# Name of the script - Example

units		metal
atom_style	atomic
boundary	p p p
pair_style	sw


#--------Reading Configuration----------


read_data   StartingSi1.xyz
mass            1       28.06

#------interaction coefficients e,sigma,cutouff----------

pair_coeff      * * Si.sw Si

#------defining groups of atoms for further processing----
#group num1 type 1
group fixed id <= 192
group mobile id <> 193 385


#----initial velocity(changed from dist gaussian to units box or lattice since bulk Si)-----

velocity mobile create 300.0 4928459 dist gaussian

#-------neighbor list rebuild parameters----------

timestep        0.00005                         
neighbor        0.5 bin                             
neigh_modify    every 1 delay 10 check yes

#-------integration method(temp Tstart Tstop Tdamp)---------------

fix 1 mobile nvt temp 300.0 300.0 10000
 

#------output files-------------------------------
#dump        myDump2 all xyz 20 dump.Starting.xyz
dump        myDump2 all xyz 20 dump.Starting.xyz

#------making restart file-----------------------
#restart 10000 dump.*.restart

thermo_style	custom step temp press pe ke etotal 
thermo  100

run	200000
unfix 1

timestep        0.001                        					
fix 1 mobile nvt temp 300.0 300.0 5000.0
thermo 100
run     400000

unfix 1
timestep        0.005                        
fix 1 mobile nvt temp 300.0 300.0 1000.0
thermo 100
run     400000