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add updated example using json molecule files

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Axel Kohlmeyer
2025-06-12 00:34:01 -04:00
parent 125389bf23
commit b15f4e5d63
10 changed files with 2523 additions and 0 deletions
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examples/PACKAGES/reaction/tiny_nylon_json/in.tiny_nylon.stabilized Normal file
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# 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
special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower
read_data tiny_nylon.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
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.json
molecule mol2 rxn1_stp1_reacted.json
molecule mol3 rxn1_stp2_unreacted.json
molecule mol4 rxn1_stp2_reacted.json
thermo 50
# dump 1 all xyz 1 test_vis.xyz
# dump_modify 1 types labels
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 rescale_charges yes
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[*]
# restart 100 restart1 restart2
run 10000
# write_restart restart_longrun
# write_data restart_longrun.data

444
examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.1 Normal file
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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-583-g5868aa095d-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# 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
special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower
read_data tiny_nylon.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
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
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
16 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
35 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.json
Read molecule template mol1:
(no title)
1 molecules
0 fragments
18 atoms with max type 0
16 bonds with max type 8
25 angles with max type 25
23 dihedrals with max type 33
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.json
Read molecule template mol2:
(no title)
1 molecules
0 fragments
18 atoms with max type 0
17 bonds with max type 11
31 angles with max type 24
39 dihedrals with max type 30
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.json
Read molecule template mol3:
(no title)
1 molecules
0 fragments
15 atoms with max type 0
14 bonds with max type 11
25 angles with max type 24
30 dihedrals with max type 30
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.json
Read molecule template mol4:
(no title)
1 molecules
0 fragments
15 atoms with max type 0
13 bonds with max type 13
19 angles with max type 26
16 dihedrals with max type 29
2 impropers with max type 5
thermo 50
# dump 1 all xyz 1 test_vis.xyz
# dump_modify 1 types labels
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 rescale_charges yes
WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[*]
# restart 100 restart1 restart2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282--3297}
}
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
@Article{Gissinger24,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {Molecular Modeling of Reactive Systems with REACTER},
journal = {Computer Physics Communications},
year = 2024,
volume = 304,
number = 109287
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23408048
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.018627396
estimated relative force accuracy = 5.6095851e-05
using double precision FFTW3
3d grid and FFT values/proc = 8000 3375
Generated 55 of 55 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 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
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) = 34 | 34 | 34 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 357.25588 0.0034851739 0 0
50 328.952 -39.291672 0.0034851739 1 0
100 311.59495 29.741131 0.0034851739 1 1
150 325.04965 -19.624049 0.0034851739 1 1
200 313.15254 15.730975 0.0034851739 1 1
250 307.88805 -22.944869 0.0034851739 1 1
300 287.9343 6.7916738 0.0034851739 1 1
350 314.40601 12.913246 0.0034851739 1 1
400 304.58587 6.9804459 0.0034851739 1 1
450 300.97668 14.68689 0.0034851739 1 1
500 345.19498 -29.961085 0.0034851739 1 1
550 229.37329 12.88087 0.0034851739 1 1
600 239.75504 -3.575567 0.0034851739 1 1
650 257.58951 -5.0844118 0.0034851739 1 1
700 249.84121 22.825491 0.0034851739 1 1
750 287.62022 28.059197 0.0034851739 1 1
800 352.31339 -50.233738 0.0034851739 1 1
850 316.12821 22.493396 0.0034851739 1 1
900 283.85252 26.129698 0.0034851739 1 1
950 290.30591 -25.743121 0.0034851739 1 1
1000 346.57856 -2.1188627 0.0034851739 1 1
1050 251.23391 20.636107 0.0034851739 1 1
1100 267.48303 -15.912571 0.0034851739 1 1
1150 282.66256 14.019753 0.0034851739 1 1
1200 227.56518 -27.076623 0.0034851739 1 1
1250 232.7204 -1.0387593 0.0034851739 1 1
1300 277.28783 32.449571 0.0034851739 1 1
1350 308.5732 -11.129035 0.0034851739 1 1
1400 264.96641 -20.93416 0.0034851739 1 1
1450 262.83931 30.82366 0.0034851739 1 1
1500 276.23182 -24.480049 0.0034851739 1 1
1550 319.00599 -9.8372065 0.0034851739 1 1
1600 316.48228 -15.940319 0.0034851739 1 1
1650 277.213 1.3856424 0.0034851739 1 1
1700 302.34736 -27.623644 0.0034851739 1 1
1750 312.06738 -52.786773 0.0034851739 1 1
1800 232.82457 -8.2208725 0.0034851739 1 1
1850 219.66312 0.0019676295 0.0034851739 1 1
1900 245.49515 -24.208901 0.0034851739 1 1
1950 262.40648 -1.8634047 0.0034851739 1 1
2000 307.5184 10.588572 0.0034851739 1 1
2050 316.54878 8.3925575 0.0034851739 1 1
2100 318.99324 29.042199 0.0034851739 1 1
2150 352.69886 18.443891 0.0034851739 1 1
2200 326.32556 -38.670826 0.0034851739 1 1
2250 333.73083 15.388091 0.0034851739 1 1
2300 258.51644 -42.524581 0.0034851739 1 1
2350 259.55019 -23.484535 0.0034851739 1 1
2400 289.75114 28.367986 0.0034851739 1 1
2450 312.34376 10.345659 0.0034851739 1 1
2500 298.65847 -14.077573 0.0034851739 1 1
2550 237.48617 -55.545493 0.0034851739 1 1
2600 266.79718 -17.165884 0.0034851739 1 1
2650 297.32794 -30.336059 0.0034851739 1 1
2700 258.77594 -1.3622741 0.0034851739 1 1
2750 240.05564 -0.4418629 0.0034851739 1 1
2800 189.88737 -13.20747 0.0034851739 1 1
2850 260.84014 -18.597276 0.0034851739 1 1
2900 299.99473 -7.3249394 0.0034851739 1 1
2950 377.90497 18.041664 0.0034851739 1 1
3000 263.92156 -54.260856 0.0034851739 1 1
3050 273.64003 26.973976 0.0034851739 1 1
3100 276.52232 -3.8583179 0.0034851739 1 1
3150 351.27802 84.899229 0.0034851739 1 1
3200 327.48822 -10.339189 0.0034851739 1 1
3250 356.11987 16.719201 0.0034851739 1 1
3300 263.01966 -18.033913 0.0034851739 1 1
3350 285.41196 -24.466282 0.0034851739 1 1
3400 233.65271 -39.293739 0.0034851739 1 1
3450 276.32895 44.300639 0.0034851739 1 1
3500 300.42687 28.489275 0.0034851739 1 1
3550 254.03142 -24.335427 0.0034851739 1 1
3600 304.6963 4.5827938 0.0034851739 1 1
3650 321.1785 -15.477109 0.0034851739 1 1
3700 256.00258 25.354176 0.0034851739 1 1
3750 356.60667 -5.4004451 0.0034851739 1 1
3800 361.31092 -1.481153 0.0034851739 1 1
3850 253.80196 -1.2120222 0.0034851739 1 1
3900 258.01895 19.280499 0.0034851739 1 1
3950 261.55352 -47.57161 0.0034851739 1 1
4000 254.54757 -8.6460339 0.0034851739 1 1
4050 301.56201 22.484551 0.0034851739 1 1
4100 304.73035 -31.321217 0.0034851739 1 1
4150 307.14343 0.5455717 0.0034851739 1 1
4200 291.05765 51.79974 0.0034851739 1 1
4250 333.73864 -24.668278 0.0034851739 1 1
4300 370.55562 -11.922425 0.0034851739 1 1
4350 408.03441 8.5963114 0.0034851739 1 1
4400 329.13138 -25.679871 0.0034851739 1 1
4450 366.98033 26.287047 0.0034851739 1 1
4500 311.80954 31.766893 0.0034851739 1 1
4550 292.28765 13.064974 0.0034851739 1 1
4600 320.72746 -49.078838 0.0034851739 1 1
4650 271.7173 -3.6846681 0.0034851739 1 1
4700 305.69502 37.947369 0.0034851739 1 1
4750 304.57521 52.411498 0.0034851739 1 1
4800 299.22173 12.555443 0.0034851739 1 1
4850 317.1756 -14.332118 0.0034851739 1 1
4900 330.62798 23.762097 0.0034851739 1 1
4950 342.34292 -21.428049 0.0034851739 1 1
5000 415.76656 10.136854 0.0034851739 1 1
5050 381.90086 18.17029 0.0034851739 1 1
5100 380.63709 28.042746 0.0034851739 1 1
5150 321.578 31.648896 0.0034851739 1 1
5200 301.22258 -29.246031 0.0034851739 1 1
5250 277.39891 -33.660526 0.0034851739 1 1
5300 259.34417 -47.78529 0.0034851739 1 1
5350 254.36079 10.616064 0.0034851739 1 1
5400 242.39213 29.468553 0.0034851739 1 1
5450 273.79403 -21.736668 0.0034851739 1 1
5500 367.30713 -6.0185517 0.0034851739 1 1
5550 309.52317 20.860119 0.0034851739 1 1
5600 316.82746 -10.339826 0.0034851739 1 1
5650 248.8707 33.659016 0.0034851739 1 1
5700 314.30152 19.05817 0.0034851739 1 1
5750 307.09966 14.458312 0.0034851739 1 1
5800 313.07936 15.825371 0.0034851739 1 1
5850 255.76382 23.890796 0.0034851739 1 1
5900 274.57947 -0.19520339 0.0034851739 1 1
5950 286.72486 -0.92397306 0.0034851739 1 1
6000 304.60873 -4.3983652 0.0034851739 1 1
6050 271.84784 -60.940602 0.0034851739 1 1
6100 283.48258 -8.2903551 0.0034851739 1 1
6150 336.07933 -8.2576526 0.0034851739 1 1
6200 363.09919 -17.309847 0.0034851739 1 1
6250 305.63822 14.475989 0.0034851739 1 1
6300 274.59195 49.13711 0.0034851739 1 1
6350 302.91015 -21.034604 0.0034851739 1 1
6400 293.87945 0.74647589 0.0034851739 1 1
6450 320.03843 47.624624 0.0034851739 1 1
6500 329.4551 -52.788127 0.0034851739 1 1
6550 320.74765 7.9598838 0.0034851739 1 1
6600 290.63144 -19.66089 0.0034851739 1 1
6650 266.9576 18.962642 0.0034851739 1 1
6700 274.61389 -9.823603 0.0034851739 1 1
6750 210.31417 -4.5767817 0.0034851739 1 1
6800 258.23732 44.233497 0.0034851739 1 1
6850 269.33119 -41.097429 0.0034851739 1 1
6900 318.88077 -21.601871 0.0034851739 1 1
6950 333.85796 26.067522 0.0034851739 1 1
7000 320.59631 -44.226656 0.0034851739 1 1
7050 348.15593 56.564077 0.0034851739 1 1
7100 291.30894 7.6597589 0.0034851739 1 1
7150 261.87574 -1.926724 0.0034851739 1 1
7200 318.17418 61.577301 0.0034851739 1 1
7250 269.73912 -41.921242 0.0034851739 1 1
7300 235.40776 -7.8606915 0.0034851739 1 1
7350 344.03017 73.910798 0.0034851739 1 1
7400 335.03212 13.288114 0.0034851739 1 1
7450 350.0822 -22.899498 0.0034851739 1 1
7500 360.69025 -78.556242 0.0034851739 1 1
7550 316.85895 -26.533434 0.0034851739 1 1
7600 271.65568 32.425371 0.0034851739 1 1
7650 264.7899 -40.230568 0.0034851739 1 1
7700 281.36612 8.9888402 0.0034851739 1 1
7750 276.96176 1.8256977 0.0034851739 1 1
7800 330.1516 -19.751957 0.0034851739 1 1
7850 325.80791 -12.52799 0.0034851739 1 1
7900 322.07086 35.21732 0.0034851739 1 1
7950 310.09493 -37.779071 0.0034851739 1 1
8000 309.87152 40.561377 0.0034851739 1 1
8050 252.91862 -27.545616 0.0034851739 1 1
8100 308.23471 -25.313089 0.0034851739 1 1
8150 278.69561 19.299388 0.0034851739 1 1
8200 270.81879 33.341696 0.0034851739 1 1
8250 312.58182 19.404863 0.0034851739 1 1
8300 302.20303 19.388391 0.0034851739 1 1
8350 299.55144 -12.952851 0.0034851739 1 1
8400 330.13129 -34.998178 0.0034851739 1 1
8450 281.66968 24.865214 0.0034851739 1 1
8500 262.4416 1.0196786 0.0034851739 1 1
8550 268.47784 44.761905 0.0034851739 1 1
8600 274.80898 8.6257741 0.0034851739 1 1
8650 264.82423 -3.9236534 0.0034851739 1 1
8700 268.88205 3.7102664 0.0034851739 1 1
8750 315.78315 -44.215318 0.0034851739 1 1
8800 280.19362 -4.2172962 0.0034851739 1 1
8850 331.88665 58.274571 0.0034851739 1 1
8900 314.70472 36.746006 0.0034851739 1 1
8950 395.82228 53.308443 0.0034851739 1 1
9000 351.95636 29.133084 0.0034851739 1 1
9050 369.74695 -37.487774 0.0034851739 1 1
9100 259.4453 -2.1826545 0.0034851739 1 1
9150 294.9952 -44.357151 0.0034851739 1 1
9200 273.94092 12.07438 0.0034851739 1 1
9250 257.18809 -29.792606 0.0034851739 1 1
9300 269.54343 -19.617554 0.0034851739 1 1
9350 301.09849 -26.979046 0.0034851739 1 1
9400 316.93675 -46.890327 0.0034851739 1 1
9450 304.52185 -8.8525101 0.0034851739 1 1
9500 371.73494 11.979311 0.0034851739 1 1
9550 291.23417 8.1900851 0.0034851739 1 1
9600 359.20912 38.693544 0.0034851739 1 1
9650 321.73443 33.448943 0.0034851739 1 1
9700 362.4237 36.54429 0.0034851739 1 1
9750 296.19875 -11.425255 0.0034851739 1 1
9800 329.9426 16.039783 0.0034851739 1 1
9850 296.79216 40.176303 0.0034851739 1 1
9900 345.63868 43.479483 0.0034851739 1 1
9950 282.27772 -49.08352 0.0034851739 1 1
10000 286.24393 -12.060687 0.0034851739 1 1
Loop time of 1.29509 on 1 procs for 10000 steps with 44 atoms
Performance: 667.133 ns/day, 0.036 hours/ns, 7721.451 timesteps/s, 339.744 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.065326 | 0.065326 | 0.065326 | 0.0 | 5.04
Bond | 0.23111 | 0.23111 | 0.23111 | 0.0 | 17.84
Kspace | 0.94073 | 0.94073 | 0.94073 | 0.0 | 72.64
Neigh | 0.0032599 | 0.0032599 | 0.0032599 | 0.0 | 0.25
Comm | 0.0013719 | 0.0013719 | 0.0013719 | 0.0 | 0.11
Output | 0.00093869 | 0.00093869 | 0.00093869 | 0.0 | 0.07
Modify | 0.049692 | 0.049692 | 0.049692 | 0.0 | 3.84
Other | | 0.002667 | | | 0.21
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 14 ave 14 max 14 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 869 ave 869 max 869 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 869
Ave neighs/atom = 19.75
Ave special neighs/atom = 6.4090909
Neighbor list builds = 209
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01

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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-583-g5868aa095d-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# 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
special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower
read_data tiny_nylon.data extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atom labelmap ...
reading bond labelmap ...
reading angle labelmap ...
reading dihedral labelmap ...
reading improper labelmap ...
reading atoms ...
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
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
16 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
35 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.006 seconds
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.json
Read molecule template mol1:
(no title)
1 molecules
0 fragments
18 atoms with max type 0
16 bonds with max type 8
25 angles with max type 25
23 dihedrals with max type 33
2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.json
Read molecule template mol2:
(no title)
1 molecules
0 fragments
18 atoms with max type 0
17 bonds with max type 11
31 angles with max type 24
39 dihedrals with max type 30
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.json
Read molecule template mol3:
(no title)
1 molecules
0 fragments
15 atoms with max type 0
14 bonds with max type 11
25 angles with max type 24
30 dihedrals with max type 30
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.json
Read molecule template mol4:
(no title)
1 molecules
0 fragments
15 atoms with max type 0
13 bonds with max type 13
19 angles with max type 26
16 dihedrals with max type 29
2 impropers with max type 5
thermo 50
# dump 1 all xyz 1 test_vis.xyz
# dump_modify 1 types labels
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 rescale_charges yes
WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[*]
# restart 100 restart1 restart2
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
@Article{Gissinger24,
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
journal = {J. Phys. Chem. B},
year = 2024,
volume = 128,
number = 13,
pages = {3282--3297}
}
- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287
@Article{Gissinger17,
author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
journal = {Polymer},
year = 2017,
volume = 128,
pages = {211--217}
}
@Article{Gissinger20,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
journal = {Macromolecules},
year = 2020,
volume = 53,
number = 22,
pages = {9953--9961}
}
@Article{Gissinger24,
author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
title = {Molecular Modeling of Reactive Systems with REACTER},
journal = {Computer Physics Communications},
year = 2024,
volume = 304,
number = 109287
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.23408048
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.018627396
estimated relative force accuracy = 5.6095851e-05
using double precision FFTW3
3d grid and FFT values/proc = 3380 960
Generated 55 of 55 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 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
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) = 33.49 | 33.72 | 34.28 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 357.25588 0.0034851739 0 0
50 328.952 -39.291672 0.0034851739 1 0
100 311.59495 29.741131 0.0034851739 1 1
150 325.04965 -19.624049 0.0034851739 1 1
200 313.15254 15.730975 0.0034851739 1 1
250 307.88805 -22.944869 0.0034851739 1 1
300 287.9343 6.7916738 0.0034851739 1 1
350 314.40601 12.913246 0.0034851739 1 1
400 304.58587 6.9804459 0.0034851739 1 1
450 300.97668 14.68689 0.0034851739 1 1
500 345.19498 -29.961085 0.0034851739 1 1
550 229.37329 12.88087 0.0034851739 1 1
600 239.75504 -3.575567 0.0034851739 1 1
650 257.58951 -5.0844118 0.0034851739 1 1
700 249.84121 22.825491 0.0034851739 1 1
750 287.62022 28.059197 0.0034851739 1 1
800 352.31339 -50.233738 0.0034851739 1 1
850 316.12821 22.493396 0.0034851739 1 1
900 283.85252 26.129698 0.0034851739 1 1
950 290.30591 -25.743121 0.0034851739 1 1
1000 346.57856 -2.1188627 0.0034851739 1 1
1050 251.23391 20.636107 0.0034851739 1 1
1100 267.48303 -15.912571 0.0034851739 1 1
1150 282.66256 14.019753 0.0034851739 1 1
1200 227.56518 -27.076623 0.0034851739 1 1
1250 232.7204 -1.0387593 0.0034851739 1 1
1300 277.28783 32.449571 0.0034851739 1 1
1350 308.5732 -11.129035 0.0034851739 1 1
1400 264.96641 -20.93416 0.0034851739 1 1
1450 262.83931 30.82366 0.0034851739 1 1
1500 276.23182 -24.480049 0.0034851739 1 1
1550 319.00599 -9.8372065 0.0034851739 1 1
1600 316.48228 -15.940319 0.0034851739 1 1
1650 277.213 1.3856424 0.0034851739 1 1
1700 302.34736 -27.623644 0.0034851739 1 1
1750 312.06738 -52.786773 0.0034851739 1 1
1800 232.82457 -8.2208725 0.0034851739 1 1
1850 219.66312 0.0019675712 0.0034851739 1 1
1900 245.49515 -24.2089 0.0034851739 1 1
1950 262.40648 -1.8634053 0.0034851739 1 1
2000 307.5184 10.588572 0.0034851739 1 1
2050 316.54878 8.3925573 0.0034851739 1 1
2100 318.99324 29.042199 0.0034851739 1 1
2150 352.69886 18.443891 0.0034851739 1 1
2200 326.32556 -38.670827 0.0034851739 1 1
2250 333.73083 15.388091 0.0034851739 1 1
2300 258.51644 -42.524579 0.0034851739 1 1
2350 259.55019 -23.484534 0.0034851739 1 1
2400 289.75114 28.367991 0.0034851739 1 1
2450 312.34376 10.34566 0.0034851739 1 1
2500 298.65847 -14.077574 0.0034851739 1 1
2550 237.48617 -55.545492 0.0034851739 1 1
2600 266.79719 -17.165888 0.0034851739 1 1
2650 297.32793 -30.336065 0.0034851739 1 1
2700 258.77594 -1.3622773 0.0034851739 1 1
2750 240.05564 -0.44186476 0.0034851739 1 1
2800 189.88736 -13.20747 0.0034851739 1 1
2850 260.84014 -18.597268 0.0034851739 1 1
2900 299.99469 -7.3249657 0.0034851739 1 1
2950 377.90515 18.041562 0.0034851739 1 1
3000 263.92164 -54.260872 0.0034851739 1 1
3050 273.63965 26.974167 0.0034851739 1 1
3100 276.52188 -3.8587984 0.0034851739 1 1
3150 351.27821 84.898762 0.0034851739 1 1
3200 327.48898 -10.338223 0.0034851739 1 1
3250 356.1212 16.719521 0.0034851739 1 1
3300 263.02135 -18.034405 0.0034851739 1 1
3350 285.4132 -24.466598 0.0034851739 1 1
3400 233.65385 -39.293822 0.0034851739 1 1
3450 276.32817 44.300742 0.0034851739 1 1
3500 300.43096 28.490491 0.0034851739 1 1
3550 254.03694 -24.336803 0.0034851739 1 1
3600 304.68561 4.5774591 0.0034851739 1 1
3650 321.19694 -15.472971 0.0034851739 1 1
3700 256.01801 25.355422 0.0034851739 1 1
3750 356.6048 -5.4033701 0.0034851739 1 1
3800 361.31685 -1.4920086 0.0034851739 1 1
3850 253.81335 -1.20491 0.0034851739 1 1
3900 257.99176 19.272863 0.0034851739 1 1
3950 261.56599 -47.578625 0.0034851739 1 1
4000 254.55501 -8.6462427 0.0034851739 1 1
4050 301.57465 22.466646 0.0034851739 1 1
4100 304.71812 -31.337506 0.0034851739 1 1
4150 307.05688 0.54710967 0.0034851739 1 1
4200 291.11678 51.789059 0.0034851739 1 1
4250 333.71702 -24.64525 0.0034851739 1 1
4300 370.53725 -11.852814 0.0034851739 1 1
4350 407.98596 8.5128018 0.0034851739 1 1
4400 329.43106 -25.637208 0.0034851739 1 1
4450 366.91557 26.250029 0.0034851739 1 1
4500 311.63134 31.61568 0.0034851739 1 1
4550 292.18008 13.020734 0.0034851739 1 1
4600 320.76549 -49.324846 0.0034851739 1 1
4650 271.72115 -3.6666938 0.0034851739 1 1
4700 305.52974 38.114013 0.0034851739 1 1
4750 304.37057 52.050863 0.0034851739 1 1
4800 300.50548 13.158616 0.0034851739 1 1
4850 317.66606 -14.951608 0.0034851739 1 1
4900 331.39591 23.823575 0.0034851739 1 1
4950 340.899 -19.557136 0.0034851739 1 1
5000 414.45112 8.7124515 0.0034851739 1 1
5050 382.95479 18.555744 0.0034851739 1 1
5100 381.26344 22.674486 0.0034851739 1 1
5150 309.88477 36.184971 0.0034851739 1 1
5200 312.4976 -31.403643 0.0034851739 1 1
5250 285.1896 -36.180241 0.0034851739 1 1
5300 249.68604 -55.078779 0.0034851739 1 1
5350 251.76542 12.156887 0.0034851739 1 1
5400 278.40908 15.846527 0.0034851739 1 1
5450 281.22116 -12.005198 0.0034851739 1 1
5500 362.38064 -14.608206 0.0034851739 1 1
5550 287.39255 38.446058 0.0034851739 1 1
5600 264.87699 -20.21112 0.0034851739 1 1
5650 300.31424 -15.899086 0.0034851739 1 1
5700 318.6444 18.688317 0.0034851739 1 1
5750 321.74224 -7.5355749 0.0034851739 1 1
5800 314.65871 33.512178 0.0034851739 1 1
5850 307.11597 -16.492491 0.0034851739 1 1
5900 259.10441 -49.668159 0.0034851739 1 1
5950 292.09045 -22.04962 0.0034851739 1 1
6000 243.99229 -15.110485 0.0034851739 1 1
6050 276.66494 -21.052012 0.0034851739 1 1
6100 328.39444 64.522811 0.0034851739 1 1
6150 289.49991 -18.518616 0.0034851739 1 1
6200 358.50076 -9.3115021 0.0034851739 1 1
6250 303.15143 -42.618735 0.0034851739 1 1
6300 297.17364 18.116143 0.0034851739 1 1
6350 254.2382 2.4963759 0.0034851739 1 1
6400 227.56255 23.535315 0.0034851739 1 1
6450 280.70805 13.243012 0.0034851739 1 1
6500 251.14485 -18.466759 0.0034851739 1 1
6550 284.32321 9.0351234 0.0034851739 1 1
6600 284.03779 -10.683306 0.0034851739 1 1
6650 315.1569 -39.736019 0.0034851739 1 1
6700 302.50424 5.9013011 0.0034851739 1 1
6750 368.279 44.343503 0.0034851739 1 1
6800 279.67266 -35.967233 0.0034851739 1 1
6850 298.98045 3.0539699 0.0034851739 1 1
6900 236.94852 0.55971293 0.0034851739 1 1
6950 303.38382 -9.1880246 0.0034851739 1 1
7000 264.56096 3.904024 0.0034851739 1 1
7050 272.26968 -44.608801 0.0034851739 1 1
7100 235.38132 13.141913 0.0034851739 1 1
7150 272.0985 26.601686 0.0034851739 1 1
7200 314.41177 -7.6236617 0.0034851739 1 1
7250 313.29915 -45.214663 0.0034851739 1 1
7300 309.20548 -11.691744 0.0034851739 1 1
7350 342.22769 18.805899 0.0034851739 1 1
7400 301.02701 32.830071 0.0034851739 1 1
7450 318.19524 48.620851 0.0034851739 1 1
7500 290.00663 -9.1444424 0.0034851739 1 1
7550 238.07666 32.654941 0.0034851739 1 1
7600 275.95317 -23.982336 0.0034851739 1 1
7650 274.54472 -29.183684 0.0034851739 1 1
7700 307.25317 11.981268 0.0034851739 1 1
7750 299.40271 -19.390542 0.0034851739 1 1
7800 314.18813 -6.0794802 0.0034851739 1 1
7850 271.14043 40.491364 0.0034851739 1 1
7900 266.43792 37.250574 0.0034851739 1 1
7950 330.21996 31.783381 0.0034851739 1 1
8000 313.80294 44.878972 0.0034851739 1 1
8050 331.1094 1.9597746 0.0034851739 1 1
8100 267.80448 26.159121 0.0034851739 1 1
8150 267.17305 16.135234 0.0034851739 1 1
8200 290.248 -13.058622 0.0034851739 1 1
8250 231.77635 -42.850795 0.0034851739 1 1
8300 233.58288 29.137765 0.0034851739 1 1
8350 270.2913 -11.177011 0.0034851739 1 1
8400 254.69873 3.1775639 0.0034851739 1 1
8450 334.88277 -27.336924 0.0034851739 1 1
8500 354.95137 -9.751911 0.0034851739 1 1
8550 327.78998 8.2348621 0.0034851739 1 1
8600 306.15772 1.3756734 0.0034851739 1 1
8650 325.68699 6.5939205 0.0034851739 1 1
8700 302.84804 13.912169 0.0034851739 1 1
8750 299.34988 10.311212 0.0034851739 1 1
8800 258.77684 -8.0783535 0.0034851739 1 1
8850 299.8835 -9.61362 0.0034851739 1 1
8900 350.28205 -34.897861 0.0034851739 1 1
8950 316.90133 -52.845562 0.0034851739 1 1
9000 337.50548 18.172556 0.0034851739 1 1
9050 306.67254 37.062973 0.0034851739 1 1
9100 310.74844 58.178538 0.0034851739 1 1
9150 301.53463 5.9650738 0.0034851739 1 1
9200 284.61384 10.677528 0.0034851739 1 1
9250 247.86475 -15.325203 0.0034851739 1 1
9300 309.74481 -60.070902 0.0034851739 1 1
9350 290.17111 5.6049467 0.0034851739 1 1
9400 268.79925 -9.2423032 0.0034851739 1 1
9450 315.80445 18.124612 0.0034851739 1 1
9500 351.58161 -14.465115 0.0034851739 1 1
9550 344.93028 43.161438 0.0034851739 1 1
9600 265.92273 0.3396608 0.0034851739 1 1
9650 261.1649 -20.46043 0.0034851739 1 1
9700 262.05627 27.187613 0.0034851739 1 1
9750 249.12463 15.911339 0.0034851739 1 1
9800 262.40626 -16.159153 0.0034851739 1 1
9850 267.48677 0.32143902 0.0034851739 1 1
9900 316.15674 40.664589 0.0034851739 1 1
9950 323.94181 20.356291 0.0034851739 1 1
10000 307.90841 4.8392456 0.0034851739 1 1
Loop time of 0.937214 on 4 procs for 10000 steps with 44 atoms
Performance: 921.881 ns/day, 0.026 hours/ns, 10669.916 timesteps/s, 469.476 katom-step/s
96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00042896 | 0.01827 | 0.04944 | 14.9 | 1.95
Bond | 0.00067626 | 0.061292 | 0.18867 | 31.0 | 6.54
Kspace | 0.50738 | 0.64527 | 0.7136 | 10.4 | 68.85
Neigh | 0.0031476 | 0.0031815 | 0.0032165 | 0.0 | 0.34
Comm | 0.01335 | 0.020817 | 0.035424 | 6.1 | 2.22
Output | 0.0010449 | 0.0012202 | 0.0016969 | 0.8 | 0.13
Modify | 0.16314 | 0.18266 | 0.20201 | 4.3 | 19.49
Other | | 0.004499 | | | 0.48
Nlocal: 11 ave 40 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 22 ave 40 max 4 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 216.5 ave 845 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 866
Ave neighs/atom = 19.681818
Ave special neighs/atom = 6.4090909
Neighbor list builds = 212
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:00

35
examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_map Normal file
View File

@ -0,0 +1,35 @@
this is a nominal superimpose file
2 edgeIDs
18 equivalences
InitiatorIDs
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

177
examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_reacted.json Normal file
View File

@ -0,0 +1,177 @@
{
"application": "LAMMPS",
"format": "molecule",
"revision": 1,
"schema": "https://download.lammps.org/json/molecule-schema.json",
"coords": {
"format": ["atom-id", "x", "y", "z"],
"data": [
[1, -5.522237178, -0.752722499, 1.631158408],
[2, -5.170398325, -0.545733378, 0.178129978],
[3, -6.469694974, -0.553071841, -0.648889109],
[4, -6.052075697, -1.721152483, 1.744647858],
[5, -6.183058842, 0.071386755, 1.971497329],
[6, -4.489339595, -1.389196844, -0.173156276],
[7, -4.637590712, 0.453703382, 0.051251954],
[8, -5.618657658, 0.13891881, 4.386106928],
[9, -4.669491736, -0.989818781, 3.943591338],
[10, -4.270193542, -0.766405234, 2.474102239],
[11, -3.348470373, -1.875393291, 2.024289246],
[12, -3.569793683, 0.564183226, 2.345995471],
[13, -5.201078949, -1.993301389, 4.044218837],
[14, -3.736681607, -0.984819193, 4.598304847],
[15, -4.255401979, 1.370923174, 2.679069013],
[16, -6.136393628, -0.339866195, -2.13677499],
[17, -6.996331494, -1.555519161, -0.517408063],
[18, -7.153308038, 0.284949373, -0.289930394]
]
},
"types": {
"format": ["atom-id", "type"],
"data": [
[1, "n"],
[2, "c2"],
[3, "c2"],
[4, "hn"],
[5, "hn"],
[6, "hc"],
[7, "hc"],
[8, "c2"],
[9, "c2"],
[10, "c_1"],
[11, "o_1"],
[12, "o"],
[13, "hc"],
[14, "hc"],
[15, "ho"],
[16, "c2"],
[17, "hc"],
[18, "hc"]
]
},
"molecules": {
"format": ["atom-id", "molecule-id"],
"data": [
[1, 1],
[2, 1],
[3, 1],
[4, 1],
[5, 1],
[6, 1],
[7, 1],
[8, 1],
[9, 1],
[10, 1],
[11, 1],
[12, 1],
[13, 1],
[14, 1],
[15, 1],
[16, 1],
[17, 1],
[18, 1]
]
},
"bonds": {
"format": ["bond-type", "atom1", "atom2"],
"data": [
["n-c2", 1, 2],
["n-hn", 1, 4],
["n-hn", 1, 5],
["n-c_1", 1, 10],
["c2-c2", 2, 3],
["c2-hc", 2, 6],
["c2-hc", 2, 7],
["c2-c2", 3, 16],
["c2-hc", 3, 17],
[ "c2-hc", 3, 18],
[ "c2-c2", 8, 9],
[ "c2-c_1", 9, 10],
[ "c2-hc", 9, 13],
[ "c2-hc", 9, 14],
[ "c_1-o_1", 10, 11],
[ "c_1-o", 10, 12],
[ "o-ho", 12, 15]
]
},
"angles": {
"format": ["angle-type", "atom1", "atom2", "atom3"],
"data": [
["c2-n-hn", 2, 1, 4],
["c2-n-hn", 2, 1, 5],
["c2-n-c_1", 2, 1, 10],
["hn-n-hn", 4, 1, 5],
["hn-n-c_1", 4, 1, 10],
["hn-n-c_1", 5, 1, 10],
["n-c2-c2", 1, 2, 3],
["n-c2-hc", 1, 2, 6],
["n-c2-hc", 1, 2, 7],
[ "c2-c2-hc", 3, 2, 6],
[ "c2-c2-hc", 3, 2, 7],
[ "hc-c2-hc", 6, 2, 7],
[ "c2-c2-c2", 2, 3, 16],
[ "c2-c2-hc", 2, 3, 17],
[ "c2-c2-hc", 2, 3, 18],
[ "c2-c2-hc", 16, 3, 17],
[ "c2-c2-hc", 16, 3, 18],
[ "hc-c2-hc", 17, 3, 18],
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}

184
examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_unreacted.json Normal file
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@ -0,0 +1,184 @@
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32
examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_map Normal file
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@ -0,0 +1,32 @@
this is a nominal superimpose file
2 edgeIDs
15 equivalences
InitiatorIDs
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

156
examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_reacted.json Normal file
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@ -0,0 +1,156 @@
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170
examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_unreacted.json Normal file
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@ -0,0 +1,170 @@
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["hc-c2-c_1-o", 13, 9, 10, 12],
["hc-c2-c_1-n", 13, 9, 10, 1],
["hc-c2-c_1-o_1", 14, 9, 10, 11],
["hc-c2-c_1-o", 14, 9, 10, 12],
["hc-c2-c_1-n", 14, 9, 10, 1],
["c2-c_1-o-ho", 9, 10, 12, 15],
["o_1-c_1-o-ho", 11, 10, 12, 15],
["n-c_1-o-ho", 1, 10, 12, 15]
]
},
"charges": {
"format": ["atom-id", "charge"],
"data": [
[1, -0.3],
[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, 0.3],
[11, 0.0],
[12, 0.0],
[13, 0.0],
[14, 0.0],
[15, 0.0]
]
}
}

820
examples/PACKAGES/reaction/tiny_nylon_json/tiny_nylon.data Normal file
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@ -0,0 +1,820 @@
LAMMPS data file via write_data, version 27 Jun 2024, timestep = 0, units = real
44 atoms
11 atom types
42 bonds
13 bond types
74 angles
26 angle types
100 dihedrals
33 dihedral types
16 impropers
5 improper types
-25 25 xlo xhi
-25 25 ylo yhi
-25 25 zlo zhi
Atom Type Labels
1 c2
2 c_1
3 o
4 hc
5 ho
6 o_1
7 na
8 hn
9 n
10 hw
11 o*
Bond Type Labels
1 c2-hc
2 c2-c2
3 c_1-o
4 c2-c_1
5 c_1-o_1
6 o-ho
7 na-c2
8 na-hn
9 n-c2
10 n-hn
11 n-c_1
12 c2-na
13 hw-o*
Angle Type Labels
1 hc-c2-hc
2 c2-c2-hc
3 c2-c2-c2
4 c2-c_1-o_1
5 o-c_1-o_1
6 c2-c_1-o
7 c_1-o-ho
8 c2-c2-c_1
9 c_1-c2-hc
10 c2-c2-na
11 na-c2-hc
12 c2-na-hn
13 hn-na-hn
14 c2-n-hn
15 c2-n-c_1
16 hn-n-hn
17 hn-n-c_1
18 n-c2-c2
19 n-c2-hc
20 hc-c2-c_1
21 n-c_1-c2
22 o_1-c_1-o
23 n-c_1-o_1
24 n-c_1-o
25 na-c2-c2
26 hw-o*-hw
Dihedral Type Labels
1 c_1-c2-c2-hc
2 hc-c2-c2-hc
3 c2-c2-c2-c_1
4 c2-c2-c2-hc
5 c2-c2-c2-c2
6 c2-c_1-o-ho
7 o_1-c_1-o-ho
8 c2-c2-c_1-o
9 hc-c2-c_1-o
10 c2-c2-c_1-o_1
11 hc-c2-c_1-o_1
12 na-c2-c2-hc
13 c2-c2-c2-na
14 c2-c2-na-hn
15 hn-na-c2-hc
16 hn-n-c2-c2
17 hn-n-c2-hc
18 c_1-n-c2-c2
19 c_1-n-c2-hc
20 c2-n-c_1-c2
21 c2-n-c_1-o_1
22 c2-n-c_1-o
23 hn-n-c_1-c2
24 hn-n-c_1-o_1
25 hn-n-c_1-o
26 n-c2-c2-c2
27 n-c2-c2-hc
28 c2-c2-c_1-n
29 hc-c2-c_1-n
30 n-c_1-o-ho
31 hn-na-c2-c2
32 hc-c2-na-hn
33 na-c2-c2-c2
Improper Type Labels
1 c2-c_1-o-o_1
2 c2-na-hn-hn
3 c2-c_1-o_1-o
4 c2-n-hn-c_1
5 n-c_1-c2-o_1
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/long
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 1.457 365.805 -699.637 998.484
8 1.006 466.74 -1073.6 1251.11
9 1.452 327.166 -547.899 526.5
10 1.01 462.75 -1053.63 1545.76
11 1.416 359.159 -558.473 1146.38
12 1.457 365.805 -699.637 998.484
13 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
10 111.91 60.7147 -13.3366 -13.0785
11 110.62 51.3137 -6.7198 -2.6003
12 110.954 50.8652 -4.4522 -10.0298
13 107.067 45.252 -7.5558 -9.512
14 113.868 45.9271 -20.0824 0
15 111.037 31.8958 -6.6942 -6.837
16 116.94 37.5749 -8.6676 0
17 117.961 37.4964 -8.1837 0
18 114.302 42.6589 -10.5464 -9.3243
19 108.937 57.401 2.9374 0
20 107.734 40.6099 -28.8121 0
21 116.926 39.4193 -10.9945 -8.7733
22 118.986 98.6813 -22.2485 10.3673
23 125.542 92.572 -34.48 -11.1871
24 125.542 92.572 -34.48 -11.1871
25 111.91 60.7147 -13.3366 -13.0785
26 103.7 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 4.6217 1.53 1.457
11 12.426 1.457 1.101
12 -6.4168 1.457 1.006
13 -1.8749 1.006 1.006
14 -3.471 1.452 1.01
15 12.1186 1.452 1.416
16 -0.5655 1.01 1.01
17 -4.3126 1.01 1.416
18 3.5446 1.452 1.53
19 15.2994 1.452 1.101
20 0.7115 1.101 1.5202
21 0 1.416 1.5202
22 0 1.202 1.3649
23 138.495 1.416 1.202
24 0 1.416 1.3649
25 4.6217 1.457 1.53
26 -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 6.0876 16.5702 1.53 1.457
11 42.4332 13.4582 1.457 1.101
12 31.8096 20.5799 1.457 1.006
13 28.0322 28.0322 1.006 1.006
14 11.8828 5.9339 1.452 1.01
15 3.7812 14.8633 1.452 1.416
16 19.8125 19.8125 1.01 1.01
17 10.8422 29.5743 1.01 1.416
18 4.6031 -5.479 1.452 1.53
19 34.8907 10.6917 1.452 1.101
20 9.1765 12.4632 1.101 1.5202
21 0 0 1.416 1.5202
22 0 0 1.202 1.3649
23 62.7124 52.4045 1.416 1.202
24 0 0 1.416 1.3649
25 16.5702 6.0876 1.457 1.53
26 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 0.1764 0 0.1766 0 -0.5206 0
14 -1.1506 0 -0.6344 0 -0.1845 0
15 -0.5187 0 -0.4837 0 -0.1692 0
16 -0.0483 0 -0.0077 0 -0.0014 0
17 -0.0148 0 -0.0791 0 -0.0148 0
18 0.0143 0 -0.0132 0 0.0091 0
19 0.0219 0 -0.026 0 0.0714 0
20 -0.7532 0 2.7392 0 0.0907 0
21 0.8297 0 3.7234 0 -0.0495 0
22 0 0 0 0 0 0
23 0 0 0 0 0 0
24 -1.6938 0 2.7386 0 -0.336 0
25 0 0 0 0 0 0
26 0.0972 0 0.0722 0 -0.2581 0
27 -0.0228 0 0.028 0 -0.1863 0
28 0.1693 0 -0.009 0 -0.0687 0
29 0.1693 0 -0.009 0 -0.0687 0
30 0 0 0 0 0 0
31 -1.1506 0 -0.6344 0 -0.1845 0
32 -0.5187 0 -0.4837 0 -0.1692 0
33 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 -27.3953 112.67 111.91
14 -7.5499 111.91 110.954
15 -10.4258 110.62 110.954
16 -4.6337 113.868 114.302
17 -6.659 113.868 108.937
18 -7.4314 111.037 114.302
19 -8.1335 111.037 108.937
20 -6.5335 111.037 116.926
21 -15.5547 111.037 125.542
22 0 111.037 0
23 -1.3234 117.961 116.926
24 -7.3186 117.961 125.542
25 0 117.961 0
26 -1.0631 114.302 112.67
27 -12.7974 114.302 110.77
28 -5.4514 108.53 116.926
29 -12.2417 107.734 116.926
30 0 0 111.254
31 -7.5499 110.954 111.91
32 -10.4258 110.954 110.62
33 -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 0.1032 0.5896 -0.4836 0.0579 -0.0043 -0.1906 1.53 1.457
14 -0.9466 0.9356 -0.5542 0.057 0.0625 0.4112 1.53 1.006
15 -1.1685 0.9266 -0.0993 0.085 0.3061 0.2104 1.101 1.006
16 -0.0992 -0.0727 -0.4139 0.132 0.0015 0.1324 1.01 1.53
17 -0.4894 0.1644 0.3105 -0.8983 0.2826 0.0881 1.01 1.101
18 -0.1245 -0.9369 0.7781 -0.2033 0.0035 0.056 1.416 1.53
19 0.2292 1.1732 -0.058 -0.3667 0.8197 0.1335 1.416 1.101
20 0.2299 -0.1141 -0.1424 0.0933 -0.4631 0.2883 1.452 1.5202
21 0.1598 0.7253 -0.1007 0.1226 -2.1326 0.5581 1.452 1.202
22 0 0 0 0 0 0 1.452 1.3649
23 0.6413 0.1676 0.144 -0.6979 0.5619 0.4212 1.01 1.5202
24 0.1214 0.1936 0.0816 -0.7604 -2.6431 1.2467 1.01 1.202
25 0 0 0 0 0 0 1.01 1.3649
26 -0.0797 -0.0406 0.0255 0.0742 0.0105 0.0518 1.452 1.53
27 0.3022 0.2513 0.4641 -0.0601 -0.3763 -0.1876 1.452 1.101
28 -0.2631 -0.0076 -0.1145 -0.2751 -0.3058 -0.1767 1.53 1.416
29 -0.0268 0.7836 0.0035 0.3552 -0.2685 0.5834 1.101 1.416
30 0 0 0 0 0 0 1.416 0.965
31 0.057 0.0625 0.4112 -0.9466 0.9356 -0.5542 1.006 1.53
32 0.085 0.3061 0.2104 -1.1685 0.9266 -0.0993 1.006 1.101
33 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 -15.4174 -7.3055 -1.0749 1.53
14 -2.2208 0.5479 -0.3527 1.457
15 -3.4611 1.6996 -0.6007 1.457
16 -3.5406 -3.3866 0.0352 1.452
17 -1.1752 2.8058 0.8083 1.452
18 -3.9501 -0.4002 -0.6798 1.452
19 -0.6899 -2.2646 1.1579 1.452
20 0 0 0 1.416
21 -8.8301 14.3079 -1.7716 1.416
22 0 0 0 1.416
23 0 0 0 1.416
24 -0.9084 6.1447 -0.4852 1.416
25 0 0 0 1.416
26 -4.2324 -3.3023 -1.3244 1.53
27 -4.1028 -0.5941 -0.047 1.53
28 0 0 0 1.5202
29 0 0 0 1.5202
30 0 0 0 1.3649
31 -2.2208 0.5479 -0.3527 1.457
32 -3.4611 1.6996 -0.6007 1.457
33 -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 1.53 1.457
14 0 1.53 1.006
15 0 1.101 1.006
16 0 1.01 1.53
17 0 1.01 1.101
18 0 1.416 1.53
19 0 1.416 1.101
20 0 1.452 1.5202
21 0 1.452 1.202
22 0 1.452 1.3649
23 0 1.01 1.5202
24 0 1.01 1.202
25 0 1.01 1.3649
26 0 1.452 1.53
27 0 1.452 1.101
28 0 1.53 1.416
29 0 1.101 1.416
30 0 1.416 0.965
31 0 1.006 1.53
32 0 1.006 1.101
33 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 -1.9225 -1.345 0.221 2.0125 0.944 -2.7612 112.67 111.91
14 -3.343 4.4558 -0.0346 0.2873 -0.8072 -0.096 111.91 110.954
15 -3.9582 2.0063 0.3213 -0.4294 -0.4442 -0.6141 110.62 110.954
16 -0.5807 0.2041 -0.1384 -2.8967 2.7084 -0.0375 113.868 114.302
17 -0.3868 0.2041 0.0445 -3.7022 1.3876 0.2393 113.868 108.937
18 -1.523 1.1296 0.7167 -0.7555 0.0564 1.2177 111.037 114.302
19 0.0372 -0.3418 -0.0775 -1.5157 2.0781 0.5364 111.037 108.937
20 5.916 1.7856 0.4052 4.2133 2.9302 3.2903 111.037 116.926
21 7.4427 2.1505 -0.2206 4.4466 4.0317 1.7129 111.037 125.542
22 0 0 0 0 0 0 111.037 0
23 1.9306 0.2105 0.0557 -2.2134 1.2909 0.9726 117.961 116.926
24 2.3848 0.703 0.1399 -2.6238 0.3606 0.5474 117.961 125.542
25 0 0 0 0 0 0 117.961 0
26 0.2039 0.1602 -0.7946 -0.5501 -1.6982 0.2485 114.302 112.67
27 -1.982 0.2325 -0.3928 -1.2469 1.6933 -1.2081 114.302 110.77
28 2.1802 -0.0335 -1.3816 2.1221 0.5032 -0.0767 108.53 116.926
29 7.095 0.0075 0.691 2.0013 0.5068 0.8406 107.734 116.926
30 0 0 0 0 0 0 0 111.254
31 0.2873 -0.8072 -0.096 -3.343 4.4558 -0.0346 110.954 111.91
32 -0.4294 -0.4442 -0.6141 -3.9582 2.0063 0.3213 110.954 110.62
33 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 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 0 0 0 116.926 123.145 125.542
Atoms # full
1 1 c2 -0.37128 12.288168 0.738732 4.37428
2 1 c_1 0.77363 13.959928 -0.883144 5.090597
3 1 o -0.68333 14.411288 -1.994419 5.68216
4 1 hc 0.20049 12.881083 0.872503 3.506176
5 1 hc 0.19609 11.232775 0.801641 3.998777
6 1 ho 0.48328 13.704366 -2.470396 6.130105
7 1 c2 -0.46692 12.489752 -0.793693 4.710639
8 1 c2 -0.38182 12.455071 1.866388 5.38587
9 1 c2 -0.47583 11.248961 1.901849 6.347664
10 1 c_1 0.78608 10.005971 2.46671 5.77284
11 1 o_1 -0.56991 14.79536 -0.034436 4.807367
12 1 o_1 -0.58244 9.115239 1.654547 5.617002
13 1 o -0.68598 9.745096 3.807654 5.573585
14 1 hc 0.20664 12.248215 -1.371492 3.808598
15 1 hc 0.21572 11.715755 -1.036825 5.500449
16 1 hc 0.18182 12.559724 2.807687 4.858452
17 1 hc 0.21541 13.299968 1.61657 6.123781
18 1 hc 0.20587 11.650505 2.330454 7.28241
19 1 hc 0.22795 10.88842 0.913219 6.637162
20 1 ho 0.48600 10.550073 4.294209 5.758192
21 2 c2 -0.38667 5.851425 1.929552 6.038335
22 2 c2 -0.17544 6.741509 3.160751 6.233074
23 2 na -0.79903 7.957761 3.12178 5.252257
24 2 na -0.79111 2.599653 -2.25894 5.985863
25 2 c2 -0.17576 3.834337 -1.907078 5.441528
26 2 c2 -0.38091 4.810793 -1.083699 6.310184
27 2 hc 0.19062 6.505912 1.182799 5.449104
28 2 hc 0.18951 5.156429 2.256468 5.348423
29 2 hc 0.17321 7.232782 3.178785 7.181911
30 2 hc 0.16772 6.251671 4.103621 6.222913
31 2 hn 0.33245 8.249909 4.070668 4.881297
32 2 hn 0.34480 7.813025 2.623184 4.400744
33 2 hn 0.33793 2.626695 -2.857547 6.817247
34 2 hn 0.33306 1.955281 -2.684319 5.32846
35 2 hc 0.17708 3.637708 -1.322842 4.469265
36 2 hc 0.15806 4.41557 -2.739689 4.997336
37 2 hc 0.18117 5.710714 -1.010014 5.642798
38 2 hc 0.18224 5.103831 -1.696423 7.160345
39 2 c2 -0.38394 5.270763 1.286629 7.308822
40 2 hc 0.17720 4.834381 2.168531 7.931687
41 2 hc 0.18425 6.118354 0.786724 7.794709
42 2 c2 -0.37058 4.273849 0.167695 6.957862
43 2 hc 0.18777 3.792544 -0.081782 7.904418
44 2 hc 0.18490 3.527495 0.674238 6.348869
Velocities
1 -0.002462698962621882 -0.0015920230003311222 -0.003062192778611524
2 0.009508241670438584 -0.006990316616750725 0.013702671335945608
3 0.0023431518493187576 -0.0029261683108242173 0.0014269399726982105
4 -0.018184451408256214 0.03110380369168796 -0.013358827768357973
5 0.026084132471017967 -0.010819576493517332 0.03040338445479488
6 -0.004731211595821874 -0.01911146239947834 -0.03679335415649756
7 -0.007506879759594987 0.006566142205596249 0.0013226575122695422
8 0.003380788138016128 0.003045873266355709 0.0022368826795446284
9 -0.0031113905793879316 0.008290886772075477 -0.001756123803949653
10 0.0024685206571693056 0.001319477620984103 -0.002804187703280044
11 -0.0034945605770565296 0.0032323777135621814 0.0016223017668450866
12 -0.006115348361284778 -0.0051534857074262185 0.0017735747357354274
13 0.0002138429678185901 -0.004539890294272967 0.006164976989441376
14 0.00250046198643734 -0.0015709184283264888 0.020837548254667757
15 0.006054793920564353 -0.012650704436910937 -0.005443075326696219
16 -0.010374605775698001 0.009140865846388924 -0.011306875858287088
17 -0.01273649912898741 -0.00917268118525065 0.005113650268546125
18 0.007674177860704811 0.01862985663545928 -0.011300096447670932
19 -0.01861613877528112 0.0010848388547730185 -0.005711843368779858
20 0.005413757224147906 -0.014564578166395727 -0.01261842044190954
21 0.005847352145231226 -0.004059528600033209 -0.0062517801580146415
22 0.0036402033824753104 -0.0014629540504663154 -0.004003071231889805
23 0.009026630501910769 -0.0027511425384659687 0.004557640256543714
24 -0.013102302415548614 -0.004728670396530579 -0.0018966887841189517
25 0.007862168262110317 -0.004204631354094957 0.000968879573747513
26 -0.004738017643833797 0.009609044194077583 -0.008759243138703934
27 0.005431165881163252 0.02003222466349599 -0.00949520764898085
28 -0.0029056381493904374 0.0033317109723156875 0.016650350064426677
29 -0.006456994403348912 0.002842398354195954 -0.026066912906505167
30 -0.022173867823429387 0.014628839880961319 -0.02333083396140238
31 0.009192571338198311 -0.0025697556639281928 -0.012822203161488303
32 -0.00832069750519279 -0.0022538429924858707 0.007762024411858031
33 0.019920685674825727 0.00503177648484941 -0.021106672824976403
34 0.014118463330250982 0.017455545466840316 -0.012482101375598437
35 -0.006111650564043797 0.013353021777303568 -0.025492434283827668
36 0.009100152156585965 0.00557377745052224 0.014573768978939985
37 0.0016523593470528035 -0.022107518020000917 0.020311423445130115
38 -0.01034627539347186 0.01605585658635179 0.005548912701926242
39 -0.0032054811383248638 0.0016779208962376315 0.002939050953753566
40 0.019649219364916443 0.004081577652322286 -0.009842244116604127
41 0.0005696169758816036 0.0007136113223474148 0.004633576422025626
42 0.0022221300208006252 0.0036217319632558197 -0.006329939850345515
43 0.002571017273484117 0.008002917981448292 0.01999298692846819
44 -0.006082758182267466 -0.011834273655641976 0.020526923045885208
Bonds
1 c2-hc 1 5
2 c2-hc 1 4
3 c2-c2 1 7
4 c2-c2 1 8
5 c_1-o 2 3
6 c_1-o_1 2 11
7 o-ho 3 6
8 c2-c_1 7 2
9 c2-hc 7 14
10 c2-hc 7 15
11 c2-c2 8 9
12 c2-hc 8 16
13 c2-hc 8 17
14 c2-c_1 9 10
15 c2-hc 9 18
16 c2-hc 9 19
17 c_1-o_1 10 12
18 c_1-o 10 13
19 o-ho 13 20
20 c2-c2 21 22
21 c2-hc 21 27
22 c2-hc 21 28
23 c2-c2 21 39
24 na-c2 22 23
25 c2-hc 22 29
26 c2-hc 22 30
27 na-hn 23 31
28 na-hn 23 32
29 na-hn 24 33
30 na-hn 24 34
31 na-c2 25 24
32 c2-c2 25 26
33 c2-hc 25 35
34 c2-hc 25 36
35 c2-hc 26 37
36 c2-hc 26 38
37 c2-c2 26 42
38 c2-hc 39 40
39 c2-hc 39 41
40 c2-c2 39 42
41 c2-hc 42 43
42 c2-hc 42 44
Angles
1 hc-c2-hc 5 1 4
2 c2-c2-hc 7 1 5
3 c2-c2-hc 8 1 5
4 c2-c2-hc 7 1 4
5 c2-c2-hc 8 1 4
6 c2-c2-c2 7 1 8
7 c2-c_1-o_1 7 2 3
8 o-c_1-o_1 3 2 11
9 c2-c_1-o 7 2 11
10 c_1-o-ho 2 3 6
11 c2-c2-c_1 1 7 2
12 c2-c2-hc 1 7 14
13 c2-c2-hc 1 7 15
14 c_1-c2-hc 2 7 14
15 c_1-c2-hc 2 7 15
16 hc-c2-hc 14 7 15
17 c2-c2-c2 1 8 9
18 c2-c2-hc 1 8 16
19 c2-c2-hc 1 8 17
20 c2-c2-hc 9 8 16
21 c2-c2-hc 9 8 17
22 hc-c2-hc 16 8 17
23 c2-c2-c_1 8 9 10
24 c2-c2-hc 8 9 18
25 c2-c2-hc 8 9 19
26 c_1-c2-hc 10 9 18
27 c_1-c2-hc 10 9 19
28 hc-c2-hc 18 9 19
29 c2-c_1-o 9 10 12
30 c2-c_1-o_1 9 10 13
31 o-c_1-o_1 13 10 12
32 c_1-o-ho 10 13 20
33 c2-c2-hc 22 21 27
34 c2-c2-hc 22 21 28
35 c2-c2-c2 22 21 39
36 hc-c2-hc 27 21 28
37 c2-c2-hc 39 21 27
38 c2-c2-hc 39 21 28
39 c2-c2-na 21 22 23
40 c2-c2-hc 21 22 29
41 c2-c2-hc 21 22 30
42 na-c2-hc 23 22 29
43 na-c2-hc 23 22 30
44 hc-c2-hc 29 22 30
45 c2-na-hn 22 23 31
46 c2-na-hn 22 23 32
47 hn-na-hn 31 23 32
48 c2-na-hn 25 24 33
49 c2-na-hn 25 24 34
50 hn-na-hn 33 24 34
51 c2-c2-na 26 25 24
52 na-c2-hc 24 25 35
53 na-c2-hc 24 25 36
54 c2-c2-hc 26 25 35
55 c2-c2-hc 26 25 36
56 hc-c2-hc 35 25 36
57 c2-c2-hc 25 26 37
58 c2-c2-hc 25 26 38
59 c2-c2-c2 25 26 42
60 hc-c2-hc 37 26 38
61 c2-c2-hc 42 26 37
62 c2-c2-hc 42 26 38
63 c2-c2-hc 21 39 40
64 c2-c2-hc 21 39 41
65 c2-c2-c2 21 39 42
66 hc-c2-hc 40 39 41
67 c2-c2-hc 42 39 40
68 c2-c2-hc 42 39 41
69 c2-c2-c2 26 42 39
70 c2-c2-hc 26 42 43
71 c2-c2-hc 26 42 44
72 c2-c2-hc 39 42 43
73 c2-c2-hc 39 42 44
74 hc-c2-hc 43 42 44
Dihedrals
1 hc-c2-c2-hc 5 1 7 14
2 hc-c2-c2-hc 5 1 7 15
3 hc-c2-c2-hc 4 1 7 14
4 hc-c2-c2-hc 4 1 7 15
5 c2-c2-c2-c_1 8 1 7 2
6 c2-c2-c2-hc 8 1 7 14
7 c2-c2-c2-hc 8 1 7 15
8 hc-c2-c2-hc 5 1 8 16
9 hc-c2-c2-hc 5 1 8 17
10 hc-c2-c2-hc 4 1 8 16
11 hc-c2-c2-hc 4 1 8 17
12 c2-c2-c2-c2 7 1 8 9
13 c2-c2-c2-hc 7 1 8 16
14 c2-c2-c2-hc 7 1 8 17
15 c2-c_1-o-ho 7 2 3 6
16 o_1-c_1-o-ho 11 2 3 6
17 c_1-c2-c2-hc 2 7 1 5
18 c_1-c2-c2-hc 2 7 1 4
19 c2-c2-c_1-o 1 7 2 3
20 hc-c2-c_1-o 14 7 2 3
21 hc-c2-c_1-o 15 7 2 3
22 c2-c2-c_1-o_1 1 7 2 11
23 hc-c2-c_1-o_1 14 7 2 11
24 hc-c2-c_1-o_1 15 7 2 11
25 c2-c2-c2-hc 9 8 1 5
26 c2-c2-c2-hc 9 8 1 4
27 c2-c2-c2-c_1 1 8 9 10
28 c2-c2-c2-hc 1 8 9 18
29 c2-c2-c2-hc 1 8 9 19
30 hc-c2-c2-hc 16 8 9 18
31 hc-c2-c2-hc 16 8 9 19
32 hc-c2-c2-hc 17 8 9 18
33 hc-c2-c2-hc 17 8 9 19
34 c_1-c2-c2-hc 10 9 8 16
35 c_1-c2-c2-hc 10 9 8 17
36 c2-c2-c_1-o_1 8 9 10 12
37 c2-c2-c_1-o 8 9 10 13
38 hc-c2-c_1-o_1 18 9 10 12
39 hc-c2-c_1-o 18 9 10 13
40 hc-c2-c_1-o_1 19 9 10 12
41 hc-c2-c_1-o 19 9 10 13
42 c2-c_1-o-ho 9 10 13 20
43 o_1-c_1-o-ho 12 10 13 20
44 hc-c2-c2-hc 27 21 22 29
45 hc-c2-c2-hc 27 21 22 30
46 hc-c2-c2-hc 28 21 22 29
47 hc-c2-c2-hc 28 21 22 30
48 c2-c2-c2-na 39 21 22 23
49 c2-c2-c2-hc 39 21 22 29
50 c2-c2-c2-hc 39 21 22 30
51 c2-c2-c2-hc 22 21 39 40
52 c2-c2-c2-hc 22 21 39 41
53 c2-c2-c2-c2 22 21 39 42
54 hc-c2-c2-hc 27 21 39 40
55 hc-c2-c2-hc 27 21 39 41
56 hc-c2-c2-hc 28 21 39 40
57 hc-c2-c2-hc 28 21 39 41
58 na-c2-c2-hc 23 22 21 27
59 na-c2-c2-hc 23 22 21 28
60 c2-c2-na-hn 21 22 23 31
61 c2-c2-na-hn 21 22 23 32
62 hn-na-c2-hc 29 22 23 31
63 hn-na-c2-hc 29 22 23 32
64 hn-na-c2-hc 30 22 23 31
65 hn-na-c2-hc 30 22 23 32
66 c2-c2-na-hn 26 25 24 33
67 hn-na-c2-hc 35 25 24 33
68 hn-na-c2-hc 36 25 24 33
69 c2-c2-na-hn 26 25 24 34
70 hn-na-c2-hc 35 25 24 34
71 hn-na-c2-hc 36 25 24 34
72 na-c2-c2-hc 24 25 26 37
73 na-c2-c2-hc 24 25 26 38
74 hc-c2-c2-hc 35 25 26 37
75 hc-c2-c2-hc 35 25 26 38
76 hc-c2-c2-hc 36 25 26 37
77 hc-c2-c2-hc 36 25 26 38
78 c2-c2-c2-na 42 26 25 24
79 c2-c2-c2-hc 42 26 25 35
80 c2-c2-c2-hc 42 26 25 36
81 c2-c2-c2-c2 25 26 42 39
82 c2-c2-c2-hc 25 26 42 43
83 c2-c2-c2-hc 25 26 42 44
84 hc-c2-c2-hc 37 26 42 43
85 hc-c2-c2-hc 37 26 42 44
86 hc-c2-c2-hc 38 26 42 43
87 hc-c2-c2-hc 38 26 42 44
88 c2-c2-c2-hc 42 39 21 27
89 c2-c2-c2-hc 42 39 21 28
90 c2-c2-c2-c2 21 39 42 26
91 c2-c2-c2-hc 21 39 42 43
92 c2-c2-c2-hc 21 39 42 44
93 hc-c2-c2-hc 40 39 42 43
94 hc-c2-c2-hc 40 39 42 44
95 hc-c2-c2-hc 41 39 42 43
96 hc-c2-c2-hc 41 39 42 44
97 c2-c2-c2-hc 39 42 26 37
98 c2-c2-c2-hc 39 42 26 38
99 c2-c2-c2-hc 26 42 39 40
100 c2-c2-c2-hc 26 42 39 41
Impropers
1 c2-na-hn-hn 7 1 4 5
2 c2-na-hn-hn 8 1 4 5
3 c2-c_1-o_1-o 7 1 8 5
4 c2-c_1-o_1-o 7 1 8 4
5 c2-c_1-o-o_1 7 2 3 11
6 c2-n-hn-c_1 1 7 2 14
7 c2-n-hn-c_1 1 7 2 15
8 c2-na-hn-hn 1 7 14 15
9 c2-c_1-o_1-o 1 8 9 16
10 c2-c_1-o_1-o 1 8 9 17
11 c2-na-hn-hn 1 8 16 17
12 c2-na-hn-hn 9 8 16 17
13 c2-n-hn-c_1 8 9 10 18
14 c2-n-hn-c_1 8 9 10 19
15 c2-na-hn-hn 8 9 18 19
16 c2-c_1-o-o_1 9 10 13 12