# LAMMPS Script: ZnO Deposition on Amorphous SiO2 using Custom ReaxFF (O-Si-Zn)
# ------------------------------------------------------------------------------

# 1. INITIALIZATION ==========================================
units           real
atom_style      charge
boundary        p p f
dimension       3
processors      * * 1
neighbor        2.0 bin
neigh_modify    every 1 delay 0 check yes

# 2. SIMULATION BOX ==========================================
region          whole block 0 50 0 50 0 60 units box
create_box      3 whole  # Atom types: O=1, Si=2, Zn=3

# 3. MASS DEFINITIONS ========================================
mass            1 15.9994   # Oxygen
mass            2 28.0855   # Silicon
mass            3 65.38     # Zinc

# 4. SiO2 SUBSTRATE CREATION =================================
# 4.1 Create amorphous SiO2 substrate
region          siO2_reg block 0 50 0 50 0 10 units box
create_atoms    2 random 500 12345 siO2_reg  # Si atoms
create_atoms    1 random 1000 67890 siO2_reg # O atoms

# 4.2 Verify stoichiometry
group           Si type 2
group           O type 1
print           "Created SiO2 substrate with [count(Si)] Si and [count(O)] O atoms"


# 5. FORCE FIELD SETUP =======================================
pair_style      reaxff NULL lgvdw yes
pair_coeff      * * ffield_O_Si_Zn_V2 O Si Zn
fix             qeq all qeq/reaxff 1 0.5 10.0 1.0e-6 reaxff maxiter 500

fix             qeq all qeq/reaxff 1 0.5 10.0 1.0e-6 reaxff maxiter 500

# 6. SYSTEM GROUPS ===========================================
group           substrate region siO2_reg
group           all type 1 2 3

# 7. OUTPUT SETTINGS =========================================
thermo          100
thermo_style    custom step temp pe ke etotal press vol density
thermo_modify   flush yes

# 8. CHARGE EQUILIBRATION ====================================
fix             qeq all qeq/reaxff 1 0.5 10.0 1.0e-6 reaxff maxiter 500

# 9. ENERGY MINIMIZATION =====================================
reset_timestep  0
min_style       cg
minimize        1.0e-6 1.0e-8 1000 10000
write_dump      all custom minimized.lammpstrj id type x y z

# 10. SiO2 AMORPHIZATION =====================================
# 10.1 Melting at 5000K
velocity        all create 5000 12345 rot yes dist gaussian
fix             nvt all nvt temp 5000 5000 100.0
fix             ave all ave/time 100 10 1000 v_temp file temp.profile
run             2000
unfix           nvt

# 10.2 Quenching to 300K
fix             nvt all nvt temp 5000 300 100.0
run             5000
unfix           nvt

# 10.3 Final relaxation
minimize        1.0e-6 1.0e-8 1000 10000
write_dump      all custom amorphous.lammpstrj id type x y z

# 11. ZnO DEPOSITION =========================================
# 11.1 Create ZnO layer
region          znO_reg block 0 50 0 50 10 15 units box
create_atoms    3 random 300 54321 znO_reg  # Zn atoms
create_atoms    1 random 300 98765 znO_reg  # O atoms

# 11.2 Verify stoichiometry
group           Zn type 3
print           "System now has [count(Zn)] Zn and [count(O)] O atoms total"

# 11.3 Energy minimization
minimize        1.0e-6 1.0e-8 1000 10000

# 11.4 Equilibration
velocity        all create 300 54321 rot yes dist gaussian
fix             nvt all nvt temp 300 300 100.0
run             2000
unfix           nvt

# 12. FINAL OUTPUT ===========================================
write_dump      all custom final.lammpstrj id type x y z
write_data      final.data
print           "ZnO/SiO2 deposition simulation completed successfully."