lammps VS Blender-FLIP-Fluids

Look into verlet lists or cell lists for your task, which are typically used with a discrete element method such as LAMMPS for what you seem to be describing.

Your choices are an n-body simulation (e.g., LAMMPS) with Coulomb interactions or, if your electrons are sufficiently sparse, a particle-in-cell (e.g., Starfish). Your best bets for visualization are going to be matplotlib or something more user-friendly like Visit or Paraview. Without a neutralizing background, however, your electrons are just going to repel each other, hit the walls, and disappear - there's not going to be much interesting to visualize. What are you actually trying to simulate? With more information maybe you could receive some more targeted advice.

Is this just a personal /learning project? I see "chemical simulations" and think quantum-espresso, LAMMPS, NWChem, etc. If this is a personal project, I apologize for my bluntness above.

Actually, the LAMMPS website has a similar example: Just hover over the "LAMMPS" logo in yellow and blue.

Modify the file to add what you need. In your case, modify the post_force functions in the files, since those will allow you to define the integration steps for the Vicsek model and its variations.

If all else fails, you may want to consider a premium addon like FLIP Fluids, which in my experience feels more stable than the default fluid sim, though it may be a bit costly. Consider trying the demo.

For troubleshooting conflicts between addons, it can help to test in a fresh Blender environment with default settings and installing/enabling addons one at a time. In case it helps, we have some instructions here for how to backup user-preferences, test in a clean environment, and then restore your original addons and settings: https://github.com/rlguy/Blender-FLIP-Fluids/wiki/Baking-Crash-Troubleshooting#testing-the-flip-fluids-addon-in-a-clean-installation-of-blender

There's a free demo if you would like to try it out: https://github.com/rlguy/Blender-FLIP-Fluids/wiki/FLIP-Fluids-Demo-Addon

The above was built from the code on the GitHub repository, which is under the GNU General Public License. This license allows for redistribution. Unfortunately, I do not have binaries for MacOS or Linux since I only use Windows. Also, note that the above download is for Blender 64-bit (which should be the default on the blender.org downloads page). The GitHub version doesn't have pre-made materials like the paid version on Blender Market. (Note: The demo file on GitHub has watermarks on the simulation. This is the full version of the addon, not to be confused with the demo.)

Make sure that your objects have correct manifold/closed/watertight geometry. See this topic for more info and how to verify geometry: https://github.com/rlguy/Blender-FLIP-Fluids/wiki/Manifold-Meshes

This is also an open source project and we provide a free version with the source code here including build/compile instructions: https://github.com/rlguy/Blender-FLIP-Fluids

Thanks! Mostly by reading through the FLIP Fluid Wiki and watching some tutorials on YouTube.

The related documentation for how to enable and use attributes (such as the color attribute) is here: https://github.com/rlguy/Blender-FLIP-Fluids/wiki/Domain-Attributes-and-Data-Settings