[lammps-users] Wired phenomenon of Oxygen penetration

Hi, all

    I have recently encountered a wired phenomenon when i try to deposit
single Oxygen atom on Silicon substrate. I fix the bottom half of silicon
substrate and let the upper half move freely. Some of the oxygen atoms just
penetrate into the interface of the fixed and unfixed silicon with no
trajectory noticed. Does anyone has any idea of this problem? Below is my
input file.


units metal
boundary p p p

atom_style full

read_data config_ox
neighbor 2.0 bin
neigh_modify delay 1 page 10000000 one 50000 binsize 0.0

pair_style tersoff
pair_coeff * * SiO.tersoff Si O #Si,O

region 1 block INF INF INF INF INF 21.72 units box # fix the bottom
group lower region 1
velocity lower set 0.0 0.0 0.0 sum no units box
fix 1 lower setforce 0 0 0

group silicon type 1
group upper subtract silicon lower
velocity upper create 300.0 4928459 rot yes dist gaussian # give the top
half initial velocity

timestep 0.0005

fix 2 all nvt temp 300.0 300.0 0.1
dump 1 all custom 1000 dump.sidi id mol type q x y z vx vy vz
thermo_style custom step temp pe ke etotal press vol
thermo 100
run 15000

unfix 1
unfix 2
undump 1

write_restart restart.1

I would just see if you can run your system with NVE first
and that the thermo and viz output are what you expect.