lammps/doc/delete_atoms.txt

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delete_atoms command :h3

[Syntax:]

delete_atoms style args :pre

style = {group} or {region} or {overlap} :ulb,l
  {group} args = group-ID
  {region} args = region-ID
  {overlap} args = distance type1 type2
    distance = delete atoms with neighbors within this cutoff (distance units)
    type1 = type of first atom in pair (optional)
    type2 = type of other atom in pair (optional)
:pre
:ule

[Examples:]

delete_atoms group edge
delete_atoms region sphere
delete_atoms overlap 0.3
delete_atoms overlap 0.3 1 1 :pre

[Description:]

Delete the specified atoms.  This command can be used to carve out
voids from a block of material or to delete created atoms that are too
close to each other (e.g. at a grain boundary).

For style {group}, all atoms belonging to the group are deleted.

For style {region}, all atoms in the region volume are deleted.

For style {overlap}, pairs of atoms within the specified cutoff
distance are searched for, and one of the 2 atoms is deleted.  If no
atom types are specified, an atom will always be deleted if the cutoff
criterion is met.  If a single atom type is specified, then one or
both of the atoms in the pair must be of the specified type for a
deletion to occur.  If two atom types are specified, the two atoms in
the pair must be of the specified types for a deletion to occur.  For
a given configuration of atoms, the only guarantee is that at the end
of the deletion operation, enough deletions will have occurred that no
atom pairs within the cutoff (and with the specified types) will
remain.  There is no guarantee that the minimum number of atoms will
be deleted, or that the same atoms will be deleted when running on
different numbers of processors.

After atoms are deleted, if the system is not molecular (no bonds),
then atom IDs are re-assigned so that they run from 1 to the number of
atoms in the system.  This is not done for molecular systems, since it
would foul up the bond connectivity that has already been assigned.

[Restrictions:]

The {overlap} style requires inter-processor communication to acquire
ghost atoms and setup a neighbor list.  This means that your system
must be ready to perform a simulation before using this command (force
fields setup, atom masses set, etc).

If the "special_bonds"_special_bonds.html command is used with a
setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
appear in the neighbor list, and thus will not be considered for
deletion by the {overlap} style.  You probably don't want to be
deleting one atom in a bonded pair anyway.

[Related commands:]

"create_atoms"_create_atoms.html

[Default:] none