LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  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

read_data large_nylon_melt.data.gz
  orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
  2 by 1 by 2 MPI processor grid
  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
  reading bonds ...
  33600 bonds
  reading angles ...
  59200 angles
  reading dihedrals ...
  80000 dihedrals
  reading impropers ...
  35200 impropers
  4 = max # of 1-2 neighbors
  6 = max # of 1-3 neighbors
  12 = max # of 1-4 neighbors
  41 = max # of special neighbors

velocity all create 800.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
  18 atoms with max type 8
  16 bonds with max type 12
  25 angles with max type 24
  23 dihedrals with max type 33
  14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
  18 atoms with max type 9
  17 bonds with max type 11
  31 angles with max type 23
  39 dihedrals with max type 30
  20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
  15 atoms with max type 9
  14 bonds with max type 11
  25 angles with max type 23
  30 dihedrals with max type 30
  16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
  15 atoms with max type 11
  13 bonds with max type 13
  19 angles with max type 25
  16 dihedrals with max type 29
  10 impropers with max type 11

thermo 50

# dump 1 all xyz 100 test_vis.xyz

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: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined

# stable at 800K
fix 1 statted_grp 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[1] f_myrxns[2] # cumulative reaction counts

# restart 100 restart1 restart2

run 200
PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.20765
  grid = 18 18 18
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0333156
  estimated relative force accuracy = 0.000100329
  using double precision FFTs
  3d grid and FFT values/proc = 4508 1620
Neighbor list info ...
  update every 1 steps, delay 10 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/newton
      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) = 81.11 | 81.13 | 81.15 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2] 
       0          800    3666.3948   0.80366765            0            0 
      50    673.95238   -9670.9169   0.80366765           31            0 
     100    697.22819   -4624.0512   0.80366765           57           22 
     150    724.40407   -17166.729   0.80366765           76           49 
     200    737.28582   -12968.224   0.80366765           84           65 
Loop time of 51.171 on 4 procs for 200 steps with 35200 atoms

Performance: 0.338 ns/day, 71.071 hours/ns, 3.908 timesteps/s
98.4% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 12.926     | 13.247     | 13.493     |   6.7 | 25.89
Bond    | 5.2132     | 5.2733     | 5.3367     |   1.9 | 10.31
Kspace  | 2.3601     | 2.6534     | 3.0067     |  16.0 |  5.19
Neigh   | 25.93      | 25.934     | 25.937     |   0.1 | 50.68
Comm    | 0.73273    | 0.75464    | 0.78505    |   2.3 |  1.47
Output  | 0.00045228 | 0.00067407 | 0.0013323  |   0.0 |  0.00
Modify  | 3.2682     | 3.2686     | 3.2692     |   0.0 |  6.39
Other   |            | 0.03995    |            |       |  0.08

Nlocal:    8800 ave 8913 max 8652 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost:    18366 ave 18461 max 18190 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs:    1.73203e+06 ave 1.77261e+06 max 1.68165e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2

Total # of neighbors = 6928132
Ave neighs/atom = 196.822
Ave special neighs/atom = 9.83608
Neighbor list builds = 200
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:52
