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 (positive integer)
    
  • zero or more keyword/value pairs may be appended

  • keyword = compress or bond or mol

    compress value = no or yes
    bond 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 482793 bond yes

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. Note that 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. However, the reset_ids command can be used after this command to accomplish the same thing.

Note that the re-assignement 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 individual processors have consecutive IDs, as the create_atoms command explains.

A molecular system with fixed bonds, angles, dihedrals, or improper interactions, is one where the topology of the interactions is typically defined in the data file read by the read_data command, and where the interactions themselves are defined with the bond_style, angle_style, etc commands. If you delete atoms from such a system, you must be careful not to end up with bonded interactions that are stored by remaining atoms but which include deleted atoms. This will cause LAMMPS to generate a “missing atoms” error when the bonded interaction is computed. The bond and mol keywords offer two ways to do that.

It the bond keyword is set to yes then any bond or angle or dihedral or improper interaction that includes a deleted atom is also removed from the lists of such interactions stored by non-deleted atoms. Note that simply deleting interactions due to dangling bonds (e.g. at a surface) may result in a inaccurate or invalid model for the remaining atoms.

It the mol keyword is set to yes, then for every atom that is deleted, all other atoms in the same molecule (with the same molecule ID) will also be deleted. This is not done for atoms with molecule ID = 0, since such an ID is assumed to flag isolated atoms that are not part of molecules.

Note

The molecule deletion operation in invoked after all individual atoms have been deleted using the rules described above for each style. This means additional atoms may be deleted that are not in the group or region, that are not required by the overlap cutoff criterion, or that will create a higher fraction of porosity than was requested.

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 the minimum force cutoff distance between any pair of atoms types (plus the neighbor skin) >= the specified overlap cutoff.

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.

The bond yes option cannot be used with molecular systems defined using molecule template files via the molecule and atom_style template commands.

Default

The option defaults are compress = yes, bond = no, mol = no.