LAMMPS (4 Nov 2022)
# two molecules DGEBA (diepoxy) and one DETA (linker)
# two crosslinking reactions

units real

boundary p p p

atom_style full

pair_style lj/class2 8

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

read_data tiny_epoxy.data
Reading data file ...
  orthogonal box = (10 -10 -15) to (30 20 10)
  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 ...
  118 atoms
  scanning bonds ...
  4 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  18 = max dihedrals/atom
  scanning impropers ...
  4 = max impropers/atom
  reading bonds ...
  123 bonds
  reading angles ...
  221 angles
  reading dihedrals ...
  302 dihedrals
  reading impropers ...
  115 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
    10 = max # of 1-3 neighbors
    19 = max # of 1-4 neighbors
    22 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.015 seconds

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_pre.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  31 atoms with max type 10
  30 bonds with max type 15
  53 angles with max type 29
  66 dihedrals with max type 39
  3 impropers with max type 5
molecule mol2 rxn1_stp1_post.molecule_template
Read molecule template mol2:
  1 molecules
  0 fragments
  31 atoms with max type 10
  30 bonds with max type 17
  55 angles with max type 36
  75 dihedrals with max type 51
  2 impropers with max type 5
molecule mol3 rxn1_stp2_post.molecule_template
Read molecule template mol3:
  1 molecules
  0 fragments
  31 atoms with max type 11
  30 bonds with max type 18
  53 angles with max type 37
  72 dihedrals with max type 53
  3 impropers with max type 5
molecule mol4 rxn2_stp1_pre.molecule_template
Read molecule template mol4:
  1 molecules
  0 fragments
  42 atoms with max type 11
  41 bonds with max type 18
  73 angles with max type 41
  96 dihedrals with max type 54
  3 impropers with max type 5
molecule mol5 rxn2_stp1_post.molecule_template
Read molecule template mol5:
  1 molecules
  0 fragments
  42 atoms with max type 11
  41 bonds with max type 18
  75 angles with max type 37
  108 dihedrals with max type 53
  2 impropers with max type 5
molecule mol6 rxn2_stp2_post.molecule_template
Read molecule template mol6:
  1 molecules
  0 fragments
  42 atoms with max type 11
  41 bonds with max type 19
  73 angles with max type 50
  102 dihedrals with max type 66
  3 impropers with max type 22

thermo 50

# dump 1 all xyz 1 test_vis.xyz

fix rxns all bond/react stabilization yes statted_grp .03   react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map   react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map   react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map   react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined


fix 1 statted_grp_REACT nvt temp 300 300 100

thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]

run 2000

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

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
  ghost atom cutoff = 10
  binsize = 5, bins = 4 6 5
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2, 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) = 16.64 | 16.64 | 16.64 Mbytes
   Step          Temp        f_rxns[1]      f_rxns[2]      f_rxns[3]      f_rxns[4]   
         0   300            0              0              0              0            
        50   378.29345      1              0              0              0            
       100   471.04152      1              1              0              0            
       150   583.79755      1              1              1              0            
       200   526.00812      1              1              1              1            
       250   429.56812      1              1              1              1            
       300   512.54655      1              1              1              1            
       350   461.18357      1              1              1              1            
       400   379.38965      1              1              1              1            
       450   424.89528      1              1              1              1            
       500   324.72257      1              1              1              1            
       550   302.91042      1              1              1              1            
       600   253.80911      1              1              1              1            
       650   252.90262      1              1              1              1            
       700   270.62628      1              1              1              1            
       750   311.64391      1              1              1              1            
       800   318.9413       1              1              1              1            
       850   354.20196      1              1              1              1            
       900   302.19641      1              1              1              1            
       950   316.97905      1              1              1              1            
      1000   303.08194      1              1              1              1            
      1050   317.51619      1              1              1              1            
      1100   287.57204      1              1              1              1            
      1150   226.72101      1              1              1              1            
      1200   283.97519      1              1              1              1            
      1250   287.0607       1              1              1              1            
      1300   327.65278      1              1              1              1            
      1350   316.06809      1              1              1              1            
      1400   337.69947      1              1              1              1            
      1450   326.12278      1              1              1              1            
      1500   300.89265      1              1              1              1            
      1550   325.2415       1              1              1              1            
      1600   294.1844       1              1              1              1            
      1650   293.98596      1              1              1              1            
      1700   317.35477      1              1              1              1            
      1750   296.97768      1              1              1              1            
      1800   274.97297      1              1              1              1            
      1850   335.36697      1              1              1              1            
      1900   315.3756       1              1              1              1            
      1950   260.65335      1              1              1              1            
      2000   354.03612      1              1              1              1            
Loop time of 0.910097 on 1 procs for 2000 steps with 118 atoms

Performance: 189.870 ns/day, 0.126 hours/ns, 2197.568 timesteps/s, 259.313 katom-step/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.10286    | 0.10286    | 0.10286    |   0.0 | 11.30
Bond    | 0.63714    | 0.63714    | 0.63714    |   0.0 | 70.01
Neigh   | 0.013949   | 0.013949   | 0.013949   |   0.0 |  1.53
Comm    | 0.0056606  | 0.0056606  | 0.0056606  |   0.0 |  0.62
Output  | 0.00055825 | 0.00055825 | 0.00055825 |   0.0 |  0.06
Modify  | 0.14629    | 0.14629    | 0.14629    |   0.0 | 16.07
Other   |            | 0.003637   |            |       |  0.40

Nlocal:            118 ave         118 max         118 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            372 ave         372 max         372 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           3487 ave        3487 max        3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3487
Ave neighs/atom = 29.550847
Ave special neighs/atom = 10.576271
Neighbor list builds = 68
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data nofix
Total wall time: 0:00:01
