compute_coord_atom.txt

"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)

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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 :ulb,l
coord/atom = style name of this compute command :l
cstyle = {cutoff} or {orientorder} :l
  {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)
  {orientorder} args = orientorderID threshold
    orientorderID = ID of an orientorder/atom compute
    threshold = minimum value of the product of two "connected" atoms :pre
:ule

[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 calculations between neighboring atoms to
determine a coordination value.  The specific calculation and the
meaning of the resulting value depend on the {cstyle} keyword used.

The {cutoff} cstyle calculates one or more traditional coordination
numbers for each atom.  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
specified group are included in the coordination number tally.

The {typeN} keywords allow specification of 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" neighbor
atoms J around each central atom I.  For this {cstyle}, connected is
defined by the orientational order parameter calculated by the
"compute orientorder/atom"_compute_orientorder_atom.html command.
This {cstyle} thus allows one to apply the ten Wolde's criterion to
identify crystal-like atoms in a system, as discussed in "ten
Wolde"_#tenWolde1.

The ID of the previously specified "compute
orientorder/atom"_compute_orientorder/atom command is specified as
{orientorderID}.  The compute must invoke its {components} option to
calculate components of the {Ybar_lm} vector for each atoms, as
described in its documentation.  Note that orientorder/atom compute
defines its own criteria for identifying neighboring atoms.  If the
scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
orientorder/atom compute is larger than the specified {threshold},
then I and J are connected, and the coordination value of I is
incremented by one.

For all {cstyle} settings, all coordination values 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:]

For {cstyle} cutoff, this compute can calculate a per-atom vector or
array.  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.

For {cstyle} orientorder, this compute calculates a per-atom vector.

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:] none

[Related commands:]

"compute cluster/atom"_compute_cluster_atom.html
"compute orientorder/atom"_compute_orientorder_atom.html

[Default:] none

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:link(tenWolde1)
[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
J. Chem. Phys. 104, 9932 (1996).