Dear lammps users,
I am trying to reproduce the oxidation of a Ge surface adding oxygen atoms bonded to the surface. I manually add them at a reasonable distance and angle from the surface (little less than 2 A and 65° from the normal to the surface). Then i mixed the tersoff potential of Ge and O and created the potential. However i see that when i run the simulation the oxygen atoms get away very fast from the surface. I put in allied an image of the initial configuration and what happens when termalization begins.
Here are the my GeO tersoff file and the part of my input file related to the potentials:
INPUT
3D germanium block simulation
boundary p p p
units metal
#farci attenzione per tutti i parametri, anche di tempo
atom_style full
bond_style harmonic
angle_style harmonic
pair_style hybrid/overlay lj/cut/coul/long 10.0 10.0 lj/cut/soft 1 0.5 10.0 tersoff
kspace_style pppm 1.0e-4
#newton on
read_data 100boxossidatobondsnowater.txt
group germanium type 1 2
group geeOx type 1 2 3
group GeO type 2
group Oox type 3
group water type 4 5
pair_coeff * * tersoff GeO.tersoff Ge Ge O NULL NULL
pair_coeff 1 1 lj/cut/coul/long 0.0 0.0 #Ge-Ge
pair_coeff 1 2 lj/cut/coul/long 0.0 0.0 #Ge-GeO
pair_coeff 1 3 lj/cut/coul/long 0.0 0.0 #Ge-Oox
pair_coeff 1 4 lj/cut/coul/long 0.0 0.0 #Ge-H
pair_coeff 2 2 lj/cut/coul/long 0.0 0.0 #GeO-GeO
pair_coeff 2 3 lj/cut/coul/long 0.0 0.0 #GeO-Oox
pair_coeff 2 4 lj/cut/coul/long 0.0 0.0 #GeO-H
pair_coeff 3 4 lj/cut/coul/long 0.0 0.0 #Oox-H
pair_coeff 4 4 lj/cut/coul/long 0.0 0.0 #H-H
pair_coeff 4 5 lj/cut/coul/long 0.0 0.0 #H-O
pair_coeff 1 5 lj/cut/soft 0.0074437 3.723 1.0 #Ge-O
pair_coeff 2 5 lj/cut/soft 0.0074437 3.723 1.0 #GeO-O
#divido le interazioni tra O e O in coulomb e lj in modo da fare fep
pair_coeff 3 5 lj/cut/soft 0.006739886 3.1655 1.0 #Oox-O
#pair_coeff 3 5 coul/long
pair_coeff 5 5 lj/cut/coul/long 0.006739886 3.1655 #O-O
#energy minimization
dump TRAJ all custom 500 dump_ossidatonowater.lammpstrj id mol type element x y z ix iy iz
dump_modify TRAJ element Ge Ge O H O
thermo_style custom step temp &
ke vol lx ly lz press epair evdwl emol etotal
thermo 5000
minimize 1.0e-6 1.0e-6 1000 10000
reset_timestep 0
variable dt equal 0.001
variable TK equal 298.15
#variable PBAR equal 1.0
neighbor 2. bin #2 angstroms oltre cutoff
neigh_modify every 2 delay 0
timestep ${dt} #0.001
velocity geeOx create {TK} 12857 #dist gaussian rot yes velocity water create {TK} 12857 #dist gaussian rot yes
fix SHAKE water shake 0.0001 20 0 b 1 a 1 #con 1000 printa ogni 1000
#fix LANG geeOx langevin {TK} {TK} 0.025 264537
#fix fixgermanium geeOx nve
fix TEMPgeOx geeOx nvt temp {TK} {TK} 0.1
fix TEMPwater water nvt temp {TK} {TK} 0.1
thermo_style custom step time temp &
pe press epair evdwl etotal
thermo 5000
run 1000000
TERSOFF FILE
format of a single entry (one or more lines):
element 1, element 2, element 3,
m, gamma, lambda3, c, d, costheta0,
n, beta, lambda2, B, R, D, lambda1, A
#The n, beta, lambda2, B, lambda1, and A parameters are only used for two-body interactions. The m, gamma, lambda3, c, d, and costheta0 #parameters are only used for three-body interactions. The R and D parameters are used for both two-body and three-body interactions.
#The non-annotated parameters are unitless. The value of m must be 3 or 1
#element 1 (the center atom in a 3-body interaction)
#element 2 (the atom bonded to the center atom)
#element 3 (the atom influencing the 1-2 bond in a bond-order sense)
Ge Ge Ge 3.0 1.0 0.0 106430.0 15.652 -0.43884
0.75627 0.00000090166 1.7047 419.23 2.95 0.15 2.4451 1769.0
O O O 3.0 1.0 0.0 64692.1 4.11127 -.845922
0.0000 0.00000 0.0000 0.000000 1.85 0.15 0.0000 0.0000
Ge O Ge 3.0 1.0 0.0 106430.0 15.652 -0.43884
0.75627 0.00000090166 2.03081 285.763 2.95 0.15 3.3081 1824.89
Ge Ge O 3.0 1.0 0.0 106430.0 15.652 -0.43884
0.75627 0.00000090166 2.03081 285.763 2.336 0.15414 3.3081 1824.89
Ge O O 3.0 1.0 0.0 106430.0 15.652 -0.43884
0.00000 0.00000 0.0000 0.000000 2.336 0.15414 0.0000 0.0000
O Ge Ge 3.0 1.0 0.0 64692.1 4.11127 -.845922
0.00000 0.00000 0.0000 0.000000 2.336 0.15414 0.0000 0.0000
O O Ge 3.0 1.0 0.0 64692.1 4.11127 -.845922
0.00000 0.00000 0.0000 0.000000 2.336 0.15414 0.0000 0.0000
O Ge O 3.0 1.0 0.0 64692.1 4.11127 -.845922
0.00000 0.00000 0.0000 0.000000 1.85 0.15 0.0000 0.0000
I activate only the Ge-Ge-Ge, Ge-O-Ge and Ge-Ge-O interactions since I am putting oxygen on the surface only so if can’t be the center of the 3 body interaction (all O- x -x interactions null) and no bonds between two oxygen is possible (Ge-O-O).
Am i mistaken in this use of the GeO.tersoff?
Thank you for your advices
Kind regards,
Lorenzo