From b15f4e5d63a5fa58d3b4b87afe0ec7ccff7085b3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 12 Jun 2025 00:34:01 -0400 Subject: [PATCH] add updated example using json molecule files --- .../tiny_nylon_json/in.tiny_nylon.stabilized | 61 ++ .../log.tiny_nylon.stabilized.12Jun2025.g++.1 | 444 ++++++++++ .../log.tiny_nylon.stabilized.12Jun2025.g++.4 | 444 ++++++++++ .../reaction/tiny_nylon_json/rxn1_stp1_map | 35 + .../tiny_nylon_json/rxn1_stp1_reacted.json | 177 ++++ .../tiny_nylon_json/rxn1_stp1_unreacted.json | 184 ++++ .../reaction/tiny_nylon_json/rxn1_stp2_map | 32 + .../tiny_nylon_json/rxn1_stp2_reacted.json | 156 ++++ .../tiny_nylon_json/rxn1_stp2_unreacted.json | 170 ++++ .../reaction/tiny_nylon_json/tiny_nylon.data | 820 ++++++++++++++++++ 10 files changed, 2523 insertions(+) create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/in.tiny_nylon.stabilized create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.1 create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.4 create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_map create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_reacted.json create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_unreacted.json create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_map create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_reacted.json create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp2_unreacted.json create mode 100644 examples/PACKAGES/reaction/tiny_nylon_json/tiny_nylon.data diff --git a/examples/PACKAGES/reaction/tiny_nylon_json/in.tiny_nylon.stabilized b/examples/PACKAGES/reaction/tiny_nylon_json/in.tiny_nylon.stabilized new file mode 100644 index 0000000000..a8a4492bfb --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon_json/in.tiny_nylon.stabilized @@ -0,0 +1,61 @@ +# 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 diff --git a/examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.1 b/examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.1 new file mode 100644 index 0000000000..eb8546b4be --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.1 @@ -0,0 +1,444 @@ +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 diff --git a/examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.4 b/examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.4 new file mode 100644 index 0000000000..158d027156 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.4 @@ -0,0 +1,444 @@ +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 diff --git a/examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_map b/examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_map new file mode 100644 index 0000000000..0de209fdfd --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_map @@ -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 diff --git a/examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_reacted.json b/examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_reacted.json new file mode 100644 index 0000000000..f8b1ed0ef1 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon_json/rxn1_stp1_reacted.json @@ -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, 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"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] + ] + }, + "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", 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-c_1", 8, 9, 10], + ["c2-c2-hc", 8, 9, 13], + ["c2-c2-hc", 8, 9, 14], + ["hc-c2-c_1", 13, 9, 10], + ["hc-c2-c_1", 14, 9, 10], + ["hc-c2-hc", 13, 9, 14], + ["c2-c_1-o_1", 9, 10, 11], + ["c2-c_1-o", 9, 10, 12], + ["n-c_1-c2", 1, 10, 9], + ["o_1-c_1-o", 11, 10, 12], + ["n-c_1-o_1", 1, 10, 11], + ["n-c_1-o", 1, 10, 12], + ["c_1-o-ho", 10, 12, 15] + ] + }, + "dihedrals": { + "format": ["dihedral-type", "atom1", "atom2", "atom3", "atom4"], + "data": [ + ["hn-n-c2-c2", 4, 1, 2, 3], + ["hn-n-c2-hc", 4, 1, 2, 6], + ["hn-n-c2-hc", 4, 1, 2, 7], + ["hn-n-c2-c2", 5, 1, 2, 3], + ["hn-n-c2-hc", 5, 1, 2, 6], + ["hn-n-c2-hc", 5, 1, 2, 7], + ["c_1-n-c2-c2", 10, 1, 2, 3], + ["c_1-n-c2-hc", 10, 1, 2, 6], + ["c_1-n-c2-hc", 10, 1, 2, 7], + ["c2-n-c_1-c2", 2, 1, 10, 9], + ["c2-n-c_1-o_1", 2, 1, 10, 11], + ["c2-n-c_1-o", 2, 1, 10, 12], + ["hn-n-c_1-c2", 4, 1, 10, 9], + ["hn-n-c_1-o_1", 4, 1, 10, 11], + ["hn-n-c_1-o", 4, 1, 10, 12], + ["hn-n-c_1-c2", 5, 1, 10, 9], + ["hn-n-c_1-o_1", 5, 1, 10, 11], + ["hn-n-c_1-o", 5, 1, 10, 12], + ["c2-c2-c_1-o_1", 8, 9, 10, 11], + ["c2-c2-c_1-o", 8, 9, 10, 12], + ["c2-c2-c_1-n", 8, 9, 10, 1], + ["hc-c2-c_1-o_1", 13, 9, 10, 11], + ["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] + ] + } +} diff --git a/examples/PACKAGES/reaction/tiny_nylon_json/tiny_nylon.data b/examples/PACKAGES/reaction/tiny_nylon_json/tiny_nylon.data new file mode 100644 index 0000000000..73c776c430 --- /dev/null +++ b/examples/PACKAGES/reaction/tiny_nylon_json/tiny_nylon.data @@ -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 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