Hi Lammps team,
I am currently using Lammps/16Mar18 and encounter the problem that Lammps doesn’t assign correct IDs for the atoms though they are within the cutoff distance.
A short cut of my data file:
why are you using this?
neigh_modify exclude molecule/intra all
this messes with your neighbor list and that will affect affect which pairs of atoms compute cluster/atom “sees”. the documentation discusses bonds and the impact of the special_bonds command. the same issue applies to explicit neighbor list exclusions. only that there is no simple workaround.
axel.