LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
  using 1 OpenMP thread(s) per MPI task
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)

boundary        p p s
units           real
atom_style      charge

read_data       data.water
Reading data file ...
  orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (src/read_data.cpp:1548)
  3000 atoms
  read_data CPU = 0.008 seconds

variable        x index 1
variable        y index 1
variable        z index 1

replicate       $x $y $z
replicate       1 $y $z
replicate       1 1 $z
replicate       1 1 1
Replication is creating a 1x1x1 = 1 times larger system...
  orthogonal box = (0 0 0.0012889577) to (31.043046 31.043046 31.045309)
  2 by 1 by 2 MPI processor grid
  3000 atoms
  replicate CPU = 0.001 seconds

pair_style      reaxff NULL safezone 3.0 mincap 150
pair_coeff      * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294)
neighbor        0.5 bin
neigh_modify    every 1 delay 0 check yes

velocity all create 300.0 4928459 rot yes dist gaussian

fix             1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix             2 all nvt temp 300 300 50.0
fix             3 all efield 0.0 0.0 1.0
fix             4 all wall/reflect zlo EDGE zhi EDGE

timestep        0.5
thermo          10
thermo_style    custom step temp press density vol

run 20

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

Your simulation uses code contributions which should be cited:

- pair reaxff command: doi:10.1016/j.parco.2011.08.005

@Article{Aktulga12,
 author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
 title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
 journal = {Parallel Computing},
 year =    2012,
 volume =  38,
 number =  {4--5},
 pages =   {245--259}
}

- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005

@Article{Aktulga12,
 author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
 title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
 journal = {Parallel Computing},
 year =    2012,
 volume =  38,
 pages =   {245--259}
}

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

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 = 6 6 6
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair reaxff, perpetual
      attributes: half, newton off, ghost
      pair build: half/bin/ghost/newtoff
      stencil: full/ghost/bin/3d
      bin: standard
  (2) fix qeq/reaxff, perpetual, copy from (1)
      attributes: half, newton off
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 188.9 | 189.5 | 190.1 Mbytes
   Step          Temp          Press         Density         Volume    
         0   300            25015.837      0.99996859     29916.212    
        10   348.83356      31131.298      0.99964273     29925.965    
        20   414.67243      27564.999      0.99979791     29921.32     
Loop time of 1.25077 on 4 procs for 20 steps with 3000 atoms

Performance: 0.691 ns/day, 34.744 hours/ns, 15.990 timesteps/s, 47.971 katom-step/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.76221    | 0.7759     | 0.78605    |   1.2 | 62.03
Neigh   | 0.083557   | 0.08496    | 0.086573   |   0.4 |  6.79
Comm    | 0.0090777  | 0.019109   | 0.032959   |   7.4 |  1.53
Output  | 3.8563e-05 | 4.1662e-05 | 5.0627e-05 |   0.0 |  0.00
Modify  | 0.36853    | 0.37036    | 0.37195    |   0.2 | 29.61
Other   |            | 0.0003959  |            |       |  0.03

Nlocal:            750 ave         757 max         738 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost:           4219 ave        4232 max        4198 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs:         230549 ave      233374 max      225849 min
Histogram: 1 0 0 0 0 0 1 0 1 1

Total # of neighbors = 922196
Ave neighs/atom = 307.39867
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:01
