# Simulation of Al sputtering deposition on Si in He gas 
 # He maintained in box via fix wall/reflect command
 # Not sticked Al allowed to escape since ppm PBC 
 processors 2 2 1
 units metal
 dimension 3
 boundary p p m 
 atom_style atomic 
log logHeAlHewBv2.lammps
 lattice    diamond 5.43
 region     box block 0 10 0 10 0 60
 create_box    4 box
 create_atoms  2 box

 region space block INF INF INF INF 3.5 60  
 group  deleteatom region space
 delete_atoms group deleteatom
 
 region  Hereg block INF INF INF INF 3.5 53
 create_atoms 3 random 100 78913942 Hereg
 
 region     sputt block 1 9 1 9 55 60 
 
 region mobile block INF INF INF INF 0.5 3
 
 variable mass1 index  26.98154
 variable mass2 index  28.0855
 variable mass3 index  4.0026
 variable mass4 index  4.0026
 
 mass 1 ${mass1}
 mass 2 ${mass2}
 mass 3 ${mass3}
 mass 4 ${mass4}
 
 group Al   type 1 
 group Si   type 2
 group He   type 3
 group HeB 	type 4
 
  variable Tg equal 300. 
  variable Ts equal 300.
  variable Tt equal 200000
  variable TB equal 600000
  
  variable vzTt equal 0.90897868*sqrt(${Tt}/${mass1})
  variable vzTB equal 0.90897868*sqrt(${TB}/${mass4})

 velocity  Si  create ${Ts} 4928459  dist gaussian units box
 velocity  He  create ${Tg} 4927459  dist gaussian units box

 pair_style hybrid tersoff eam/fs lj/cut 10.0 table linear 4999 
 pair_coeff  * * tersoff   Si.tersoff        NULL Si   NULL NULL
 pair_coeff  * * eam/fs    Al_mm.eam.fs      Al   NULL NULL NULL 
 pair_coeff  1 2 lj/cut 0.0828250  3.223         # Al-Si  
 pair_coeff  1 3 lj/cut 0.0185836  2.59          # Al-He
 pair_coeff  1 4 lj/cut 0.0185836  2.59          # Al-HeB
 pair_coeff  2 3 lj/cut 0.0039265  3.193         # Si-He
 pair_coeff  2 4 lj/cut 0.0185836  2.59          # Al-HeB
 pair_coeff  3 3 table  He_He_JW2013.table  HeHe # He-He
 pair_coeff  3 4 lj/cut 0.000881  2.56           # He-HeB
 pair_coeff  4 4 table  He_He_JW2013.table  HeHe # HeB-HeB
 

 
 neighbor 0.3 bin
 neigh_modify delay 10 every 10 check yes

 timestep	0.00025

 compute  add    Al temp
 compute_modify	add dynamic/dof yes extra/dof 0
 compute  mobile Si temp
 compute  vapor  He  temp
 compute  totaltemp all temp

 fix         1  all nve
 fix         2  Si langevin ${Ts} ${Ts} 0.1 48279
 fix_modify  2  temp mobile
 fix         3  He langevin ${Tg} ${Tg} 0.1 48259
 fix_modify  3  temp mobile
  fix         4 He wall/reflect zhi EDGE
 
 thermo		8000
 thermo_modify	temp mobile

 dump        1 all    xyz 40000 dumpAlwHeBv2.xyz #because varying output atom number
 dump_modify 1 element Al Si He N
 #dump        2 all custom 800000 dumpAlwHeB.lammpstrj id type x y z vx vy vz
 
 
 variable        i loop 1000
 label loopa
 variable        s1 equal floor(random(2101,6017,45997))
 variable        s2 equal floor(random(2101,6017,45987))
 variable        s3 equal random(0.00001,0.99999,45995)
 variable        s4 equal random(0.00001,0.99999,45985)
 variable        s5 equal random(0.00001,0.99999,45975)
 variable        s6 equal random(0.00001,0.99999,45965)
 variable        s7 equal random(0.00001,0.99999,45955)
 variable        s8 equal random(0.00001,0.99999,45945) 
 
 variable vzAl   equal -${vzTt}*sqrt(-2*ln(${s3}))*abs(cos(2*PI*${s4}))
 variable vxAl   equal  ${vzTt}*sqrt(-2*ln(${s5}))*cos(2*PI*${s6})
 variable vyAl   equal  ${vzTt}*sqrt(-2*ln(${s5}))*sin(2*PI*${s6})
 
 print  "${vxAl} ${vyAl} ${vzAl} "
 
 variable vzHeB  equal -${vzTB}*sqrt(-2*ln(${s3}))*abs(sin(2*PI*${s4}))
 variable vxHeB  equal  ${vzTB}*sqrt(-2*ln(${s7}))*cos(2*PI*${s8})
 variable vyHeB  equal  ${vzTB}*sqrt(-2*ln(${s7}))*sin(2*PI*${s8})
 
 print  "${vxHeB} ${vyHeB} ${vzHeB} "
 
 fix         5 Al  deposit 10 1 8000 ${s1} region sputt vx ${vxAl} ${vxAl} vy ${vyAl} ${vyAl} vz ${vzAl} ${vzAl} near 2.0 units box
 thermo_style custom step c_mobile c_vapor c_add c_totaltemp pe etotal press vol
 run 80000
 unfix 5 
 fix         5 HeB deposit 1  4 8000 ${s2} region sputt vx ${vxHeB} ${vxHeB} vy ${vyHeB} ${vyHeB} vz ${vzHeB} ${vzHeB} near 2.0 units box
 thermo_style custom step c_mobile c_vapor c_add c_totaltemp pe etotal press vol
 run 8000
 unfix 5
 next    i  
 jump SELF loopa