -0.2083 107.734 123.145
12 -1.1075 0.282 0.8318 0.5111 1.6328 -1.0155 111.91 110.77
13 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
14 -1.9225 -1.345 0.221 2.0125 0.944 -2.7612 112.67 111.91
15 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
16 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
17 -3.343 4.4558 -0.0346 0.2873 -0.8072 -0.096 111.91 110.954
18 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.62 110.954
19 -0.5807 0.2041 -0.1384 -2.8967 2.7084 -0.0375 113.868 114.302
20 -0.3868 0.2041 0.0445 -3.7022 1.3876 0.2393 113.868 108.937
21 -1.523 1.1296 0.7167 -0.7555 0.0564 1.2177 111.037 114.302
22 0.0372 -0.3418 -0.0775 -1.5157 2.0781 0.5364 111.037 108.937
23 5.916 1.7856 0.4052 4.2133 2.9302 3.2903 111.037 116.926
24 7.4427 2.1505 -0.2206 4.4466 4.0317 1.7129 111.037 125.542
25 0 0 0 0 0 0 111.037 0
26 1.9306 0.2105 0.0557 -2.2134 1.2909 0.9726 117.961 116.926
27 2.3848 0.703 0.1399 -2.6238 0.3606 0.5474 117.961 125.542
28 0 0 0 0 0 0 117.961 0
29 0.2039 0.1602 -0.7946 -0.5501 -1.6982 0.2485 114.302 112.67
30 -1.982 0.2325 -0.3928 -1.2469 1.6933 -1.2081 114.302 110.77
31 2.1802 -0.0335 -1.3816 2.1221 0.5032 -0.0767 108.53 116.926
32 7.095 0.0075 0.691 2.0013 0.5068 0.8406 107.734 116.926
33 0 0 0 0 0 0 0 111.254
34 0.2873 -0.8072 -0.096 -3.343 4.4558 -0.0346 110.954 111.91
35 -0.4294 -0.4442 -0.6141 -3.9582 2.0063 0.3213 110.954 110.62
36 2.0125 0.944 -2.7612 -1.9225 -1.345 0.221 111.91 112.67
Improper Coeffs # class2
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
7 0 0
8 0 0
9 0 0
10 0 0
11 0 0
12 0 0
13 24.3329 0
AngleAngle Coeffs
1 0 0 0 0 118.985 123.145
2 0.2738 -0.4825 0.2738 110.77 107.66 110.77
3 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
4 2.0403 -1.8202 1.0827 108.53 107.734 110.77
5 -3.3867 -3.4976 -3.3867 107.734 107.66 107.734
6 0 0 0 110.954 107.067 110.954
7 0.2738 -0.4825 0.2738 110.77 107.66 110.77
8 -1.3199 -1.3199 0.1184 112.67 110.77 110.77
9 -2.5301 0.5381 2.4286 111.91 110.62 110.77
10 2.4321 -3.5496 2.4321 110.62 107.66 110.62
11 0 0 0 123.145 118.985 0
12 0 0 0 113.868 117.961 111.037
13 0 0 0 116.926 123.145 125.542
Atoms # full
1 1 1 0.0000000000000000e+00 12.288168 0.738732 4.374280 0 0 0
2 1 2 2.9999999999999999e-01 13.959928 -0.883144 5.090597 0 0 0
3 1 3 0.0000000000000000e+00 14.411288 -1.994419 5.682160 0 0 0
4 1 4 0.0000000000000000e+00 12.881083 0.872503 3.506176 0 0 0
5 1 4 0.0000000000000000e+00 11.232775 0.801641 3.998777 0 0 0
6 1 5 0.0000000000000000e+00 13.704366 -2.470396 6.130105 0 0 0
7 1 1 0.0000000000000000e+00 12.489752 -0.793693 4.710639 0 0 0
8 1 1 0.0000000000000000e+00 12.455071 1.866388 5.385870 0 0 0
9 1 1 0.0000000000000000e+00 11.248961 1.901849 6.347664 0 0 0
10 1 2 2.9999999999999999e-01 10.005971 2.466710 5.772840 -1 1 0
11 1 6 0.0000000000000000e+00 14.795360 -0.034436 4.807367 0 0 0
12 1 6 0.0000000000000000e+00 9.115239 1.654547 5.617002 -1 0 0
13 1 3 0.0000000000000000e+00 9.745096 3.807654 5.573585 -1 1 0
14 1 4 0.0000000000000000e+00 12.248215 -1.371492 3.808598 0 0 0
15 1 4 0.0000000000000000e+00 11.715755 -1.036825 5.500449 0 0 0
16 1 4 0.0000000000000000e+00 12.559724 2.807687 4.858452 0 1 0
17 1 4 0.0000000000000000e+00 13.299968 1.616570 6.123781 0 0 0
18 1 4 0.0000000000000000e+00 11.650505 2.330454 7.282410 0 1 0
19 1 4 0.0000000000000000e+00 10.888420 0.913219 6.637162 -1 0 0
20 1 5 0.0000000000000000e+00 10.550073 4.294209 5.758192 -1 1 0
21 2 1 0.0000000000000000e+00 5.851425 1.929552 6.038335 0 0 0
22 2 1 0.0000000000000000e+00 6.741509 3.160751 6.233074 0 0 0
23 2 7 -2.9999999999999999e-01 7.957761 3.121780 5.252257 1 0 0
24 2 7 -2.9999999999999999e-01 2.599653 -2.258940 5.985863 0 -1 0
25 2 1 0.0000000000000000e+00 3.834337 -1.907078 5.441528 0 -1 0
26 2 1 0.0000000000000000e+00 4.810793 -1.083699 6.310184 0 -1 0
27 2 4 0.0000000000000000e+00 6.505912 1.182799 5.449104 0 0 0
28 2 4 0.0000000000000000e+00 5.156429 2.256468 5.348423 0 0 0
29 2 4 0.0000000000000000e+00 7.232782 3.178785 7.181911 0 0 0
30 2 4 0.0000000000000000e+00 6.251671 4.103621 6.222913 0 0 0
31 2 8 0.0000000000000000e+00 8.249909 4.070668 4.881297 1 0 0
32 2 8 0.0000000000000000e+00 7.813025 2.623184 4.400744 1 0 0
33 2 8 0.0000000000000000e+00 2.626695 -2.857547 6.817247 0 -1 0
34 2 8 0.0000000000000000e+00 1.955281 -2.684319 5.328460 0 -1 0
35 2 4 0.0000000000000000e+00 3.637708 -1.322842 4.469265 0 -1 0
36 2 4 0.0000000000000000e+00 4.415570 -2.739689 4.997336 0 -1 0
37 2 4 0.0000000000000000e+00 5.710714 -1.010014 5.642798 0 -1 0
38 2 4 0.0000000000000000e+00 5.103831 -1.696423 7.160345 0 -1 0
39 2 1 0.0000000000000000e+00 5.270763 1.286629 7.308822 0 0 0
40 2 4 0.0000000000000000e+00 4.834381 2.168531 7.931687 0 0 1
41 2 4 0.0000000000000000e+00 6.118354 0.786724 7.794709 0 0 1
42 2 1 0.0000000000000000e+00 4.273849 0.167695 6.957862 0 -1 0
43 2 4 0.0000000000000000e+00 3.792544 -0.081782 7.904418 0 -1 1
44 2 4 0.0000000000000000e+00 3.527495 0.674238 6.348869 0 0 0
Velocities
1 -2.4626989626218821e-03 -1.5920230003311222e-03 -3.0621927786115238e-03
2 9.5082416704385837e-03 -6.9903166167507250e-03 1.3702671335945608e-02
3 2.3431518493187576e-03 -2.9261683108242173e-03 1.4269399726982105e-03
4 -1.8184451408256214e-02 3.1103803691687960e-02 -1.3358827768357973e-02
5 2.6084132471017967e-02 -1.0819576493517332e-02 3.0403384454794881e-02
6 -4.7312115958218744e-03 -1.9111462399478338e-02 -3.6793354156497558e-02
7 -7.5068797595949869e-03 6.5661422055962489e-03 1.3226575122695422e-03
8 3.3807881380161281e-03 3.0458732663557089e-03 2.2368826795446284e-03
9 -3.1113905793879316e-03 8.2908867720754773e-03 -1.7561238039496530e-03
10 2.4685206571693056e-03 1.3194776209841030e-03 -2.8041877032800441e-03
11 -3.4945605770565296e-03 3.2323777135621814e-03 1.6223017668450866e-03
12 -6.1153483612847778e-03 -5.1534857074262185e-03 1.7735747357354274e-03
13 2.1384296781859011e-04 -4.5398902942729667e-03 6.1649769894413760e-03
14 2.5004619864373401e-03 -1.5709184283264888e-03 2.0837548254667757e-02
15 6.0547939205643532e-03 -1.2650704436910937e-02 -5.4430753266962190e-03
16 -1.0374605775698001e-02 9.1408658463889240e-03 -1.1306875858287088e-02
17 -1.2736499128987409e-02 -9.1726811852506501e-03 5.1136502685461254e-03
18 7.6741778607048112e-03 1.8629856635459279e-02 -1.1300096447670932e-02
19 -1.8616138775281121e-02 1.0848388547730185e-03 -5.7118433687798576e-03
20 5.4137572241479059e-03 -1.4564578166395727e-02 -1.2618420441909540e-02
21 5.8473521452312256e-03 -4.0595286000332086e-03 -6.2517801580146415e-03
22 3.6402033824753104e-03 -1.4629540504663154e-03 -4.0030712318898046e-03
23 9.0266305019107689e-03 -2.7511425384659687e-03 4.5576402565437142e-03
24 -1.3102302415548614e-02 -4.7286703965305791e-03 -1.8966887841189517e-03
25 7.8621682621103171e-03 -4.2046313540949568e-03 9.6887957374751301e-04
26 -4.7380176438337968e-03 9.6090441940775827e-03 -8.7592431387039336e-03
27 5.4311658811632517e-03 2.0032224663495989e-02 -9.4952076489808503e-03
28 -2.9056381493904374e-03 3.3317109723156875e-03 1.6650350064426677e-02
29 -6.4569944033489122e-03 2.8423983541959541e-03 -2.6066912906505167e-02
30 -2.2173867823429387e-02 1.4628839880961319e-02 -2.3330833961402380e-02
31 9.1925713381983114e-03 -2.5697556639281928e-03 -1.2822203161488303e-02
32 -8.3206975051927905e-03 -2.2538429924858707e-03 7.7620244118580314e-03
33 1.9920685674825727e-02 5.0317764848494097e-03 -2.1106672824976403e-02
34 1.4118463330250982e-02 1.7455545466840316e-02 -1.2482101375598437e-02
35 -6.1116505640437966e-03 1.3353021777303568e-02 -2.5492434283827668e-02
36 9.1001521565859649e-03 5.5737774505222404e-03 1.4573768978939985e-02
37 1.6523593470528035e-03 -2.2107518020000917e-02 2.0311423445130115e-02
38 -1.0346275393471860e-02 1.6055856586351790e-02 5.5489127019262424e-03
39 -3.2054811383248638e-03 1.6779208962376315e-03 2.9390509537535661e-03
40 1.9649219364916443e-02 4.0815776523222859e-03 -9.8422441166041274e-03
41 5.6961697588160361e-04 7.1361132234741477e-04 4.6335764220256257e-03
42 2.2221300208006252e-03 3.6217319632558197e-03 -6.3299398503455151e-03
43 2.5710172734841170e-03 8.0029179814482924e-03 1.9992986928468189e-02
44 -6.0827581822674656e-03 -1.1834273655641976e-02 2.0526923045885208e-02
Bonds
1 1 1 5
2 1 1 4
3 2 1 7
4 2 1 8
5 3 2 3
6 5 2 11
7 6 3 6
8 4 7 2
9 1 7 14
10 1 7 15
11 2 8 9
12 1 8 16
13 1 8 17
14 4 9 10
15 1 9 18
16 1 9 19
17 5 10 12
18 3 10 13
19 6 13 20
20 7 21 22
21 8 21 27
22 8 21 28
23 7 21 39
24 9 22 23
25 8 22 29
26 8 22 30
27 10 23 31
28 10 23 32
29 10 24 33
30 10 24 34
31 9 25 24
32 7 25 26
33 8 25 35
34 8 25 36
35 8 26 37
36 8 26 38
37 7 26 42
38 8 39 40
39 8 39 41
40 7 39 42
41 8 42 43
42 8 42 44
Angles
1 1 5 1 4
2 2 7 1 5
3 2 8 1 5
4 2 7 1 4
5 2 8 1 4
6 3 7 1 8
7 4 7 2 3
8 5 3 2 11
9 6 7 2 11
10 7 2 3 6
11 8 1 7 2
12 2 1 7 14
13 2 1 7 15
14 9 2 7 14
15 9 2 7 15
16 1 14 7 15
17 3 1 8 9
18 2 1 8 16
19 2 1 8 17
20 2 9 8 16
21 2 9 8 17
22 1 16 8 17
23 8 8 9 10
24 2 8 9 18
25 2 8 9 19
26 9 10 9 18
27 9 10 9 19
28 1 18 9 19
29 6 9 10 12
30 4 9 10 13
31 5 13 10 12
32 7 10 13 20
33 10 22 21 27
34 10 22 21 28
35 11 22 21 39
36 12 27 21 28
37 10 39 21 27
38 10 39 21 28
39 13 21 22 23
40 10 21 22 29
41 10 21 22 30
42 14 23 22 29
43 14 23 22 30
44 12 29 22 30
45 15 22 23 31
46 15 22 23 32
47 16 31 23 32
48 15 25 24 33
49 15 25 24 34
50 16 33 24 34
51 13 26 25 24
52 14 24 25 35
53 14 24 25 36
54 10 26 25 35
55 10 26 25 36
56 12 35 25 36
57 10 25 26 37
58 10 25 26 38
59 11 25 26 42
60 12 37 26 38
61 10 42 26 37
62 10 42 26 38
63 10 21 39 40
64 10 21 39 41
65 11 21 39 42
66 12 40 39 41
67 10 42 39 40
68 10 42 39 41
69 11 26 42 39
70 10 26 42 43
71 10 26 42 44
72 10 39 42 43
73 10 39 42 44
74 12 43 42 44
Dihedrals
1 2 5 1 7 14
2 2 5 1 7 15
3 2 4 1 7 14
4 2 4 1 7 15
5 3 8 1 7 2
6 4 8 1 7 14
7 4 8 1 7 15
8 2 5 1 8 16
9 2 5 1 8 17
10 2 4 1 8 16
11 2 4 1 8 17
12 5 7 1 8 9
13 4 7 1 8 16
14 4 7 1 8 17
15 6 7 2 3 6
16 7 11 2 3 6
17 1 2 7 1 5
18 1 2 7 1 4
19 8 1 7 2 3
20 9 14 7 2 3
21 9 15 7 2 3
22 10 1 7 2 11
23 11 14 7 2 11
24 11 15 7 2 11
25 4 9 8 1 5
26 4 9 8 1 4
27 3 1 8 9 10
28 4 1 8 9 18
29 4 1 8 9 19
30 2 16 8 9 18
31 2 16 8 9 19
32 2 17 8 9 18
33 2 17 8 9 19
34 1 10 9 8 16
35 1 10 9 8 17
36 10 8 9 10 12
37 8 8 9 10 13
38 11 18 9 10 12
39 9 18 9 10 13
40 11 19 9 10 12
41 9 19 9 10 13
42 6 9 10 13 20
43 7 12 10 13 20
44 13 27 21 22 29
45 13 27 21 22 30
46 13 28 21 22 29
47 13 28 21 22 30
48 14 39 21 22 23
49 15 39 21 22 29
50 15 39 21 22 30
51 15 22 21 39 40
52 15 22 21 39 41
53 16 22 21 39 42
54 13 27 21 39 40
55 13 27 21 39 41
56 13 28 21 39 40
57 13 28 21 39 41
58 12 23 22 21 27
59 12 23 22 21 28
60 17 21 22 23 31
61 17 21 22 23 32
62 18 29 22 23 31
63 18 29 22 23 32
64 18 30 22 23 31
65 18 30 22 23 32
66 17 26 25 24 33
67 18 35 25 24 33
68 18 36 25 24 33
69 17 26 25 24 34
70 18 35 25 24 34
71 18 36 25 24 34
72 12 24 25 26 37
73 12 24 25 26 38
74 13 35 25 26 37
75 13 35 25 26 38
76 13 36 25 26 37
77 13 36 25 26 38
78 14 42 26 25 24
79 15 42 26 25 35
80 15 42 26 25 36
81 16 25 26 42 39
82 15 25 26 42 43
83 15 25 26 42 44
84 13 37 26 42 43
85 13 37 26 42 44
86 13 38 26 42 43
87 13 38 26 42 44
88 15 42 39 21 27
89 15 42 39 21 28
90 16 21 39 42 26
91 15 21 39 42 43
92 15 21 39 42 44
93 13 40 39 42 43
94 13 40 39 42 44
95 13 41 39 42 43
96 13 41 39 42 44
97 15 39 42 26 37
98 15 39 42 26 38
99 15 26 42 39 40
100 15 26 42 39 41
Impropers
1 2 7 1 4 5
2 2 8 1 4 5
3 3 7 1 8 5
4 3 7 1 8 4
5 1 7 2 3 11
6 4 1 7 2 14
7 4 1 7 2 15
8 2 1 7 14 15
9 5 2 7 14 15
10 3 1 8 9 16
11 3 1 8 9 17
12 2 1 8 16 17
13 2 9 8 16 17
14 4 8 9 10 18
15 4 8 9 10 19
16 2 8 9 18 19
17 5 10 9 18 19
18 1 9 10 13 12
19 7 22 21 27 28
20 8 22 21 39 27
21 8 22 21 39 28
22 7 39 21 28 27
23 9 21 22 23 29
24 9 21 22 23 30
25 7 21 22 29 30
26 10 23 22 29 30
27 6 22 23 31 32
28 6 25 24 33 34
29 9 26 25 24 35
30 9 26 25 24 36
31 10 24 25 35 36
32 7 26 25 35 36
33 7 25 26 37 38
34 8 25 26 42 37
35 8 25 26 42 38
36 7 42 26 38 37
37 7 21 39 40 41
38 8 21 39 42 40
39 8 21 39 42 41
40 7 42 39 41 40
41 8 26 42 39 43
42 8 26 42 39 44
43 7 26 42 43 44
44 7 39 42 43 44

44
examples/USER/misc/bond_react/tiny_polystyrene/2styrene_map
View File

@ -1,44 +0,0 @@
this is a map file
0 edgeIDs
32 equivalences
BondingIDs
4
30
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31
32 32

312
examples/USER/misc/bond_react/tiny_polystyrene/2styrene_reacted.data_template
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@ -1,312 +0,0 @@
2styrene_reacted
32 atoms
33 bonds
54 angles
79 dihedrals
22 impropers
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 2
32 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 0.035400
32 0.035400
Coords
1 13.465810 0.682530 -1.658940
2 14.397820 1.221530 -1.658940
3 12.235820 1.392530 -1.658940
4 12.235820 2.892530 -1.658940
5 11.005820 0.682530 -1.658940
6 10.073820 1.221530 -1.658940
7 11.005820 -0.737470 -1.658940
8 10.073820 -1.276460 -1.658940
9 12.235820 -1.447460 -1.658940
10 12.235820 -2.524470 -1.658940
11 13.465810 -0.737470 -1.658940
12 14.397820 -1.276460 -1.658940
13 13.101820 3.297530 -1.301940
14 10.957820 3.441530 -2.220940
15 11.007810 4.183540 -2.319940
16 10.314820 2.618530 -2.514940
17 18.663521 0.855480 -1.372130
18 19.595510 1.394480 -1.372130
19 17.433510 1.565480 -1.372130
20 17.433510 3.065480 -1.372130
21 16.203510 0.855480 -1.372130
22 15.271510 1.394480 -1.372130
23 16.203510 -0.564520 -1.372130
24 15.271510 -1.103520 -1.372130
25 17.433510 -1.274520 -1.372130
26 17.433510 -2.351520 -1.372130
27 18.663521 -0.564520 -1.372130
28 19.595510 -1.103520 -1.372130
29 18.299509 3.470480 -1.015130
30 16.155510 3.614480 -1.934130
31 16.205509 4.356480 -2.033130
32 15.512510 2.791480 -2.228130
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 7 3 4
5 2 3 5
6 8 13 4
7 9 4 14
8 9 4 30
9 1 5 6
10 2 5 7
11 1 7 8
12 2 7 9
13 1 9 10
14 2 9 11
15 1 11 12
16 10 15 14
17 10 16 14
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 20 30
25 1 21 22
26 2 21 23
27 1 23 24
28 2 23 25
29 1 25 26
30 2 25 27
31 1 27 28
32 10 31 30
33 10 32 30
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 9 1 3 4
5 2 1 3 5
6 9 5 3 4
7 10 3 4 13
8 11 3 4 14
9 11 3 4 30
10 12 13 4 14
11 12 13 4 30
12 13 14 4 30
13 1 3 5 6
14 2 3 5 7
15 1 7 5 6
16 1 5 7 8
17 2 5 7 9
18 1 9 7 8
19 1 7 9 10
20 2 7 9 11
21 1 11 9 10
22 2 1 11 9
23 1 1 11 12
24 1 9 11 12
25 14 15 14 4
26 14 16 14 4
27 15 15 14 16
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 12 29 20 30
37 1 19 21 22
38 2 19 21 23
39 1 23 21 22
40 1 21 23 24
41 2 21 23 25
42 1 25 23 24
43 1 23 25 26
44 2 23 25 27
45 1 27 25 26
46 2 17 27 25
47 1 17 27 28
48 1 25 27 28
49 16 4 30 20
50 14 31 30 4
51 14 32 30 4
52 14 31 30 20
53 14 32 30 20
54 15 31 30 32
Dihedrals
1 10 2 1 3 4
2 2 5 3 1 2
3 11 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 12 1 3 4 13
10 13 1 3 4 14
11 13 1 3 4 30
12 12 5 3 4 13
13 13 5 3 4 14
14 13 5 3 4 30
15 2 1 3 5 6
16 4 1 3 5 7
17 10 6 5 3 4
18 11 7 5 3 4
19 14 3 4 14 15
20 14 3 4 14 16
21 15 13 4 14 15
22 15 13 4 14 16
23 16 30 4 14 15
24 16 30 4 14 16
25 17 3 4 30 20
26 14 3 4 30 31
27 14 3 4 30 32
28 18 13 4 30 20
29 15 13 4 30 31
30 15 13 4 30 32
31 19 14 4 30 20
32 16 14 4 30 31
33 16 14 4 30 32
34 2 3 5 7 8
35 4 3 5 7 9
36 5 6 5 7 8
37 2 9 7 5 6
38 2 5 7 9 10
39 4 5 7 9 11
40 5 8 7 9 10
41 2 11 9 7 8
42 4 7 9 11 1
43 2 7 9 11 12
44 2 1 11 9 10
45 5 10 9 11 12
46 10 18 17 19 20
47 2 21 19 17 18
48 11 27 17 19 20
49 4 27 17 19 21
50 2 25 27 17 18
51 5 18 17 27 28
52 4 19 17 27 25
53 2 19 17 27 28
54 12 17 19 20 29
55 13 17 19 20 30
56 12 21 19 20 29
57 13 21 19 20 30
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 17 19 20 30 4
63 14 19 20 30 31
64 14 19 20 30 32
65 18 29 20 30 4
66 15 29 20 30 31
67 15 29 20 30 32
68 2 19 21 23 24
69 4 19 21 23 25
70 5 22 21 23 24
71 2 25 23 21 22
72 2 21 23 25 26
73 4 21 23 25 27
74 5 24 23 25 26
75 2 27 25 23 24
76 4 23 25 27 17
77 2 23 25 27 28
78 2 17 27 25 26
79 5 26 25 27 28
Impropers
1 1 3 1 11 2
2 5 1 3 5 4
3 1 3 5 7 6
4 1 5 7 9 8
5 1 7 9 11 10
6 1 1 11 9 12
7 6 15 14 16 4
8 1 19 17 27 18
9 5 17 19 21 20
10 7 19 20 29 30
11 1 19 21 23 22
12 1 21 23 25 24
13 1 23 25 27 26
14 1 17 27 25 28
15 1 3 4 13 14
16 1 3 4 13 30
17 1 3 4 14 30
18 1 13 4 14 30
19 1 31 30 20 4
20 1 32 30 20 4
21 1 31 30 32 4
22 1 31 30 32 20

284
examples/USER/misc/bond_react/tiny_polystyrene/2styrene_unreacted.data_template
View File

@ -1,284 +0,0 @@
2styrene_unreacted
32 atoms
32 bonds
48 angles
64 dihedrals
16 impropers
Types
1 1
2 2
3 1
4 3
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 4
15 2
16 2
17 1
18 2
19 1
20 3
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 4
31 2
32 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 0.035400
32 0.035400
Coords
1 13.465815 0.682534 -1.658941
2 14.397816 1.221534 -1.658941
3 12.235815 1.392534 -1.658941
4 12.235815 2.892534 -1.658941
5 11.005816 0.682534 -1.658941
6 10.073815 1.221534 -1.658941
7 11.005816 -0.737466 -1.658941
8 10.073815 -1.276465 -1.658941
9 12.235815 -1.447465 -1.658941
10 12.235815 -2.524465 -1.658941
11 13.465815 -0.737466 -1.658941
12 14.397816 -1.276465 -1.658941
13 13.101815 3.297535 -1.301941
14 10.957815 3.441535 -2.220941
15 11.007814 4.183536 -2.319941
16 10.314816 2.618534 -2.514940
17 18.663515 0.855482 -1.372128
18 19.595514 1.394482 -1.372128
19 17.433512 1.565481 -1.372128
20 17.433512 3.065482 -1.372128
21 16.203512 0.855482 -1.372128
22 15.271511 1.394482 -1.372128
23 16.203512 -0.564518 -1.372128
24 15.271511 -1.103518 -1.372128
25 17.433512 -1.274518 -1.372128
26 17.433512 -2.351518 -1.372128
27 18.663515 -0.564518 -1.372128
28 19.595514 -1.103518 -1.372128
29 18.299513 3.470482 -1.015128
30 16.155512 3.614482 -1.934128
31 16.205513 4.356482 -2.033128
32 15.512512 2.791482 -2.228127
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 3 3 4
5 2 3 5
6 4 13 4
7 5 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 6 15 14
16 6 16 14
17 1 17 18
18 2 17 19
19 2 17 27
20 3 19 20
21 2 19 21
22 4 29 20
23 5 20 30
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 6 31 30
32 6 32 30
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 3 1 3 4
5 2 1 3 5
6 3 5 3 4
7 4 3 4 13
8 5 3 4 14
9 6 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 7 15 14 4
23 7 16 14 4
24 8 15 14 16
25 1 19 17 18
26 1 27 17 18
27 2 19 17 27
28 3 17 19 20
29 2 17 19 21
30 3 21 19 20
31 4 19 20 29
32 5 19 20 30
33 6 29 20 30
34 1 19 21 22
35 2 19 21 23
36 1 23 21 22
37 1 21 23 24
38 2 21 23 25
39 1 25 23 24
40 1 23 25 26
41 2 23 25 27
42 1 27 25 26
43 2 17 27 25
44 1 17 27 28
45 1 25 27 28
46 7 31 30 20
47 7 32 30 20
48 8 31 30 32
Dihedrals
1 1 2 1 3 4
2 2 5 3 1 2
3 3 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 6 1 3 4 13
10 7 1 3 4 14
11 6 5 3 4 13
12 7 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 1 6 5 3 4
16 3 7 5 3 4
17 8 3 4 14 15
18 8 3 4 14 16
19 9 13 4 14 15
20 9 13 4 14 16
21 2 3 5 7 8
22 4 3 5 7 9
23 5 6 5 7 8
24 2 9 7 5 6
25 2 5 7 9 10
26 4 5 7 9 11
27 5 8 7 9 10
28 2 11 9 7 8
29 4 7 9 11 1
30 2 7 9 11 12
31 2 1 11 9 10
32 5 10 9 11 12
33 1 18 17 19 20
34 2 21 19 17 18
35 3 27 17 19 20
36 4 27 17 19 21
37 2 25 27 17 18
38 5 18 17 27 28
39 4 19 17 27 25
40 2 19 17 27 28
41 6 17 19 20 29
42 7 17 19 20 30
43 6 21 19 20 29
44 7 21 19 20 30
45 2 17 19 21 22
46 4 17 19 21 23
47 1 22 21 19 20
48 3 23 21 19 20
49 8 19 20 30 31
50 8 19 20 30 32
51 9 29 20 30 31
52 9 29 20 30 32
53 2 19 21 23 24
54 4 19 21 23 25
55 5 22 21 23 24
56 2 25 23 21 22
57 2 21 23 25 26
58 4 21 23 25 27
59 5 24 23 25 26
60 2 27 25 23 24
61 4 23 25 27 17
62 2 23 25 27 28
63 2 17 27 25 26
64 5 26 25 27 28
Impropers
1 1 3 1 11 2
2 2 1 3 5 4
3 3 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 4 15 14 16 4
9 1 19 17 27 18
10 2 17 19 21 20
11 3 19 20 29 30
12 1 19 21 23 22
13 1 21 23 25 24
14 1 23 25 27 26
15 1 17 27 25 28
16 4 31 30 32 20

67
examples/USER/misc/bond_react/tiny_polystyrene/chain_chain_map
View File

@ -1,67 +0,0 @@
this is a map file
2 edgeIDs
50 equivalences
EdgeIDs
17
34
BondingIDs
14
38
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31
32 32
33 33
34 34
35 35
36 36
37 37
38 38
39 39
40 40
41 41
42 42
43 43
44 44
45 45
46 46
47 47
48 48
49 49
50 50

497
examples/USER/misc/bond_react/tiny_polystyrene/chain_chain_reacted.data_template
View File

@ -1,497 +0,0 @@
chain_chain_reacted
50 atoms
52 bonds
90 angles
135 dihedrals
42 impropers
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 5
18 6
19 2
20 2
21 1
22 2
23 1
24 5
25 1
26 2
27 1
28 2
29 1
30 2
31 1
32 2
33 2
34 6
35 1
36 2
37 1
38 5
39 1
40 2
41 1
42 2
43 1
44 2
45 1
46 2
47 2
48 6
49 2
50 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 -0.018200
18 -0.069600
19 0.035400
20 0.035400
21 -0.129000
22 0.123700
23 0.026600
24 -0.018200
25 -0.129000
26 0.123700
27 -0.173400
28 0.140300
29 -0.113400
30 0.128800
31 -0.173400
32 0.140300
33 0.051600
34 -0.069600
35 -0.129000
36 0.123700
37 0.026600
38 -0.018200
39 -0.129000
40 0.123700
41 -0.173400
42 0.140300
43 -0.113400
44 0.128800
45 -0.173400
46 0.140300
47 0.051600
48 -0.069600
49 0.035400
50 0.035400
Coords
1 24.391510 0.871570 -1.658940
2 25.323530 1.410570 -1.658940
3 23.161520 1.581570 -1.658940
4 23.161520 3.081570 -1.658940
5 21.931530 0.871570 -1.658940
6 20.999531 1.410570 -1.658940
7 21.931530 -0.548430 -1.658940
8 20.999531 -1.087420 -1.658940
9 23.161520 -1.258420 -1.658940
10 23.161520 -2.335430 -1.658940
11 24.391510 -0.548430 -1.658940
12 25.323530 -1.087420 -1.658940
13 24.027519 3.486570 -1.301940
14 21.883520 3.630570 -2.220940
15 21.933510 4.372580 -2.319940
16 21.240520 2.807570 -2.514940
17 28.359209 3.254520 -1.372130
18 27.081209 3.803520 -1.934130
19 27.131210 4.545520 -2.033130
20 26.438219 2.980520 -2.228130
21 13.465810 0.682530 -1.658940
22 14.397820 1.221530 -1.658940
23 12.235820 1.392530 -1.658940
24 12.235820 2.892530 -1.658940
25 11.005820 0.682530 -1.658940
26 10.073820 1.221530 -1.658940
27 11.005820 -0.737470 -1.658940
28 10.073820 -1.276460 -1.658940
29 12.235820 -1.447460 -1.658940
30 12.235820 -2.524470 -1.658940
31 13.465810 -0.737470 -1.658940
32 14.397820 -1.276460 -1.658940
33 13.101820 3.297530 -1.301940
34 10.957820 3.441530 -2.220940
35 18.663521 0.855480 -1.372130
36 19.595510 1.394480 -1.372130
37 17.433510 1.565480 -1.372130
38 17.433510 3.065480 -1.372130
39 16.203510 0.855480 -1.372130
40 15.271510 1.394480 -1.372130
41 16.203510 -0.564520 -1.372130
42 15.271510 -1.103520 -1.372130
43 17.433510 -1.274520 -1.372130
44 17.433510 -2.351520 -1.372130
45 18.663521 -0.564520 -1.372130
46 19.595510 -1.103520 -1.372130
47 18.299509 3.470480 -1.015130
48 16.155510 3.614480 -1.934130
49 16.205509 4.356480 -2.033130
50 15.512510 2.791480 -2.228130
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 7 3 4
5 2 3 5
6 8 13 4
7 9 4 14
8 9 4 18
9 1 5 6
10 2 5 7
11 1 7 8
12 2 7 9
13 1 9 10
14 2 9 11
15 1 11 12
16 10 15 14
17 10 16 14
18 9 38 14
19 9 17 18
20 10 19 18
21 10 20 18
22 1 21 22
23 2 21 23
24 2 21 31
25 7 23 24
26 2 23 25
27 8 33 24
28 9 24 34
29 9 24 48
30 1 25 26
31 2 25 27
32 1 27 28
33 2 27 29
34 1 29 30
35 2 29 31
36 1 31 32
37 1 35 36
38 2 35 37
39 2 35 45
40 7 37 38
41 2 37 39
42 8 47 38
43 9 38 48
44 1 39 40
45 2 39 41
46 1 41 42
47 2 41 43
48 1 43 44
49 2 43 45
50 1 45 46
51 10 49 48
52 10 50 48
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 9 1 3 4
5 2 1 3 5
6 9 5 3 4
7 10 3 4 13
8 11 3 4 14
9 11 3 4 18
10 12 13 4 14
11 12 13 4 18
12 13 14 4 18
13 1 3 5 6
14 2 3 5 7
15 1 7 5 6
16 1 5 7 8
17 2 5 7 9
18 1 9 7 8
19 1 7 9 10
20 2 7 9 11
21 1 11 9 10
22 2 1 11 9
23 1 1 11 12
24 1 9 11 12
25 14 15 14 4
26 14 16 14 4
27 16 4 14 38
28 15 15 14 16
29 14 15 14 38
30 14 16 14 38
31 16 4 18 17
32 14 19 18 4
33 14 20 18 4
34 14 19 18 17
35 14 20 18 17
36 15 19 18 20
37 1 23 21 22
38 1 31 21 22
39 2 23 21 31
40 9 21 23 24
41 2 21 23 25
42 9 25 23 24
43 10 23 24 33
44 11 23 24 34
45 11 23 24 48
46 12 33 24 34
47 12 33 24 48
48 13 34 24 48
49 1 23 25 26
50 2 23 25 27
51 1 27 25 26
52 1 25 27 28
53 2 25 27 29
54 1 29 27 28
55 1 27 29 30
56 2 27 29 31
57 1 31 29 30
58 2 21 31 29
59 1 21 31 32
60 1 29 31 32
61 1 37 35 36
62 1 45 35 36
63 2 37 35 45
64 9 35 37 38
65 2 35 37 39
66 9 39 37 38
67 11 37 38 14
68 12 47 38 14
69 13 14 38 48
70 10 37 38 47
71 11 37 38 48
72 12 47 38 48
73 1 37 39 40
74 2 37 39 41
75 1 41 39 40
76 1 39 41 42
77 2 39 41 43
78 1 43 41 42
79 1 41 43 44
80 2 41 43 45
81 1 45 43 44
82 2 35 45 43
83 1 35 45 46
84 1 43 45 46
85 16 24 48 38
86 14 49 48 24
87 14 50 48 24
88 14 49 48 38
89 14 50 48 38
90 15 49 48 50
Dihedrals
1 10 2 1 3 4
2 2 5 3 1 2
3 11 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 12 1 3 4 13
10 13 1 3 4 14
11 13 1 3 4 18
12 12 5 3 4 13
13 13 5 3 4 14
14 13 5 3 4 18
15 2 1 3 5 6
16 4 1 3 5 7
17 10 6 5 3 4
18 11 7 5 3 4
19 14 3 4 14 15
20 14 3 4 14 16
21 17 3 4 14 38
22 15 13 4 14 15
23 15 13 4 14 16
24 18 13 4 14 38
25 16 18 4 14 15
26 16 18 4 14 16
27 19 18 4 14 38
28 17 3 4 18 17
29 14 3 4 18 19
30 14 3 4 18 20
31 18 13 4 18 17
32 15 13 4 18 19
33 15 13 4 18 20
34 19 14 4 18 17
35 16 14 4 18 19
36 16 14 4 18 20
37 2 3 5 7 8
38 4 3 5 7 9
39 5 6 5 7 8
40 2 9 7 5 6
41 2 5 7 9 10
42 4 5 7 9 11
43 5 8 7 9 10
44 2 11 9 7 8
45 4 7 9 11 1
46 2 7 9 11 12
47 2 1 11 9 10
48 5 10 9 11 12
49 17 37 38 14 4
50 18 47 38 14 4
51 19 48 38 14 4
52 14 37 38 14 15
53 15 47 38 14 15
54 16 48 38 14 15
55 14 37 38 14 16
56 15 47 38 14 16
57 16 48 38 14 16
58 10 22 21 23 24
59 2 25 23 21 22
60 11 31 21 23 24
61 4 31 21 23 25
62 2 29 31 21 22
63 5 22 21 31 32
64 4 23 21 31 29
65 2 23 21 31 32
66 12 21 23 24 33
67 13 21 23 24 34
68 13 21 23 24 48
69 12 25 23 24 33
70 13 25 23 24 34
71 13 25 23 24 48
72 2 21 23 25 26
73 4 21 23 25 27
74 10 26 25 23 24
75 11 27 25 23 24
76 17 23 24 48 38
77 14 23 24 48 49
78 14 23 24 48 50
79 18 33 24 48 38
80 15 33 24 48 49
81 15 33 24 48 50
82 19 34 24 48 38
83 16 34 24 48 49
84 16 34 24 48 50
85 2 23 25 27 28
86 4 23 25 27 29
87 5 26 25 27 28
88 2 29 27 25 26
89 2 25 27 29 30
90 4 25 27 29 31
91 5 28 27 29 30
92 2 31 29 27 28
93 4 27 29 31 21
94 2 27 29 31 32
95 2 21 31 29 30
96 5 30 29 31 32
97 10 36 35 37 38
98 2 39 37 35 36
99 11 45 35 37 38
100 4 45 35 37 39
101 2 43 45 35 36
102 5 36 35 45 46
103 4 37 35 45 43
104 2 37 35 45 46
105 13 35 37 38 14
106 12 35 37 38 47
107 13 35 37 38 48
108 13 39 37 38 14
109 12 39 37 38 47
110 13 39 37 38 48
111 2 35 37 39 40
112 4 35 37 39 41
113 10 40 39 37 38
114 11 41 39 37 38
115 19 14 38 48 24
116 16 14 38 48 49
117 16 14 38 48 50
118 17 37 38 48 24
119 14 37 38 48 49
120 14 37 38 48 50
121 18 47 38 48 24
122 15 47 38 48 49
123 15 47 38 48 50
124 2 37 39 41 42
125 4 37 39 41 43
126 5 40 39 41 42
127 2 43 41 39 40
128 2 39 41 43 44
129 4 39 41 43 45
130 5 42 41 43 44
131 2 45 43 41 42
132 4 41 43 45 35
133 2 41 43 45 46
134 2 35 45 43 44
135 5 44 43 45 46
Impropers
1 1 3 1 11 2
2 5 1 3 5 4
3 1 3 5 7 6
4 1 5 7 9 8
5 1 7 9 11 10
6 1 1 11 9 12
7 1 23 21 31 22
8 5 21 23 25 24
9 1 23 25 27 26
10 1 25 27 29 28
11 1 27 29 31 30
12 1 21 31 29 32
13 1 37 35 45 36
14 5 35 37 39 38
15 1 37 39 41 40
16 1 39 41 43 42
17 1 41 43 45 44
18 1 35 45 43 46
19 1 3 4 13 14
20 1 3 4 13 18
21 1 3 4 14 18
22 1 13 4 14 18
23 1 15 14 16 4
24 1 15 14 4 38
25 1 16 14 4 38
26 1 15 14 16 38
27 1 19 18 17 4
28 1 20 18 17 4
29 1 19 18 20 4
30 1 19 18 20 17
31 1 23 24 33 34
32 1 23 24 33 48
33 1 23 24 34 48
34 1 33 24 34 48
35 1 37 38 47 14
36 1 37 38 14 48
37 1 47 38 14 48
38 1 37 38 47 48
39 1 49 48 38 24
40 1 50 48 38 24
41 1 49 48 50 24
42 1 49 48 50 38

467
examples/USER/misc/bond_react/tiny_polystyrene/chain_chain_unreacted.data_template
View File

@ -1,467 +0,0 @@
chain_chain_unreacted
50 atoms
51 bonds
84 angles
118 dihedrals
36 impropers
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 5
18 6
19 2
20 2
21 1
22 2
23 1
24 5
25 1
26 2
27 1
28 2
29 1
30 2
31 1
32 2
33 2
34 6
35 1
36 2
37 1
38 5
39 1
40 2
41 1
42 2
43 1
44 2
45 1
46 2
47 2
48 6
49 2
50 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 -0.018200
18 -0.069600
19 0.035400
20 0.035400
21 -0.129000
22 0.123700
23 0.026600
24 -0.018200
25 -0.129000
26 0.123700
27 -0.173400
28 0.140300
29 -0.113400
30 0.128800
31 -0.173400
32 0.140300
33 0.051600
34 -0.069600
35 -0.129000
36 0.123700
37 0.026600
38 -0.018200
39 -0.129000
40 0.123700
41 -0.173400
42 0.140300
43 -0.113400
44 0.128800
45 -0.173400
46 0.140300
47 0.051600
48 -0.069600
49 0.035400
50 0.035400
Coords
1 24.391510 0.871570 -1.658940
2 25.323530 1.410570 -1.658940
3 23.161520 1.581570 -1.658940
4 23.161520 3.081570 -1.658940
5 21.931530 0.871570 -1.658940
6 20.999531 1.410570 -1.658940
7 21.931530 -0.548430 -1.658940
8 20.999531 -1.087420 -1.658940
9 23.161520 -1.258420 -1.658940
10 23.161520 -2.335430 -1.658940
11 24.391510 -0.548430 -1.658940
12 25.323530 -1.087420 -1.658940
13 24.027519 3.486570 -1.301940
14 21.883520 3.630570 -2.220940
15 21.933510 4.372580 -2.319940
16 21.240520 2.807570 -2.514940
17 28.359209 3.254520 -1.372130
18 27.081209 3.803520 -1.934130
19 27.131210 4.545520 -2.033130
20 26.438219 2.980520 -2.228130
21 13.465810 0.682530 -1.658940
22 14.397820 1.221530 -1.658940
23 12.235820 1.392530 -1.658940
24 12.235820 2.892530 -1.658940
25 11.005820 0.682530 -1.658940
26 10.073820 1.221530 -1.658940
27 11.005820 -0.737470 -1.658940
28 10.073820 -1.276460 -1.658940
29 12.235820 -1.447460 -1.658940
30 12.235820 -2.524470 -1.658940
31 13.465810 -0.737470 -1.658940
32 14.397820 -1.276460 -1.658940
33 13.101820 3.297530 -1.301940
34 10.957820 3.441530 -2.220940
35 18.663521 0.855480 -1.372130
36 19.595510 1.394480 -1.372130
37 17.433510 1.565480 -1.372130
38 17.433510 3.065480 -1.372130
39 16.203510 0.855480 -1.372130
40 15.271510 1.394480 -1.372130
41 16.203510 -0.564520 -1.372130
42 15.271510 -1.103520 -1.372130
43 17.433510 -1.274520 -1.372130
44 17.433510 -2.351520 -1.372130
45 18.663521 -0.564520 -1.372130
46 19.595510 -1.103520 -1.372130
47 18.299509 3.470480 -1.015130
48 16.155510 3.614480 -1.934130
49 16.205509 4.356480 -2.033130
50 15.512510 2.791480 -2.228130
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 7 3 4
5 2 3 5
6 8 13 4
7 9 4 14
8 9 4 18
9 1 5 6
10 2 5 7
11 1 7 8
12 2 7 9
13 1 9 10
14 2 9 11
15 1 11 12
16 10 15 14
17 10 16 14
18 9 17 18
19 10 19 18
20 10 20 18
21 1 21 22
22 2 21 23
23 2 21 31
24 7 23 24
25 2 23 25
26 8 33 24
27 9 24 34
28 9 24 48
29 1 25 26
30 2 25 27
31 1 27 28
32 2 27 29
33 1 29 30
34 2 29 31
35 1 31 32
36 1 35 36
37 2 35 37
38 2 35 45
39 7 37 38
40 2 37 39
41 8 47 38
42 9 38 48
43 1 39 40
44 2 39 41
45 1 41 42
46 2 41 43
47 1 43 44
48 2 43 45
49 1 45 46
50 10 49 48
51 10 50 48
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 9 1 3 4
5 2 1 3 5
6 9 5 3 4
7 10 3 4 13
8 11 3 4 14
9 11 3 4 18
10 12 13 4 14
11 12 13 4 18
12 13 14 4 18
13 1 3 5 6
14 2 3 5 7
15 1 7 5 6
16 1 5 7 8
17 2 5 7 9
18 1 9 7 8
19 1 7 9 10
20 2 7 9 11
21 1 11 9 10
22 2 1 11 9
23 1 1 11 12
24 1 9 11 12
25 14 15 14 4
26 14 16 14 4
27 15 15 14 16
28 16 4 18 17
29 14 19 18 4
30 14 20 18 4
31 14 19 18 17
32 14 20 18 17
33 15 19 18 20
34 1 23 21 22
35 1 31 21 22
36 2 23 21 31
37 9 21 23 24
38 2 21 23 25
39 9 25 23 24
40 10 23 24 33
41 11 23 24 34
42 11 23 24 48
43 12 33 24 34
44 12 33 24 48
45 13 34 24 48
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 1 25 27 28
50 2 25 27 29
51 1 29 27 28
52 1 27 29 30
53 2 27 29 31
54 1 31 29 30
55 2 21 31 29
56 1 21 31 32
57 1 29 31 32
58 1 37 35 36
59 1 45 35 36
60 2 37 35 45
61 9 35 37 38
62 2 35 37 39
63 9 39 37 38
64 10 37 38 47
65 11 37 38 48
66 12 47 38 48
67 1 37 39 40
68 2 37 39 41
69 1 41 39 40
70 1 39 41 42
71 2 39 41 43
72 1 43 41 42
73 1 41 43 44
74 2 41 43 45
75 1 45 43 44
76 2 35 45 43
77 1 35 45 46
78 1 43 45 46
79 16 24 48 38
80 14 49 48 24
81 14 50 48 24
82 14 49 48 38
83 14 50 48 38
84 15 49 48 50
Dihedrals
1 10 2 1 3 4
2 2 5 3 1 2
3 11 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 12 1 3 4 13
10 13 1 3 4 14
11 13 1 3 4 18
12 12 5 3 4 13
13 13 5 3 4 14
14 13 5 3 4 18
15 2 1 3 5 6
16 4 1 3 5 7
17 10 6 5 3 4
18 11 7 5 3 4
19 14 3 4 14 15
20 14 3 4 14 16
21 15 13 4 14 15
22 15 13 4 14 16
23 16 18 4 14 15
24 16 18 4 14 16
25 17 3 4 18 17
26 14 3 4 18 19
27 14 3 4 18 20
28 18 13 4 18 17
29 15 13 4 18 19
30 15 13 4 18 20
31 19 14 4 18 17
32 16 14 4 18 19
33 16 14 4 18 20
34 2 3 5 7 8
35 4 3 5 7 9
36 5 6 5 7 8
37 2 9 7 5 6
38 2 5 7 9 10
39 4 5 7 9 11
40 5 8 7 9 10
41 2 11 9 7 8
42 4 7 9 11 1
43 2 7 9 11 12
44 2 1 11 9 10
45 5 10 9 11 12
46 10 22 21 23 24
47 2 25 23 21 22
48 11 31 21 23 24
49 4 31 21 23 25
50 2 29 31 21 22
51 5 22 21 31 32
52 4 23 21 31 29
53 2 23 21 31 32
54 12 21 23 24 33
55 13 21 23 24 34
56 13 21 23 24 48
57 12 25 23 24 33
58 13 25 23 24 34
59 13 25 23 24 48
60 2 21 23 25 26
61 4 21 23 25 27
62 10 26 25 23 24
63 11 27 25 23 24
64 17 23 24 48 38
65 14 23 24 48 49
66 14 23 24 48 50
67 18 33 24 48 38
68 15 33 24 48 49
69 15 33 24 48 50
70 19 34 24 48 38
71 16 34 24 48 49
72 16 34 24 48 50
73 2 23 25 27 28
74 4 23 25 27 29
75 5 26 25 27 28
76 2 29 27 25 26
77 2 25 27 29 30
78 4 25 27 29 31
79 5 28 27 29 30
80 2 31 29 27 28
81 4 27 29 31 21
82 2 27 29 31 32
83 2 21 31 29 30
84 5 30 29 31 32
85 10 36 35 37 38
86 2 39 37 35 36
87 11 45 35 37 38
88 4 45 35 37 39
89 2 43 45 35 36
90 5 36 35 45 46
91 4 37 35 45 43
92 2 37 35 45 46
93 12 35 37 38 47
94 13 35 37 38 48
95 12 39 37 38 47
96 13 39 37 38 48
97 2 35 37 39 40
98 4 35 37 39 41
99 10 40 39 37 38
100 11 41 39 37 38
101 17 37 38 48 24
102 14 37 38 48 49
103 14 37 38 48 50
104 18 47 38 48 24
105 15 47 38 48 49
106 15 47 38 48 50
107 2 37 39 41 42
108 4 37 39 41 43
109 5 40 39 41 42
110 2 43 41 39 40
111 2 39 41 43 44
112 4 39 41 43 45
113 5 42 41 43 44
114 2 45 43 41 42
115 4 41 43 45 35
116 2 41 43 45 46
117 2 35 45 43 44
118 5 44 43 45 46
Impropers
1 1 3 1 11 2
2 5 1 3 5 4
3 1 3 5 7 6
4 1 5 7 9 8
5 1 7 9 11 10
6 1 1 11 9 12
7 6 15 14 16 4
8 1 23 21 31 22
9 5 21 23 25 24
10 1 23 25 27 26
11 1 25 27 29 28
12 1 27 29 31 30
13 1 21 31 29 32
14 1 37 35 45 36
15 5 35 37 39 38
16 7 37 38 47 48
17 1 37 39 41 40
18 1 39 41 43 42
19 1 41 43 45 44
20 1 35 45 43 46
21 1 3 4 13 14
22 1 3 4 13 18
23 1 3 4 14 18
24 1 13 4 14 18
25 1 19 18 17 4
26 1 20 18 17 4
27 1 19 18 20 4
28 1 19 18 20 17
29 1 23 24 33 34
30 1 23 24 33 48
31 1 23 24 34 48
32 1 33 24 34 48
33 1 49 48 38 24
34 1 50 48 38 24
35 1 49 48 50 24
36 1 49 48 50 38

62
examples/USER/misc/bond_react/tiny_polystyrene/chain_plus_styrene_map
View File

@ -1,62 +0,0 @@
this is a map file
1 edgeIDs
46 equivalences
EdgeIDs
30
BondingIDs
14
34
Equivalences
1 1
2 2
3 3
4 4
5 5
6 6
7 7
8 8
9 9
10 10
11 11
12 12
13 13
14 14
15 15
16 16
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
31 31
32 32
33 33
34 34
35 35
36 36
37 37
38 38
39 39
40 40
41 41
42 42
43 43
44 44
45 45
46 46

451
examples/USER/misc/bond_react/tiny_polystyrene/chain_plus_styrene_reacted.data_template
View File

@ -1,451 +0,0 @@
chain_plus_styrene_reacted
46 atoms
48 bonds
81 angles
121 dihedrals
35 impropers
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

422
examples/USER/misc/bond_react/tiny_polystyrene/chain_plus_styrene_unreacted.data_template
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@ -1,422 +0,0 @@
chain_plus_styrene_unreacted
46 atoms
47 bonds
75 angles
105 dihedrals
29 impropers
Types
1 1
2 2
3 1
4 3
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 4
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 3 3 4
5 2 3 5
6 4 13 4
7 5 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 6 15 14
16 6 16 14
17 1 17 18
18 2 17 19
19 2 17 27
20 7 19 20
21 2 19 21
22 8 29 20
23 9 20 30
24 9 20 44
25 1 21 22
26 2 21 23
27 1 23 24
28 2 23 25
29 1 25 26
30 2 25 27
31 1 27 28
32 1 31 32
33 2 31 33
34 2 31 41
35 7 33 34
36 2 33 35
37 8 43 34
38 9 34 44
39 1 35 36
40 2 35 37
41 1 37 38
42 2 37 39
43 1 39 40
44 2 39 41
45 1 41 42
46 10 45 44
47 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 3 1 3 4
5 2 1 3 5
6 3 5 3 4
7 4 3 4 13
8 5 3 4 14
9 6 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 7 15 14 4
23 7 16 14 4
24 8 15 14 16
25 1 19 17 18
26 1 27 17 18
27 2 19 17 27
28 9 17 19 20
29 2 17 19 21
30 9 21 19 20
31 10 19 20 29
32 11 19 20 30
33 11 19 20 44
34 12 29 20 30
35 12 29 20 44
36 13 30 20 44
37 1 19 21 22
38 2 19 21 23
39 1 23 21 22
40 1 21 23 24
41 2 21 23 25
42 1 25 23 24
43 1 23 25 26
44 2 23 25 27
45 1 27 25 26
46 2 17 27 25
47 1 17 27 28
48 1 25 27 28
49 1 33 31 32
50 1 41 31 32
51 2 33 31 41
52 9 31 33 34
53 2 31 33 35
54 9 35 33 34
55 10 33 34 43
56 11 33 34 44
57 12 43 34 44
58 1 33 35 36
59 2 33 35 37
60 1 37 35 36
61 1 35 37 38
62 2 35 37 39
63 1 39 37 38
64 1 37 39 40
65 2 37 39 41
66 1 41 39 40
67 2 31 41 39
68 1 31 41 42
69 1 39 41 42
70 16 20 44 34
71 14 45 44 20
72 14 46 44 20
73 14 45 44 34
74 14 46 44 34
75 15 45 44 46
Dihedrals
1 1 2 1 3 4
2 2 5 3 1 2
3 3 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 6 1 3 4 13
10 7 1 3 4 14
11 6 5 3 4 13
12 7 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 1 6 5 3 4
16 3 7 5 3 4
17 8 3 4 14 15
18 8 3 4 14 16
19 9 13 4 14 15
20 9 13 4 14 16
21 2 3 5 7 8
22 4 3 5 7 9
23 5 6 5 7 8
24 2 9 7 5 6
25 2 5 7 9 10
26 4 5 7 9 11
27 5 8 7 9 10
28 2 11 9 7 8
29 4 7 9 11 1
30 2 7 9 11 12
31 2 1 11 9 10
32 5 10 9 11 12
33 10 18 17 19 20
34 2 21 19 17 18
35 11 27 17 19 20
36 4 27 17 19 21
37 2 25 27 17 18
38 5 18 17 27 28
39 4 19 17 27 25
40 2 19 17 27 28
41 12 17 19 20 29
42 13 17 19 20 30
43 13 17 19 20 44
44 12 21 19 20 29
45 13 21 19 20 30
46 13 21 19 20 44
47 2 17 19 21 22
48 4 17 19 21 23
49 10 22 21 19 20
50 11 23 21 19 20
51 17 19 20 44 34
52 14 19 20 44 45
53 14 19 20 44 46
54 18 29 20 44 34
55 15 29 20 44 45
56 15 29 20 44 46
57 19 30 20 44 34
58 16 30 20 44 45
59 16 30 20 44 46
60 2 19 21 23 24
61 4 19 21 23 25
62 5 22 21 23 24
63 2 25 23 21 22
64 2 21 23 25 26
65 4 21 23 25 27
66 5 24 23 25 26
67 2 27 25 23 24
68 4 23 25 27 17
69 2 23 25 27 28
70 2 17 27 25 26
71 5 26 25 27 28
72 10 32 31 33 34
73 2 35 33 31 32
74 11 41 31 33 34
75 4 41 31 33 35
76 2 39 41 31 32
77 5 32 31 41 42
78 4 33 31 41 39
79 2 33 31 41 42
80 12 31 33 34 43
81 13 31 33 34 44
82 12 35 33 34 43
83 13 35 33 34 44
84 2 31 33 35 36
85 4 31 33 35 37
86 10 36 35 33 34
87 11 37 35 33 34
88 17 33 34 44 20
89 14 33 34 44 45
90 14 33 34 44 46
91 18 43 34 44 20
92 15 43 34 44 45
93 15 43 34 44 46
94 2 33 35 37 38
95 4 33 35 37 39
96 5 36 35 37 38
97 2 39 37 35 36
98 2 35 37 39 40
99 4 35 37 39 41
100 5 38 37 39 40
101 2 41 39 37 38
102 4 37 39 41 31
103 2 37 39 41 42
104 2 31 41 39 40
105 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 2 1 3 5 4
3 3 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 4 15 14 16 4
9 1 19 17 27 18
10 5 17 19 21 20
11 1 19 21 23 22
12 1 21 23 25 24
13 1 23 25 27 26
14 1 17 27 25 28
15 1 33 31 41 32
16 5 31 33 35 34
17 7 33 34 43 44
18 1 33 35 37 36
19 1 35 37 39 38
20 1 37 39 41 40
21 1 31 41 39 42
22 1 19 20 29 30
23 1 19 20 29 44
24 1 19 20 30 44
25 1 29 20 30 44
26 1 45 44 34 20
27 1 46 44 34 20
28 1 45 44 46 20
29 1 45 44 46 34

56
examples/USER/misc/bond_react/tiny_polystyrene/in.tiny_polystyrene.stabilized
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@ -1,56 +0,0 @@
# 20 styrene molecules
# three reactions defined
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data tiny_polystyrene.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
molecule mol1 2styrene_unreacted.data_template
molecule mol2 2styrene_reacted.data_template
molecule mol3 chain_plus_styrene_unreacted.data_template
molecule mol4 chain_plus_styrene_reacted.data_template
molecule mol5 chain_chain_unreacted.data_template
molecule mol6 chain_chain_reacted.data_template
thermo 100
# dump 1 all xyz 5 test_vis.xyz
fix rxn1 all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100 &
react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100 &
react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]
run 10000
# write_restart restart_longrun nofix
# write_data restart_longrun.data

245
examples/USER/misc/bond_react/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.1
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LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573)
1 by 1 by 1 MPI processor grid
reading atoms ...
320 atoms
reading velocities ...
320 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
22 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
320 bonds
reading angles ...
480 angles
reading dihedrals ...
640 dihedrals
reading impropers ...
160 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
39 = max # of special neighbors
special bonds CPU = 0.000929056 secs
read_data CPU = 0.00930568 secs
Read molecule mol1:
32 atoms with max type 4
32 bonds with max type 6
48 angles with max type 8
64 dihedrals with max type 9
16 impropers with max type 4
Read molecule mol2:
32 atoms with max type 6
33 bonds with max type 10
54 angles with max type 16
79 dihedrals with max type 19
22 impropers with max type 7
Read molecule mol3:
46 atoms with max type 6
47 bonds with max type 10
75 angles with max type 16
105 dihedrals with max type 19
29 impropers with max type 7
Read molecule mol4:
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
Read molecule mol5:
50 atoms with max type 6
51 bonds with max type 10
84 angles with max type 16
118 dihedrals with max type 19
36 impropers with max type 7
Read molecule mol6:
50 atoms with max type 6
52 bonds with max type 10
90 angles with max type 16
135 dihedrals with max type 19
42 impropers with max type 5
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304)
using 12-bit tables for long-range coulomb (../kspace.cpp:323)
G vector (1/distance) = 0.255611
grid = 6 6 6
stencil order = 5
estimated absolute RMS force accuracy = 0.00974692
estimated relative force accuracy = 2.93525e-05
using double precision FFTs
3d grid and FFT values/proc = 1331 216
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 = 4 4 4
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) = 31.14 | 31.14 | 31.14 Mbytes
Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
0 320.13638 -376.0844 0.76796752 0 0 0
100 520.00782 3952.7008 0.76796752 8 0 0
200 499.9174 2360.8219 0.76796752 8 3 1
300 583.93895 2453.7374 0.76796752 8 3 2
400 560.65536 -2243.3464 0.76796752 8 3 3
500 556.27995 3598.7044 0.76796752 8 3 3
600 570.8397 -3340.1826 0.76796752 8 4 4
700 456.89894 -1087.8081 0.76796752 8 4 4
800 572.91817 -776.19188 0.76796752 8 4 4
900 530.13621 -246734.46 0.76796752 8 4 5
1000 542.34698 1044.0793 0.76796752 8 4 5
1100 562.86339 1207.1715 0.76796752 8 4 5
1200 520.1559 2725.6523 0.76796752 8 4 5
1300 534.01667 951.0972 0.76796752 8 4 5
1400 478.68681 1184.9224 0.76796752 8 4 5
1500 509.05445 2020.5224 0.76796752 8 4 5
1600 549.5382 810.17577 0.76796752 8 4 5
1700 549.46882 -6349.7751 0.76796752 8 4 5
1800 496.77334 3953.1043 0.76796752 8 4 5
1900 522.28719 -2271.7599 0.76796752 8 4 6
2000 569.95975 5633.4352 0.76796752 8 4 6
2100 590.8418 2355.8447 0.76796752 8 4 6
2200 537.64787 6459.6743 0.76796752 8 4 6
2300 548.38487 -1566.3528 0.76796752 8 4 6
2400 533.50353 6755.664 0.76796752 8 4 6
2500 512.57053 325.30968 0.76796752 8 4 6
2600 498.4597 -2468.1165 0.76796752 8 4 6
2700 559.03937 2428.3446 0.76796752 8 4 6
2800 585.85721 -2896.3607 0.76796752 8 4 6
2900 523.18635 1391.254 0.76796752 8 4 6
3000 524.62076 375.02973 0.76796752 8 4 6
3100 534.65688 -1522.7879 0.76796752 8 4 6
3200 499.42665 3725.5476 0.76796752 8 4 6
3300 514.36972 1725.8329 0.76796752 8 4 6
3400 482.52662 4648.5013 0.76796752 8 4 6
3500 495.36836 967.3482 0.76796752 8 4 6
3600 583.28736 745.21794 0.76796752 8 4 6
3700 531.99717 -804.39572 0.76796752 8 4 6
3800 555.08359 -2381.363 0.76796752 8 4 6
3900 520.1818 -547.34169 0.76796752 8 4 6
4000 444.38804 -2488.7881 0.76796752 8 4 6
4100 518.65622 -3135.9573 0.76796752 8 4 6
4200 484.15227 -1040.2447 0.76796752 8 4 6
4300 514.58006 550.14626 0.76796752 8 4 6
4400 579.81405 -849.81454 0.76796752 8 4 6
4500 522.8698 5222.654 0.76796752 8 4 6
4600 490.78275 3251.2892 0.76796752 8 4 6
4700 492.64299 3785.3482 0.76796752 8 4 6
4800 500.11059 4441.8978 0.76796752 8 4 6
4900 536.80009 965.33724 0.76796752 8 4 6
5000 516.98575 -3794.4213 0.76796752 8 4 6
5100 516.76648 -3593.9106 0.76796752 8 4 6
5200 521.6379 -6532.7773 0.76796752 8 4 6
5300 535.64798 2931.412 0.76796752 8 4 6
5400 559.83266 7628.1659 0.76796752 8 4 6
5500 538.91756 2841.6746 0.76796752 8 4 6
5600 539.13999 10445.173 0.76796752 8 4 6
5700 501.56603 -2106.3309 0.76796752 8 4 6
5800 496.72952 -4831.0565 0.76796752 8 4 6
5900 536.12979 -3916.8197 0.76796752 8 4 6
6000 553.10092 3142.6871 0.76796752 8 4 6
6100 558.09546 3154.584 0.76796752 8 4 6
6200 523.48472 9807.0034 0.76796752 8 4 6
6300 551.80343 -3608.2078 0.76796752 8 4 6
6400 484.28359 2255.4675 0.76796752 8 4 6
6500 560.68443 -4826.4868 0.76796752 8 4 6
6600 604.50797 402.32183 0.76796752 8 4 6
6700 538.84714 -7670.3312 0.76796752 8 4 6
6800 528.82853 -380.32058 0.76796752 8 4 6
6900 579.30919 4438.4574 0.76796752 8 4 6
7000 540.3406 3738.0524 0.76796752 8 4 6
7100 519.53645 -1825.5563 0.76796752 8 4 6
7200 474.136 1657.3863 0.76796752 8 4 6
7300 485.55159 -221.84939 0.76796752 8 4 6
7400 527.38494 1037.1777 0.76796752 8 4 6
7500 517.14767 -2313.5823 0.76796752 8 4 6
7600 517.95967 -4763.4709 0.76796752 8 4 6
7700 513.63507 4819.0253 0.76796752 8 4 6
7800 503.56828 1295.1212 0.76796752 8 4 6
7900 520.87804 1506.9417 0.76796752 8 4 6
8000 509.46453 -5800.0971 0.76796752 8 4 6
8100 566.67059 6065.4607 0.76796752 8 4 6
8200 592.53068 1097.2277 0.76796752 8 4 6
8300 529.55235 -580.81757 0.76796752 8 4 6
8400 518.22587 560.45589 0.76796752 8 4 6
8500 521.94561 5325.9459 0.76796752 8 4 6
8600 510.54416 -1929.1967 0.76796752 8 4 6
8700 562.71252 -629.90392 0.76796752 8 4 6
8800 540.23123 -3484.3893 0.76796752 8 4 6
8900 513.82411 -5227.152 0.76796752 8 4 6
9000 534.3307 -3299.088 0.76796752 8 4 6
9100 509.24467 -5676.2775 0.76796752 8 4 6
9200 506.3216 -7043.8493 0.76796752 8 4 7
9300 480.37682 2380.4696 0.76796752 8 4 7
9400 546.15532 1831.0103 0.76796752 8 4 7
9500 567.18341 3839.9843 0.76796752 8 4 7
9600 536.14883 4258.5304 0.76796752 8 4 7
9700 496.04153 3321.3561 0.76796752 8 4 7
9800 531.78927 3124.9156 0.76796752 8 4 7
9900 530.91395 38.987859 0.76796752 8 4 7
10000 551.22761 1027.5706 0.76796752 8 4 7
Loop time of 57.7096 on 1 procs for 10000 steps with 320 atoms
Performance: 14.972 ns/day, 1.603 hours/ns, 173.281 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 | 11.621 | 11.621 | 11.621 | 0.0 | 20.14
Bond | 11.151 | 11.151 | 11.151 | 0.0 | 19.32
Kspace | 2.2403 | 2.2403 | 2.2403 | 0.0 | 3.88
Neigh | 25.467 | 25.467 | 25.467 | 0.0 | 44.13
Comm | 0.90467 | 0.90467 | 0.90467 | 0.0 | 1.57
Output | 0.0017984 | 0.0017984 | 0.0017984 | 0.0 | 0.00
Modify | 6.2622 | 6.2622 | 6.2622 | 0.0 | 10.85
Other | | 0.06192 | | | 0.11
Nlocal: 320 ave 320 max 320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3240 ave 3240 max 3240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 54336 ave 54336 max 54336 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 54336
Ave neighs/atom = 169.8
Ave special neighs/atom = 11.3063
Neighbor list builds = 10000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:58

255
examples/USER/misc/bond_react/tiny_polystyrene/log.20Nov19.tiny_polystyrene.stabilized.g++.4
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LAMMPS (20 Nov 2019)
WARNING-WARNING-WARNING-WARNING-WARNING
This LAMMPS executable was compiled using C++98 compatibility.
Please report the compiler info below at https://github.com/lammps/lammps/issues/1659
GNU C++ 4.8.5
WARNING-WARNING-WARNING-WARNING-WARNING
Reading data file ...
orthogonal box = (1.74267 1.74267 1.74267) to (18.2573 18.2573 18.2573)
1 by 2 by 2 MPI processor grid
reading atoms ...
320 atoms
reading velocities ...
320 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
18 = max angles/atom
scanning dihedrals ...
22 = max dihedrals/atom
scanning impropers ...
26 = max impropers/atom
reading bonds ...
320 bonds
reading angles ...
480 angles
reading dihedrals ...
640 dihedrals
reading impropers ...
160 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
3 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
39 = max # of special neighbors
special bonds CPU = 0.000751222 secs
read_data CPU = 0.0268223 secs
Read molecule mol1:
32 atoms with max type 4
32 bonds with max type 6
48 angles with max type 8
64 dihedrals with max type 9
16 impropers with max type 4
Read molecule mol2:
32 atoms with max type 6
33 bonds with max type 10
54 angles with max type 16
79 dihedrals with max type 19
22 impropers with max type 7
Read molecule mol3:
46 atoms with max type 6
47 bonds with max type 10
75 angles with max type 16
105 dihedrals with max type 19
29 impropers with max type 7
Read molecule mol4:
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
Read molecule mol5:
50 atoms with max type 6
51 bonds with max type 10
84 angles with max type 16
118 dihedrals with max type 19
36 impropers with max type 7
Read molecule mol6:
50 atoms with max type 6
52 bonds with max type 10
90 angles with max type 16
135 dihedrals with max type 19
42 impropers with max type 5
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:304)
using 12-bit tables for long-range coulomb (../kspace.cpp:323)
G vector (1/distance) = 0.255611
grid = 6 6 6
stencil order = 5
estimated absolute RMS force accuracy = 0.00974692
estimated relative force accuracy = 2.93525e-05
using double precision FFTs
3d grid and FFT values/proc = 704 72
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 = 4 4 4
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) = 30.66 | 30.68 | 30.69 Mbytes
Step Temp Press Density f_rxn1[1] f_rxn1[2] f_rxn1[3]
0 320.13638 -376.0844 0.76796752 0 0 0
100 522.71544 6623.0579 0.76796752 8 0 0
200 500.86716 -9439.5519 0.76796752 8 3 2
300 594.60588 6714.1323 0.76796752 8 3 3
400 598.68768 683.70457 0.76796752 8 3 3
500 563.1011 3576.6857 0.76796752 8 3 4
600 510.29713 -196148.37 0.76796752 8 3 5
700 494.14346 -118517.45 0.76796752 8 3 6
800 565.62849 7678.1235 0.76796752 8 3 6
900 515.74468 554.84571 0.76796752 8 3 6
1000 500.64636 450.15932 0.76796752 8 3 6
1100 463.34973 6023.8346 0.76796752 8 3 6
1200 529.88483 2748.185 0.76796752 8 3 6
1300 546.84049 1353.4891 0.76796752 8 3 6
1400 552.27356 1446.5807 0.76796752 8 3 6
1500 557.70874 -2745.1523 0.76796752 8 3 6
1600 572.0005 629.36722 0.76796752 8 3 6
1700 503.96569 5937.0231 0.76796752 8 3 6
1800 491.34262 -1175.8104 0.76796752 8 3 6
1900 538.24798 -81.197397 0.76796752 8 3 6
2000 523.89324 2857.2466 0.76796752 8 3 6
2100 515.1424 2288.2405 0.76796752 8 3 6
2200 546.80854 3807.1038 0.76796752 8 3 6
2300 500.31231 -135.33933 0.76796752 8 4 6
2400 497.16354 5516.857 0.76796752 8 4 6
2500 545.34187 3485.5645 0.76796752 8 4 6
2600 522.70122 3114.1284 0.76796752 8 4 6
2700 531.76604 6633.5518 0.76796752 8 4 6
2800 521.97643 -279.83682 0.76796752 8 4 6
2900 497.29575 7052.9409 0.76796752 8 4 6
3000 524.5942 2284.8918 0.76796752 8 4 6
3100 567.61329 -3667.4557 0.76796752 8 4 6
3200 506.82452 -2934.4936 0.76796752 8 4 6
3300 510.8521 313.36263 0.76796752 8 4 6
3400 516.70206 3671.1899 0.76796752 8 4 6
3500 535.12788 2645.2564 0.76796752 8 4 6
3600 580.14214 2604.3079 0.76796752 8 4 6
3700 529.77869 2684.0812 0.76796752 8 4 6
3800 502.93191 2838.6698 0.76796752 8 4 6
3900 585.91492 5308.0828 0.76796752 8 4 6
4000 548.89917 5262.5775 0.76796752 8 4 6
4100 550.7662 -1066.6807 0.76796752 8 4 6
4200 519.19198 2777.5276 0.76796752 8 4 6
4300 521.46332 -3429.7171 0.76796752 8 4 6
4400 532.64173 2301.3135 0.76796752 8 4 6
4500 528.96107 1369.0991 0.76796752 8 4 6
4600 564.66443 9687.2531 0.76796752 8 4 6
4700 558.49446 2322.6085 0.76796752 8 4 6
4800 497.78614 -442.45053 0.76796752 8 4 6
4900 511.09435 -10251.159 0.76796752 8 4 6
5000 525.6642 -1202.0584 0.76796752 8 4 6
5100 521.76974 1821.7811 0.76796752 8 4 6
5200 555.9859 7256.9632 0.76796752 8 4 6
5300 551.51971 -122893.16 0.76796752 8 4 7
5400 524.34705 2905.1033 0.76796752 8 4 7
5500 567.09396 2896.4824 0.76796752 8 4 7
5600 487.57746 1417.1715 0.76796752 8 4 7
5700 547.37304 3900.8734 0.76796752 8 4 7
5800 536.17647 -4048.7522 0.76796752 8 4 7
5900 536.85051 4497.9847 0.76796752 8 4 7
6000 548.58212 -4880.4979 0.76796752 8 4 7
6100 500.94692 6004.2105 0.76796752 8 4 7
6200 486.82494 402.5875 0.76796752 8 4 7
6300 478.09381 6600.767 0.76796752 8 4 7
6400 559.90398 2868.0805 0.76796752 8 4 7
6500 526.01866 -3398.4788 0.76796752 8 4 7
6600 539.68471 -1202.0012 0.76796752 8 4 7
6700 507.51217 -378.71164 0.76796752 8 4 7
6800 526.15958 -4536.9888 0.76796752 8 4 7
6900 511.37134 -2522.3553 0.76796752 8 4 7
7000 538.86918 -2028.0323 0.76796752 8 4 7
7100 523.25566 2911.9962 0.76796752 8 4 7
7200 513.28464 -1000.4758 0.76796752 8 4 7
7300 510.19826 5181.7976 0.76796752 8 4 7
7400 493.46528 -1166.3996 0.76796752 8 4 7
7500 491.51305 5669.2213 0.76796752 8 4 7
7600 506.72032 -2840.301 0.76796752 8 4 7
7700 513.4319 2802.1719 0.76796752 8 4 7
7800 543.7658 -7477.3623 0.76796752 8 4 7
7900 527.35619 -3182.3155 0.76796752 8 4 7
8000 533.50993 613.16561 0.76796752 8 4 7
8100 512.44958 -5037.3414 0.76796752 8 4 7
8200 494.88981 1799.3513 0.76796752 8 4 7
8300 554.81474 -2436.0507 0.76796752 8 4 7
8400 523.22917 364.30593 0.76796752 8 4 7
8500 515.12395 525.24581 0.76796752 8 4 7
8600 511.6321 -1679.8669 0.76796752 8 4 7
8700 531.6327 -1168.1215 0.76796752 8 4 7
8800 548.14438 -5222.7573 0.76796752 8 4 7
8900 517.72579 2073.9695 0.76796752 8 4 7
9000 543.11894 -5307.0759 0.76796752 8 4 7
9100 521.13747 -5546.8552 0.76796752 8 4 7
9200 509.66142 -1584.019 0.76796752 8 4 7
9300 488.73821 -277.85847 0.76796752 8 4 7
9400 513.67282 989.60653 0.76796752 8 4 7
9500 509.98833 -1754.8786 0.76796752 8 4 7
9600 558.72497 5616.6969 0.76796752 8 4 7
9700 533.74988 811.48871 0.76796752 8 4 7
9800 510.94641 -3136.5876 0.76796752 8 4 7
9900 517.80127 -1962.0837 0.76796752 8 4 7
10000 477.50428 -3768.1653 0.76796752 8 4 7
Loop time of 20.9963 on 4 procs for 10000 steps with 320 atoms
Performance: 41.150 ns/day, 0.583 hours/ns, 476.276 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.4968 | 3.0329 | 3.3607 | 18.6 | 14.45
Bond | 2.3164 | 2.8835 | 3.456 | 26.0 | 13.73
Kspace | 1.3332 | 2.2082 | 3.285 | 48.0 | 10.52
Neigh | 7.4831 | 7.4922 | 7.5012 | 0.3 | 35.68
Comm | 1.2809 | 1.3121 | 1.3297 | 1.6 | 6.25
Output | 0.0012138 | 0.0013506 | 0.0017552 | 0.6 | 0.01
Modify | 4.0269 | 4.0301 | 4.0335 | 0.1 | 19.19
Other | | 0.03583 | | | 0.17
Nlocal: 80 ave 94 max 66 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2243.75 ave 2260 max 2221 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 13658.5 ave 17096 max 9421 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 54634
Ave neighs/atom = 170.731
Ave special neighs/atom = 11.3063
Neighbor list builds = 10000
Dangerous builds = 0
System init for write_data ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:323)
G vector (1/distance) = 0.255611
grid = 6 6 6
stencil order = 5
estimated absolute RMS force accuracy = 0.00974692
estimated relative force accuracy = 2.93525e-05
using double precision FFTs
3d grid and FFT values/proc = 704 72
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:21

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examples/USER/misc/bond_react/tiny_polystyrene/tiny_polystyrene.data
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