LAMMPS (27 May 2021)
# Demonstrate MLIAP interface to SNAP nn Cu potential

# Initialize simulation

variable nsteps index 100
variable nrep equal 4
variable a equal 3.621262
units           metal

# generate the box and atom positions using a FCC lattice

variable nx equal ${nrep}
variable nx equal 4
variable ny equal ${nrep}
variable ny equal 4
variable nz equal ${nrep}
variable nz equal 4

boundary        p p p

lattice         fcc $a
lattice         fcc 3.621262
Lattice spacing in x,y,z = 3.6212620 3.6212620 3.6212620
region          box block 0 ${nx} 0 ${ny} 0 ${nz}
region          box block 0 4 0 ${ny} 0 ${nz}
region          box block 0 4 0 4 0 ${nz}
region          box block 0 4 0 4 0 4
create_box      1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.485048 14.485048 14.485048)
  1 by 2 by 2 MPI processor grid
create_atoms    1 box
Created 256 atoms
  create_atoms CPU = 0.000 seconds

mass 1 63.546

# choose potential

pair_style mliap model nn Cu.nn.mliap.model descriptor sna Cu.snap.mliap.descriptor
Reading potential file Cu.nn.mliap.model with DATE: 2021-03-03
Reading potential file Cu.snap.mliap.descriptor with DATE: 2021-03-03
SNAP keyword rcutfac 5.0 
SNAP keyword twojmax 6 
SNAP keyword nelems 1 
SNAP keyword elems Cu 
SNAP keyword radelems 0.5 
SNAP keyword welems 1.0 
SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 
SNAP keyword bzeroflag 0 
SNAP keyword switchflag 1 
pair_coeff * * Cu

# Setup output

compute  eatom all pe/atom
compute  energy all reduce sum c_eatom

compute  satom all stress/atom NULL
compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)

thermo_style    custom step temp epair c_energy etotal press v_press
thermo          10
thermo_modify norm yes

# Set up NVE run

timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes

# Run MD

velocity all create 300.0 4928459 loop geom
fix 1 all nve
run             ${nsteps}
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 = 6
  ghost atom cutoff = 6
  binsize = 3, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair mliap, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 30.85 | 30.85 | 30.85 Mbytes
Step Temp E_pair c_energy TotEng Press v_press 
       0          300   -4.0935581   -4.0935581   -4.0549315   -2916.7505    2916.7505 
      10    294.11049   -4.0927998   -4.0927998   -4.0549315   -2654.7826    2654.7826 
      20    276.89115   -4.0905826   -4.0905826   -4.0549314   -1879.2872    1879.2872 
      30    249.71134   -4.0870829   -4.0870829   -4.0549312   -627.47006    627.47006 
      40    214.92415   -4.0826036   -4.0826036    -4.054931    995.44801   -995.44801 
      50    175.86879   -4.0775747   -4.0775747   -4.0549307    2811.6019   -2811.6019 
      60    136.62706   -4.0725218   -4.0725218   -4.0549303    4640.4144   -4640.4144 
      70    101.48566   -4.0679968   -4.0679968     -4.05493    6313.5871   -6313.5871 
      80    74.248664   -4.0644897   -4.0644897   -4.0549298    7644.1364   -7644.1364 
      90    57.500423   -4.0623332   -4.0623332   -4.0549297    8514.2222   -8514.2222 
     100    52.104609   -4.0616385   -4.0616385   -4.0549298    8870.8923   -8870.8923 
Loop time of 1.25021 on 4 procs for 100 steps with 256 atoms

Performance: 3.455 ns/day, 6.946 hours/ns, 79.987 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.2256     | 1.2347     | 1.2415     |   0.5 | 98.76
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.0074687  | 0.014311   | 0.023481   |   4.8 |  1.14
Output  | 0.00060678 | 0.00062859 | 0.00066781 |   0.0 |  0.05
Modify  | 8.7976e-05 | 9.7811e-05 | 0.00010943 |   0.0 |  0.01
Other   |            | 0.0004484  |            |       |  0.04

Nlocal:        64.0000 ave          64 max          64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:        843.000 ave         843 max         843 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs:      4992.00 ave        4992 max        4992 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 19968
Ave neighs/atom = 78.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01
