Ion-implantation in bulk silicon substrates simulation


I'm a new learner of MD simulation, and recently I want to simulate an ion-implantation process to bulk silicon substrates, and obtain the ion's penetration depth.
I have some questions about LAMMPS input file coding.

Q1:To create a bulk silicon substrates in room temperature,

-----------------------LAMMPS code-----------------------
units metal

boundary p p f

atom_style atomic

atom_modify map array

lattice diamond 5.43

region simbox block -10 10 -10 10 -550 5

region target block -10 10 -10 10 -550 0

create_box 2 simbox

create_atoms 1 region target

mass 1 28.0

group group_si region target

pair_style sw

pair_coeff * * Si.sw Si

>fix 1 group_si nvt 300 300 100
>velocity group_si create 300.0 4929 dist gaussian units box

the bulk silicon substrate's temperature drops to about 150[K].
I cant understand that behavior.

Search for "Equipartition theorem" (half of your initial inetic energy
goes into potential energy).
Run longer and wait!

Q2: I want to set some pair potential interactions,

Check the docs here:

Try reduce your tdamp, too. Default timestep size with metal units is
0.001 ps, so that tdamp of 100 is way too big, which will take a lot
longer to equilibrate.


Dear Ray

Thank you for your answering so fast.
I will study equipartition theorem in more detail.

I tried to reduce the value of "tdamp" 100->50, 10, 1 , 0.1 ...
,and I had a error message that is "ERROR: Lost atoms: original 176081 current 1760411 (thermo.cpp:385)"
value '1760411' change when I change value of tdamp or initial ion position.
What has happened in my simulation ??

Thanks for helping me!!