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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1053 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2007-10-16 18:49:13 +00:00
parent 1e414cd924
commit 1a3ac720df
2 changed files with 23 additions and 12 deletions
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18
doc/fix_viscosity.html
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@ -98,12 +98,13 @@ momentum and kinetic energy. Thus you should not need to thermostat
the system. If you do use a thermostat, you may want to apply it only
to the non-swapped dimensions (other than <I>vdim</I>).
</P>
<P>You should not swap velocities of atoms that are in constrained
molecules, e.g. via <A HREF = "fix_shake.html">fix shake</A> or <A HREF = "fix_rigid.html">fix
rigid</A>, since application of the constraints will alter
the amount of transferred momentum. You should, however, be able to
use flexible molecules with this approach. LAMMPS does not check that
this advice is followed.
<P>LAMMPS does not check, but you should not use this fix to swap
velocities of atoms that are in constrained molecules, e.g. via <A HREF = "fix_shake.html">fix
shake</A> or <A HREF = "fix_rigid.html">fix rigid</A>. This is because
application of the constraints will alter the amount of transferred
momentum. You should, however, be able to use flexible molecules.
See the <A HREF = "#Maginn">Maginn paper</A> for an example of using this algorithm
in a computation of alcohol molecule properties.
</P>
<P>When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta bewteen
@ -122,4 +123,9 @@ nvt/sllod</A>
<P><B>(Muller-Plathe)</B> Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
</P>
<A NAME = "Maginn"></A>
<P><B>(Maginn)</B> Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
260, 218-231 (2007).
</P>
</HTML>

17
doc/fix_viscosity.txt
View File

@ -95,12 +95,13 @@ momentum and kinetic energy. Thus you should not need to thermostat
the system. If you do use a thermostat, you may want to apply it only
to the non-swapped dimensions (other than {vdim}).
You should not swap velocities of atoms that are in constrained
molecules, e.g. via "fix shake"_fix_shake.html or "fix
rigid"_fix_rigid.html, since application of the constraints will alter
the amount of transferred momentum. You should, however, be able to
use flexible molecules with this approach. LAMMPS does not check that
this advice is followed.
LAMMPS does not check, but you should not use this fix to swap
velocities of atoms that are in constrained molecules, e.g. via "fix
shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because
application of the constraints will alter the amount of transferred
momentum. You should, however, be able to use flexible molecules.
See the "Maginn paper"_#Maginn for an example of using this algorithm
in a computation of alcohol molecule properties.
When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta bewteen
@ -117,3 +118,7 @@ nvt/sllod"_fix_nvt_sllod.html
:link(Muller-Plathe)
[(Muller-Plathe)] Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
:link(Maginn)
[(Maginn)] Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
260, 218-231 (2007).