Implementing a Repulsive Circular Wall in 2D Brownian Dynamics Simulation

Hello LAMMPS Community,

I am working on a 2D Brownian dynamics simulation where I need to confine ellipsoidal particles inside a circular boundary, with the boundary acting as a repulsive wall. While I have set up a simulation where particles move within a rectangular box, I am encountering challenges in introducing a repulsive circular wall.

Below is the relevant portion of my LAMMPS script:

single particle brownian dynamics

sample LAMMPS input script for diffusion of 2d LJ liquid

mean-squared displacement via compute msd

problem setup

units lj
dimension 2
boundary f f p
atom_style ellipsoid
neigh_modify every 1
region Sphere sphere 0 0 0 5 side in
region Box block -5 5 -5 5 -0.5 0.5
region circle intersect 2 Sphere Box
lattice sq 0.500
create_box 1 circle
create_atoms 1 region circle
set atom * mass 1
set atom * shape 1 1 1
velocity all create 1.0 97287
neighbor 0.40 bin
neigh_modify every 1 delay 1 check yes
pair_style lj/cut 1.12246
pair_modify shift yes
pair_coeff 1 1 1.0 1 1.12246

fix 1 all nve/asphere
fix 2 all langevin 1.0 1.0 0.010 498094 angmom 3.33333
fix active_group all propel/self quat 120.0
fix wallxlo all wall/lj93 xlo EDGE 2.0 1.0 2.5 units lattice
fix wallxhi all wall/lj93 xhi EDGE 2.0 1.0 2.5 units lattice
fix wallylo all wall/lj93 ylo EDGE 2.0 1.0 2.5 units lattice
fix wallyhi all wall/lj93 yhi EDGE 2.0 1.0 2.5 units lattice
fix 3 all enforce2d

equilibration run

thermo 1000
#run 5000
reset_timestep 0
dump 4 all movie 100 movie.mpg type type zoom 1 size 3040 2480 view 20 250
dump_modify 4 backcolor white
#dump_modify 4 acolor 1 green
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
timestep 0.001
run 10000000

I am aiming to implement a repulsive potential that acts on the ellipsoidal particles when they approach the circular boundary. I considered using the fix wall/region command with the Lennard-Jones 9-3 potential (lj93) for the circle region, but I am unsure if this is the best approach.

Could anyone provide guidance on how to properly set up a repulsive circular wall for my simulation? Any insights, suggestions, or code modifications would be highly appreciated.

Thank you in advance for your time and assistance!

Warm regards,
Gokul Upadhyay

What challenges?

If you are not sure, make tests and confirm that results are as expected. If you need a more flexible wall potential, you could compute the wall potential with an atom-style variable expression and then use fix addforce.

In the video, I observe that the initial atoms are created inside the circle. However, subsequently, they seem to experience repulsion from the box. I have also experimented with a periodic boundary. When the repulsion using the fix wall is turned off, the periodic boundary is applied along the box and not the circle. I suspect that it interprets the simulation box as the intersection of the sphere and the box.

This is too vague and convoluted to give advice directly. You need to create a suitable (small, fast, easy to run) input deck that demonstrates what you are concerned about, and then people can have a look. Other than that, you will be mostly on your own or have to consult with your adviser/tutor/supervisor or anybody else familiar with your research since we are not (and don’t really aim to be).

I want to confine ellipsoidal particles within a circle, where the boundary of the circle acts as a repulsive wall using the LJ93 potential.

That is the same, vague description and does not demonstrate any concerns. I have already explained what you have to do. People first need to understand where you get unexpected results and how.

So far, all what your posts amount to is a somewhat disguised version of “please do my job for me”.