Problem with equilibrating Silicon

Dear Developers/Users,

I am a beginner in using Lammps. I am trying to thermally equilibrate a silicon nanostructure at 300 K. I am using Tersoff potential and Stillinger-Waber potential (distributed with the LAMMPS package). The structure is periodic in X,Y-Z direction and clamped in X direction (by setting force on the first layer of unit cell equal to zero). The structure is free to vibrate in X direction.

The problem I have is that during heating using NVT ensemble (in 20 ns) to reach 300 K from 1 K, (timestep 1fs) few atoms escape from the structure and move towards the wall of the box. I have tried different TDamp for the thermostat (10 fs,100 fs,1000 fs) and also tried using timestep of 0.5 fs, but the problem persists. Can anyone shed some light on this problem. I have searched the mail-list but could not figure out a solution.

The script I use is the following

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

units metal
atom_style atomic
boundary p p p

lattice diamond 5.43 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &

region box block 0 18 -4 4 -4 4

create_box 1 box
create_atoms 1 box

mass 1 28.055

pair_style tersoff
pair_coeff * * Si.tersoff Si

timestep 0.001

region RDel block 13 18 -4 4 -4 4

group gRDel region RDel

delete_atoms group gRDel

region LFix block 0 1 -4 4 -4 4
group gLFix region LFix

region NFix block 1 13 -4 4 -4 4
group gNFix region NFix

region RFix1 block 12.5 13 -4 4 -4 4

thermo 1
thermo_style custom step temp pe vol pxx pyy pzz

fix f1 gLFix setforce 0 0 0
fix nveFix gLFix nve

velocity gNFix create 1 1005698 mom yes rot yes dist gaussian

fix NVT gNFix nvt temp 1 300 0.1

run 20000000

fix nvt0 gNFix nvt temp 300 300 0.1

run 2000000

%%%%%%%%%%%%%%

Thanks

Sankha Mukherjee

Dear Developers/Users,

I am a beginner in using Lammps. I am trying to thermally equilibrate a
silicon nanostructure at 300 K. I am using Tersoff potential and
Stillinger-Waber potential (distributed with the LAMMPS package). The
structure is periodic in X,Y-Z direction and clamped in X direction (by
setting force on the first layer of unit cell equal to zero). The structure
is free to vibrate in X direction.

The problem I have is that during heating using NVT ensemble (in 20 ns) to
reach 300 K from 1 K, (timestep 1fs) few atoms escape from the structure and
move towards the wall of the box. I have tried different TDamp for the
thermostat (10 fs,100 fs,1000 fs) and also tried using timestep of 0.5 fs,
but the problem persists. Can anyone shed some light on this problem. I have
searched the mail-list but could not figure out a solution.

visualize your structure with periodicity enabled. very likely there
are some "bad contacts" or some other way that those atoms moving away
have a very high potential energy. i don't think it has anything to do
with thermalization.

axel.