Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/doc2/compute_temp_asphere.html
07554c8efe48lammm-devel

Last Change
Raw File

compute_temp_asphere.html
View Options

<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>
<PRE>compute ID group-ID temp/asphere keyword value ...
</PRE>
<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
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>
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all temp/asphere
compute myTemp mobile temp/asphere bias tempCOM
compute myTemp mobile temp/asphere dof rotate
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the temperature of a group of
aspherical particles, including a contribution from both their
translational and rotational kinetic energy. This differs from the
usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes point
particles with only translational kinetic energy.
</P>
<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).
</P>
<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
<A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
accordingly.
</P>
<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.
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.
</P>
<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.
</P>
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
as ellipsoids, not ellipses, meaning their moments of inertia will be
the same as in 3d.
</P>
<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.
</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.
</P>
<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
thermostatting.
</P>
<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 flow 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>
<P><B>Output info:</B>
</P>
<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
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
vector values are "extensive".
</P>
<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>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
c4science · Help