LAMMPS (19 Sep 2019)
# Ar in real units

# simulation params in reduced units
# settable from command line
# epsilon, sigma, mass set below

variable	x index 5
variable	y index 5
variable	z index 5
variable        rhostar index 0.8842
variable        dt index 0.005
variable        cutoff index 2.5
variable        skin index 0.3
variable        tinitial index 1.0
variable        nthermo index 10
variable        nsteps index 100

# physical constants from update.cpp

variable        kb index 0.0019872067         # kB in Kcal/mole/K
variable        avogadro index 6.02214129e23  # Avogadro's number

# Ar properties in real units

variable        epskb index 117.7             # LJ epsilon/kB in degrees K
variable        sigma index 3.504             # LJ sigma in Angstroms
variable        epsilon equal ${epskb}*${kb}  # LJ epsilon in Kcal/mole
variable        epsilon equal 117.7*${kb}  
variable        epsilon equal 117.7*0.0019872067  
variable        mass index 39.95              # mass in g/mole

# scale factors

# sigma = scale factor on distance, converts reduced distance to Angs
# epsilon = scale factor on energy, converts reduced energy to Kcal/mole
# tmpscale = scale factor on temperature, converts reduced temp to degrees K
# tscale = scale factor on time, converts reduced time to fs
#   formula is t = t* / sqrt(epsilon/mass/sigma^2), but need t in fs
#   use epsilon (Joule/mole), mass (kg/mole), sigma (meter) to get t in seconds
# pscale = scale factor on pressure, converts reduced pressure to atmospheres
#   formula is P = P* / (sigma^3/epsilon), but need P in atmospheres
#   use sigma (meter), epsilon (Joule) to get P in nt/meter^2, convert to atms

variable        KcaltoJoule index 4.1868e3    # convert Kcals to Joules
variable        NtMtoAtm equal 1.0/1.0135e5   # convert Nt/meter^2 to Atmospheres

variable        tmpscale equal ${epskb}
variable        tmpscale equal 117.7
variable        epsJmole equal ${epsilon}*${KcaltoJoule}
variable        epsJmole equal 0.23389422859*${KcaltoJoule}
variable        epsJmole equal 0.23389422859*4.1868e3
variable        massKgmole equal ${mass}/1000.0
variable        massKgmole equal 39.95/1000.0
variable        sigmaM equal ${sigma}/1.0e10
variable        sigmaM equal 3.504/1.0e10
variable        sigmaMsq equal ${sigmaM}*${sigmaM}
variable        sigmaMsq equal 3.504e-10*${sigmaM}
variable        sigmaMsq equal 3.504e-10*3.504e-10
variable        tscale equal 1.0e15/sqrt(${epsJmole}/${massKgmole}/${sigmaMsq})
variable        tscale equal 1.0e15/sqrt(979.268356260612/${massKgmole}/${sigmaMsq})
variable        tscale equal 1.0e15/sqrt(979.268356260612/0.03995/${sigmaMsq})
variable        tscale equal 1.0e15/sqrt(979.268356260612/0.03995/1.2278016e-19)
variable        sigmaM3 equal ${sigmaM}*${sigmaM}*${sigmaM}
variable        sigmaM3 equal 3.504e-10*${sigmaM}*${sigmaM}
variable        sigmaM3 equal 3.504e-10*3.504e-10*${sigmaM}
variable        sigmaM3 equal 3.504e-10*3.504e-10*3.504e-10
variable        pscale equal ${NtMtoAtm}/(${sigmaM3}/(${epsJmole}/${avogadro}))
variable        pscale equal 9.86679822397632e-06/(${sigmaM3}/(${epsJmole}/${avogadro}))
variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(${epsJmole}/${avogadro}))
variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/${avogadro}))
variable        pscale equal 9.86679822397632e-06/(4.3022168064e-29/(979.268356260612/6.02214129e23))

# variables
# alat = lattice constant in Angs (at reduced density rhostar)
# temp = reduced temperature for output
# epair,emol,etotal = reduced epair,emol,etotal energies for output
# press = reduced pressure for output

variable        alat equal (4.0*${sigma}*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable        alat equal (4.0*3.504*${sigma}*${sigma}/${rhostar})^(1.0/3.0)
variable        alat equal (4.0*3.504*3.504*${sigma}/${rhostar})^(1.0/3.0)
variable        alat equal (4.0*3.504*3.504*3.504/${rhostar})^(1.0/3.0)
variable        alat equal (4.0*3.504*3.504*3.504/0.8842)^(1.0/3.0)
variable        temp equal temp/${tmpscale}
variable        temp equal temp/117.7
variable        epair equal epair/${epsilon}
variable        epair equal epair/0.23389422859
variable        emol equal emol/${epsilon}
variable        emol equal emol/0.23389422859
variable        etotal equal etotal/${epsilon}
variable        etotal equal etotal/0.23389422859
variable        press equal press/${pscale}
variable        press equal press/372.936366301003

# same script as in.ar.lj

units		real
atom_style	atomic

lattice		fcc ${alat}
lattice		fcc 5.79518437579763
Lattice spacing in x,y,z = 5.79518 5.79518 5.79518
region		box block 0 $x 0 $y 0 $z
region		box block 0 5 0 $y 0 $z
region		box block 0 5 0 5 0 $z
region		box block 0 5 0 5 0 5
create_box	1 box
Created orthogonal box = (0 0 0) to (28.9759 28.9759 28.9759)
  1 by 2 by 2 MPI processor grid
create_atoms	1 box
Created 500 atoms
  create_atoms CPU = 0.000664949 secs
mass		1 ${mass}
mass		1 39.95

velocity	all create $(v_tinitial*v_epskb) 12345
velocity	all create 117.70000000000000284 12345

pair_style	lj/cut $(v_cutoff*v_sigma)
pair_style	lj/cut 8.7599999999999997868
pair_coeff	1 1 ${epsilon} ${sigma}
pair_coeff	1 1 0.23389422859 ${sigma}
pair_coeff	1 1 0.23389422859 3.504

neighbor	$(v_skin*v_sigma) bin
neighbor	1.0511999999999999122 bin
neigh_modify	delay 0 every 20 check no

fix		1 all nve

timestep	$(v_dt*v_tscale)
timestep	11.190297512378050371

# columns 2,3,4 = temp,pe,press in real units
# columns 5-9 = temp,energy.press in reduced units, compare to in.ar.lj
# need to include real unit output to enable use of reduced variables

thermo_style    custom step temp pe press v_temp v_epair v_emol v_etotal v_press
thermo_modify	norm yes
thermo		${nthermo}
thermo		10

run		${nsteps}
run		100
Neighbor list info ...
  update every 20 steps, delay 0 steps, check no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 9.8112
  ghost atom cutoff = 9.8112
  binsize = 4.9056, bins = 6 6 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.609 | 2.609 | 2.609 Mbytes
Step Temp PotEng Press v_temp v_epair v_emol v_etotal v_press 
       0        117.7   -1.6612661   -1909.5509            1   -7.1026383            0   -5.6056383   -5.1203128 
      10    86.674156   -1.5707707   -1152.1077   0.73639895    -6.715731            0   -5.6133417   -3.0892877 
      20    42.104452   -1.4412091   -141.16344   0.35772687   -6.1617986            0   -5.6262815  -0.37851883 
      30    55.478223   -1.4819221   -410.58592   0.47135278   -6.3358644            0   -5.6302493   -1.1009544 
      40     54.54231   -1.4793231   -409.58446    0.4634011   -6.3247524            0    -5.631041    -1.098269 
      50    57.354168   -1.4876242   -457.34719   0.48729115   -6.3602431            0   -5.6307682   -1.2263411 
      60    59.835295   -1.4949249   -512.38519   0.50837124    -6.391457            0   -5.6304252   -1.3739212 
      70    60.005554   -1.4954174     -525.858   0.50981779   -6.3935625            0   -5.6303653   -1.4100475 
      80    63.469566    -1.505493   -614.29111   0.53924865   -6.4366403            0   -5.6293851   -1.6471741 
      90    65.064012   -1.5100983   -656.32951   0.55279535   -6.4563301            0   -5.6287955   -1.7598968 
     100     64.63774   -1.5088033   -644.51211   0.54917366   -6.4507932            0   -5.6286803   -1.7282093 
Loop time of 0.0285767 on 4 procs for 100 steps with 500 atoms

Performance: 3383.318 ns/day, 0.007 hours/ns, 3499.350 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.012398   | 0.014826   | 0.016774   |   1.6 | 51.88
Neigh   | 0.001797   | 0.0021547  | 0.0025899  |   0.6 |  7.54
Comm    | 0.0079622  | 0.010444   | 0.013427   |   2.3 | 36.55
Output  | 0.00042987 | 0.00047708 | 0.00059676 |   0.0 |  1.67
Modify  | 0.00028896 | 0.00038844 | 0.00049448 |   0.0 |  1.36
Other   |            | 0.0002864  |            |       |  1.00

Nlocal:    125 ave 133 max 117 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost:    1099 ave 1107 max 1091 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs:    4908.75 ave 5493 max 4644 min
Histogram: 1 2 0 0 0 0 0 0 0 1

Total # of neighbors = 19635
Ave neighs/atom = 39.27
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00
