LAMMPS (13 Feb 2017)
# Demonstrate SNAP Ta 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 2 by 2 MPI processor grid
create_atoms	1 box
Created 128 atoms
mass 1 183.84
mass 2 4.0026

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	helium	type 2
5 atoms in group helium
# choose potential

include W.SNAP_HePair.pot
# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63
#
# Definition of SNAP+ZBL+Tabulated potential.
variable zblcutinner equal 4
variable zblcutouter equal 4.8
variable zblz equal 74

# Specify hybrid with SNAP, ZBL, and long-range Coulomb

pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000
pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000
pair_coeff 	1 1 zbl ${zblz} ${zblz}
pair_coeff 	1 1 zbl 74 ${zblz}
pair_coeff 	1 1 zbl 74 74
pair_coeff 	* * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL
Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20
SNAP Element = W, Radius 0.5, Weight 1 
Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20
SNAP keyword rcutfac 4.73442 
SNAP keyword twojmax 8 
SNAP keyword gamma 1 
SNAP keyword rfac0 0.99363 
SNAP keyword rmin0 0 
SNAP keyword diagonalstyle 3 
pair_coeff      2 2 table 1 He_He_JW2013.table HeHe
Reading potential file He_He_JW2013.table with DATE: 2017-02-20
WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr.
  Should only be flagged at inflection points (../pair_table.cpp:476)
pair_coeff      1 2 table 2 W_He_JW2013.table WHe
Reading potential file W_He_JW2013.table with DATE: 2017-02-20
WARNING: 3 of 325 force values in table are inconsistent with -dE/dr.
  Should only be flagged at inflection points (../pair_table.cpp:476)
#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here
#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here.


# 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 = 5.8
  ghost atom cutoff = 5.8
  binsize = 2.9, bins = 5 5 5
  6 neighbor lists, perpetual/occasional/extra = 6 0 0
  (1) pair zbl, perpetual, half/full from (2)
      attributes: half, newton on
      pair build: halffull/newton/skip
      stencil: none
      bin: none
  (2) pair snap, perpetual, skip from (6)
      attributes: full, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) pair table, perpetual, skip from (5)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (4) pair table, perpetual, skip from (5)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (5) neighbor class addition, perpetual, half/full from (6)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
  (6) neighbor class addition, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Memory usage per processor = 7.65426 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          300   -10.438105            0    -10.39963   -5445.2808 
      10    292.13979   -10.437097            0    -10.39963   -5516.3963 
      20    272.55728   -10.434585            0   -10.399629   -5460.4268 
      30    245.06559   -10.431059            0   -10.399629   -5016.6351 
      40    212.79459    -10.42692            0   -10.399629   -3924.2175 
      50    178.03903   -10.422462            0   -10.399629   -2354.5485 
      60    141.62155   -10.417791            0   -10.399628   -595.41345 
      70    107.24843   -10.413383            0   -10.399628    1138.4107 
      80    79.985938   -10.409886            0   -10.399628    2392.1106 
      90    62.568933   -10.407652            0   -10.399628    3141.7027 
     100    56.697933   -10.406899            0   -10.399628    3583.9538 
Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms

Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.7363     | 2.8122     | 2.8636     |   2.9 | 97.79
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.011014   | 0.062439   | 0.13842    |  19.3 |  2.17
Output  | 0.00023842 | 0.00025076 | 0.0002861  |   0.0 |  0.01
Modify  | 9.2506e-05 | 9.9301e-05 | 0.00010395 |   0.0 |  0.00
Other   |            | 0.0006654  |            |       |  0.02

Nlocal:    32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:    431 ave 431 max 431 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs:    856.25 ave 885 max 818 min
Histogram: 1 0 0 0 1 0 0 0 1 1
FullNghs:  1712.5 ave 1738 max 1658 min
Histogram: 1 0 0 0 0 0 0 0 2 1

Total # of neighbors = 6850
Ave neighs/atom = 53.5156
Neighbor list builds = 0
Dangerous builds = 0

Total wall time: 0:00:02
