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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12818 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2014-12-05 22:05:01 +00:00
parent 473353997b
commit 2f2f9abcd2
2 changed files with 30 additions and 2 deletions
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16
doc/fix_gle.html
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@ -50,7 +50,8 @@ vibrational modes in the system to inexpensive (approximate)
modelling of nuclear quantum effects. Contrary to
<A HREF = "fix_langevin.html">fix langevin</A>, this fix performs both
thermostatting and evolution of the Hamiltonian equations of motion, so it
does not need to be used together with <A HREF = "fix_nve.html">fix nve</A>.
should not be used together with <A HREF = "fix_nve.html">fix nve</A> -- at least not
on the same atom groups.
</P>
<P>Each degree of freedom in the thermostatted group is supplemented
with Ns additional degrees of freedom s, and the equations of motion
@ -93,6 +94,14 @@ generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
</P>
<P>Note also that the Generalized Langevin Dynamics scheme that is
implemented by the <A HREF = "fix_gld.html">fix gld</A> scheme is closely related
to the present one. In fact, it should be always possible to cast the
Prony series form of the memory kernel used by GLD into an appropriate
input matrix for <A HREF = "fix_gle.html">fix_gle</A>. While the GLE scheme is more
general, the form used by <A HREF = "fix_gld.html">fix gld</A> can be more directly
related to the representation of an implicit solvent environment.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>The instantaneous values of the extended variables are written to
@ -127,6 +136,11 @@ with rigid bodies, SHAKE or RATTLE. It is expected that all the
thermostatted degrees of freedom are fully flexible, and the sampled
ensemble will not be correct otherwise.
</P>
<P>In order to perform constant-pressure simulations please use
<A HREF = "fix_press_berendsen.html">fix press/berendsen</A>, rather than
<A HREF = "fix_npt.html">fix_npt</A>, to avoid duplicate integration of the
equations of motion.
</P>
<P>This fix is part of the USER-MISC package. It is only enabled if LAMMPS
was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.

16
doc/fix_gle.txt
View File

@ -40,7 +40,8 @@ vibrational modes in the system to inexpensive (approximate)
modelling of nuclear quantum effects. Contrary to
"fix langevin"_fix_langevin.html, this fix performs both
thermostatting and evolution of the Hamiltonian equations of motion, so it
does not need to be used together with "fix nve"_fix_nve.html.
should not be used together with "fix nve"_fix_nve.html -- at least not
on the same atom groups.
Each degree of freedom in the thermostatted group is supplemented
with Ns additional degrees of freedom s, and the equations of motion
@ -83,6 +84,14 @@ generate its own unique seed and its own stream of random numbers.
Thus the dynamics of the system will not be identical on two runs on
different numbers of processors.
Note also that the Generalized Langevin Dynamics scheme that is
implemented by the "fix gld"_fix_gld.html scheme is closely related
to the present one. In fact, it should be always possible to cast the
Prony series form of the memory kernel used by GLD into an appropriate
input matrix for "fix_gle"_fix_gle.html. While the GLE scheme is more
general, the form used by "fix gld"_fix_gld.html can be more directly
related to the representation of an implicit solvent environment.
[Restart, fix_modify, output, run start/stop, minimize info:]
The instantaneous values of the extended variables are written to
@ -117,6 +126,11 @@ with rigid bodies, SHAKE or RATTLE. It is expected that all the
thermostatted degrees of freedom are fully flexible, and the sampled
ensemble will not be correct otherwise.
In order to perform constant-pressure simulations please use
"fix press/berendsen"_fix_press_berendsen.html, rather than
"fix_npt"_fix_npt.html, to avoid duplicate integration of the
equations of motion.
This fix is part of the USER-MISC package. It is only enabled if LAMMPS
was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.