LAMMPS (7 Aug 2019)
# 3d Lennard-Jones melt
#
# This example requires that the KIM Portable Model (PM)
# SW_StillingerWeber_1985_Si__MO_405512056662_005
# is installed.  This can be done with the command
#   kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
# 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).
#
# Or, 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	SW_StillingerWeber_1985_Si__MO_405512056662_005 real
#=== BEGIN kim-init ==========================================
units real
#=== END kim-init ============================================


lattice		fcc 4.4300
Lattice spacing in x,y,z = 4.43 4.43 4.43
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 0 0) to (88.6 88.6 88.6)
  1 by 2 by 2 MPI processor grid
create_atoms	1 box
Created 32000 atoms
  create_atoms CPU = 0.000997 secs

kim_interactions Si
#=== BEGIN kim_interactions ==================================
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
pair_coeff * * Si 
#=== 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
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.07118
  ghost atom cutoff = 4.07118
  binsize = 2.03559, bins = 44 44 44
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair kim, perpetual
      attributes: full, newton off, cut 4.07118
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Setting up Verlet run ...
  Unit style    : real
  Current step  : 0
  Time step     : 1
Per MPI rank memory allocation (min/avg/max) = 3.517 | 3.517 | 3.517 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          200   -85249.847            0   -66173.259   -33302.387 
     100    253.43357    -90346.68            0   -66173.441   -14888.698 
Loop time of 19.0287 on 4 procs for 100 steps with 32000 atoms

Performance: 0.454 ns/day, 52.857 hours/ns, 5.255 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 18.81      | 18.838     | 18.883     |   0.6 | 99.00
Neigh   | 0.018598   | 0.01914    | 0.020732   |   0.7 |  0.10
Comm    | 0.10341    | 0.1475     | 0.17393    |   7.1 |  0.78
Output  | 6e-05      | 6.225e-05  | 6.7e-05    |   0.0 |  0.00
Modify  | 0.014839   | 0.014925   | 0.015047   |   0.1 |  0.08
Other   |            | 0.008997   |            |       |  0.05

Nlocal:    8000 ave 8014 max 7988 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost:    3374.75 ave 3389 max 3361 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:    0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:  100588 ave 100856 max 100392 min
Histogram: 1 0 1 0 1 0 0 0 0 1

Total # of neighbors = 402352
Ave neighs/atom = 12.5735
Neighbor list builds = 4
Dangerous builds = 0

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

Total wall time: 0:00:19
