# 2d Lennard-Jones melt

variable    x index 1
variable    y index 1
variable    z index 1

variable    xx equal 40*$x
variable    yy equal 20*$y
variable    zz equal 20*$z

units        lj
atom_style    atomic
dimension 2
timestep 0.0032

#lattice       hex 0.8442 #Set the lattice vector
region        box block 0 ${xx} 0 ${yy} 0 1 # Make region for the periodic box
#region        two block 5 15 5 15 0 1 # Make a region for where the atoms will begin
create_box    1 box
#create_atoms    1 region two # Create the atoms
create_atoms 1 random 50 1 NULL
mass        1 1.0

velocity    all create 1.44 87994 loop geom # Set their initial velocity which will be scaled during the simulation

pair_style    lj/cut 2.5 # Define the intermolecular interaction with the Lennard-Jones function with a cutoff of 2.5
pair_coeff    1 1 1.0 1.0 2.5 # Setting the sigma and epsilon values

# This neighbor list improves the efficiency of the calculation by only calculating interactions with particles within cutoff+0.3
#neighbor    0.3 bin 
#neigh_modify    delay 0 every 1 check no

#dump pdump all xyz 100 dump.lj #Saves the trajectory to a file to open in VMD
dump xdump all custom 1 dumpx.lj x y z
#dump xtcdump all xtc 1 dumpxtc.lj 
#dump sdump all custom 1 dumps.lj xs ys zs
dump vdump all custom 1 dumpv.lj vx vy vz
#dump fdump all custom 1 dumpf.lj fx fy fz

dump_modify xdump format float %.20g sort id#40g
#dump_modify sdump format float %.34g
dump_modify vdump format float %.20g sort id
#dump_modify fdump format float %.15g

#dump    3 all movie 100 movie.mpg type type &
#    zoom 1.6 adiam 1.5
#dump_modify 3 pad 5

#thermo 1000

# Velocity Verlet
run_style verlet

fix        1 all nve # Performs an integration to move the sample through time
fix        2 all enforce2d # Make sure there is no forces in the z direction 
fix        bfix all temp/berendsen 0.5 0.5 0.0032#0.5 0.5 0.0032

#dump tdump all custom 1 dumptemp.lj c_3_temp
thermo 1
thermo_style custom c_bfix_temp c_thermo_temp
thermo_modify format float %1.35f

run        50 #run for this number of steps the default timestep for lj is 0.005 tau