Implementing a Repulsive Circular Wall in 2D Brownian Dynamics Simulation

LAMMPS LAMMPS General Discussion
1

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

2

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.

3

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.

4

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).

5

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

6

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”.