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 1 by 1 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 = 7.6729 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          300   -10.438105            0    -10.39963   -5445.2808 
      10    290.48923   -10.436885            0   -10.399629   -5646.4813 
      20    271.18868   -10.434409            0   -10.399629   -5654.4646 
      30     246.2601   -10.431212            0   -10.399629   -5281.8873 
      40    218.69918   -10.427677            0   -10.399629   -4343.3636 
      50    189.12519   -10.423885            0   -10.399629   -2903.1138 
      60    155.55701   -10.419579            0   -10.399629   -1402.2278 
      70    118.83581   -10.414869            0   -10.399629   -146.36141 
      80    85.903126   -10.410645            0   -10.399628    857.74986 
      90    65.223651   -10.407993            0   -10.399628    1494.2746 
     100    59.833542   -10.407302            0   -10.399628    1938.9164 
Loop time of 11.0736 on 1 procs for 100 steps with 128 atoms

Performance: 0.390 ns/day, 61.520 hours/ns, 9.030 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 11.072     | 11.072     | 11.072     |   0.0 | 99.99
Neigh   | 0.00041604 | 0.00041604 | 0.00041604 |   0.0 |  0.00
Comm    | 0.00046253 | 0.00046253 | 0.00046253 |   0.0 |  0.00
Output  | 0.0001657  | 0.0001657  | 0.0001657  |   0.0 |  0.00
Modify  | 0.0002265  | 0.0002265  | 0.0002265  |   0.0 |  0.00
Other   |            | 0.0003119  |            |       |  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:    3425 ave 3425 max 3425 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:  6850 ave 6850 max 6850 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 6850
Ave neighs/atom = 53.5156
Neighbor list builds = 1
Dangerous builds = 0

Total wall time: 0:00:11
