compute cluster/atom command
compute fragment/atom command
compute aggregate/atom command
compute ID group-ID cluster/atom cutoff compute ID group-ID fragment/atom compute ID group-ID aggregate/atom cutoff
- ID, group-ID are documented in compute command
- cluster/atom or fragment/atom or aggregate/atom = style name of this compute command
- cutoff = distance within which to label atoms as part of same cluster (distance units)
compute 1 all cluster/atom 3.5 compute 1 all fragment/atom compute 1 all aggregate/atom 3.5
Define a computation that assigns each atom a cluster, fragment, or aggregate 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.
A fragment is similarly defined as a set of atoms, each of which has an explicit bond (i.e. defined via a data file, the create_bonds command, or through fixes like fix bond/create, fix bond/swap, or fix bond/break). The cluster ID or fragment ID of every atom in the cluster will be set to the smallest atom ID of any atom in the cluster or fragment, respectively.
An aggregate is defined by combining the rules for clusters and fragments, i.e. a set of atoms, where each of it is within the cutoff distance from one or more atoms within a fragment that is part of the same cluster. This measure can be used to track molecular assemblies like micelles.
Only atoms in the compute group are clustered and assigned cluster IDs. Atoms not in the compute group are assigned a cluster ID = 0. For fragments, only bonds where both atoms of the bond are included in the compute group are assigned to fragments, so that only fragments are detected where all atoms are in the compute group. Thus atoms may be included in the compute group, yes still have a fragment ID of 0.
For computes cluster/atom and aggregate/atom 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 cluster/atom or aggregate/atom style.
If you have a bonded system, then the settings of special_bonds command can remove pairwise interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds command, and means those pairwise interactions do not appear in the neighbor list. Because this fix uses the neighbor list, it also means those pairs will not be included when computing the clusters. This does not apply when using long-range coulomb (coul/long, coul/msm, coul/wolf or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another workaround is to write a dump file, and use the rerun command to compute the clusters for snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list.
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 6.15 for an overview of LAMMPS output options.
The per-atom vector values will be an ID > 0, as explained above.