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 perfoming 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).
Note that the resetting of IDs is not really 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_ids so that subsequent communication is not inefficient.