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rLAMMPS lammps
compute_gyration.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 gyration command
</H3>
<P><B>
Syntax:
</B>
</P>
<PRE>
compute ID group-ID gyration
</PRE>
<UL><LI>
ID, group-ID are documented in
<A
HREF =
"compute.html"
>
compute
</A>
command
<LI>
gyration = style name of this compute command
</UL>
<P><B>
Examples:
</B>
</P>
<PRE>
compute 1 molecule gyration
</PRE>
<P><B>
Description:
</B>
</P>
<P>
Define a computation that calculates the radius of gyration Rg of the
group of atoms, including all effects due to atoms passing thru
periodic boundaries.
</P>
<P>
Rg is a measure of the size of the group of atoms, and is computed as
the square root of the Rg^2 value in this formula
</P>
<CENTER><IMG
SRC =
"Eqs/compute_gyration.jpg"
>
</CENTER>
<P>
where M is the total mass of the group, Rcm is the center-of-mass
position of the group, and the sum is over all atoms in the group.
</P>
<P>
A Rg^2 tensor, stored as a 6-element vector, is also calculated by
this compute. The formula for the components of the tensor is the
same as the above formula, except that (Ri - Rcm)^2 is replaced by
(Rix - Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6
components of the vector are ordered xx, yy, zz, xy, xz, yz. Note
that unlike the scalar Rg, each of the 6 values of the tensor is
effectively a "squared" value, since the cross-terms may be negative
and taking a sqrt() would be invalid.
</P>
<P>
IMPORTANT NOTE: The coordinates of an atom contribute to Rg in
"unwrapped" form, by using the image flags associated with each atom.
See the
<A
HREF =
"dump.html"
>
dump custom
</A>
command for a discussion of
"unwrapped" coordinates. See the Atoms section of the
<A
HREF =
"read_data.html"
>
read_data
</A>
command for a discussion of image flags and
how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this compute by using the
<A
HREF =
"set.html"
>
set
image
</A>
command.
</P>
<P><B>
Output info:
</B>
</P>
<P>
This compute calculates a global scalar (Rg) and a global vector of
length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These
values can be used by any command that uses a global scalar value or
vector 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 scalar and vector values calculated by this compute are
"intensive". The scalar and vector values will be in distance and
distance^2
<A
HREF =
"units.html"
>
units
</A>
respectively.
</P>
<P><B>
Restrictions:
</B>
none
</P>
<P><B>
Related commands:
</B>
</P>
<P><A
HREF =
"compute_gyration_chunk.html"
>
compute gyration/chunk
</A>
</P>
<P><B>
Default:
</B>
none
</P>
</HTML>
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