compute ID group-ID cluster/atom cutoff
compute 1 all cluster/atom 1.0
Define a computation that assigns each atom a cluster ID.
A cluster is defined as a set of atoms, each of which is within the cutoff distance from one or more other atoms in the cluster. If an atom has no neighbors within the cutoff distance, then it is a 1-atom cluster. The ID of every atom in the cluster will be the smallest atom ID of any atom in the cluster.
Only atoms in the compute group are clustered and assigned cluster IDs. Atoms not in the compute group are assigned a cluster ID = 0.
The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a clsuter/atom style.
This compute calculates a per-atom vector, which can be accessed by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.
The per-atom vector values will be an ID > 0, as explained above.