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lammps/doc/src/compute_coord_atom.txt
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"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
compute coord/atom command :h3
[Syntax:]
compute ID group-ID coord/atom cstyle args ... :pre
ID, group-ID are documented in "compute"_compute.html command
coord/atom = style name of this compute command
one cstyle must be appended :ul
cstyle = {cutoff} or {orientorder}
{cutoff} args = cutoff typeN
cutoff = distance within which to count coordination neighbors (distance units)
typeN = atom type for Nth coordination count (see asterisk form below) :pre
{orientorder} args = orientorderID threshold
orientorderID = ID of a previously defined orientorder/atom compute
threshold = minimum value of the scalar product between two 'connected' atoms (see text for explanation) :pre
[Examples:]
compute 1 all coord/atom cutoff 2.0
compute 1 all coord/atom cutoff 6.0 1 2
compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
compute 1 all coord/atom orientorder 2 0.5 :pre
[Description:]
This compute performs generic calculations between neighboring atoms. So far,
there are two cstyles implemented: {cutoff} and {orientorder}.
The {cutoff} cstyle calculates one or more coordination numbers
for each atom in a group.
A coordination number is defined as the number of neighbor atoms with
specified atom type(s) that are within the specified cutoff distance
from the central atom. Atoms not in the group are included in a
coordination number of atoms in the group.
The {typeN} keywords allow you to specify which atom types contribute
to each coordination number. One coordination number is computed for
each of the {typeN} keywords listed. If no {typeN} keywords are
listed, a single coordination number is calculated, which includes
atoms of all types (same as the "*" format, see below).
The {typeN} keywords can be specified in one of two ways. An explicit
numeric value can be used, as in the 2nd example above. Or a
wild-card asterisk can be used to specify a range of atom types. This
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
atom types, then an asterisk with no numeric values means all types
from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
The {orientorder} cstyle calculates the number of 'connected' atoms j
around each atom i. The atom j is connected to i if the scalar product
({Ybar_lm(i)},{Ybar_lm(j)}) is larger than {threshold}. Thus, this cstyle
will work only if a "compute orientorder/atom"_compute_orientorder_atom.html
has been previously defined. This cstyle allows one to apply the
ten Wolde's criterion to identify cristal-like atoms in a system
(see "ten Wolde et al."_#tenWolde).
The value of all coordination numbers will be 0.0 for atoms not in the
specified compute group.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the "special_bonds"_special_bonds.html
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the coordination count. One way
to get around this, is to write a dump file, and use the
"rerun"_rerun.html command to compute the coordination for snapshots
in the dump file. The rerun script can use a
"special_bonds"_special_bonds.html command that includes all pairs in
the neighbor list.
[Output info:]
If single {type1} keyword is specified (or if none are specified),
this compute calculates a per-atom vector. If multiple {typeN}
keywords are specified, this compute calculates a per-atom array, with
N columns. These values can be accessed by any command that uses
per-atom values from a compute as input. See "Section
6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The per-atom vector or array values will be a number >= 0.0, as
explained above.
[Restrictions:]
The cstyle {orientorder} can only be used if a
"compute orientorder/atom"_compute_orientorder_atom.html command
was previously defined. Otherwise, an error message will be issued.
[Related commands:]
"compute cluster/atom"_compute_cluster_atom.html
"compute orientorder/atom"_compute_orientorder_atom.html
[Default:] none
:line
:link(tenWolde)
[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
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