hello sir
I want to build a two-dimensional substrate to create interaction potential between substrate and two-dimensional active Brownian particles in lammps. can someone help me?
I tried this… but I don’t know I am right or wrong?
units lj
dimension 2
boundary p p p
atom_style sphere 0
It is not clear what you want to achieve, nor what it means to be wrong. Anyway, the obvious problem is that your setup fills the simulation box with the substrate, leaving no room for other particles. Also, you may want to add at least another atom type to play with the interaction between the substrate and the Brownian particles. Here is my suggestion for you to work on. Good luck, and remember to study in detail the documentation of each keyword. There is no shortcut for building understanding.
units lj
dimension 2
boundary p p p
atom_style sphere 0
lattice sq 0.4
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
region substrate block 0 20 0 2 -0.5 .5
lattice sq 0.4
create_atoms 1 region substrate
group substrate region substrate
fix 5 substrate freeze
region particles block 0 20 2.5 20 -.5 .5
create_atoms 2 random 400 228221 particles
set type 1 diameter 2
set type 2 diameter 1.2
Whether you are doing the research that you are supposed to be doing is a discussion that you have to have with your adviser/supervisor/tutor. Most of the instructions that you have to follow are available in the documentation. As a rule of thumb, any kind of question of the kind “is this correct?” is not a question that you should be asking here. Typically, a suitable question for this kind of forum is more of the kind: I ran these input, the documentation says “…”, but when I look at the trajectory I see “…” or when I compute property “…” or “…” I get “…” but I expect it to be “…” because of “…”.
Also, the skill of validating that your calculations are doing what you expect and whether you get the results that are consistent with the physics/model you want to realize is something that you have to develop yourself. You will not be able to do meaningful research without. One - obvious - way to verify whether you get what you want to do is to write out the coordinates and visualize them. And again, if this is not what you expect, you can ask about it here for help, provided that you first explain why you wrote the input like you did and back this up with references to the documentation.