forked from lijiext/lammps
124 lines
5.1 KiB
Plaintext
124 lines
5.1 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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delete_atoms command :h3
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[Syntax:]
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delete_atoms style args keyword value ... :pre
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style = {group} or {region} or {overlap} or {porosity} :ulb,l
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{group} args = group-ID
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{region} args = region-ID
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{overlap} args = cutoff group1-ID group2-ID
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cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
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group1-ID = one atom in pair must be in this group
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group2-ID = other atom in pair must be in this group
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{porosity} args = region-ID fraction seed
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region-ID = region within which to perform deletions
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fraction = delete this fraction of atoms
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seed = random number seed (positive integer) :pre
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zero or more keyword/value pairs may be appended :l
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keyword = {compress} or {mol} :l
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{compress} value = {no} or {yes}
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{mol} value = {no} or {yes} :pre
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:ule
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[Examples:]
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delete_atoms group edge
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delete_atoms region sphere compress no
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delete_atoms overlap 0.3 all all
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delete_atoms overlap 0.5 solvent colloid
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delete_atoms porosity cube 0.1 482793 :pre
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[Description:]
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Delete the specified atoms. This command can be used to carve out
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voids from a block of material or to delete created atoms that are too
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close to each other (e.g. at a grain boundary).
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For style {group}, all atoms belonging to the group are deleted.
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For style {region}, all atoms in the region volume are deleted.
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Additional atoms can be deleted if they are in a molecule for which
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one or more atoms were deleted within the region; see the {mol}
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keyword discussion below.
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For style {overlap} pairs of atoms whose distance of separation is
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within the specified cutoff distance are searched for, and one of the
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2 atoms is deleted. Only pairs where one of the two atoms is in the
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first group specified and the other atom is in the second group are
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considered. The atom that is in the first group is the one that is
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deleted.
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Note that it is OK for the two group IDs to be the same (e.g. group
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{all}), or for some atoms to be members of both groups. In these
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cases, either atom in the pair may be deleted. Also note that if
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there are atoms which are members of both groups, the only guarantee
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is that at the end of the deletion operation, enough deletions will
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have occurred that no atom pairs within the cutoff will remain
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(subject to the group restriction). There is no guarantee that the
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minimum number of atoms will be deleted, or that the same atoms will
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be deleted when running on different numbers of processors.
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For style {porosity} a specified {fraction} of atoms are deleted
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within the specified region. For example, if fraction is 0.1, then
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10% of the atoms will be deleted. The atoms to delete are chosen
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randomly. There is no guarantee that the exact fraction of atoms will
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be deleted, or that the same atoms will be deleted when running on
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different numbers of processors.
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If the {compress} keyword is set to {yes}, then after atoms are
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deleted, then atom IDs are re-assigned so that they run from 1 to the
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number of atoms in the system. This is not done for molecular systems
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(see the "atom_style"_atom_style.html command), regardless of the
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{compress} setting, since it would foul up the bond connectivity that
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has already been assigned.
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It the {mol} keyword is set to {yes}, then for every atom that is
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deleted, all other atoms in the same molecule (with the same molecule
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ID) will also be deleted. This is not done for atoms with molecule ID
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= 0, since it is assumed to flag isolated atoms that are not part of
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molecules. This is a way to insure that entire molecules are deleted
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instead of only a subset of atoms in the molecule which will typically
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lead to errors because of bond, angle, or dihedral interactions stored
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by remaining atoms which reference deleted atoms.
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IMPORTANT NOTE: The molecule deletion operation in invoked after all
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individual atoms have been deleted using the rules described above for
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each style. This means additional atoms may be deleted that are not
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in the group or region, that are not required by the overlap cutoff
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criterion, or that will create a higher fraction of porosity than was
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requested.
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[Restrictions:]
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The {overlap} styles requires inter-processor communication to acquire
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ghost atoms and build a neighbor list. This means that your system
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must be ready to perform a simulation before using this command (force
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fields setup, atom masses set, etc). Since a neighbor list is used to
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find overlapping atom pairs, it also means that you must define a
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"pair style"_pair_style.html with force cutoffs greater than or equal
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to the desired overlap cutoff between pairs of relevant atom types,
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even though the pair potential will not be evaluated.
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If the "special_bonds"_special_bonds.html command is used with a
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setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
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appear in the neighbor list, and thus will not be considered for
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deletion by the {overlap} styles. You probably don't want to be
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deleting one atom in a bonded pair anyway.
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[Related commands:]
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"create_atoms"_create_atoms.html
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[Default:]
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The option defaults are compress = yes and mol = no.
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