I have created a simulation for 3 atoms but the output (OVITO) shows only 1,is there any possible explanation?

LAMMPS LAMMPS Beginners
4

I have four comments or suggestions:

  1. Please have a closer look at this post (again?) to learn how to correctly quote text in this forum. What you are currently doing is not correct and special characters are interpreted as markup (e.g. to make text bold or italic). It also explains what information to provide and how to explain things so that people can help you. I have already explained to you how important that is, yet you are making the same mistake here. E.g. there are not 3 atoms but 3 atom types. This distinction is crucial here.
  2. Please carefully check your output/log file. All the important information was already given there, e.g. that you have created 4000 atoms 3 times and then 8000 of those atoms were deleted. It is extremely likely that the delete_atoms command is still deleting some of the atoms you created with the changed input.
  3. Your system creation with 3 create_atoms command with different lattices makes no sense at all. You are just overlaying 3 different incompatible lattices within the same region. If you want to create a specific lattice of a compound, you probably need to create a custom lattice where the relative positions of the different atom types are listed. The lattice definitions that you are using are for mono-atomic systems. Thus what you are doing will create a big mess in any case. This is a clear indication that you are lacking the necessary understanding in crystallography and how geometries of crystals are specified. This is something that you cannot learn here, but need to acquire elsewhere. There are plenty of textbooks and you can consult with your adviser or more experienced colleagues. It is not rocket science but you are wasting your (and our!) time by continuing and just making what looks like almost random(?) changes without really understanding what you are doing. You will not get somebody here to tell you exactly which input commands with which arguments you have to use and thus effectively doing your job for you.
  4. You need to find yourself a (local) tutor that gets you started on MD simulations and you need to start with simulating simpler systems. A good way is to start from available tutorials and not only just look at them and then try to use them at template for your system of interest, but study them line by line, command by command in combination with the manual until you have fully understood each step. Only then can you advance to a more complex system, but do it in multiple stages until you reach your final system of interest. Otherwise, you will have far too many “moving parts” and thus will be overwhelmed to figure out what is causing you issues, since most of the time there will not be just one problem (and thus a simple solution) but a combination of problem that often will need to be addresses in the correct order to fully (and efficiently!) resolve them. If you continue on your current trajectory in the same way without improving, you will see the level of support you are getting to drop to zero rather quickly. Nobody likes to give advice to a person that doesn’t pay attention and doesn’t make an active effort to improve on mistakes that have been pointed out.