# 3d EAM surface for global HD

# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92
# hop event on (100) surface is same distance
# exchange event is 2 atoms moving same distance

variable        Tequil index 800.0
variable        Vmax index 0.3
variable        qfactor index 0.3
variable        cutbond index 3.2
variable        cutevent index 1.1
variable        steps index 1000 
variable        zoom index 1.8

units           metal
atom_style	atomic
atom_modify     map array
boundary        p p p

lattice		fcc 3.92
region		box block 0 6 0 6 0 4
create_box	3 box
create_atoms	1 box

mass            * 1.0

change_box      all z final -0.1 5.0 boundary p p f 
create_atoms    2 single 3.5 3.5 4

# define frozen substrate and mobile atoms

group           adatom type 2
region          base block INF INF INF INF 0 1.8
set             region base type 3
group           base type 3
group           mobile type 1 2

# pair style

pair_style	eam/alloy
pair_coeff	* * ptvoterlammps.eam Pt Pt Pt

neighbor	0.5 bin
neigh_modify    every 1 delay 5 check yes

fix		1 mobile nve
fix		2 mobile langevin ${Tequil} ${Tequil} 1.0 4879387 zero yes

timestep	0.005

compute         tmobile mobile temp

thermo		100
thermo_modify   temp tmobile

# thermal equilibration

run             1000
reset_timestep  0

# pin base so will not move during quenches

fix             freeze base setforce 0.0 0.0 0.0

# event detection

compute         event all event/displace ${cutevent}

# hyper/global

fix             HG mobile hyper/global ${cutbond} ${qfactor} ${Vmax} ${Tequil}

# thermo output

thermo_style    custom step temp pe f_HG &
                f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] &
                f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11]

thermo_modify   lost ignore
thermo_modify   temp tmobile

thermo          100

# dump output options

region          substrate block INF INF INF INF 1.8 3.8
region          adatoms block INF INF INF INF 3.8 INF
variable        acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms)

dump		1 all custom 10000000 dump.* id type x y z
dump_modify	1 pad 6

dump		5 all image 10000000 static.*.ppm v_acolor type &
		zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01
dump_modify	5 pad 9 amap 1 3 sa 1 3 blue red green

# run

hyper           ${steps} 100 HG event min 1.0e-6 1.0e-6 100 100 dump 1 dump 5