Cluster/atom doesn't group atoms within cutoff

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.