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#
# 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