reset_atom_ids keyword values ... * zero or more keyword/value pairs may be appended * keyword = *sort*
sort value = yes or no
reset_atom_ids reset_atom_ids sort yes
Reset atom IDs for the system, including all the global IDs stored for bond, angle, dihedral, improper topology data. This will create a set of IDs that are numbered contiguously from 1 to N for a N atoms system.
This can be useful to do after performing a “delete_atoms” command for a molecular system. The delete_atoms compress yes option will not perform this operation due to the existence of bond topology. It can also be useful to do after any simulation which has lost atoms, e.g. due to atoms moving outside a simulation box with fixed boundaries (see the “boundary command”), or due to evaporation (see the “fix evaporate” command).
If the sort keyword is used with a setting of yes, then the assignment of new atom IDs will be the same no matter how many processors LAMMPS is running on. This is done by first doing a spatial sort of all the atoms into bins and sorting them within each bin. Because the set of bins is independent of the number of processors, this enables a consistent assignment of new IDs to each atom.
This can be useful to do after using the “create_atoms” command and/or “replicate” command. In general those commands do not guarantee assignment of the same atom ID to the same physical atom when LAMMPS is run on different numbers of processors. Enforcing consistent IDs can be useful for debugging or comparing output from two different runs.
Note that the spatial sort requires communication of atom IDs and coordinates between processors in an all-to-all manner. This is done efficiently in LAMMPS, but it is more expensive than how atom IDs are reset without sorting.
Note that whether sorting or not, the resetting of IDs is not a compression, where gaps in atom IDs are removed by decrementing atom IDs that are larger. Instead the IDs for all atoms are erased, and new IDs are assigned so that the atoms owned by an individual processor have consecutive IDs, as the create_atoms command explains.
If this command is used before a pair style is defined, an error about bond topology atom IDs not being found may result. This is because the cutoff distance for ghost atom communication was not sufficient to find atoms in bonds, angles, etc that are owned by other processors. The comm_modify cutoff command can be used to correct this issue. Or you can define a pair style before using this command. If you do the former, you should unset the comm_modify cutoff after using reset_atom_ids so that subsequent communication is not inefficient.
By default, sort is no.