From 75cb5f13709b700b7be2b46dd78632bd704b3b4d Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 22 Oct 2010 21:24:33 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5097
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/compute.html    |  3 ++-
 doc/compute.txt     |  3 ++-
 doc/pair_gauss.html | 14 +++++++++++++-
 doc/pair_gauss.txt  | 14 +++++++++++++-
 4 files changed, 30 insertions(+), 4 deletions(-)

diff --git a/doc/compute.html b/doc/compute.html
index 2e2d5c5b56..0e8f7a687c 100644
--- a/doc/compute.html
+++ b/doc/compute.html
@@ -210,7 +210,8 @@ available in LAMMPS:
 <LI><A HREF = "compute_temp_profile.html">temp/profile</A> - temperature excluding a binned velocity profile
 <LI><A HREF = "compute_temp_ramp.html">temp/ramp</A> - temperature excluding ramped velocity component
 <LI><A HREF = "compute_temp_region.html">temp/region</A> - temperature of a region of atoms
-<LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles 
+<LI><A HREF = "compute_temp_sphere.html">temp/sphere</A> - temperature of spherical particles
+<LI><A HREF = "compute_ti.html">ti</A> - thermodyanmic integration free energy values 
 </UL>
 <P>There are also additional compute styles submitted by users which are
 included in the LAMMPS distribution.  The list of these with links to
diff --git a/doc/compute.txt b/doc/compute.txt
index cc7c436959..c9e5895379 100644
--- a/doc/compute.txt
+++ b/doc/compute.txt
@@ -205,7 +205,8 @@ available in LAMMPS:
 "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
 "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
 "temp/region"_compute_temp_region.html - temperature of a region of atoms
-"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles :ul
+"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
+"ti"_compute_ti.html - thermodyanmic integration free energy values :ul
 
 There are also additional compute styles submitted by users which are
 included in the LAMMPS distribution.  The list of these with links to
diff --git a/doc/pair_gauss.html b/doc/pair_gauss.html
index 696a48b6b9..c6ceaae2ae 100644
--- a/doc/pair_gauss.html
+++ b/doc/pair_gauss.html
@@ -71,13 +71,25 @@ to be specified in an input script that reads a restart file.
 <A HREF = "run_style.html">run_style respa</A> command.  It does not support the
 <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
 </P>
+<P>This pair style tallies an "occupancy" count of how many Gaussian-well
+sites have an atom within the distance at which the force is a maximum
+= sqrt(0.5/b).  This quantity can be accessed via the <A HREF = "compute_pair.html">compute
+pair</A> command as a vector of values of length 1.
+</P>
+<P>To print this quantity to the log file (with a descriptive column
+heading) the following commands could be included in an input script:
+</P>
+<PRE>compute gauss all pair gauss
+variable occ equal c_gauss[1]
+thermo_style custom step temp epair v_occ 
+</PRE>
 <HR>
 
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_adapt.html">fix adapt</A>
+<P><A HREF = "pair_coeff.html">pair_coeff</A>
 </P>
 <P><B>Default:</B> none
 </P>
diff --git a/doc/pair_gauss.txt b/doc/pair_gauss.txt
index 809bb7d237..85fa1feea5 100644
--- a/doc/pair_gauss.txt
+++ b/doc/pair_gauss.txt
@@ -68,12 +68,24 @@ This pair style can only be used via the {pair} keyword of the
 "run_style respa"_run_style.html command.  It does not support the
 {inner}, {middle}, {outer} keywords.
 
+This pair style tallies an "occupancy" count of how many Gaussian-well
+sites have an atom within the distance at which the force is a maximum
+= sqrt(0.5/b).  This quantity can be accessed via the "compute
+pair"_compute_pair.html command as a vector of values of length 1.
+
+To print this quantity to the log file (with a descriptive column
+heading) the following commands could be included in an input script:
+
+compute gauss all pair gauss
+variable occ equal c_gauss\[1\]
+thermo_style custom step temp epair v_occ :pre
+
 :line
 
 [Restrictions:] none
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html, "fix adapt"_fix_adapt.html
+"pair_coeff"_pair_coeff.html
 
 [Default:] none