#
#  define units
#
units       lj

#
#  specify periodic boundary conditions
#
boundary p p p

#
#  define atom_style
#  full covers everything
#
atom_style  full 

#
# Setup the simulatioon box  
#
variable blen      equal 12.5
region      boxid block 0.0       ${blen}      0.0       ${blen}      0.0       ${blen}
create_box  2 boxid

#
#  Split the simulation into two regions
#
variable    half_x equal ${blen}/2.0
region      boxa  block 0.0       ${half_x} 0.0 ${blen} 0.0 ${blen} 
region      boxb  block ${half_x} ${blen}      0.0 ${blen} 0.0 ${blen} 

#
#  specify initial positions of atoms
#  sc = simple cubic
#  0.5 = density in lj units
#
lattice     sc 0.50
#  place atoms of type 1 in boxa
#  place atoms of type 2 in boxb
create_atoms    1 region boxa
create_atoms    2 region boxb

#
#   define mass
#
#   mass of atom type 1
mass        1 1.0
mass        2 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
pair_coeff  2 2 1.2 0.9 2.5

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

#
# Specify timestep
#
timestep 0.001

#
# Write thermodynamic parameters to log
#
thermo_style custom step pe ke etotal temp press density
thermo 1000
thermo_modify norm no

#
# Setup plumed and that we are going to run npt equilibration
#
fix     1 all plumed plumedfile plumed.dat outfile p.log
fix     2 all npt temp 1.0 1.0 0.1 iso 0.0 0.0 0.4

#
#   save trajectory and restart file
#   dumpid = 1
#   filename = output.xyz
#
dump    1       all xyz 1000 output.xyz
dump_modify 1 element Ar Ne
restart 100000 lj.equilibration.restart

#
# Run 5000000 of equilibration
#
run     100000