Can someone explain the difference between these two keywords？ I cannot figure out
One is for storing atoms of a bond/angle/dihedral/improper interaction, the other is for storing excluded neighbors. The latter may not be part of any of the former.
Just check out the output of a regular run with bonded interactions, e.g. here lammps/log.27Nov18.peptide.g++.1 at ceb9466172398e9a20cb510528b4b17f719c7cf2 · lammps/lammps · GitHub
It reports how much space for each of those is being allocated since by default LAMMPS will allocate only the minimum required by a given system.
Could you please explain what “storing excluded neighbors” means？Thanks
Please see the special_bonds command — LAMMPS documentation
and read up about the use of exclusions in molecular force fields your favorite text book on molecular dynamics and force fields.