Renamed InP potential files and create standard log files

LAMMPS (2 Jun 2020)

# Demonstrate SNAP InP potential

# Initialize simulation

variable nsteps index 100

variable nrep equal 4

variable a equal 5.83

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         diamond $a

lattice         diamond 5.83

Lattice spacing in x,y,z = 5.83 5.83 5.83

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 0.0 0.0) to (23.32 23.32 23.32)

  1 by 1 by 1 MPI processor grid

create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2

Created 512 atoms

  create_atoms CPU = 0.000 seconds

mass 1 114.76

mass 2 30.98

# choose potential

include InP_JCPA2020.snap

# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)

# Definition of SNAP+ZBL potential.

variable zblcutinner equal 4

variable zblcutouter equal 4.2

variable zblz1 equal 49

variable zblz2 equal 15

# 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 4.2 snap

pair_coeff 1 1 zbl ${zblz1} ${zblz1}

pair_coeff 1 1 zbl 49 ${zblz1}

pair_coeff 1 1 zbl 49 49

pair_coeff 1 2 zbl ${zblz1} ${zblz2}

pair_coeff 1 2 zbl 49 ${zblz2}

pair_coeff 1 2 zbl 49 15

pair_coeff 2 2 zbl ${zblz2} ${zblz2}

pair_coeff 2 2 zbl 15 ${zblz2}

pair_coeff 2 2 zbl 15 15

pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P

Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01

SNAP Element = In, Radius 3.81205, Weight 1 

SNAP Element = P, Radius 3.82945, Weight 0.929316 

Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01

SNAP keyword rcutfac 1.0 

SNAP keyword twojmax 6 

SNAP keyword rfac0 0.99363 

SNAP keyword rmin0 0.0 

SNAP keyword bzeroflag 1 

SNAP keyword quadraticflag 0 

SNAP keyword wselfallflag 1 

SNAP keyword alloyflag 1 

# 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 = 8.6589

  ghost atom cutoff = 8.6589

  binsize = 4.32945, bins = 6 6 6

  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) = 6.027 | 6.027 | 6.027 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          300   -3.4805794            0   -3.4418771    1353.5968 

      10    286.42264   -3.4788274            0   -3.4418767    1586.4881 

      20    250.14148   -3.4741459            0   -3.4418757    2219.0344 

      30    202.52417   -3.4680017            0   -3.4418745    2982.7272 

      40    157.39113   -3.4621782            0   -3.4418735    3631.0936 

      50     126.7004   -3.4582183            0    -3.441873    4053.7725 

      60    117.00722   -3.4569679            0    -3.441873    4204.9542 

      70    127.65968   -3.4583427            0   -3.4418736    4106.3112 

      80    151.50217   -3.4614195            0   -3.4418745    3840.7205 

      90    177.67607    -3.464797            0   -3.4418754    3527.9794 

     100    195.30359   -3.4670717            0   -3.4418761    3300.3795 

Loop time of 18.1983 on 1 procs for 100 steps with 512 atoms

Performance: 0.237 ns/day, 101.102 hours/ns, 5.495 timesteps/s

99.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 18.196     | 18.196     | 18.196     |   0.0 | 99.99

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0.00104    | 0.00104    | 0.00104    |   0.0 |  0.01

Output  | 0.000262   | 0.000262   | 0.000262   |   0.0 |  0.00

Modify  | 0.000576   | 0.000576   | 0.000576   |   0.0 |  0.00

Other   |            | 0.000486   |            |       |  0.00

Nlocal:    512 ave 512 max 512 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    1959 ave 1959 max 1959 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    31232 ave 31232 max 31232 min

Histogram: 1 0 0 0 0 0 0 0 0 0

FullNghs:  62464 ave 62464 max 62464 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 62464

Ave neighs/atom = 122

Neighbor list builds = 0

Dangerous builds = 0

Total wall time: 0:00:18

LAMMPS (2 Jun 2020)

# Demonstrate SNAP InP potential

# Initialize simulation

variable nsteps index 100

variable nrep equal 4

variable a equal 5.83

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         diamond $a

lattice         diamond 5.83

Lattice spacing in x,y,z = 5.83 5.83 5.83

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 0.0 0.0) to (23.32 23.32 23.32)

  1 by 2 by 2 MPI processor grid

create_atoms    1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2

Created 512 atoms

  create_atoms CPU = 0.001 seconds

mass 1 114.76

mass 2 30.98

# choose potential

include InP_JCPA2020.snap

# DATE: 2020-06-01 CONTRIBUTOR: Mary Alice Cusentino mcusent@sandia.gov CITATION: M.A. Cusentino, M. A. Wood, and A.P. Thompson, "Explicit Multi-element Extension of the Spectral Neighbor Analysis Potential for Chemically Complex Systems", J. Phys. Chem. A, xxxxxx (2020)

# Definition of SNAP+ZBL potential.

variable zblcutinner equal 4

variable zblcutouter equal 4.2

variable zblz1 equal 49

variable zblz2 equal 15

# 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 4.2 snap

pair_coeff 1 1 zbl ${zblz1} ${zblz1}

pair_coeff 1 1 zbl 49 ${zblz1}

pair_coeff 1 1 zbl 49 49

pair_coeff 1 2 zbl ${zblz1} ${zblz2}

pair_coeff 1 2 zbl 49 ${zblz2}

pair_coeff 1 2 zbl 49 15

pair_coeff 2 2 zbl ${zblz2} ${zblz2}

pair_coeff 2 2 zbl 15 ${zblz2}

pair_coeff 2 2 zbl 15 15

pair_coeff * * snap InP_JCPA2020.snapcoeff InP_JCPA2020.snapparam In P

Reading potential file InP_JCPA2020.snapcoeff with DATE: 2020-06-01

SNAP Element = In, Radius 3.81205, Weight 1 

SNAP Element = P, Radius 3.82945, Weight 0.929316 

Reading potential file InP_JCPA2020.snapparam with DATE: 2020-06-01

SNAP keyword rcutfac 1.0 

SNAP keyword twojmax 6 

SNAP keyword rfac0 0.99363 

SNAP keyword rmin0 0.0 

SNAP keyword bzeroflag 1 

SNAP keyword quadraticflag 0 

SNAP keyword wselfallflag 1 

SNAP keyword alloyflag 1 

# 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 = 8.6589

  ghost atom cutoff = 8.6589

  binsize = 4.32945, bins = 6 6 6

  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) = 4.587 | 4.587 | 4.587 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          300   -3.4805794            0   -3.4418771    1353.5968 

      10    286.58246    -3.478848            0   -3.4418767     1582.995 

      20    250.70996   -3.4742192            0   -3.4418757    2207.7507 

      30    203.58199   -3.4681382            0   -3.4418746    2968.5206 

      40    158.84622    -3.462366            0   -3.4418736    3619.0285 

      50    128.30488   -3.4584254            0   -3.4418731     4047.173 

      60    118.40349   -3.4571481            0   -3.4418731    4203.3421 

      70    128.48973   -3.4584499            0   -3.4418737    4109.0296 

      80    151.54241   -3.4614247            0   -3.4418746    3847.4617 

      90    176.92084   -3.4646996            0   -3.4418755    3548.7811 

     100     193.9555   -3.4668978            0   -3.4418761    3342.8083 

Loop time of 5.73708 on 4 procs for 100 steps with 512 atoms

Performance: 0.753 ns/day, 31.873 hours/ns, 17.430 timesteps/s

99.3% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 5.5736     | 5.5812     | 5.591      |   0.3 | 97.28

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0.14432    | 0.15366    | 0.16168    |   1.6 |  2.68

Output  | 0.000187   | 0.00024775 | 0.000419   |   0.0 |  0.00

Modify  | 0.000293   | 0.00038075 | 0.000582   |   0.0 |  0.01

Other   |            | 0.00161    |            |       |  0.03

Nlocal:    128 ave 128 max 128 min

Histogram: 4 0 0 0 0 0 0 0 0 0

Nghost:    1099 ave 1099 max 1099 min

Histogram: 4 0 0 0 0 0 0 0 0 0

Neighs:    7808 ave 7808 max 7808 min

Histogram: 4 0 0 0 0 0 0 0 0 0

FullNghs:  15616 ave 15616 max 15616 min

Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 62464

Ave neighs/atom = 122

Neighbor list builds = 0

Dangerous builds = 0

Total wall time: 0:00:05