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/partial 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/partial xflag yflag zflag
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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/partial = style name of this compute command
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<LI>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>compute newT flow temp/partial 1 1 0
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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 compute to calculate the temperature of a group of atoms,
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after excluding one or more velocity components. A compute of this
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style 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>, <A HREF = "fix_npt.html">fix npt</A>, etc.
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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 = dimensionality of the simulation, N = number of atoms in the
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group, k = Boltzmann constant, and T = temperature. The calculation
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of KE excludes the x, y, or z dimensions if xflag, yflag, or zflag =
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0. The dim parameter is adjusted to give the correct number of
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degrees of freedom.
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</P>
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<P>A 6-component kinetic energy tensor is also calculated by this compute
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for use in the calculation of a pressure tensor. The formula for the
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components of the tensor is the same as the above formula, except that
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v^2 is replaced by vx * vy for the xy component, etc.
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</P>
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<P>The number of atoms contributing to the temperature is assumed to be
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constant for the duration of the run; use the <I>dynamic</I> option of the
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<A HREF = "compute_modify.html">compute_modify</A> command if this is not the case.
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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 velocity components by this fix is essentially
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computing the temperature after a "bias" has been removed from the
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velocity of the atoms. If this compute is used with a fix command
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that performs thermostatting then this bias will be subtracted from
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each atom, thermostatting of the remaining thermal velocity will be
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performed, and the bias will be added back in. Thermostatting fixes
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that work in this way include <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
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temp/rescale</A>, <A HREF = "fix_temp_berendsen">fix
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temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
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langevin</A>.
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</P>
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2007-02-10 05:40:32 +08:00
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<P>This compute subtracts 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>. This means the temperature of groups of
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atoms that include these constraints will be computed correctly. If
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needed, the subtracted degrees-of-freedom can be altered using the
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<I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
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</P>
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2008-04-05 05:15:50 +08:00
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<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
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discussion of different ways to compute temperature and perform
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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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<P>The scalar value calculated by this compute is "intensive", meaning it
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is independent of the number of atoms in the simulation. The vector
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values are "extensive", meaning they scale with the number of atoms in
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the simulation.
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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_temp_region.html">compute
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temp/region</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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