LAMMPS (10 Feb 2021)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Simulator Model (PM)
# `Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000`
# is installed. This can be done with the command
#   kim-api-collections-management install user Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# If this command does not work, you may need to setup your PATH to find the utility.
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
# (where the current working directory is assumed to be the LAMMPS build directory)
#   source ./kim_build-prefix/bin/kim-api-activate
# If you installed the kim-api using the LAMMPS Make build, you can do the following
# (where the current working directory is assumed to be the LAMMPS src directory)
#   source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
#
# See `https://openkim.org/doc/obtaining-models` for alternative options.
#

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

variable     xx equal 20*$x
variable     xx equal 20*1
variable     yy equal 20*$y
variable     yy equal 20*1
variable     zz equal 20*$z
variable     zz equal 20*1

kim          init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real
#=== BEGIN kim init ==========================================
# Using KIM Simulator Model : Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000
# For Simulator             : LAMMPS 28 Feb 2019
# Running on                : LAMMPS 10 Feb 2021
#
units real
neighbor 2.0 bin   # Angstroms
timestep 1.0       # femtoseconds
atom_style charge
neigh_modify one 4000
#=== END kim init ============================================


lattice      fcc 4.4300
Lattice spacing in x,y,z = 4.4300000 4.4300000 4.4300000
region       box block 0 ${xx} 0 ${yy} 0 ${zz}
region       box block 0 20 0 ${yy} 0 ${zz}
region       box block 0 20 0 20 0 ${zz}
region       box block 0 20 0 20 0 20
create_box   1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (88.600000 88.600000 88.600000)
  1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 32000 atoms
  create_atoms CPU = 0.003 seconds

kim          interactions O
#=== BEGIN kim interactions ==================================
variable kim_periodic equal 1
pair_style reax/c /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/lmp_control safezone 2.0 mincap 100
pair_coeff * * /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/ffield.reax.rdx O
Reading potential file /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/ffield.reax.rdx with DATE: 2010-02-19
fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 /var/tmp/kim-shared-library-parameter-file-directory-SLT21lwwgINS/param.qeq
#=== END kim interactions ====================================


mass         1 39.95
velocity     all create 200.0 232345 loop geom

neighbor     0.3 bin
neigh_modify delay 0 every 1 check yes

fix          1 all nve
#fix         1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0

run          100

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

Your simulation uses code contributions which should be cited:

- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6

@Article{tadmor:elliott:2011,
 author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
 title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
 journal = {{JOM}},
 year =    2011,
 volume =  63,
 number =  17,
 pages =   {17},
 doi =     {10.1007/s11837-011-0102-6}
}

- OpenKIM potential: https://openkim.org/cite/SM_107643900657_000#item-citation

@Comment
{
\documentclass{article}
\usepackage{url}
\begin{document}
This Simulator Model originally published in \cite{SM_107643900657_000a} is archived in OpenKIM~\cite{SM_107643900657_000, tadmor:elliott:2011, elliott:tadmor:2011}.
\bibliographystyle{vancouver}
\bibliography{kimcite-SM_107643900657_000.bib}
\end{document}
}

@Misc{SM_107643900657_000,
  author       = {Ellad Tadmor},
  title        = {{LAMMPS} {R}eax{FF} potential for {RDX} ({C}-{H}-{N}-{O}) systems developed by {S}trachan et al. (2003) v000},
  doi          = {10.25950/acd3fc89},
  howpublished = {OpenKIM, \url{https://doi.org/10.25950/acd3fc89}},
  keywords     = {OpenKIM, Simulator Model, SM_107643900657_000},
  publisher    = {OpenKIM},
  year         = 2019,
}

@Article{tadmor:elliott:2011,
  author    = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
  title     = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
  journal   = {{JOM}},
  year      = {2011},
  volume    = {63},
  number    = {7},
  pages     = {17},
  doi       = {10.1007/s11837-011-0102-6},
}

@Misc{elliott:tadmor:2011,
  author       = {Ryan S. Elliott and Ellad B. Tadmor},
  title        = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
  howpublished = {\url{https://openkim.org/kim-api}},
  publisher    = {OpenKIM},
  year         = 2011,
  doi          = {10.25950/ff8f563a},
}

@Article{SM_107643900657_000a,
  author = {Strachan, Alejandro and van Duin, Adri C. T. and Chakraborty, Debashis and Dasgupta, Siddharth and Goddard, William A.},
  doi = {10.1103/PhysRevLett.91.098301},
  issue = {9},
  journal = {Physical Review Letters},
  month = {Aug},
  numpages = {4},
  pages = {098301},
  publisher = {American Physical Society},
  title = {Shock Waves in High-Energy Materials: {T}he Initial Chemical Events in Nitramine {RDX}},
  volume = {91},
  year = {2003},
}
- pair reax/c command:

@Article{Aktulga12,
 author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
 title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
 journal = {Parallel Computing},
 year =    2012,
 volume =  38,
 pages =   {245--259}
}

- fix qeq/reax command:

@Article{Aktulga12,
 author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
 title = {Parallel reactive molecular dynamics: Numerical 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: 4000, page size: 100000
  master list distance cutoff = 10.3
  ghost atom cutoff = 10.3
  binsize = 5.15, bins = 18 18 18
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair reax/c, perpetual
      attributes: half, newton off, ghost
      pair build: half/bin/newtoff/ghost
      stencil: half/ghost/bin/3d/newtoff
      bin: standard
  (2) fix qeq/reax, perpetual, copy from (1)
      attributes: half, newton off, ghost
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 1803.0 | 1803.0 | 1803.0 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          200   -39091.147            0   -20014.559    19501.107 
     100    63.198252   -26042.062            0   -20014.027    21497.661 
Loop time of 38.6526 on 1 procs for 100 steps with 32000 atoms

Performance: 0.224 ns/day, 107.368 hours/ns, 2.587 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 23.493     | 23.493     | 23.493     |   0.0 | 60.78
Neigh   | 0.4498     | 0.4498     | 0.4498     |   0.0 |  1.16
Comm    | 0.020568   | 0.020568   | 0.020568   |   0.0 |  0.05
Output  | 6.8e-05    | 6.8e-05    | 6.8e-05    |   0.0 |  0.00
Modify  | 14.677     | 14.677     | 14.677     |   0.0 | 37.97
Other   |            | 0.01223    |            |       |  0.03

Nlocal:        32000.0 ave       32000 max       32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        26825.0 ave       26825 max       26825 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3.73924e+06 ave 3.73924e+06 max 3.73924e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3739236
Ave neighs/atom = 116.85112
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:39
