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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1648 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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doc/fix_nvt_sphere.html
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@ -9,15 +9,15 @@
<HR>
<H3>fix nvt/asphere command
<H3>fix nvt/sphere command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID nvt/asphere Tstart Tstop Tdamp keyword value ...
<PRE>fix ID group-ID nvt/sphere Tstart Tstop Tdamp keyword value ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>nvt/asphere = style name of this fix command
<LI>nvt/sphere = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
@ -33,16 +33,26 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all nvt/asphere 300.0 300.0 100.0
fix 1 all nvt/asphere 300.0 300.0 100.0 drag 0.2
<PRE>fix 1 all nvt/sphere 300.0 300.0 100.0
fix 1 all nvt/sphere 300.0 300.0 100.0 drag 0.2
</PRE>
<P><B>Description:</B>
</P>
<P>Perform constant NVT integration to update positions, velocities,
and angular velocities each timestep for aspherical or ellipsoidal
particles in the group using a Nose/Hoover temperature thermostat.
V is volume; T is temperature. This creates a system trajectory
consistent with the canonical ensemble.
<P>Perform constant NVT integration to update position, velocity, and
angular velocity each timestep for extended spherical particles in the
group using a Nose/Hoover temperature thermostat. V is volume; T is
temperature. This creates a system trajectory consistent with the
canonical ensemble.
</P>
<P>This fix differs from the <A HREF = "fix_nvt.html">fix nvt</A> command, which
assumes point particles and only updates their position and velocity.
</P>
<P>The thermostat is applied to both the translational and rotational
degrees of freedom for the spherical particles, assuming a compute is
used which calculates a temperature that includes the rotational
degrees of freedom (see below). The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
@ -62,12 +72,12 @@ to determine if the drag term is working. Typically a value between
0.2 to 2.0 is sufficient to damp oscillations after a few periods.
</P>
<P>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style "temp/asphere", as if this command
creates its own compute of style "temp/sphere", as if this command
had been issued:
</P>
<PRE>compute fix-ID_temp group-ID temp/asphere
<PRE>compute fix-ID_temp group-ID temp/sphere
</PRE>
<P>See the <A HREF = "compute_temp_asphere.html">compute temp/asphere</A> command for
<P>See the <A HREF = "compute_temp_sphere.html">compute temp/sphere</A> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + "temp", and the group for the new compute is the same as
the fix group.
@ -82,6 +92,21 @@ custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, this fix can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
@ -112,9 +137,10 @@ commands</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
<P>This fix requires that particles be represented as extended spheres
and not point particles. This means they will have an angular
velocity and a diameter which is determined by the <A HREF = "shape.html">shape</A>
command.
</P>
<P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in
@ -122,8 +148,9 @@ the Nose/Hoover formulation.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
<P><A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_nve_sphere.html">fix nve_sphere</A>, <A HREF = "fix_nvt_asphere.html">fix
nvt_asphere</A>, <A HREF = "fix_npt_sphere.html">fix
npt_sphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B>
</P>