[Lammps Users request] Help about msd

Hi all,

I have a question concerning the set of atom displacement. I my project I ‘m trying
to investigate de diffusive behavior of BaTiO3 including oxygen vacancies in the
temperature range 773-673K.
I was minimized the structure but when I try to run MD under PBC and nph ensemble
controlling the temperature with Berendsen Thermostat, to obtain msd of oxygen ion,
not diffuse. I believe that the problem is concerning to the pressure values, I want
to do it under atmospheric pressure (P=0GPa). I used the Virial correction to input
the pressure but nothing.
I did these simulations before by suing other software but LAMMPS is faster and I
want to learn.

Attached are two files: the minimization and equilibration and the MD run input files:

Waiting for your help
Yohandys

####--------------in.min------------------------------------------------------------------------####

# minimization

units metal
dimension 3
atom_style charge
boundary p p p
atom_modify map array sort 0 10.0
neighbor 0.5 bin # I don't know if it is correct
neigh_modify delay 0 every 1 check no

lattice custom 16.04 a1 1 0 0 a2 0 1.0 0 a3 0 0 1 basis 0 0 0
read_data BT4x4x4.dat # 4x4x4 BaTiO3 unit cell

##########################################################################-----------------------Atoms
Definitions----------------------####
###################################################################### group Ti
type 1 group o type 3
group Ba type 2

set group o charge -2.0
set group Ti charge 4.0
set group Ba charge 2.0

mass 1 47.88
mass 2 137.33
mass 3 16.00

in.min (3.13 KB)

in.dyn (2.16 KB)

What is your question? If you simply want to measure the MSD, then
there is a compute MSD which does it. See the compute msd doc
page and read Section 6.15 of the manual for info on how to use
the output of the compute.

Steve

Hi Yohandys,

I think that if you are interested in dynamical properties you should use not-folded positions for the coordinate particles/molecules, in otherwise you will see not diffusion

Regards,

HVS