Homec4science
Diffusion lammps (HEAD -> master) Browse

lammps/doc/compute_temp_partial.html
0cc1d090f44eHEAD -> master

Last Change
Raw File

compute_temp_partial.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/partial command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID temp/partial xflag yflag zflag
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>temp/partial = style name of this compute command
<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute newT flow temp/partial 1 1 0
</PRE>
<P><B>Description:</B>
</P>
<P>Define a compute to calculate the temperature of a group of atoms,
after excluding one or more velocity components. A compute of this
style can be used by any command that computes a temperature,
e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_npt.html">fix npt</A>, etc.
</P>
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
dim = dimensionality of the simulation, N = number of atoms in the
group, k = Boltzmann constant, and T = temperature. The calculation
of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
0. The dim parameter is adjusted to give the correct number of
degrees of freedom.
</P>
<P>A 6-component kinetic energy tensor is also calculated by this compute
for use in the calculation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
v^2 is replaced by vx * vy for the xy component, etc.
</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>The removal of velocity components by this fix is essentially
computing the temperature after a "bias" has been removed from the
velocity of the atoms. If this compute is used with a fix command
that performs thermostatting then this bias will be subtracted from
each atom, thermostatting of the remaining thermal velocity will be
performed, and the bias will be added back in. Thermostatting fixes
that work in this way include <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>
<P>This compute subtracts out 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#4_16">this howto section</A> of the manual for a
discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P><B>Output info:</B>
</P>
<P>The scalar value calculated by this compute is "intensive", meaning it
is independent of the number of atoms in the simulation. The vector
values are "extensive", meaning they scale with the number of atoms in
the simulation.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_region.html">compute
temp/region</A>, <A HREF = "compute_pressure.html">compute
pressure</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
c4science · Help