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rLAMMPS lammps
compute_hexorder_atom.html
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<HTML>
<CENTER><A
HREF =
"http://lammps.sandia.gov"
>
LAMMPS WWW Site
</A>
-
<A
HREF =
"Manual.html"
>
LAMMPS Documentation
</A>
-
<A
HREF =
"Section_commands.html#comm"
>
LAMMPS Commands
</A>
</CENTER>
<HR>
<H3>
compute hexorder/atom command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
compute ID group-ID hexorder/atom keyword values ...
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"compute.html"
>
compute
</A>
command
<LI>
hexorder/atom = style name of this compute command
<LI>
zero or more keyword/value pairs may be appended
<LI>
keyword =
<I>
degree
</I>
<PRE>
<I>
n
</I>
value = degree of order parameter
</PRE>
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
compute 1 all hexorder/atom
compute 1 all hexorder/atom n 4
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Define a computation that calculates
<I>
qn
</I>
the bond-orientational
order parameter for each atom in a group. The hexatic (
<I>
n
</I>
= 6) order
parameter was introduced by
<A
HREF =
"#Nelson"
>
Nelson and Halperin
</A>
as a way to detect
hexagonal symmetry in two-dimensional systems. For each atom,
<I>
qn
</I>
is a complex number (stored as two real numbers) defined as follows:
</P>
<CENTER><IMG
SRC =
"Eqs/hexorder.jpg"
>
</CENTER>
<P>
where the sum is over the
<I>
n
</I>
nearest neighbors
of the central atom. The angle theta
is formed by the bond vector rij and the
<I>
x
</I>
axis. theta is calculated
only using the
<I>
x
</I>
and
<I>
y
</I>
components, whereas the distance from the
central atom is calculated using all three
<I>
x
</I>
,
<I>
y
</I>
, and
<I>
z
</I>
components of the bond vector.
Neighbor atoms not in the group
are included in the order parameter of atoms in the group.
</P>
<P>
The optional keyword
<I>
n
</I>
sets the degree of the order parameter.
The default value is 6. For a perfect hexagonal lattice,
<I>
q
</I>
6 = exp(6 i phi) for all atoms, where the constant 0
< phi
<
pi
/
3
depends
only
on
the
orientation
of
the
lattice
relative
to
the
x
axis
.
In
an
isotropic
liquid
,
local
neighborhoods
may
still
exhibit
weak
hexagonal
symmetry
,
but
because
the
orientational
correlation
decays
quickly
with
distance
,
the
value
of
phi
will
be
different
for
different
atoms
,
and
|<<
I
>
q
</I>
6>|
<
< 1
.
</
P
>
<P>
The value of
<I>
qn
</I>
will be zero for atoms not in the
specified compute group. If the atom has less than
<I>
n
</I>
neighbors (within
the potential cutoff), then
<I>
qn
</I>
is set to zero.
</P>
<P>
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.
</P>
<P>
IMPORTANT NOTE: If you have a bonded system, then the settings of
<A
HREF =
"special_bonds.html"
>
special_bonds
</A>
command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the
<A
HREF =
"special_bonds.html"
>
special_bonds
</A>
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 order parameter. One way
to get around this, is to write a dump file, and use the
<A
HREF =
"rerun.html"
>
rerun
</A>
command to compute the order parameter for snapshots
in the dump file. The rerun script can use a
<A
HREF =
"special_bonds.html"
>
special_bonds
</A>
command that includes all pairs in
the neighbor list.
</P>
<P><B>
Output info:
</B>
</P>
<P>
This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts of
<I>
qn
</I>
, respectively.
</P>
<P>
These values can be accessed by any command that uses
per-atom values from a compute as input. See
<A
HREF =
"Section_howto.html#howto_15"
>
Section_howto
15
</A>
for an overview of LAMMPS output
options.
</P>
<P>
The per-atom array contain pairs of numbers representing the
real and imaginary parts of
<I>
qn
</I>
, a complex number subject to the
constraint |
<I>
qn
</I>
|
<
= 1.
</P>
<P><B>
Restrictions:
</B>
none
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"compute_coord_atom.html"
>
compute coord/atom
</A>
,
<A
HREF =
"compute_centro_atom.html"
>
compute centro/atom
</A>
</P>
<P><B>
Default:
</B>
</P>
<P>
The option default is
<I>
n
</I>
= 6.
</P>
<HR>
<A
NAME =
"Nelson"
></A>
<P><B>
(Nelson)
</B>
Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
</P>
</HTML>
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