ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Added hexatic bond orientational order parameter

Browse Source 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14236 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
2015-11-05 06:53:08 +00:00
parent d212245359
commit 3bc7350704
5 changed files with 61 additions and 23 deletions
Download Patch File Download Diff File Expand all files Collapse all files

43
doc/compute_hexorder_atom.txt
View File

@ -10,26 +10,31 @@ compute hexorder/atom command :h3
[Syntax:]
compute ID group-ID hexorder/atom :pre
compute ID group-ID hexorder/atom keyword values ... :pre
ID, group-ID are documented in "compute"_compute.html command
hexorder/atom = style name of this compute command
ID, group-ID are documented in "compute"_compute.html command :ulb,l
hexorder/atom = style name of this compute command :l
zero or more keyword/value pairs may be appended :l
keyword = {degree} :l
{n} value = degree of order parameter :pre
:ule
[Examples:]
compute 1 all hexorder/atom :pre
compute 1 all hexorder/atom
compute 1 all hexorder/atom n 4 :pre
[Description:]
Define a computation that calculates {q}6 the hexatic bond-orientational
order parameter for each atom in a group. This order
Define a computation that calculates {qn} the bond-orientational
order parameter for each atom in a group. The hexatic ({n} = 6) order
parameter was introduced by "Nelson and Halperin"_#Nelson as a way to detect
hexagonal symmetry in two-dimensional systems. For each atom, {q}6
hexagonal symmetry in two-dimensional systems. For each atom, {qn}
is a complex number (stored as two real numbers) defined as follows:
:c,image(Eqs/hexorder.jpg)
where the sum is over the six nearest neighbors
where the sum is over the {n} nearest neighbors
of the central atom. The angle theta
is formed by the bond vector rij and the {x} axis. theta is calculated
only using the {x} and {y} components, whereas the distance from the
@ -38,16 +43,16 @@ central atom is calculated using all three
Neighbor atoms not in the group
are included in the order parameter of atoms in the group.
If the neighbors of the central atom lie on a hexagonal lattice,
then |{q}6| = 1.
The optional keyword {n} sets the degree of the order parameter.
The default value is 6. If the neighbors of the central atom
lie on a hexagonal lattice, then |{q}6| = 1.
The complex phase of {q}6 depends on the orientation of the
lattice relative to the {x} axis. For a liquid in which the
atomic neighborhood lacks orientational symmetry, |{q}6| << 1.
The value of all order parameters will be zero for atoms not in the
specified compute group. If the atom does not have 6 neighbors (within
the potential cutoff), then its centro-symmetry parameter is set to
zero.
The value of {qn} will be zero for atoms not in the
specified compute group. If the atom has less than {n} neighbors (within
the potential cutoff), then {qn} is set to zero.
The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
@ -70,7 +75,7 @@ the neighbor list.
[Output info:]
This compute calculates a per-atom array with 2 columns, giving the
real and imaginary parts of {q}6, respectively.
real and imaginary parts of {qn}, respectively.
These values can be accessed by any command that uses
per-atom values from a compute as input. See "Section_howto
@ -78,8 +83,8 @@ per-atom values from a compute as input. See "Section_howto
options.
The per-atom array contain pairs of numbers representing the
real and imaginary parts of {q}6, a complex number subject to the
constraint |{q}6| <= 1.
real and imaginary parts of {qn}, a complex number subject to the
constraint |{qn}| <= 1.
[Restrictions:] none
@ -87,7 +92,9 @@ constraint |{q}6| <= 1.
"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html
[Default:] none
[Default:]
The option default is {n} = 6.
:line