LAMMPS (7 Aug 2019)
# Demonstrate SNAP W-Be potential

# Initialize simulation

variable nsteps index 100
variable nrep equal 4
variable a equal 3.1803
units		metal

# generate the box and atom positions using a BCC 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         bcc $a
lattice         bcc 3.1803
Lattice spacing in x,y,z = 3.1803 3.1803 3.1803
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	2 box
Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 128 atoms
  create_atoms CPU = 0.000234842 secs
mass 1 183.84
mass 2 9.012182

set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He
  5 settings made for type/fraction
group	tungsten 	 type 1
123 atoms in group tungsten
group	beryllium	 type 2
5 atoms in group beryllium
# choose potential

include WBe_Wood_PRB2019.snap
# Definition of SNAP+ZBL potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz1 equal 74
variable zblz2 equal 4

# Specify hybrid with SNAP and ZBL

pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap
pair_style hybrid/overlay zbl 4 4.8 snap
pair_coeff 1 1 zbl ${zblz1} ${zblz1}
pair_coeff 1 1 zbl 74 ${zblz1}
pair_coeff 1 1 zbl 74 74
pair_coeff 1 2 zbl ${zblz1} ${zblz2}
pair_coeff 1 2 zbl 74 ${zblz2}
pair_coeff 1 2 zbl 74 4
pair_coeff 2 2 zbl ${zblz2} ${zblz2}
pair_coeff 2 2 zbl 4 ${zblz2}
pair_coeff 2 2 zbl 4 4
pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be
SNAP Element = W, Radius 0.5, Weight 1 
SNAP Element = Be, Radius 0.417932, Weight 0.959049 
SNAP keyword rcutfac 4.8123 
SNAP keyword twojmax 8 
SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 
SNAP keyword bzeroflag 1 
SNAP keyword quadraticflag 0 


# Setup output

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
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 = 5.8123
  ghost atom cutoff = 5.8123
  binsize = 2.90615, bins = 5 5 5
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair zbl, perpetual, half/full from (2)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
  (2) pair snap, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          300   -8.5980876            0   -8.5596125   -35284.855 
      10    299.29029   -8.5979965            0   -8.5596125   -35299.259 
      20    288.99334   -8.5966759            0   -8.5596124   -35004.093 
      30    269.91027   -8.5942284            0   -8.5596123   -34447.077 
      40    243.57361   -8.5908505            0   -8.5596121   -33687.105 
      50    212.21385   -8.5868284            0   -8.5596119   -32821.864 
      60    178.77144   -8.5825391            0   -8.5596116    -31971.17 
      70    146.71854    -8.578428            0   -8.5596113    -31245.51 
      80    119.50956   -8.5749383            0   -8.5596111   -30724.137 
      90    99.872785   -8.5724197            0    -8.559611   -30440.244 
     100    89.604584   -8.5711027            0   -8.5596109   -30392.805 
Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms

Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s
199.5% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.1672     | 3.1672     | 3.1672     |   0.0 | 99.97
Neigh   | 0.00030208 | 0.00030208 | 0.00030208 |   0.0 |  0.01
Comm    | 0.00029612 | 0.00029612 | 0.00029612 |   0.0 |  0.01
Output  | 0.00019813 | 0.00019813 | 0.00019813 |   0.0 |  0.01
Modify  | 0.00014448 | 0.00014448 | 0.00014448 |   0.0 |  0.00
Other   |            | 0.0001433  |            |       |  0.00

Nlocal:    128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    727 ave 727 max 727 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    3710 ave 3710 max 3710 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  7420 ave 7420 max 7420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 7420
Ave neighs/atom = 57.9688
Neighbor list builds = 1
Dangerous builds = 0

Total wall time: 0:00:03
