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
# 20 styrene molecules
# three reactions defined

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

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

variable T equal 530

read_data tiny_polystyrene.data    extra/bond/per/atom 5   extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334)
  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 ...
  320 atoms
  reading velocities ...
  320 velocities
  scanning bonds ...
  8 = max bonds/atom
  scanning angles ...
  18 = max angles/atom
  scanning dihedrals ...
  22 = max dihedrals/atom
  scanning impropers ...
  26 = max impropers/atom
  orthogonal box = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  320 bonds
  reading angles ...
  480 angles
  reading dihedrals ...
  640 dihedrals
  reading impropers ...
  160 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        1       
  special bond factors coul:  0        0        1       
     3 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    34 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.018 seconds

molecule mol1 M-M_pre.mol
Read molecule template mol1:
2styrene_unreacted
  1 molecules
  0 fragments
  0 bodies
  32 atoms with max type 4
  32 bonds with max type 11
  48 angles with max type 19
  64 dihedrals with max type 21
  16 impropers with max type 8
molecule mol2 M-M_post.mol
Read molecule template mol2:
2styrene_reacted
  1 molecules
  0 fragments
  0 bodies
  32 atoms with max type 6
  33 bonds with max type 13
  54 angles with max type 22
  79 dihedrals with max type 19
  14 impropers with max type 7
molecule mol3 M-P_pre.mol
Read molecule template mol3:
chain_plus_styrene_unreacted
  1 molecules
  0 fragments
  0 bodies
  46 atoms with max type 6
  47 bonds with max type 13
  75 angles with max type 22
  105 dihedrals with max type 21
  21 impropers with max type 8
molecule mol4 M-P_post.mol
Read molecule template mol4:
chain_plus_styrene_reacted
  1 molecules
  0 fragments
  0 bodies
  46 atoms with max type 6
  48 bonds with max type 13
  81 angles with max type 22
  121 dihedrals with max type 19
  19 impropers with max type 7
molecule mol5 P-P_pre.mol
Read molecule template mol5:
chain_chain_unreacted
  1 molecules
  0 fragments
  0 bodies
  50 atoms with max type 6
  51 bonds with max type 13
  84 angles with max type 22
  118 dihedrals with max type 19
  20 impropers with max type 7
molecule mol6 P-P_post.mol
Read molecule template mol6:
chain_chain_reacted
  1 molecules
  0 fragments
  0 bodies
  50 atoms with max type 6
  52 bonds with max type 13
  90 angles with max type 22
  135 dihedrals with max type 19
  18 impropers with max type 2

# dump 1 all xyz 5 test_vis.xyz
# dump_modify 1 types labels

fix rxn1 all bond/react stabilization yes statted_grp .03  react M-M all 1 0 3.0 mol1 mol2 M-M.rxnmap stabilize_steps 100  react M-P all 1 0 3.0 mol3 mol4 M-P.rxnmap stabilize_steps 100  react P-P all 1 0 5.0 mol5 mol6 P-P.rxnmap stabilize_steps 100
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100

fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1

thermo_style custom step temp press density f_rxn1[*]
thermo_modify colname auto

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: 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 ...
WARNING: System is not charge neutral, net charge = -0.004
For more information see https://docs.lammps.org/err0029 (src/kspace.cpp:329)
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.25561147
  grid = 6 6 6
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0097469157
  estimated relative force accuracy = 2.9352547e-05
  using double precision KISS FFT
  3d grid and FFT values/proc = 1331 216
Generated 21 of 21 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 = 4 4 4
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      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) = 31.07 | 31.07 | 31.07 Mbytes
   Step          Temp          Press         Density       f_rxn1:M-M     f_rxn1:M-P     f_rxn1:P-P  
         0   320.13638      8863.4109      0.76796752     0              0              0            
     10000   529.74892      7400.5017      0.76796752     7              1              3            
Loop time of 16.4177 on 1 procs for 10000 steps with 320 atoms

Performance: 52.626 ns/day, 0.456 hours/ns, 609.097 timesteps/s, 194.911 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.778      | 6.778      | 6.778      |   0.0 | 41.28
Bond    | 4.0389     | 4.0389     | 4.0389     |   0.0 | 24.60
Kspace  | 1.045      | 1.045      | 1.045      |   0.0 |  6.36
Neigh   | 0.65857    | 0.65857    | 0.65857    |   0.0 |  4.01
Comm    | 0.11532    | 0.11532    | 0.11532    |   0.0 |  0.70
Output  | 0.00046322 | 0.00046322 | 0.00046322 |   0.0 |  0.00
Modify  | 3.7598     | 3.7598     | 3.7598     |   0.0 | 22.90
Other   |            | 0.02174    |            |       |  0.13

Nlocal:            320 ave         320 max         320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           3401 ave        3401 max        3401 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          54998 ave       54998 max       54998 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 54998
Ave neighs/atom = 171.86875
Ave special neighs/atom = 9.275
Neighbor list builds = 457
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data nofix
Total wall time: 0:00:16
