2007-04-20 07:25:27 +08:00
|
|
|
<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 temp/asphere command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
2011-04-30 00:27:56 +08:00
|
|
|
<PRE>compute ID group-ID temp/asphere keyword value ...
|
2007-04-20 07:25:27 +08:00
|
|
|
</PRE>
|
2011-04-30 00:27:56 +08:00
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
|
|
|
|
|
|
|
|
|
<LI>temp/asphere = style name of this compute command
|
|
|
|
|
|
|
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
|
|
|
|
|
|
|
|
|
<LI>keyword = <I>bias</I> or <I>dof</I>
|
|
|
|
|
|
|
|
|
|
<PRE> <I>bias</I> value = bias-ID<I>uniform</I> or <I>gaussian</I>
|
|
|
|
|
bias-ID = ID of a temperature compute that removes a velocity bias
|
|
|
|
|
<I>dof</I> value = <I>all</I> or <I>rotate</I>
|
|
|
|
|
all = compute temperature of translational and rotational degrees of freedom
|
|
|
|
|
rotate = compute temperature of just rotational degrees of freedom
|
|
|
|
|
</PRE>
|
|
|
|
|
|
2007-04-20 07:25:27 +08:00
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute 1 all temp/asphere
|
2011-04-30 00:27:56 +08:00
|
|
|
compute myTemp mobile temp/asphere bias tempCOM
|
|
|
|
|
compute myTemp mobile temp/asphere dof rotate
|
2007-04-20 07:25:27 +08:00
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Define a computation that calculates the temperature of a group of
|
2008-03-18 08:23:39 +08:00
|
|
|
aspherical particles, including a contribution from both their
|
|
|
|
|
translational and rotational kinetic energy. This differs from the
|
2008-03-19 04:39:07 +08:00
|
|
|
usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes point
|
|
|
|
|
particles with only translational kinetic energy.
|
2008-03-18 08:23:39 +08:00
|
|
|
</P>
|
2009-07-02 22:39:37 +08:00
|
|
|
<P>Only finite-size particles (aspherical or spherical) can be included
|
|
|
|
|
in the group. For 3d finite-size particles, each has 6 degrees of
|
|
|
|
|
freedom (3 translational, 3 rotational). For 2d finite-size
|
|
|
|
|
particles, each has 3 degrees of freedom (2 translational, 1
|
|
|
|
|
rotational).
|
2008-03-18 08:23:39 +08:00
|
|
|
</P>
|
2009-07-02 22:39:37 +08:00
|
|
|
<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
|
|
|
|
|
all finite-size aspherical or spherical particles in your model will
|
|
|
|
|
freely rotate, sampling all their rotational dof. It is possible to
|
|
|
|
|
use a combination of interaction potentials and fixes that induce no
|
|
|
|
|
torque or otherwise constrain some of all of your particles so that
|
|
|
|
|
this is not the case. Then there are less dof and you should use the
|
2009-06-27 02:41:31 +08:00
|
|
|
<A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
|
|
|
|
|
accordingly.
|
2008-03-18 08:23:39 +08:00
|
|
|
</P>
|
2011-04-14 05:39:34 +08:00
|
|
|
<P>For example, an aspherical particle with all three of its shape
|
|
|
|
|
parameters the same is a sphere. If it does not rotate, then it
|
|
|
|
|
should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
|
|
|
|
|
uniaxial aspherical particle has two of its three shape parameters the
|
|
|
|
|
same. If it does not rotate around the axis perpendicular to its
|
|
|
|
|
circular cross section, then it should have 5 dof instead of 6 in 3d.
|
2013-03-14 02:48:49 +08:00
|
|
|
The latter is the case for uniaxial ellipsoids in a <A HREF = "pair_gayberne.html">GayBerne
|
|
|
|
|
model</A> since there is no induced torque around the
|
|
|
|
|
optical axis. It will also be the case for biaxial ellipsoids when
|
|
|
|
|
exactly two of the semiaxes have the same length and the corresponding
|
|
|
|
|
relative well depths are equal.
|
2008-03-18 08:23:39 +08:00
|
|
|
</P>
|
2009-04-30 00:54:14 +08:00
|
|
|
<P>The translational kinetic energy is computed the same as is described
|
|
|
|
|
by the <A HREF = "compute_temp.html">compute temp</A> command. The rotational
|
|
|
|
|
kinetic energy is computed as 1/2 I w^2, where I is the inertia tensor
|
|
|
|
|
for the aspherical particle and w is its angular velocity, which is
|
|
|
|
|
computed from its angular momentum.
|
2008-03-19 04:39:07 +08:00
|
|
|
</P>
|
2008-03-19 05:02:30 +08:00
|
|
|
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
|
2008-03-19 04:39:07 +08:00
|
|
|
as ellipsoids, not ellipses, meaning their moments of inertia will be
|
|
|
|
|
the same as in 3d.
|
2008-03-18 08:23:39 +08:00
|
|
|
</P>
|
2009-12-04 07:58:11 +08:00
|
|
|
<P>A kinetic energy 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 v^2 and w^2 are
|
|
|
|
|
replaced by vx*vy and wx*wy for the xy component, and the appropriate
|
|
|
|
|
elements of the inertia tensor are used. The 6 components of the
|
|
|
|
|
vector are ordered xx, yy, zz, xy, xz, yz.
|
2008-03-18 08:23:39 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The number of atoms contributing to the temperature is assumed to be
|
|
|
|
|
constant for the duration of the run; use the <I>dynamic</I> option of the
|
|
|
|
|
<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This compute subtracts out translational degrees-of-freedom due to
|
|
|
|
|
fixes that constrain molecular motion, such as <A HREF = "fix_shake.html">fix
|
|
|
|
|
shake</A> and <A HREF = "fix_rigid.html">fix rigid</A>. This means the
|
|
|
|
|
temperature of groups of atoms that include these constraints will be
|
|
|
|
|
computed correctly. If needed, the subtracted degrees-of-freedom can
|
|
|
|
|
be altered using the <I>extra</I> option of the
|
|
|
|
|
<A HREF = "compute_modify.html">compute_modify</A> command.
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
2011-08-26 01:01:01 +08:00
|
|
|
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
|
|
|
|
|
a discussion of different ways to compute temperature and perform
|
2008-04-07 23:58:34 +08:00
|
|
|
thermostatting.
|
|
|
|
|
</P>
|
2011-04-30 00:27:56 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<P>The keyword/value option pairs are used in the following ways.
|
|
|
|
|
</P>
|
|
|
|
|
<P>For the <I>bias</I> keyword, <I>bias-ID</I> refers to the ID of a temperature
|
|
|
|
|
compute that removes a "bias" velocity from each atom. This allows
|
|
|
|
|
compute temp/sphere to compute its thermal temperature after the
|
|
|
|
|
translational kinetic energy components have been altered in a
|
|
|
|
|
prescribed way, e.g. to remove a velocity profile. Thermostats that
|
|
|
|
|
use this compute will work with this bias term. See the doc pages for
|
|
|
|
|
individual computes that calculate a temperature and the doc pages for
|
|
|
|
|
fixes that perform thermostatting for more details.
|
|
|
|
|
</P>
|
|
|
|
|
<P>For the <I>dof</I> keyword, a setting of <I>all</I> calculates a temperature
|
|
|
|
|
that includes both translational and rotational degrees of freedom. A
|
|
|
|
|
setting of <I>rotate</I> calculates a temperature that includes only
|
|
|
|
|
rotational degrees of freedom.
|
|
|
|
|
</P>
|
|
|
|
|
<HR>
|
|
|
|
|
|
2008-01-03 03:25:15 +08:00
|
|
|
<P><B>Output info:</B>
|
|
|
|
|
</P>
|
2009-12-04 07:58:11 +08:00
|
|
|
<P>This compute calculates a global scalar (the temperature) and a global
|
|
|
|
|
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
|
|
|
|
These values can be used by any command that uses global scalar or
|
2011-08-26 01:01:01 +08:00
|
|
|
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
|
2009-12-04 07:58:11 +08:00
|
|
|
section</A> for an overview of LAMMPS output
|
|
|
|
|
options.
|
|
|
|
|
</P>
|
2010-03-03 05:51:16 +08:00
|
|
|
<P>The scalar value calculated by this compute is "intensive". The
|
|
|
|
|
vector values are "extensive".
|
2008-01-03 03:25:15 +08:00
|
|
|
</P>
|
2010-01-24 07:20:05 +08:00
|
|
|
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
|
|
|
|
|
vector values will be in energy <A HREF = "units.html">units</A>.
|
|
|
|
|
</P>
|
2007-04-20 07:25:27 +08:00
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
2011-08-27 02:53:00 +08:00
|
|
|
<P>This compute is part of the ASPHERE package. It is only enabled if
|
2011-08-26 00:46:23 +08:00
|
|
|
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
2011-04-14 05:39:34 +08:00
|
|
|
LAMMPS</A> section for more info.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This compute requires that atoms store angular momementum and a
|
|
|
|
|
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
|
|
|
|
|
command.
|
|
|
|
|
</P>
|
|
|
|
|
<P>All particles in the group must be finite-size. They cannot be point
|
|
|
|
|
particles, but they can be aspherical or spherical as defined by their
|
|
|
|
|
shape attribute.
|
2007-04-20 07:25:27 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "compute_temp.html">compute temp</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
