# sample surface deposition script for molecules

units		lj
atom_style      bond
boundary        p p f

lattice		fcc 1.0
region          box block 0 5 0 5 0 10
create_box      3 box bond/types 1 extra/bond/per/atom 1

region		substrate block INF INF INF INF INF 3
create_atoms	1 region substrate

pair_style	lj/cut 2.5
pair_coeff	* * 1.0 1.0
pair_coeff	1 2 1.0 1.0 5.0
mass		* 1.0

bond_style	harmonic
bond_coeff      1 5.0 1.0

neigh_modify	delay 0

group		addatoms type 2
region          mobile block 0 5 0 5 2 INF
group		mobile region mobile

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

fix		1 addatoms nve
fix		2 mobile langevin 0.1 0.1 0.1 587283
fix		3 mobile nve

molecule        dimer molecule.dimer.shake
region          slab block 0 5 0 5 8 9
fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
                mol dimer vz -1.0 -1.0 shake 6
fix		5 addatoms wall/reflect zhi EDGE
fix             6 all shake 0.0001 20 1000 b 1 mol dimer

thermo_style	custom step atoms temp epair etotal press
thermo          100
thermo_modify	temp add lost/bond ignore lost warn

#dump		1 all atom 50 dump.deposit.atom

#dump		2 all image 50 image.*.jpg type type &
#		axes yes 0.8 0.02 view 80 -30
#dump_modify	2 pad 5

#dump		3 all movie 50 tmp.mpg type type &
#		axes yes 0.8 0.02 view 80 -30
#dump_modify	3 pad 5

run             10000