I’m trying to simulate the attached work. I have looked into LAMMPS example script for kappa(for lj liquids) but not sure if modifying that will work for Bi2Te3. I’ve tried thermal tool plugin but it seems like this only works for 2D materials specifically and my results came out very inceherent. Kind of clueless at this point. Any insight on how can I simulate the system will be very appreciable thanks 
Large thermal conductivity decrease in point defective Bi 2 Te 3 bulk materials
and superlattices.pdf|attachment (3.2 MB)
What you are asking for is that people in this forum will be tutoring / advising you on how to do your research. That is not likely to happen since it is the job of your adviser / supervisor to train your or find you a tutor that can do so and is interested in the research you would be doing.
In general, your question seems to indicate that you have limited experience with using MD and LAMMPS and thus it is generally recommended, that you gain significant experience in basic simulation techniques first before tackling an advanced problem like computing thermal conductivitiy. There is not simple “do this, not that” kind of advice that can be given here, anyway.