# Create T = Temperature and r=density variables (reduced in LJ units)
variable T equal 0.80
variable r equal 0.80 
 
# Create variable for sampling frequency (in timesteps): DCD trajectory, MSD, RDF, Thermodynamic Properties
variable f equal 10
 
# Create variable for the number of timesteps to equilibrate
variable e equal 1000
 
# Create variable for the number of timesteps for production
variable n equal 2000
 
# Units for simulation
units  lj

# set the boundaries to be fixed
boundary f f f
 
# Simulation style 
atom_style atomic
 
# Create lattice for atom placement (lattice type and "scale")
# For LJ units scale is reduced density
# For non-LJ units scale is the lattice constant
lattice fcc $r
 
# Define variable for box length (reduced by lattice constant - determined automatically from density for LJ units)
variable L equal 7.0
 
# Create a region for the box [-L,L] in x,y,z-directions
region box block -$L $L -$L $L -$L $L
 
 
# Create the box (id, region)
create_box 1 box
 
# Specifiy the mass of atoms (atom id, mass (reduced))
mass 1 1.0
 
# Create the atoms (id, region)
create_atoms 1 box
 
# Define the potential style (smooths LJ potential to zero between 4.5 and 5.0 sigma)
pair_style lj/smooth 4.5 5.0
 
# Define pair coefficients (for pair 1-1:  eps = 1.0 and sig = 1.0) 
pair_coeff 1 1 1.0 1.0
 
# Set neighbor list skin distance (keep list 1 sigma beyond force cutoff)
neighbor 1.0 bin
 
# Assign initial velocities (T* = $T, random seed = 1234)
velocity all create $T 1234 
 
# Fix the integrator for the atoms (id, atoms, T* initial, T* finial, Drag Coeff)
# Note: Uses Nose-Hoover thermostat
fix 1 all nvt temp $T $T 0.005
 
# Implementing a reflective wall
#fix 2 all wall/reflect xlo -$L xhi $L ylo -$L yhi $L zlo -$L zhi $L 
fix 2 all wall/reflect xlo EDGE xhi EDGE ylo EDGE yhi EDGE zlo EDGE zhi EDGE
 
# Write thermo properties to log (frequency (timesteps))
thermo $f

# create a dcd file
dump 1 all dcd $f movie_luis.dcd 

# generate the initial configuration of the system
dump 2 all xyz $n initial.xyz
 
# Run simulation to equilibrate the system (no. timesteps, default timestep for LJ units is 0.005tau)
run $e
 
# Run simulation for the production phase (no. timesteps, default timestep for LJ units is 0.005tau)
run $n