From 1a3ac720dfefcdd3feefc5c4b234e8caf766be4a Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Tue, 16 Oct 2007 18:49:13 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1053
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/fix_viscosity.html | 18 ++++++++++++------
 doc/fix_viscosity.txt  | 17 +++++++++++------
 2 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/doc/fix_viscosity.html b/doc/fix_viscosity.html
index 2f7fada686..3ae2b1ce58 100644
--- a/doc/fix_viscosity.html
+++ b/doc/fix_viscosity.html
@@ -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>
diff --git a/doc/fix_viscosity.txt b/doc/fix_viscosity.txt
index 2a50fbc945..d4dbc512b2 100644
--- a/doc/fix_viscosity.txt
+++ b/doc/fix_viscosity.txt
@@ -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).