d1cbced715
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14292 f3b2605a-c512-4ea7-a41b-209d697bcdaa
132 lines
5.4 KiB
HTML
132 lines
5.4 KiB
HTML
<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 orientorder/atom command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>compute ID group-ID orientorder/atom keyword values ...
|
|
</PRE>
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
|
|
|
<LI>orientorder/atom = style name of this compute command
|
|
|
|
<LI>one or more keyword/value pairs may be appended
|
|
|
|
<PRE>keyword = <I>cutoff</I> or <I>nnn</I> or <I>ql</I>
|
|
<I>cutoff</I> value = distance cutoff
|
|
<I>nnn</I> value = number of nearest neighbors
|
|
<I>degrees</I> values = nlvalues, l1, l2,...
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>compute 1 all orientorder/atom
|
|
compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Define a computation that calculates a set of bond-orientational
|
|
order parameters <I>Ql</I> for each atom in a group. These order parameters
|
|
were introduced by <A HREF = "#Steinhardt">Steinhardt et al.</A> as a way to
|
|
characterize the local orientational order in atomic structures.
|
|
For each atom, <I>Ql</I> is a real number defined as follows:
|
|
</P>
|
|
<CENTER><IMG SRC = "Eqs/orientorder.jpg">
|
|
</CENTER>
|
|
<P>The first equation defines the spherical harmonic order parameters.
|
|
These are complex number components of the 3D analog of the 2D order
|
|
parameter <I>qn</I>, which is implemented as LAMMPS compute
|
|
<A HREF = "compute_hexorder_atom.html">hexorder/atom</A>.
|
|
The summation is over the <I>nnn</I> nearest
|
|
neighbors of the central atom.
|
|
The angles theta and phi are the standard spherical polar angles
|
|
defining the direction of the bond vector <I>rij</I>.
|
|
The second equation defines <I>Ql</I>, which is a
|
|
rotationally invariant scalar quantity obtained by summing
|
|
over all the components of degree <I>l</I>.
|
|
</P>
|
|
<P>The optional keyword <I>cutoff</I> defines the distance cutoff
|
|
used when searching for neighbors. The default value, also
|
|
the maximum allowable value, is the cutoff specified
|
|
by the pair style.
|
|
</P>
|
|
<P>The optional keyword <I>nnn</I> defines the number of nearest
|
|
neighbors used to calculate <I>Ql</I>. The default value is 12.
|
|
If the value is NULL, then all neighbors up to the
|
|
specified distance cutoff are used.
|
|
</P>
|
|
<P>The optional keyword <I>degrees</I> defines the list of order parameters to
|
|
be computed. The first argument <I>nlvalues</I> is the number of order
|
|
parameters. This is followed by that number of integers giving the
|
|
degree of each order parameter. Because <I>Q</I>2 and all odd-degree
|
|
order parameters are zero for atoms in cubic crystals
|
|
(see <A HREF = "#Steinhardt">Steinhardt</A>), the default order parameters
|
|
are <I>Q</I>4, <I>Q</I>6, <I>Q</I>8, <I>Q</I>10, and <I>Q</I>12. For the
|
|
FCC crystal with <I>nnn</I>=12, <I>Q</I>4 = sqrt(7/3)/8 = 0.19094....
|
|
The numerical values of all order parameters up to <I>Q</I>12
|
|
for a range of commonly encountered high-symmetry structures are given
|
|
in Table I of <A HREF = "#Mickel">Mickel et al.</A>.
|
|
</P>
|
|
<P>The value of <I>Ql</I> is set to zero for atoms not in the
|
|
specified compute group, as well as for atoms that have less than
|
|
<I>nnn</I> neighbors within the distance cutoff.
|
|
</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. This difficulty
|
|
can be circumvented by writing a dump file, and using 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 <I>nlvalues</I> columns, giving the
|
|
<I>Ql</I> values for each atom, which are real numbers on the range 0 <= <I>Ql</I> <= 1.
|
|
</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><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>, <A HREF = "compute_hexorder_atom.html">compute hexorder/atom</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The option defaults are <I>cutoff</I> = pair style cutoff, <I>nnn</I> = 12, <I>degrees</I> = 5 4 6 8 9 10 12 i.e. <I>Q</I>4, <I>Q</I>6, <I>Q</I>8, <I>Q</I>10, and <I>Q</I>12.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "Steinhardt"></A>
|
|
|
|
<A NAME = "Mickel"></A><B>(Steinhardt)</B> P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
|
|
|
|
|
|
<P><B>(Mickel)</B> W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
|
|
</P>
|
|
</HTML>
|