2008-03-06 02:17:18 +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/com command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute ID group-ID temp/com
|
|
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
|
|
|
|
<LI>temp/com = style name of this compute command
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>compute 1 all temp/com
|
|
|
|
|
compute myTemp mobile temp/com
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Define a computation that calculates the temperature of a group of
|
|
|
|
|
atoms, after subtracting out the center-of-mass velocity of the group.
|
|
|
|
|
This is useful if the group is expected to have a non-zero net
|
|
|
|
|
velocity for some reason. 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>
|
2009-04-30 00:54:14 +08:00
|
|
|
<P>After the center-of-mass velocity has been subtracted from each atom,
|
|
|
|
|
the temperature is calculated by the formula KE = dim/2 N k T, where
|
2008-03-06 02:17:18 +08:00
|
|
|
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
|
|
|
|
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
|
|
|
|
|
in the group, k = Boltzmann constant, and T = temperature.
|
|
|
|
|
</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 for use in the computation 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. The 6 components of the vector are ordered xx, yy,
|
|
|
|
|
zz, xy, xz, yz.
|
2008-03-06 02:17:18 +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>
|
2008-03-12 00:37:01 +08:00
|
|
|
<P>The removal of the center-of-mass velocity 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>
|
2008-03-06 02:17:18 +08:00
|
|
|
<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>
|
2008-04-05 05:15:50 +08:00
|
|
|
<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>
|
2008-03-06 02:17:18 +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
|
|
|
|
|
vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
|
|
|
|
|
section</A> for an overview of LAMMPS output
|
|
|
|
|
options.
|
|
|
|
|
</P>
|
2008-03-06 02:17:18 +08:00
|
|
|
<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>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
|
|
|
|
</HTML>
|
