From dd84b1464401d48b13f4fd1b0a3a6f7cf7e33a5d Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 7 May 2010 16:29:19 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4113
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/Section_intro.html |  2 +-
 doc/Section_intro.txt  |  2 +-
 doc/Section_tools.html |  2 +-
 doc/Section_tools.txt  |  2 +-
 doc/pair_dpd.html      | 14 +++++++-------
 doc/pair_dpd.txt       | 12 ++++++------
 doc/variable.html      | 16 ++++++++--------
 doc/variable.txt       | 14 +++++++-------
 8 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/doc/Section_intro.html b/doc/Section_intro.html
index 8165316b0e..1bf786324f 100644
--- a/doc/Section_intro.html
+++ b/doc/Section_intro.html
@@ -319,7 +319,7 @@ debugging purposes.  For high-quality visualization we recommend the
 following packages:
 </P>
 <UL><LI><A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>
-<LI><A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A>
+<LI><A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
 <LI><A HREF = "http://pymol.sourceforge.net">PyMol</A>
 <LI><A HREF = "http://www.bmsc.washington.edu/raster3d/raster3d.html">Raster3d</A>
 <LI><A HREF = "http://www.openrasmol.org">RasMol</A> 
diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt
index 77d27e4bee..61c8790c21 100644
--- a/doc/Section_intro.txt
+++ b/doc/Section_intro.txt
@@ -315,7 +315,7 @@ debugging purposes.  For high-quality visualization we recommend the
 following packages:
 
 "VMD"_http://www.ks.uiuc.edu/Research/vmd
-"AtomEye"_http://164.107.79.177/Archive/Graphics/A
+"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
 "PyMol"_http://pymol.sourceforge.net
 "Raster3d"_http://www.bmsc.washington.edu/raster3d/raster3d.html
 "RasMol"_http://www.openrasmol.org :ul
diff --git a/doc/Section_tools.html b/doc/Section_tools.html
index 71104c2256..93da911d15 100644
--- a/doc/Section_tools.html
+++ b/doc/Section_tools.html
@@ -209,7 +209,7 @@ Kohlmeyer (akohlmey at cmm.chem.upenn.edu) at U Penn.
 post-processing LAMMPS output.  The scripts include readers for log
 and dump files, a reader for EAM potential files, and a converter that
 reads LAMMPS dump files and produces CFG files that can be visualized
-with the <A HREF = "http://164.107.79.177/Archive/Graphics/A">AtomEye</A>
+with the <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</A>
 visualizer.
 </P>
 <P>See the README.pdf file for more information.
diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt
index 4cccfa734a..a672c23a72 100644
--- a/doc/Section_tools.txt
+++ b/doc/Section_tools.txt
@@ -205,7 +205,7 @@ The matlab sub-directory contains several "MATLAB"_matlab scripts for
 post-processing LAMMPS output.  The scripts include readers for log
 and dump files, a reader for EAM potential files, and a converter that
 reads LAMMPS dump files and produces CFG files that can be visualized
-with the "AtomEye"_http://164.107.79.177/Archive/Graphics/A
+with the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
 visualizer.
 
 See the README.pdf file for more information.
diff --git a/doc/pair_dpd.html b/doc/pair_dpd.html
index de94d0293a..065b8c73d3 100644
--- a/doc/pair_dpd.html
+++ b/doc/pair_dpd.html
@@ -40,13 +40,13 @@ pair_coeff 1 1 1.0 1.0
 </P>
 <P>Style <I>dpd/tstat</I> invokes a DPD thermostat on pairwise interactions,
 which is equivalent to the non-conservative portion of the DPD force
-field.  This thermostat can be used in conjunction with any <A HREF = "doc/pair_style.html">pair
-style</A>, and in leiu of per-particle thermostats
-like <A HREF = "fix_langevin.html">fix langevin</A> or ensemble thermostats like
-Nose Hoover as implemented by <A HREF = "fix_nvt.html">fix nvt</A>.  To use
-<I>dpd/stat</I> with another pair style, use the <A HREF = "pair_hybrid.html">pair_style
+field.  This thermostat can be used in conjunction with any <A HREF = "pair_style.html">pair
+style</A>, and in leiu of per-particle thermostats like
+<A HREF = "fix_langevin.html">fix langevin</A> or ensemble thermostats like Nose
+Hoover as implemented by <A HREF = "fix_nh.html">fix nvt</A>.  To use <I>dpd/stat</I>
+with another pair style, use the <A HREF = "pair_hybrid.html">pair_style
 hybrid/overlay</A> command to compute both the desired
-pair interaction and the thermostat for each pair of particles.  
+pair interaction and the thermostat for each pair of particles.
 </P>
 <P>For style <I>dpd</I>, the force on atom I due to atom J is given as a sum
 of 3 terms
@@ -148,7 +148,7 @@ atoms.
 </P>
 <P><B>Related commands:</B>
 </P>
-<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_langevin.html">fix
+<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_langevin.html">fix
 langevin</A>
 </P>
 <P><B>Default:</B> none
diff --git a/doc/pair_dpd.txt b/doc/pair_dpd.txt
index 94e325a559..4b2d1081d6 100644
--- a/doc/pair_dpd.txt
+++ b/doc/pair_dpd.txt
@@ -37,12 +37,12 @@ Style {dpd} computes a force field for dissipative particle dynamics
 Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions,
 which is equivalent to the non-conservative portion of the DPD force
 field.  This thermostat can be used in conjunction with any "pair
-style"_doc/pair_style.html, and in leiu of per-particle thermostats
-like "fix langevin"_fix_langevin.html or ensemble thermostats like
-Nose Hoover as implemented by "fix nvt"_fix_nvt.html.  To use
-{dpd/stat} with another pair style, use the "pair_style
+style"_pair_style.html, and in leiu of per-particle thermostats like
+"fix langevin"_fix_langevin.html or ensemble thermostats like Nose
+Hoover as implemented by "fix nvt"_fix_nh.html.  To use {dpd/stat}
+with another pair style, use the "pair_style
 hybrid/overlay"_pair_hybrid.html command to compute both the desired
-pair interaction and the thermostat for each pair of particles.  
+pair interaction and the thermostat for each pair of particles.
 
 For style {dpd}, the force on atom I due to atom J is given as a sum
 of 3 terms
@@ -144,7 +144,7 @@ atoms.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html, "fix nvt"_fix_nvt.html, "fix
+"pair_coeff"_pair_coeff.html, "fix nvt"_fix_nh.html, "fix
 langevin"_fix_langevin.html
 
 [Default:] none
diff --git a/doc/variable.html b/doc/variable.html
index 2983d975b5..f253e530f1 100644
--- a/doc/variable.html
+++ b/doc/variable.html
@@ -76,11 +76,11 @@ which when evaluated produces a single numeric value which can be
 output either directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix
 print</A>, and <A HREF = "run.html">run every</A> commands) or as part
 of thermodynamic output (see the <A HREF = "thermo_style.html">thermo_style</A>
-command), or used as input to an averaging fix (see the <A HREF = "fix_ave_time">fix
-ave/time</A> command).  Variables of style <I>atom</I> store a
-formula which when evaluated produces one numeric value per atom which
-can be output to a dump file (see the <A HREF = "dump.html">dump custom</A> command)
-or used as input to an averaging fix (see the <A HREF = "fix_ave_spatial.html">fix
+command), or used as input to an averaging fix (see the <A HREF = "fix_ave_time.html">fix
+ave/time</A> command).  Variables of style <I>atom</I> store
+a formula which when evaluated produces one numeric value per atom
+which can be output to a dump file (see the <A HREF = "dump.html">dump custom</A>
+command) or used as input to an averaging fix (see the <A HREF = "fix_ave_spatial.html">fix
 ave/spatial</A> and <A HREF = "fix_ave_atom.html">fix ave/atom</A>
 commands).
 </P>
@@ -461,9 +461,9 @@ define the variable "v" as
 this will assign the initial volume to the variable "v".  That is not
 the case.  Rather it assigns a formula which evaluates the volume
 (using the thermo_style keyword "vol") to the variable "v".  If you
-use the variable "v" in some other command like "fix ave/time" then
-the current volume of the box will be evaluated continuously during
-the run.
+use the variable "v" in some other command like <A HREF = "fix_ave_time.html">fix
+ave/time</A> then the current volume of the box will be
+evaluated continuously during the run.
 </P>
 <P>If you want to store the initial volume of the system, you can do it
 this way:
diff --git a/doc/variable.txt b/doc/variable.txt
index 5eb2889376..93032f5162 100644
--- a/doc/variable.txt
+++ b/doc/variable.txt
@@ -71,10 +71,10 @@ output either directly (see the "print"_print.html, "fix
 print"_fix_print.html, and "run every"_run.html commands) or as part
 of thermodynamic output (see the "thermo_style"_thermo_style.html
 command), or used as input to an averaging fix (see the "fix
-ave/time"_fix_ave_time command).  Variables of style {atom} store a
-formula which when evaluated produces one numeric value per atom which
-can be output to a dump file (see the "dump custom"_dump.html command)
-or used as input to an averaging fix (see the "fix
+ave/time"_fix_ave_time.html command).  Variables of style {atom} store
+a formula which when evaluated produces one numeric value per atom
+which can be output to a dump file (see the "dump custom"_dump.html
+command) or used as input to an averaging fix (see the "fix
 ave/spatial"_fix_ave_spatial.html and "fix ave/atom"_fix_ave_atom.html
 commands).
 
@@ -450,9 +450,9 @@ before a run where the simulation box size changes.  You might think
 this will assign the initial volume to the variable "v".  That is not
 the case.  Rather it assigns a formula which evaluates the volume
 (using the thermo_style keyword "vol") to the variable "v".  If you
-use the variable "v" in some other command like "fix ave/time" then
-the current volume of the box will be evaluated continuously during
-the run.
+use the variable "v" in some other command like "fix
+ave/time"_fix_ave_time.html then the current volume of the box will be
+evaluated continuously during the run.
 
 If you want to store the initial volume of the system, you can do it
 this way: