2007-02-10 05:40:32 +08:00
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<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>
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<HR>
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<H3>compute temp/region command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID temp/region region-ID
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>temp/region = style name of this compute command
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<LI>region-ID = ID of region to use for choosing atoms
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</UL>
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<P><B>Examples:</B>
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</P>
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2010-05-14 23:08:14 +08:00
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<PRE>compute mine flow temp/region boundary
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2007-02-10 05:40:32 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Define a computation that calculates the temperature of a group of
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atoms in a geometric region. This can be useful for thermostatting
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one portion of the simulation box. E.g. a McDLT simulation where one
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side is cooled, and the other side is heated. A compute of this style
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can be used by any command that computes a temperature,
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e.g. <A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "fix_temp_rescale.html">fix
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temp/rescale</A>, etc.
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</P>
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<P>Note that a <I>region</I>-style temperature can be used to thermostat with
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<A HREF = "fix_temp_rescale.html">fix temp/rescale</A> or <A HREF = "fix_langevin.html">fix
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langevin</A>, but should probably not be used with
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2010-04-03 00:51:06 +08:00
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Nose/Hoover style fixes (<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_nh.html">fix
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npt</A>, or <A HREF = "fix_nh.html">fix nph</A>), if the
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2007-02-10 05:40:32 +08:00
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degrees-of-freedom included in the computed T varies with time.
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</P>
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<P>The temperature is calculated by the formula KE = dim/2 N k T, where
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KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
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dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
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in both the group and region, k = Boltzmann constant, and T =
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temperature.
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</P>
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2009-12-04 07:58:11 +08:00
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<P>A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz.
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2007-02-10 05:40:32 +08:00
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</P>
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<P>The number of atoms contributing to the temperature is compute each
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time the temperature is evaluated since it is assumed atoms can
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enter/leave the region. Thus there is no need to use the <I>dynamic</I>
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option of the <A HREF = "compute_modify.html">compute_modify</A> command for this
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compute style.
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</P>
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2008-03-12 00:37:01 +08:00
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<P>The removal of atoms outside the region by this fix is essentially
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computing the temperature after a "bias" has been removed, which in
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this case is the velocity of any atoms outside the region. If this
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compute is used with a fix command that performs thermostatting then
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this bias will be subtracted from each atom, thermostatting of the
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remaining thermal velocity will be performed, and the bias will be
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added back in. Thermostatting fixes that work in this way include
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2010-05-07 23:11:21 +08:00
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<A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
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2008-03-12 00:37:01 +08:00
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temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
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2008-03-12 02:05:41 +08:00
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langevin</A>. This means any of the thermostatting
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2008-03-12 00:37:01 +08:00
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fixes can operate on a geometric region of atoms, as defined by this
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compute.
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</P>
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2007-02-10 05:40:32 +08:00
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<P>Unlike other compute styles that calculate temperature, this compute
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does NOT currently subtract out degrees-of-freedom due to fixes that
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constrain molecular motion, such as <A HREF = "fix_shake.html">fix shake</A> and
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<A HREF = "fix_rigid.html">fix rigid</A>. If needed the subtracted
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degrees-of-freedom can be altered using the <I>extra</I> option of the
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<A HREF = "compute_modify.html">compute_modify</A> command.
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</P>
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2011-08-26 01:01:01 +08:00
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<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
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a discussion of different ways to compute temperature and perform
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2008-04-05 05:15:50 +08:00
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thermostatting.
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</P>
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2008-01-03 03:25:15 +08:00
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<P><B>Output info:</B>
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</P>
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2009-12-04 07:58:11 +08:00
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<P>This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
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These values can be used by any command that uses global scalar or
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2011-08-26 01:01:01 +08:00
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vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
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2009-12-04 07:58:11 +08:00
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section</A> for an overview of LAMMPS output
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options.
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</P>
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2010-03-03 05:51:16 +08:00
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<P>The scalar value calculated by this compute is "intensive". The
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vector values are "extensive".
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2008-01-03 03:25:15 +08:00
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</P>
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2010-01-24 07:20:05 +08:00
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<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
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vector values will be in energy <A HREF = "units.html">units</A>.
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</P>
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2007-02-10 05:40:32 +08:00
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_pressure.html">compute
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pressure</A>
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</P>
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<P><B>Default:</B> none
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</P>
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</HTML>
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