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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 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>). to the non-swapped dimensions (other than <I>vdim</I>).
</P> </P>
<P>You should not swap velocities of atoms that are in constrained <P>LAMMPS does not check, but you should not use this fix to swap
molecules, e.g. via <A HREF = "fix_shake.html">fix shake</A> or <A HREF = "fix_rigid.html">fix velocities of atoms that are in constrained molecules, e.g. via <A HREF = "fix_shake.html">fix
rigid</A>, since application of the constraints will alter shake</A> or <A HREF = "fix_rigid.html">fix rigid</A>. This is because
the amount of transferred momentum. You should, however, be able to application of the constraints will alter the amount of transferred
use flexible molecules with this approach. LAMMPS does not check that momentum. You should, however, be able to use flexible molecules.
this advice is followed. See the <A HREF = "#Maginn">Maginn paper</A> for an example of using this algorithm
in a computation of alcohol molecule properties.
</P> </P>
<P>When running a simulation with large, massive particles or molecules <P>When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta bewteen 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><B>(Muller-Plathe)</B> Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
</P> </P>
<A NAME = "Maginn"></A>
<P><B>(Maginn)</B> Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria,
260, 218-231 (2007).
</P>
</HTML> </HTML>

17
doc/fix_viscosity.txt
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@ -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 the system. If you do use a thermostat, you may want to apply it only
to the non-swapped dimensions (other than {vdim}). to the non-swapped dimensions (other than {vdim}).
You should not swap velocities of atoms that are in constrained LAMMPS does not check, but you should not use this fix to swap
molecules, e.g. via "fix shake"_fix_shake.html or "fix velocities of atoms that are in constrained molecules, e.g. via "fix
rigid"_fix_rigid.html, since application of the constraints will alter shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because
the amount of transferred momentum. You should, however, be able to application of the constraints will alter the amount of transferred
use flexible molecules with this approach. LAMMPS does not check that momentum. You should, however, be able to use flexible molecules.
this advice is followed. 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 When running a simulation with large, massive particles or molecules
in a background solvent, you may want to only exchange momenta bewteen 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) :link(Muller-Plathe)
[(Muller-Plathe)] Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999). [(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).