\(\renewcommand{\AA}{\text{Å}}\)

reset_mol_ids command

Syntax

reset_mol_ids group-ID keyword value ...
  • group-ID = ID of group of atoms whose molecule IDs will be reset

  • zero or more keyword/value pairs may be appended

  • keyword = compress or offset or single

    compress value = yes or no
    offset value = Noffset >= -1
    single value = yes or no to treat single atoms (no bonds) as molecules

Examples

reset_mol_ids all
reset_mol_ids all offset 10 single yes
reset_mol_ids solvent compress yes offset 100
reset_mol_ids solvent compress no

Description

Reset molecule IDs for a group of atoms based on current bond connectivity. This will typically create a new set of molecule IDs for atoms in the group. Only molecule IDs for atoms in the specified group are reset; molecule IDs for atoms not in the group are not changed.

For purposes of this operation, molecules are identified by the current bond connectivity in the system, which may or may not be consistent with the current molecule IDs. A molecule in this context is a set of atoms connected to each other with explicit bonds. The specific algorithm used is the one of compute fragment/atom Once the molecules are identified and a new molecule ID computed for each, this command will update the current molecule ID for all atoms in the group with the new molecule ID. Note that if the group excludes atoms within molecules, one (physical) molecule may become two or more (logical) molecules. For example if the group excludes atoms in the middle of a linear chain, then each end of the chain is considered an independent molecule and will be assigned a different molecule ID.

This can be a useful operation to perform after running reactive molecular dynamics run with fix bond/react, fix bond/create, or fix bond/break, all of which can change molecule topologies. It can also be useful after molecules have been deleted with the delete_atoms command or after a simulation which has lost molecules, e.g. via the fix evaporate command.

The compress keyword determines how new molecule IDs are computed. If the setting is yes (the default) and there are N molecules in the group, the new molecule IDs will be a set of N contiguous values. See the offset keyword for details on selecting the range of these values. If the setting is no, the molecule ID of every atom in the molecule will be set to the smallest atom ID of any atom in the molecule.

The single keyword determines whether single atoms (not bonded to another atom) are treated as one-atom molecules or not, based on the yes or no setting. If the setting is no (the default), their molecule IDs are set to 0. This setting can be important if the new molecule IDs will be used as input to other commands such as compute chunk/atom molecule or fix rigid molecule.

The offset keyword is only used if the compress setting is yes. Its default value is Noffset = -1. In that case, if the specified group is all, then the new compressed molecule IDs will range from 1 to N. If the specified group is not all and the largest molecule ID of atoms outside that group is M, then the new compressed molecule IDs will range from M+1 to M+N, to avoid collision with existing molecule IDs. If an Noffset >= 0 is specified, then the new compressed molecule IDs will range from Noffset+1 to Noffset+N. If the group is not all there may be collisions with the molecule IDs of other atoms.

Note

The same as explained for the compute fragment/atom command, molecules are identified using the current bond topology. This will not account for bonds broken by the bond_style quartic command because it does not perform a full update of the bond topology data structures within LAMMPS.

Restrictions

none

Default

The default keyword settings are compress = yes, single = no, and offset = -1.