.. index:: delete_atoms delete_atoms command ==================== Syntax """""" .. parsed-literal:: delete_atoms style args keyword value ... * style = *group* or *region* or *overlap* or *porosity* .. parsed-literal:: *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* .. parsed-literal:: *compress* value = *no* or *yes* *mol* value = *no* or *yes* Examples """""""" .. parsed-literal:: 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 :doc:`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 :doc:`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 :doc:`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. Related commands """""""""""""""" :doc:`create_atoms ` Default """"""" The option defaults are compress = yes and mol = no. .. _liws: http://www.cfdem.com .. _ld: Manual.html .. _lc: Section_commands.html#comm