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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2781 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2009-04-29 16:54:14 +00:00
parent 16ef076c31
commit c0b782aaa2
18 changed files with 136 additions and 99 deletions
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30
doc/Section_howto.html
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@ -1178,6 +1178,7 @@ pressure</A> command calculates pressure.
<LI><A HREF = "compute_temp_com.html">compute temp/com</A>
<LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
<LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
<LI><A HREF = "compute_temp_profile.html">compute temp/profile</A>
<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
<LI><A HREF = "compute_temp_region.html">compute temp/region</A>
</UL>
@ -1186,9 +1187,10 @@ velocities) that are removed when computing the thermal temperature.
<A HREF = "fix_temp_sphere.html">Fix temp/sphere</A> and <A HREF = "fix_temp_asphere.html">fix
temp/asphere</A> compute kinetic energy for
extended particles that includes rotational degrees of freedom. They
both allow, as an extra argument, another temperature compute that
subtracts a velocity bias, so the translational velocity of extended
spherical or aspherical particles can be adjusted in prescribed ways.
both allow, as an extra argument, which is another temperature compute
that subtracts a velocity bias. This allows the translational
velocity of extended spherical or aspherical particles to be adjusted
in prescribed ways.
</P>
<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>. Four
thermostatting fixes are currently available: Nose-Hoover (nvt),
@ -1203,7 +1205,7 @@ Berendsen, Langevin, and direct rescaling (temp/rescale):
<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
</UL>
<P><A HREF = "fix_nvt.html">Fix nvt</A> only thermostats the translational velocity of
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> does as well, except
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the <A HREF = "#4_13">NEMD
simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
@ -1225,8 +1227,9 @@ the x and z components of velocity by using it in conjunction with
<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
they update the velocities and positions of particles due to forces
and velocities respectively. The other thermostat fixes only adjust
velocities; they do NOT perform time integration. Thus they should be
used in conjunction with a constant NVE integration fix such as these:
velocities; they do NOT perform time integration updates. Thus they
should be used in conjunction with a constant NVE integration fix such
as these:
</P>
<UL><LI><A HREF = "fix_nve.html">fix nve</A>
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
@ -1258,12 +1261,15 @@ and aspherical particles.
</P>
<P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
pressure</A> compute to calculate a current
pressure. The barostatting fixes can also use temperature computes
that remove bias for the purpose of computing the current temperature
which contributes to the current pressure. 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 or pressure compute to a
barostatting fix.
pressure. By default, this compute is created with a simple <A HREF = "compute_temp.html">compute
temp</A> (see the last argument of the <A HREF = "compute_pressure.html">compute
pressure</A> command), which is used to calculated
the kinetic componenet of the pressure. The barostatting fixes can
also use temperature computes that remove bias for the purpose of
computing the kinetic componenet which contributes to the current
pressure. 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 or pressure compute to a barostatting fix.
</P>
<P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_npt.html">fix
npt</A> and <A HREF = "fix_nph.html">fix nph</A>) perform time