"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line delete_atoms command :h3 [Syntax:] delete_atoms style args keyword value ... :pre style = {group} or {region} or {overlap} or {porosity} :ulb,l {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) :pre zero or more keyword/value pairs may be appended :l keyword = {compress} or {bond} or {mol} :l {compress} value = {no} or {yes} {bond} value = {no} or {yes} {mol} value = {no} or {yes} :pre :ule [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 :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. 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"_atom_style.html command), regardless of the {compress} setting, since it would foul up the bond connectivity that has already been assigned. 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"_read_data.html command, and where the interactions themselves are defined with the "bond_style"_bond_style.html, "angle_style"_angle_style.html, 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"_pair_style.html with the minimum force cutoff distance between any pair of atoms types (plus the "neighbor"_neighbor.html skin) >= the specified overlap cutoff. 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} 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"_molecule.html and "atom_style template"_atom_style.html commands. [Related commands:] "create_atoms"_create_atoms.html [Default:] The option defaults are compress = yes, bond = no, mol = no.