I have a periodic prism box of 4 stacked 2D surfaces. These surfaces have ions in between them(provided in the attachment). Using the tutorial(8.5.8. Tutorial for Thermalized Drude oscillators in LAMMPS — LAMMPS documentation) and documentation I could run the required simulations by adding a drude particle to each of these ions.
I have used the “polarizer.py” code to prepare the drude systems but for some reason after increasing the number of ions above a certain threshold, the code starts to add bonds between different ions and different satellite particles. I’ve checked the code but I couldn’t find the reason behind this. Also vmd’s distance based bond creation code gives desired results by finding bond between each ion and their corresponding drude particle. Could there be a bug in “polarizer.py” file for large enough systems?
This tool is specific to the DRUDE package, so you need to talk to somebody that has experience with that and possibly the developer(s) of the tool in question. Please note that a lot of code in LAMMPS is contributed by researchers across the globe and often those are the most competent to help or to debug and improve the tools in question or to educate about incorrect usage.
The names and contact info of contributing authors is usually provided in the individual files and in the information of the LAMMPS package in question in the manual. Please keep in mind that people in science have a tendency to migrate, so you may need to look up an updated affiliation and contact details. I have often found Google Scholar a good place to keep track of people in academia…
