# Name of the script - Example

units		metal
atom_style	atomic
boundary	p p p
pair_style	sw

variable a equal 5.4379
lattice         custom $a               &
                a1 1.0 0.0 0.0          &
                a2 0.0 1.0 0.0          &
                a3 0.0 0.0 1.0          &
                basis 0.0 0.0 0.0       &
                basis 0.0 0.5 0.5       &
                basis 0.5 0.0 0.5       &
                basis 0.5 0.5 0.0       &
                basis 0.25 0.25 0.25    &
                basis 0.25 0.75 0.75    &
                basis 0.75 0.25 0.75    &
                basis 0.75 0.75 0.25

region 	myreg block		0 4  &  
				0 3  &  
				0 4 


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

#read_restart   dump.90000.restart
#create_atoms 1 single 10 19 10
#create_atoms 1 single 10.87 11.16 10.87 units lattice
#fix 1 all deposit 1 1 500000 12345 region myreg global 10.875 11.16 10.875 vz 0 -11.7 units lattice


create_box      1 myreg
create_atoms    1 region myreg	

mass            1       28.06				


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

pair_style	sw
pair_coeff      * * Si.sw Si

#------defining groups of atoms for further processing----

group fixed id <= 192
group mobile id <> 193 384

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

velocity fixed set 0.0 0.0 0.0
velocity mobile create 300.0 4928459 dist gaussian


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

timestep        0.005                            
neighbor        0.2 bin                             
neigh_modify    every 1 delay 10 check yes

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

fix 1 mobile nvt temp 300.0 300.0 100.0    ##Thermo_style dumps only the temp pertaining to the mobile compute group.

#------output files-------------------------------
#dump		myDump1 num1 custom 100 exmp_n1.dump.bin id x y z
#dump		myDump1 num1 custom 100 exmp_n2.dump xu yu zu
#dump		myDump4 num2 xyz 20 exmp.movie_p2.xyz

##dump		 all 20 exmp.movie_p1 id type x y z vx vy vz
dump        myDump2 all xyz 20 dump.movie.xyz
#dump        myDump2 all custom 20 dump.movie id type x y z vx vy vz


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


#min_style cg
#minimize 1e-25 1e-25 5000 10000
thermo_style	custom step temp press pe ke etotal 
thermo  100

run	500000

unfix 1

# fix ID group-ID deposit N type M seed keyword values. This is used to add the extra atom.

fix 1 all deposit 1 1 500000 29494 region myreg local 13.02094 18.38892 13.9674 vx 0 0 vy 0 -11.7 vz 0 0 units box
dump        myDump2 all xyz 20 dump.movie.xyz
thermo 150

run 550000