# SiH4/NH3 deposition on Si simulation
# Initialize
clear
units metal
dimension 3
boundary p p f
atom_style atomic

# Create atoms
read_data data.GAAS_progresivo

# SW Potential
pair_style sw
pair_coeff * * parametros.sw Ga As


# Define Settings
region r_bottom block INF INF INF INF INF 3.0 units box
group g_bottom region r_bottom
region r_middle block INF INF INF INF 3.0 49.0 units box
group g_middle region r_middle
region r_top block INF INF INF INF 65.0 INF units box
group g_top region r_top
region r_deposition block INF INF INF INF 50.9 64.9 units box
group g_deposition region r_deposition
region r_gas block INF INF INF INF 65.0 INF units box
group g_gas region r_gas

#parametros 
velocity g_gas create 1000 492459 rot yes dist gaussian


fix nve_deposition g_deposition nve
fix fix_bottom g_bottom setforce 0.0 0.0 0.0
fix nvt_middle g_middle nvt temp 600 800 0.1
fix nvt_gas g_gas nvt temp 1000 1200 0.1
fix muro all wall/reflect zhi EDGE

thermo 5000
#thermo_style custom step temp pe etotal

thermo_modify lost ignore

# Diffusion run

dump salidadump all atom 20000 dump.salidaprogresiva
#si el paso es mas grade da NaN (0.05 fallaba).
timestep 0.001

#restart 100000 deposicion.restart
run 1000000

undump salidadump
dump dumpfinal all atom 100000 dump.finalprogresiva
minimize     1.0e-4 1.0e-6 1000 10000