delete_atoms command¶

Syntax¶

delete_atoms style args keyword value ...

style = group or region or overlap or porosity

group args = group-ID
region args = region-ID
overlap args = cutoff group1-ID group2-ID
  cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
  group1-ID = one atom in pair must be in this group
  group2-ID = other atom in pair must be in this group
porosity args = region-ID fraction seed
  region-ID = region within which to perform deletions
  fraction = delete this fraction of atoms
  seed = random number seed (prime number greater 10000)

zero or more keyword/value pairs may be appended
keyword = compress or mol

compress value = no or yes
mol value = no or yes

Examples¶

delete_atoms group edge
delete_atoms region sphere compress no
delete_atoms overlap 0.3 all all
delete_atoms overlap 0.5 solvent colloid
delete_atoms porosity cube 0.1 123457

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. Additional atoms can be deleted if they are in a molecule for which one or more atoms were deleted within the region; see the mol keyword discussion below.

For style overlap pairs of atoms whose distance of separation is within the specified cutoff distance are searched for, and one of the 2 atoms is deleted. Only pairs where one of the two atoms is in the first group specified and the other atom is in the second group are considered. The atom that is in the first group is the one that is deleted.

Note that it is OK for the two group IDs to be the same (e.g. group all), or for some atoms to be members of both groups. In these cases, either atom in the pair may be deleted. Also note that if there are atoms which are members of both groups, the only guarantee is that at the end of the deletion operation, enough deletions will have occurred that no atom pairs within the cutoff will remain (subject to the group restriction). 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.

For style porosity a specified fraction of atoms are deleted within the specified region. For example, if fraction is 0.1, then 10% of the atoms will be deleted. The atoms to delete are chosen randomly. There is no guarantee that the exact fraction of atoms will be deleted, or that the same atoms will be deleted when running on different numbers of processors.

If the compress keyword is set to yes, then after atoms are deleted, 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 (see the atom_style command), regardless of the compress setting, since it would foul up the bond connectivity that has already been assigned.

It the mol keyword is set to yes, then for every atom that is deleted, all other atoms in the same molecule will also be deleted. This keyword is only used by the region style. It is a way to insure that entire molecules are deleted instead of only a subset of atoms in a bond or angle or dihedral interaction.

Restrictions¶

The overlap styles requires inter-processor communication to acquire ghost atoms and build 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). Since a neighbor list is used to find overlapping atom pairs, it also means that you must define a pair style with force cutoffs greater than or equal to the desired overlap cutoff between pairs of relevant atom types, even though the pair potential will not be evaluated.

If the special_bonds 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 styles. You probably don’t want to be deleting one atom in a bonded pair anyway.

Default¶

The option defaults are compress = yes and mol = no.