# 3d collision simulation

units		metal

dimension	3
boundary	p p p

atom_style	atomic
neighbor	0.5 bin
neigh_modify	every 1 delay 2 check yes

# create geometry

lattice		fcc 4.0800 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region		box block -2 2 -2 2 -2 30
create_box	2 box
 
mass		1 1.008        
mass		2 196.97         

# atom regions
region		target block -2 2 -2 2 0 20
 
# create atoms
create_atoms 	1 single 0 0.1 -1.5 units lattice
create_atoms	2 region target

# Morse, Moliere and EAM potentials
pair_style hybrid morse 0.5 table linear 8000 eam

# H-H interaction with dummy Morse, to use for molecular impacts
#pair_style morse 1.0
pair_coeff 1 1 morse 0.00001 1.0 1.0 

#H-Au interaction with Moliere
#pair_style table linear 8000
pair_coeff 1 2 table MoliereAuH.table AuH

#Au-Au interaction by EAM
#pair_style	eam
pair_coeff	2 2 eam Au_u3.eam

# define groups
group		ion type 1
group		film region target
group		film type 2
group		mobile union film ion 

# initial velocities
fix		1 all nve

compute 1 film ke/atom
compute 2 film centro/atom
compute 3 film pe/atom
compute 4 film stress/atom pair
compute 5 ion ke/atom
compute		new3d film temp

velocity	film create 1.0 5812775 temp new3d
velocity	ion set 0.0000 0.0000 0.0000 

thermo		100
thermo_style	custom step temp pe ke etotal press vol
thermo_modify	temp new3d norm yes

timestep	0.001
### Begin bombardment run
reset_timestep	0

## Add stopping force as a viscous force 
##(proportional to velocity). Q viscous is 0.3 in atomic units. NIMB 164-165 (2000) 268.
## Note that this will act before it hits target and therefore has to check enntry&exit energy
## solution: put a loop and check z coordinate of projectile to fix-unfix viscous
fix 3 ion viscous 0.000710

timestep	0.001
fix 4 all dt/reset 1 0.000001 0.005 0.03 units box

thermo		500
thermo_style	custom step temp pe ke etotal press vol
thermo_modify	temp new3d norm yes
dump		rasmol film custom 4500 DUMP/dump.col.* x y z c_1 c_2 type vx vy vz id c_3 c_4[1] c_4[2] c_4[3]
dump		rasmolI ion custom 400 DUMPIon/dumpIon.col x y z c_5 type vx vy vz id 
dump		rasmolII ion custom 4500 DUMPIon/dumpIon.col.Final x y z c_5 type vx vy vz id 
restart		4500000 restart.*

variable Rseed equal 5812773

variable i loop 10000
label loop
variable Rseed equal (${Rseed}+1)

delete_atoms      group ion
delete_atoms      group film

#create and equilibrate 
create_atoms	2 region target
group		film region target
group		film type 2
fix 2 film temp/rescale 1 1.0 1.0 0.1 1.0
run		500
unfix		2

### create displaced atom
create_atoms 	1 single 0 0.1 -1.5 units lattice
group		ion type 1
displace_atoms ion random 1.0 1.0 0. ${Rseed} units lattice
print		"DIAG2 - loop i is ${i} ${Rseed}"
#10000 A/ps ~ 5.2 keV
velocity	ion set 0.0 0.0 10000.0 sum yes units box
# Assume that in 4000 steps ion traverses sample
run		4000

next i
# THIS LINE MUST CHANGE IF YOU CHANGE THE FILENAME.....
jump in.coll loop
# END OF LOOP