#  define units
units       lj

#  specify periodic boundary conditions
boundary p p p

#  define atom_style
#  full covers everything
atom_style  full 

#  define simulation volume 
#  If I want N = 512 atoms 
#  and I want a density of rho = 0.5 atoms/lj-sigma^3
#  Then I can determine the size of a cube by 
#  size = (N/rho)^(1/3)
variable side      equal 10.0793684
region      boxid block 0.0 ${side} 0.0 ${side} 0.0 ${side}
create_box  1 boxid

#  specify initial positions of atoms
#  sc = simple cubic
#  0.5 = density in lj units
lattice     sc 0.50

#  place atoms of type 1 in boxid
create_atoms    1 box

#   define mass of atom type 1
mass        1 1.0

#  specify initial velocity of atoms
#  group = all
#  reduced temperature is T = 1.0 = lj-eps/kb 
#  seed for random number generator
#  distribution is gaussian (e.g. Maxwell-Boltzmann)
velocity    all create 1.0 87287 dist gaussian

#  specify interaction potential
#  pairwise interaction via the Lennard-Jones potential with a cut-off at 2.5 lj-sigma
pair_style  lj/cut 2.5

#  specify parameters between atoms of type 1 with an atom of type 1
#  epsilon = 1.0, sigma = 1.0, cutoff = 2.5
pair_coeff  1 1 1.0 1.0 2.5

# add long-range tail correction
pair_modify tail yes

#  specify parameters for neighbor list 
#  rnbr = rcut + 0.3
neighbor    0.3 bin

#  specify thermodynamic properties to be output
#  pe = potential energy
#  ke = kinetic energy
#  etotal = pe + ke
#  temp = temperature
#  press = pressure
#  density = number density
#  output every thousand steps
#  norm = normalize by # of atoms (yes or no)
thermo_style custom step pe ke etotal temp press density

# report instantaneous thermo values every 100 steps
thermo 100

# normalize thermo properties by number of atoms (yes or no)
thermo_modify norm no

#  specify ensemble
#  fixid = 1
#  atoms = all
#  ensemble = nve or nvt
fix     1 all nve

#  define time step
timestep 0.005

# run 1000 steps in the NVE ensemble
# (this equilibrates positions)
run 1000

#  stop fix with given fixid
#  fixid = 1
unfix 1

#  specify ensemble
#  fixid = 2
#  atoms = all
#  ensemble = nvt
#  temp = temperature
#  initial temperature = 1.0
#  final temperature = 1.0
#  thermostat controller gain = 0.1 (units of time, bigger is less tight control)
fix     2 all nvt temp 1.0 1.0 0.1 

# run 1000 steps in the NVT ensemble
# (this equilibrates thermostat)
run     1000

#   save configurations
#   dumpid = 1
#   all atoms
#   atomic symbol is Ar
#   save positions every 100 steps
#   filename = output.xyz
#
dump    1       all xyz 100 output.xyz
dump_modify 1 element Ar

# run 1000 more steps in the NVT ensemble
# (this is data production, from which configurations are saved) 
run     2000