If you want helpful answers, you have to write posts that people can make sense of, that properly describe the problem and provide sufficient detail that somebody from remote, who does not know what you are doing and cannot look over your shoulder, can understand what happened and then make a suggestion.
All that can be found out from your post is that you have done some simulation of an unknown system which apparently contains some nitrogen atoms and then did some kind of analysis and the results are not what you expect.
What is extremely confusing is that you say the number of atoms is increasing. That cannot be unless your simulation contains commands that add atoms. Since we don’t know what system you are simulating how and also don’t know what kind of analysis you are doing with what software, there is nothing that can be recommended.
This question makes no sense without context. The number of atoms is an input parameter of a simulation.
There rarely is a case where adding a single (magic) command that can “fix” a problem. However, in this case it is completely unclear what the problem as such is. However, understanding the problem is a prerequisite to figuring out a solution.
What has a digested mailing list message containing 16(!) emails to do with your problem?
Do you seriously expect that just copying your input file without any explanations and without providing any answers or responses to the questions and requests posed to you, will get you the kind of help you are looking for? Not to mention, that this is incomplete because it lacks the data file, so it is still not even possible to guess what you are doing and concerned about.
This is showing a serious lack of respect for the people that volunteer their time and take the effort to help you and others. If a person does not make any significant effort when asking for help, then there is no motivation to provide help.
Being a beginner with LAMMPS is no excuse for skipping over basic scientific principles and not providing explanations and answering questions being asked. This is just common sense.
The fact that you have been running LAMMPS and OVITO does not really explain anything.
If you are unable to provide the (rather basic) details and explanations being asked for, you are not ready to do simulations and have to go back and learn more about the fundamentals of doing research first.
Bottom line, to be able to help you, you need to help us (much) more.
I cannot help you because I do not understand what you are asking.
I have asked for a more detailed explanation and also explained why. Instead you are just repeating what you have written before and that simply does not make sense.
Moreover, it appears that your problem is more of an OVITO problem than a LAMMPS problem.
Beginner or not. As I have already pointed out to you, if you cannot describe your problem, you cannot do research. Teaching basic research skills is beyond the scope of this forum. Please discuss with your adviser how to get more training and how to become more skilled in describing your work and your problems.
Please note that sending the same message to my personal email does not improve your situation.
On the contrary, you are making me upset because this is not stuff I like to see in my inbox, and you are in no way entitled to get personal consulting from me. Ignoring my advice and my requests are just disrespectful and annoying.
I have now multiple times explained that I cannot help you because you cannot describe your problem in a way that I can understand it.
All I can deduce from your posts is that you have a problem interpreting the analysis you are doing with OVITO. That makes it not even a LAMMPS problem and you are posting in the wrong forum.