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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13078 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-02-06 23:40:25 +00:00
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26
doc/Section_howto.html
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@ -1617,15 +1617,15 @@ pressure</A> command calculates pressure.
<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
</UL>
<P>All but the first 3 calculate velocity biases (i.e. advection
<P>All but the first 3 calculate velocity biases directly (e.g. advection
velocities) that are removed when computing the thermal temperature.
<A HREF = "compute_temp_sphere.html">Compute temp/sphere</A> and <A HREF = "compute_temp_asphere.html">compute
temp/asphere</A> compute kinetic energy for
finite-size particles that includes rotational degrees of freedom.
They both allow, as an extra argument, which is another temperature
compute that subtracts a velocity bias. This allows the translational
velocity of spherical or aspherical particles to be adjusted in
prescribed ways.
They both allow for velocity biases indirectly, via an optional extra
argument, another temperature compute that subtracts a velocity bias.
This allows the translational velocity of spherical or aspherical
particles to be adjusted in prescribed ways.
</P>
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>, or in one
case by a pair style. Several thermostatting fixes are available:
@ -1658,15 +1658,21 @@ to the per-particle thermostatting of <A HREF = "fix_langevin.html">fix
langevin</A>.
</P>
<P>Any of the thermostatting fixes can use temperature computes that
remove bias for two purposes: (a) computing the current temperature to
compare to the requested target temperature, and (b) adjusting only
the thermal temperature component of the particle's velocities. See
the doc pages for the individual fixes and for the
remove bias which has two effects. First, the current calculated
temperature, which is compared to the requested target temperature, is
caluclated with the velocity bias removed. Second, the thermostat
adjusts only the thermal temperature component of the particle's
velocities, which are the velocities with the bias removed. The
removed bias is then added back to the adjusted velocities. See the
doc pages for the individual fixes and for the
<A HREF = "fix_modify.html">fix_modify</A> command for instructions on how to assign
a temperature compute to a thermostatting fix. For example, you can
apply a thermostat to only the x and z components of velocity by using
it in conjunction with <A HREF = "compute_temp_partial.html">compute
temp/partial</A>.
temp/partial</A>. Of you could thermostat only
the thermal temperature of a streaming flow of particles without
affecting the streaming velocity, by using <A HREF = "compute_temp_profile.html">compute
temp/profile</A>.
</P>
<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces