LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

read_data tiny_nylon.data   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
  reading bonds ...
  42 bonds
  reading angles ...
  74 angles
  reading dihedrals ...
  100 dihedrals
  reading impropers ...
  44 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    12 = max # of 1-4 neighbors
    41 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.008 seconds


velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  18 atoms with max type 8
  16 bonds with max type 10
  25 angles with max type 28
  23 dihedrals with max type 36
  2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
  1 molecules
  0 fragments
  18 atoms with max type 9
  17 bonds with max type 13
  31 angles with max type 27
  39 dihedrals with max type 33
  0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
  1 molecules
  0 fragments
  15 atoms with max type 9
  14 bonds with max type 13
  25 angles with max type 27
  30 dihedrals with max type 33
  0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
  1 molecules
  0 fragments
  15 atoms with max type 11
  13 bonds with max type 15
  19 angles with max type 29
  16 dihedrals with max type 32
  2 impropers with max type 13

thermo 50

# dump 1 all xyz 1 test_vis.xyz

fix myrxns all bond/react stabilization no   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined

fix 1 all nve/limit .03

thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]

# restart 100 restart1 restart2

run 1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012

@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}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.05345967
  grid = 2 2 2
  stencil order = 5
  estimated absolute RMS force accuracy = 0.040225597
  estimated relative force accuracy = 0.00012113819
  using double precision KISS FFT
  3d grid and FFT values/proc = 343 8
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric 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
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.72 | 33.72 | 33.72 Mbytes
   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
         0   300            346.78165      0.0034851739   0              0            
        50   530.51001     -15.418012      0.0034851739   1              0            
       100   677.21327      16.545108      0.0034851739   1              1            
       150   386.79268     -28.445486      0.0034851739   1              1            
       200   380.29074      1.8065066      0.0034851739   1              1            
       250   353.27609     -7.3505628      0.0034851739   1              1            
       300   357.84405     -7.0569         0.0034851739   1              1            
       350   337.65224      54.441683      0.0034851739   1              1            
       400   322.54035      20.338902      0.0034851739   1              1            
       450   316.91217      44.76973       0.0034851739   1              1            
       500   345.40444     -8.2133383      0.0034851739   1              1            
       550   296.22085     -30.331582      0.0034851739   1              1            
       600   263.8024      -36.834323      0.0034851739   1              1            
       650   284.05699      1.2532577      0.0034851739   1              1            
       700   274.86269      4.6881357      0.0034851739   1              1            
       750   298.72284     -18.225831      0.0034851739   1              1            
       800   292.72143     -5.1622029      0.0034851739   1              1            
       850   279.30224     -10.72513       0.0034851739   1              1            
       900   284.97331      30.268801      0.0034851739   1              1            
       950   262.46089      16.98134       0.0034851739   1              1            
      1000   297.55359      28.583097      0.0034851739   1              1            
Loop time of 0.175951 on 1 procs for 1000 steps with 44 atoms

Performance: 491.045 ns/day, 0.049 hours/ns, 5683.388 timesteps/s, 250.069 katom-step/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.022992   | 0.022992   | 0.022992   |   0.0 | 13.07
Bond    | 0.1045     | 0.1045     | 0.1045     |   0.0 | 59.39
Kspace  | 0.034057   | 0.034057   | 0.034057   |   0.0 | 19.36
Neigh   | 0.0013592  | 0.0013592  | 0.0013592  |   0.0 |  0.77
Comm    | 0.00040677 | 0.00040677 | 0.00040677 |   0.0 |  0.23
Output  | 0.00030929 | 0.00030929 | 0.00030929 |   0.0 |  0.18
Modify  | 0.01121    | 0.01121    | 0.01121    |   0.0 |  6.37
Other   |            | 0.001118   |            |       |  0.64

Nlocal:             44 ave          44 max          44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              8 ave           8 max           8 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            810 ave         810 max         810 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 810
Ave neighs/atom = 18.409091
Ave special neighs/atom = 9.9090909
Neighbor list builds = 28
Dangerous builds = 0

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