#metal units: mass = grams/mole, distance = Angstroms, time = picoseconds
#             energy = eV, temperature = Kelvin, pressure = bars

units		    metal
atom_style      bond
boundary        p p f


region         box block -1.3152898809742837 75.05575668095013 -0.7720498783018925 43.344980278297996 -0.9914731218710244 100
create_box     3 box bond/types 1 extra/bond/per/atom 1

read_data       amorphous.data add merge


pair_style	    hybrid tersoff rebo lj/cut 5

pair_coeff	    * * tersoff SiO.tersoff Si O NULL 
pair_coeff	    * * rebo CH.rebo NULL NULL C

pair_coeff      1 3 lj/cut 0.5 3.629    #Si-C
pair_coeff      2 3 lj/cut 0.4 3.275    #O-C


mass		    1 28.0855        #mass of Si
mass            2 16             #mass of O
mass            3 12.1           #mass of C

neigh_modify	delay 0

group		    addCaratoms type 3
region          heat-bath block -1.3152898809742837 75.05575668095013 -0.7720498783018925 43.344980278297996 20 40
group		    middle region heat-bath

region          free      block -1.3152898809742837 75.05575668095013 -0.7720498783018925 43.344980278297996 40.1 66
group           upper region free

region          RoughnessProD block -1.3152898809742837 75.05575668095013 19 25 50 60
group		    Surface region RoughnessProD

compute         RougD Surface property/atom x z 

compute		    add addCaratoms temp
compute_modify	add dynamic/dof yes extra/dof 0

compute         MSD upper msd 
compute         den all chunk/atom bin/1d z lower 0.2 bound z 0 80  # DLC density is 1.6-2.2 g cm^-3
compute         1 addCaratoms coord/atom cutoff 1.75 group addCaratoms


fix		        1 addCaratoms nve

fix		        2 middle langevin 300 300 0.1 587283
fix		        3 middle nve

fix             4 upper nve
fix             5 upper ave/time 100 10 1000 c_MSD[*] file MSD.text ave one


region          slab block -1.3152898809742837 75.05575668095013 -0.7720498783018925 43.344980278297996 80 81
fix		        6 addCaratoms deposit 10000 3 5 12345 region slab near 3 vz -353.55 -353.55

fix             7 all ave/chunk 100 10 1000 den density/mass ave one file den-1D.test


thermo_style   custom step atoms temp epair press etotal ke pe c_MSD[3]
thermo         500
thermo_modify  temp add lost/bond ignore lost warn

dump		   1 all atom 100 dump.deposit.atom
dump		   3 Surface custom 1000 rough.text id type x z 
dump           4 addCaratoms custom 1000 coordination.text id type x y z c_1

run            10000

write_data     Final.data