read_from_file.in

include current_inputs.var
# Atomify commands start with #/

# Move camera to a nice position
#/camera position 15.0 21.8 66.5
#/camera target 13.7 15.4 10.5

# Set atom size and color
#/atom 1 1.0 #ffffff
#/atom 2 1.5 #ff0000

variable L equal 3
variable Lhalf equal $(0.5*v_L)
variable thickness equal 2.0

units lj
atom_style atomic
lattice fcc 0.5

# Create regions to place atoms
variable left equal 0.5*$L-0.5*${thickness}
variable right equal 0.5*$L+0.5*${thickness}
region system block 0 $L 0 $L 0 ${Lhalf}
region boxinside block ${left} ${right} 0 $L 0 ${Lhalf}
region boxoutside block ${left} ${right} 0 $L 0 ${Lhalf} side out

# Create a box with 2 atom types in the region system
create_box 2 system
# Create atoms of type 1 inside the inner region
create_atoms 1 region boxinside
# Create atoms of type 2 inside the outer region
create_atoms 2 region boxoutside

# Set atom masses 
mass 1 1.0
mass 2 4.0

# Give initial velocity, T=3.00, seed = 1337
velocity all create 3.00 1337 loop geom

# Choose LJ with 2.5sigma cutoff
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
neigh_modify every 1 delay 0 check yes

# Create two groups for computing diffusion coefficients
group light type 1
group heavy type 2

# Measure mean square displacement and diffusion coefficient
compute msd_light light msd com yes
variable diffusion_coeff_light equal c_msd_light[4]/6/(step*dt+1.0e-6)
variable msd_light equal c_msd_light[4]

compute msd_heavy heavy msd com yes
variable msd_heavy equal c_msd_heavy[4]
variable diffusion_coeff_heavy equal c_msd_heavy[4]/6/(step*dt+1.0e-6)

thermo ${thermo}
thermo_style custom step v_diffusion_coeff_light v_msd_light v_diffusion_coeff_heavy v_msd_heavy
fix 1 all nve
compute displace all displace/atom
compute compute_ix all property/atom ix iy iz
compute compute_xu all property/atom xu yu zu