Added W-Be example to example/snap folder

../../potentials/WBe_Wood_PRB2019.snap

 No newline at end of file

../../potentials/WBe_Wood_PRB2019.snapcoeff

 No newline at end of file

../../potentials/WBe_Wood_PRB2019.snapparam

 No newline at end of file

# 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 ny equal ${nrep}

variable nz equal ${nrep}

boundary	p p p

lattice         bcc $a

region		box block 0 ${nx} 0 ${ny} 0 ${nz}

create_box	2 box

create_atoms	1 box

mass 1 183.84

mass 2 9.012182

set	group all type/fraction 2 0.05 3590153 # Change 5% of W to He

group	tungsten 	 type 1

group	beryllium	 type 2

# choose potential

include WBe_Wood_PRB2019.snap

# 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}

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