# LAMMPS Script: ZnO Deposition on Amorphous SiO2 with Embedded ReaxFF Parameters # LAMMPS Script with Embedded ReaxFF Parameters - CORRECTED VERSION # ------------------------------------------------------------------------------ # 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 ================================= 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 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 # Define ReaxFF parameters through pair_coeff commands # First: General parameters (39 values) pair_coeff * * reaxff \ general \ 50.0000 9.5469 1.6725 1.7224 6.8702 60.4850 1.0588 4.6000 \ 12.1176 13.3056 -40.0000 0.0000 10.0000 2.8793 33.8667 6.0891 \ 1.0563 2.0384 6.1431 6.9290 0.3989 3.9954 -2.4837 5.7796 \ 10.0000 1.9487 -1.2327 2.1645 1.5591 0.1000 1.7602 0.6991 \ 50.0000 1.8512 0.5000 20.0000 5.0000 0.0000 0.7903 # Second: Atom parameters (3 atoms) pair_coeff * * reaxff \ atom \ O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 0.0000 \ Si 2.0175 4.0000 28.0600 2.0473 0.1835 0.8925 1.2962 0.0000 \ Zn 1.8862 2.0000 65.3900 1.9200 0.2998 0.4828 -1.6836 0.0000 # Third: Bond parameters (6 types) pair_coeff * * reaxff \ bond \ 1 1 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051 \ 0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000 \ 1 2 272.8709 18.4462 0.0000 -0.6107 -0.3000 1.0000 36.0000 0.8270 \ 10.2334 -0.5495 29.9954 1.0000 -0.1277 7.5863 1.0000 0.0000 \ 2 2 78.0276 54.0531 30.0000 0.5398 -0.3000 1.0000 16.0000 0.0476 \ 0.2865 -0.8055 7.1248 1.0000 -0.0681 8.6957 0.0000 0.0000 \ 1 3 159.9755 0.0000 0.0000 -0.4548 -0.5000 0.0000 35.0000 0.0375 \ 1.3099 -0.5000 25.0000 0.0000 -0.4787 4.6717 0.0000 0.0000 \ 2 3 108.3910 95.0233 0.0000 0.1129 -0.5558 1.0000 17.2117 0.4568 \ 0.2424 -0.2378 10.1163 1.0000 -0.1020 5.7156 1.0000 0.0000 \ 3 3 38.4643 0.0000 0.0000 -0.6944 -0.2000 0.0000 16.0000 0.2129 \ 0.5059 -0.2000 15.0000 0.0000 -0.0814 6.0333 0.0000 0.0000 # Fourth: Off-diagonal terms (3 pairs) pair_coeff * * reaxff \ offdiag \ 1 2 0.1330 2.0545 10.8315 1.7043 1.3773 -1.0000 \ 1 3 0.2744 2.1414 9.7703 1.9804 -1.0000 -1.0000 \ 2 3 0.1500 2.1000 10.0000 1.6500 -1.0000 -1.0000 # Fifth: Angle parameters (13 angles) pair_coeff * * reaxff \ angle \ 1 1 1 89.1221 20.1779 1.4145 0.0000 2.9881 0.0000 1.0929 \ 2 2 2 71.0490 32.4076 1.2648 0.0000 0.0133 0.0000 1.2899 \ 1 2 2 99.8997 26.6610 2.1237 0.0000 0.0100 0.0000 1.4341 \ 1 2 1 98.2184 38.9429 0.7727 0.0000 1.1658 0.0000 2.2641 \ 2 1 2 144.0000 1.3068 5.6478 0.0000 3.8972 0.0000 3.0000 \ 1 1 2 82.7397 32.1198 1.8862 0.0000 0.1058 0.0000 1.5443 \ 1 3 1 109.4700 38.9915 0.7072 0.0000 2.0000 0.0000 2.6162 \ 3 1 3 109.4700 32.3525 0.2657 0.0000 0.4403 0.0000 1.1000 \ 1 3 3 16.9624 30.3241 0.2697 0.0000 2.0000 0.0000 3.0708 \ 1 1 3 60.0000 20.0000 0.5000 0.0000 1.0000 0.0000 2.0000 \ 2 1 3 80.0000 15.0000 4.0000 0.0000 0.5000 0.0000 2.0000 \ 2 3 2 105.0000 30.0000 1.5000 0.0000 0.0000 0.0000 2.0000 \ 3 2 3 120.0000 25.0000 2.0000 0.0000 0.0000 0.0000 1.5000 # Sixth: Torsion parameters (2 torsions) pair_coeff * * reaxff \ torsion \ 1 1 1 1 0.1000 1.0000 0.3000 -2.5000 -0.9000 0.0000 0.0000 \ 0 1 1 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000 # Charge equilibration 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."