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sjplimp 2012-08-23 00:10:10 +00:00
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9
doc/fix_nh.html
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@ -445,6 +445,15 @@ space measure of the underlying non-Hamiltonian equations of motion.
</P>
<HR>
<P>The fix npt and fix nph commands can be used with rigid bodies or
mixtures of rigid bodies and non-rigid particles (e.g. solvent). But
there are also <A HREF = "fix_rigid.html">fix rigid/npt</A> and <A HREF = "fix_rigid.html">fix
rigid/nph</A> commands, which are typically a more natural
choice. See the doc page for those commands for more discussion of
the various ways to do this.
</P>
<HR>
<P>Styles with a <I>cuda</I> suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in

9
doc/fix_nh.txt
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@ -436,6 +436,15 @@ space measure of the underlying non-Hamiltonian equations of motion.
:line
The fix npt and fix nph commands can be used with rigid bodies or
mixtures of rigid bodies and non-rigid particles (e.g. solvent). But
there are also "fix rigid/npt"_fix_rigid.html and "fix
rigid/nph"_fix_rigid.html commands, which are typically a more natural
choice. See the doc page for those commands for more discussion of
the various ways to do this.
:line
Styles with a {cuda} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in

58
doc/fix_rigid.html
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@ -465,6 +465,64 @@ described below.
</P>
<HR>
<P>If your simlulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with <A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix
nvt</A>, <A HREF = "fix_nh.html">fix npt</A>, and <A HREF = "fix_nh.html">fix nph</A>.
</P>
<P>If you wish to perform NVE dynamics (no thermostatting or
barostatting), use fix rigid or fix rigid/nve to integrate the rigid
bodies, and <A HREF = "fix_nve.html">fix nve</A> to integrate the non-rigid
particles.
</P>
<P>If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use fix rigid/nvt for the rigid bodies, and any
thermostatting fix for the non-rigid particles (<A HREF = "fix_nh.html">fix nvt</A>,
<A HREF = "fix_langevin.html">fix langevin</A>, <A HREF = "fix_temp_berendsen.html">fix
temp/berendsen</A>). You can also use fix rigid
or fix rigid/nve for the rigid bodies and thermostat them using <A HREF = "fix_langevin.html">fix
langevin</A> on the group that contains all the
particles in the rigid bodies. The net force added by <A HREF = "fix_langevin.html">fix
langevin</A> to each rigid body effectively thermostats
its translational center-of-mass motion. Not sure how well it does at
thermostatting its rotational motion.
</P>
<P>If you with to perform NPT or NPH dynamics (barostatting), you cannot
use both <A HREF = "fix_nh.html">fix npt</A> and fix rigid/npt (or the nph
variants). This is because there can only be one fix which monitors
the global pressure and changes the simulation box dimensions. So you
have 3 choices:
</P>
<UL><LI>Use fix rigid/npt for the rigid bodies. Use the <I>dilate</I> all option
so that it will dilate the positions of the non-rigid particles as
well. Use <A HREF = "fix_nh.html">fix nvt</A> (or any other thermostat) for the
non-rigid particles.
<LI>Use <A HREF = "fix_nh.html">fix npt</A> for the group of non-rigid particles. Use
the <I>dilate</I> all option so that it will dilate the center-of-mass
positions of the rigid bodies as well. Use fix rigid/nvt for the
rigid bodies.
<LI>Use <A HREF = "fix_press_berendsen.html">fix press/berendsen</A> to compute the
pressure and change the box dimensions. Use fix rigid/nvt for the
rigid bodies. Use <A HREF = "fix_nh.thml">fix nvt</A> (or any other thermostat) for
the non-rigid particles.
</UL>
<P>In all case, the rigid bodies and non-rigid particles both contribute
to the global pressure and the box is scaled the same by any of the
barostatting fixes.
</P>
<P>You could even use the 2nd and 3rd options for a non-hybrid simulation
consisting of only rigid bodies, assuming you give <A HREF = "fix_nh.html">fix
npt</A> an empty group, though it's an odd thing to do. The
barostatting fixes (<A HREF = "fix_nh.html">fix npt</A> and <A HREF = "fix_press_berendsen.html">fix
press/berensen</A>) will monitor the pressure
and change the box dimensions, but not time integrate any particles.
The integration of the rigid bodies will be performed by fix
rigid/nvt.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about the <I>rigid</I> and <I>rigid/nve</I> fixes are written to

58
doc/fix_rigid.txt
View File

@ -452,6 +452,64 @@ described below.
:line
If your simlulation is a hybrid model with a mixture of rigid bodies
and non-rigid particles (e.g. solvent) there are several ways these
rigid fixes can be used in tandem with "fix nve"_fix_nve.html, "fix
nvt"_fix_nh.html, "fix npt"_fix_nh.html, and "fix nph"_fix_nh.html.
If you wish to perform NVE dynamics (no thermostatting or
barostatting), use fix rigid or fix rigid/nve to integrate the rigid
bodies, and "fix nve"_fix_nve.html to integrate the non-rigid
particles.
If you wish to perform NVT dynamics (thermostatting, but no
barostatting), you can use fix rigid/nvt for the rigid bodies, and any
thermostatting fix for the non-rigid particles ("fix nvt"_fix_nh.html,
"fix langevin"_fix_langevin.html, "fix
temp/berendsen"_fix_temp_berendsen.html). You can also use fix rigid
or fix rigid/nve for the rigid bodies and thermostat them using "fix
langevin"_fix_langevin.html on the group that contains all the
particles in the rigid bodies. The net force added by "fix
langevin"_fix_langevin.html to each rigid body effectively thermostats
its translational center-of-mass motion. Not sure how well it does at
thermostatting its rotational motion.
If you with to perform NPT or NPH dynamics (barostatting), you cannot
use both "fix npt"_fix_nh.html and fix rigid/npt (or the nph
variants). This is because there can only be one fix which monitors
the global pressure and changes the simulation box dimensions. So you
have 3 choices:
Use fix rigid/npt for the rigid bodies. Use the {dilate} all option
so that it will dilate the positions of the non-rigid particles as
well. Use "fix nvt"_fix_nh.html (or any other thermostat) for the
non-rigid particles. :ulb,l
Use "fix npt"_fix_nh.html for the group of non-rigid particles. Use
the {dilate} all option so that it will dilate the center-of-mass
positions of the rigid bodies as well. Use fix rigid/nvt for the
rigid bodies. :l
Use "fix press/berendsen"_fix_press_berendsen.html to compute the
pressure and change the box dimensions. Use fix rigid/nvt for the
rigid bodies. Use "fix nvt"_fix_nh.thml (or any other thermostat) for
the non-rigid particles. :l,ule
In all case, the rigid bodies and non-rigid particles both contribute
to the global pressure and the box is scaled the same by any of the
barostatting fixes.
You could even use the 2nd and 3rd options for a non-hybrid simulation
consisting of only rigid bodies, assuming you give "fix
npt"_fix_nh.html an empty group, though it's an odd thing to do. The
barostatting fixes ("fix npt"_fix_nh.html and "fix
press/berensen"_fix_press_berendsen.html) will monitor the pressure
and change the box dimensions, but not time integrate any particles.
The integration of the rigid bodies will be performed by fix
rigid/nvt.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about the {rigid} and {rigid/nve} fixes are written to