From 89e4db00f2651c61f53b02a6fe5806eaa442d438 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 1 Oct 2010 16:18:09 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4935
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
doc/Section_example.html | 8 +++-----
doc/Section_example.txt | 8 +++-----
doc/Section_tools.html | 1 +
doc/Section_tools.txt | 1 +
4 files changed, 8 insertions(+), 10 deletions(-)
diff --git a/doc/Section_example.html b/doc/Section_example.html
index 71f3cd60d5..5e32f0ca3c 100644
--- a/doc/Section_example.html
+++ b/doc/Section_example.html
@@ -45,6 +45,7 @@ Site</A>.
<TR><TD >micelle</TD><TD > self-assembly of small lipid-like molecules into 2d bilayers</TD></TR>
<TR><TD >min</TD><TD > energy minimization of 2d LJ melt</TD></TR>
<TR><TD >msst</TD><TD > MSST shock dynamics</TD></TR>
+<TR><TD >neb</TD><TD > nudged elastic band (NEB) calculation for barrier finding</TD></TR>
<TR><TD >nemd</TD><TD > non-equilibrium MD of 2d sheared system</TD></TR>
<TR><TD >obstacle</TD><TD > flow around two voids in a 2d channel</TD></TR>
<TR><TD >peptide</TD><TD > dynamics of a small solvated peptide chain (5-mer)</TD></TR>
@@ -53,7 +54,8 @@ Site</A>.
<TR><TD >prd</TD><TD > parallel replica dynamics of a vacancy diffusion in bulk Si</TD></TR>
<TR><TD >reax</TD><TD > RDX and TATB models using the ReaxFF</TD></TR>
<TR><TD >rigid</TD><TD > rigid bodies modeled as independent or coupled</TD></TR>
-<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void
+<TR><TD >shear</TD><TD > sideways shear applied to 2d solid, with and without a void</TD></TR>
+<TR><TD >srd</TD><TD > stochastic rotation dynamics (SRD) particles as solvent
</TD></TR></TABLE></DIV>
<P>Here is how you might run and visualize one of the sample problems:
@@ -69,10 +71,6 @@ lmp_linux < in.indent # run the problem
</PRE>
<HR>
-<P>There is also a COUPLE directory which has examples of how to link to
-LAMMPS as a library and drive it from a wrapper program. See the
-README file for more info.
-</P>
<P>There is also an ELASTIC directory with an example script for
computing elastic constants, using a zero temperature Si example. See
the in.elastic file for more info.
diff --git a/doc/Section_example.txt b/doc/Section_example.txt
index 468e8e8f0a..241f01f70b 100644
--- a/doc/Section_example.txt
+++ b/doc/Section_example.txt
@@ -41,6 +41,7 @@ melt: rapid melt of 3d LJ system
micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt
msst: MSST shock dynamics
+neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer)
@@ -49,7 +50,8 @@ pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of a vacancy diffusion in bulk Si
reax: RDX and TATB models using the ReaxFF
rigid: rigid bodies modeled as independent or coupled
-shear: sideways shear applied to 2d solid, with and without a void :tb(s=:)
+shear: sideways shear applied to 2d solid, with and without a void
+srd: stochastic rotation dynamics (SRD) particles as solvent :tb(s=:)
Here is how you might run and visualize one of the sample problems:
@@ -64,10 +66,6 @@ Running the simulation produces the files {dump.indent} and
:line
-There is also a COUPLE directory which has examples of how to link to
-LAMMPS as a library and drive it from a wrapper program. See the
-README file for more info.
-
There is also an ELASTIC directory with an example script for
computing elastic constants, using a zero temperature Si example. See
the in.elastic file for more info.
diff --git a/doc/Section_tools.html b/doc/Section_tools.html
index 556e55ef8e..e48547c76d 100644
--- a/doc/Section_tools.html
+++ b/doc/Section_tools.html
@@ -338,6 +338,7 @@ that perform common LAMMPS post-processing tasks, like
<UL><LI>extract thermodynamic info from a log file as columns of numbers
<LI>plot two columns of thermodynamic info from a log file using GnuPlot
<LI>sort the snapshots in a dump file by atom ID
+<LI>convert multiple <A HREF = "neb.html">NEB</A> dump files into one dump file for viz
<LI>convert dump files into XYZ, CFG, or PDB format for viz by other packages
</UL>
<P>These are simple scripts built on <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> modules. See the
diff --git a/doc/Section_tools.txt b/doc/Section_tools.txt
index 73c4140539..f57f8f7d32 100644
--- a/doc/Section_tools.txt
+++ b/doc/Section_tools.txt
@@ -334,6 +334,7 @@ that perform common LAMMPS post-processing tasks, like
extract thermodynamic info from a log file as columns of numbers
plot two columns of thermodynamic info from a log file using GnuPlot
sort the snapshots in a dump file by atom ID
+convert multiple "NEB"_neb.html dump files into one dump file for viz
convert dump files into XYZ, CFG, or PDB format for viz by other packages :ul
These are simple scripts built on "Pizza.py"_pizza modules. See the
--
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