How to remove the overlaping of ellipsoidal particles?

LAMMPS LAMMPS General Discussion
1

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

Gaybern
Gaybern1666Ă—1690 203 KB

2

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.

3

hi Anuj, which software are you using to visualize these non spherical particles and please tell me how to set parameters to obtain such image of ellipsoidal particles in the visualizing software
?

4

You can use Ovito to visualise ellipsoids. Your dump should contain the following information:

compute q all property/atom quatw quati quatj quatk
compute diameter all property/atom shapex shapey shapez
dump TRJ all custom 1000 test.dump id type xu yu zu c_q[1] c_q[2] c_q[3] c_q[4] c_diameter[1] c_diameter[2] c_diameter[3] vx vy vz angmomx angmomy angmomz mol
dump_modify TRJ colname c_q[1] quatw colname c_q[2] quati colname c_q[3] quatj colname c_q[4] quatk

PS For @akohlmey: the above snippet breaks the syntax highlighting! It seems the culprits are the c_q[1].

1 Like
5

yes hothello, I will be back again after considering the above said modification. One more thing I want to know is that in Basic version of Ovito software how can I set particle shape parameter? Actually I am facing problem in choosing Ellipsoid type in the particle section of Ovito. please help with the issues . thank your for your valuable reply above

Picture2
Picture21021Ă—744 62.8 KB

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6

Your script successfully executed. I greatly appreciate your assistance, and I’m truly thankful. Your help has made me very happy. Thank you very much sir hothello. I attached the snapshot below .

Picture4
Picture41020Ă—755 94.4 KB

7

I have no control over syntax highlighting, and specifically don’t know what syntax is applied by default.
You can follow the usual markup convention to specify the language after the triple quotes, e.g. I have changed it in the above example from ``` to ```c++. I sometimes use ```xxx to turn the highlighting off when it is distracting.

8

I see, thanks for clarifying.