git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4935 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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.

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.

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

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