How to remove the overlaping of ellipsoidal particles?

Dear LAMMPS User

I am doing simulations for ellipsoidal particles taking gayberne potential. But, there was an overlapping of ellipsoids at their ends and also on the sides. How to avoid any kind of overlapping of ellipsoidal particles?

My script is attached below.

units lj
atom_style ellipsoid
dimension 2
boundary p p p
region my_box block 0.0 30 0.0 30 -0.5 0.5

create_box 1 my_box
create_atoms 1 random 270 18765 my_box
group lc type 1

set group lc shape 0.9 0.3 0.3
set group all quat 0.0 0.0 0.0 1.0

pair_style gayberne 1.0 1.0 3.0 4.0
pair_coeff * * 1.0 1.0 1.0 1.0 0.2 1.0 1.0 0.2 4.0

comm_modify mode single vel yes #cutoff 20.0
neighbor 0.3 bin #multi
neigh_modify every 1 delay 0 check yes page 5000000 one 500000

minimize 1.0e-4 1.0e-5 1000 100000
velocity lc create 1.0 91259 loop geom

fix 1 lc langevin 1.0 1.0 1.25 84279 zero yes angmom 1.5
fix 4 all nve/asphere
fix 5 all enforce2d

compute rot lc temp/asphere dof all
compute mytemp all temp/asphere dof all

compute q all property/atom quatw quati quatj quatk
compute sh all property/atom shapex shapey shapez

thermo_style custom step temp c_rot pe ke press density
thermo_modify temp mytemp

dump 2 all custom 500 dump.dipole_ellips id type x y z c_q[1] c_q[2] c_q[3] c_q[4] c_sh[1] c_sh[2] c_sh[3]
thermo 500

timestep 0.0001
run 100000

You may be misunderstanding your model. The Gay-Berne potential is a “soft” interaction model that is essentially extending the Lennard-Jones model to ellipsoids. So there is quite a bit of overlap that is tolerable. Furthermore, the “size” of such particles is defined by the potential parameters, not the shape settings. Thus from your dump file it is impossible to derive what is the actual diameter of your ellipsoids. Their effective radii may be (much?) smaller than what you see.

How much overlap you will get during a simulation depends on the simulation settings and whether that is physical depends on the choice of parameters, too. If there would be unphysical choices, you would have excessive potential energy and the energy conservation would be bad. To determine the latter, you would have to run without a thermostat after an initial equilibration run.