LAMMPS (10 Dec 2025 - Development - patch_10Dec2025-120-ga51f9ba0e7-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
# 35,000 atom nylon melt example

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower

read_data large_nylon_melt.data.gz   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 = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
  2 by 1 by 2 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  35200 atoms
  reading velocities ...
  35200 velocities
  scanning bonds ...
  9 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  31 = max dihedrals/atom
  scanning impropers ...
  29 = max impropers/atom
  orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
  2 by 1 by 2 MPI processor grid
  reading bonds ...
  33600 bonds
  reading angles ...
  59200 angles
  reading dihedrals ...
  80000 dihedrals
  reading impropers ...
  35200 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 = 0.007 seconds
  read_data CPU = 0.748 seconds

velocity all create 800.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
this is a molecule template for: initial nylon crosslink, pre-reacting
  1 molecules
  0 fragments
  0 bodies
  18 atoms with max type 8
  16 bonds with max type 12
  25 angles with max type 24
  23 dihedrals with max type 33
  2 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
this is a molecule template for: initial nylon crosslink, post-reacting
  1 molecules
  0 fragments
  0 bodies
  18 atoms with max type 9
  17 bonds with max type 11
  31 angles with max type 23
  39 dihedrals with max type 30
  0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
this is a molecule template for: water condensation, pre-reacting
  1 molecules
  0 fragments
  0 bodies
  15 atoms with max type 9
  14 bonds with max type 11
  25 angles with max type 23
  30 dihedrals with max type 30
  0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
this is a molecule template for: water condensation, post-reacting
  1 molecules
  0 fragments
  0 bodies
  15 atoms with max type 11
  13 bonds with max type 13
  19 angles with max type 25
  16 dihedrals with max type 29
  2 impropers with max type 11

thermo 50

# dump 1 all xyz 100 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
WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2630)
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2630)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

# stable at 800K
fix 1 statted_grp_REACT nvt temp 800 800 100

# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1

thermo_style custom step temp press density f_myrxns[*] # cumulative reaction counts
thermo_modify colname auto

# restart 100 restart1 restart2

run 200

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: https://reacter.org, https://doi.org/10.1016/j.polymer.2017.09.038, https://doi.org/10.1021/acs.macromol.0c02012, https://doi.org/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
  G vector (1/distance) = 0.20765034
  grid = 18 18 18
  stencil order = 5
  estimated absolute RMS force accuracy = 0.033315619
  estimated relative force accuracy = 0.000100329
  using double precision KISS FFT
  3d grid and FFT values/proc = 4508 1458
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 = 15 15 15
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      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) = 79.97 | 79.98 | 79.99 Mbytes
   Step          Temp          Press         Density     f_myrxns:rxn1  f_myrxns:rxn2 
         0   800            9347.3909      0.80366765     0              0            
        50   685.33063     -9882.8359      0.80366765     34             0            
       100   711.35475     -6916.8177      0.80366765     58             28           
       150   731.39207     -5172.8555      0.80366765     79             55           
       200   741.77172     -6737.2807      0.80366765     94             74           
Loop time of 14.742 on 4 procs for 200 steps with 35200 atoms

Performance: 1.172 ns/day, 20.475 hours/ns, 13.567 timesteps/s, 477.547 katom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.1959     | 4.3131     | 4.415      |   4.8 | 29.26
Bond    | 1.8618     | 1.8955     | 1.9242     |   1.8 | 12.86
Kspace  | 0.48599    | 0.61712    | 0.76457    |  15.6 |  4.19
Neigh   | 6.0426     | 6.0489     | 6.0553     |   0.3 | 41.03
Comm    | 0.19496    | 0.20421    | 0.21318    |   1.8 |  1.39
Output  | 0.00025729 | 0.00028156 | 0.00035095 |   0.0 |  0.00
Modify  | 1.6375     | 1.6379     | 1.6384     |   0.0 | 11.11
Other   |            | 0.02493    |            |       |  0.17

Nlocal:           8800 ave        8903 max        8678 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost:        18363.8 ave       18442 max       18189 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs:    1.73187e+06 ave 1.77044e+06 max 1.68762e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2

Total # of neighbors = 6927463
Ave neighs/atom = 196.80293
Ave special neighs/atom = 5.4301136
Neighbor list builds = 140
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data nofix
Total wall time: 0:00:15
