git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2955 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_example.html

@@ -47,6 +47,7 @@ Site</A>.
 <TR><TD >peptide</TD><TD >  dynamics of a small solvated peptide chain (5-mer)</TD></TR>
 <TR><TD >peri</TD><TD >     Peridynamics example of cylinder hit by projectile</TD></TR>
 <TR><TD >pour</TD><TD >     pouring of granular particles into a 3d box, then chute flow</TD></TR>
+<TR><TD >reax</TD><TD >     simple example for ReaxFF force field</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 
 </TD></TR></TABLE></DIV>

doc/Section_example.txt

@@ -43,6 +43,7 @@ obstacle: flow around two voids in a 2d channel
 peptide:  dynamics of a small solvated peptide chain (5-mer)
 peri:     Peridynamics example of cylinder hit by projectile
 pour:     pouring of granular particles into a 3d box, then chute flow
+reax:     simple example for ReaxFF force field
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void :tb(s=:)
 

doc/Section_history.html

@@ -31,11 +31,13 @@ GranFlow for granular materials.
 are being worked on; some haven't been implemented because of lack of
 time or interest; others are just a lot of work!
 </P>
-<UL><LI>NPT with changing box shape (Parinello-Rahman)
-<LI>long-range point dipole solver
-<LI>torsional shear boundary conditions and temperature calculation
-<LI>charge equilibration
-<LI>ReaxFF force field from Bill Goddard's group 
+<UL><LI>coupling to finite elements
+<LI>new ReaxFF implementation (in addition to existing one)
+<LI>stochastic rotation dynamics
+<LI>Stokesian dynamics via fast lubrication dynamics
+<LI>NPT with changing box shape (Parinello-Rahman)
+<LI>long-range point-dipole solver
+<LI>torsional shear boundary conditions and temperature calculation 
 </UL>
 <HR>
 

doc/Section_history.txt

@@ -28,11 +28,13 @@ These are new features we'd like to eventually add to LAMMPS.  Some
 are being worked on; some haven't been implemented because of lack of
 time or interest; others are just a lot of work!
 
+coupling to finite elements
+new ReaxFF implementation (in addition to existing one)
+stochastic rotation dynamics
+Stokesian dynamics via fast lubrication dynamics
 NPT with changing box shape (Parinello-Rahman)
-long-range point dipole solver
-torsional shear boundary conditions and temperature calculation
-charge equilibration
-ReaxFF force field from Bill Goddard's group :ul
+long-range point-dipole solver
+torsional shear boundary conditions and temperature calculation :ul
 
 :line
 

doc/Section_intro.html

@@ -192,6 +192,11 @@ commands)
 <LI>  rRESPA hierarchical timestepping
 <LI>  parallel tempering (replica exchange) 
 </UL>
+<P>Diagnostics: h4
+(<A HREF = "fix.html">fix</A> command, <A HREF = "compute.html">compute</A> command) 
+</P>
+<P>  see the various flavors of the fix and compute commands
+</P>
 <H4>Output 
 </H4>
 <P>(<A HREF = "dump.html">dump</A>, <A HREF = "restart.html">restart</A> commands) 
@@ -208,9 +213,9 @@ commands)
 <H4>Pre- and post-processing 
 </H4>
 <P>Our group has also written and released a separate toolkit called
-<A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
+<A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which provides tools for doing setup, analysis,
 plotting, and visualization for LAMMPS simulations.  Pizza.py is
-written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">the
+written in <A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the
 Pizza.py WWW site</A>.
 </P>
 
@@ -246,10 +251,10 @@ section</A>.  However, many people use other codes or
 write their own tools for these tasks.
 </P>
 <P>As noted above, our group has also written and released a separate
-toolkit called <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which addresses some of the listed
+toolkit called <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A> which addresses some of the listed
 bullets.  It provides tools for doing setup, analysis, plotting, and
 visualization for LAMMPS simulations.  Pizza.py is written in
-<A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.cs.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW
+<A HREF = "http://www.python.org">Python</A> and is available for download from <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">the Pizza.py WWW
 site</A>.
 </P>
 <P>LAMMPS requires as input a list of initial atom coordinates and types,
@@ -471,6 +476,14 @@ the list.
 
 
 <DIV ALIGN=center><TABLE  BORDER=1 >
+<TR><TD >compute heat/flux for Green-Kubo </TD><TD > Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)</TD></TR>
+<TR><TD >region cone </TD><TD > Pim Schravendijk</TD></TR>
+<TR><TD >fix reax/bonds </TD><TD > Aidan Thompson (Sandia)</TD></TR>
+<TR><TD >pair born/coul/long </TD><TD > Ahmed Ismail (Sandia)</TD></TR>
+<TR><TD >fix ttm </TD><TD > Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)</TD></TR>
+<TR><TD >fix box/relax </TD><TD > Aidan Thompson and David Olmsted (Sandia)</TD></TR>
+<TR><TD >ReaxFF potential </TD><TD > Aidan Thompson (Sandia) and Hansohl Cho (MIT)</TD></TR>
+<TR><TD >compute cna/atom </TD><TD > Wan Liang (Chinese Academy of Sciences)</TD></TR>
 <TR><TD >Tersoff/ZBL potential </TD><TD > Dave Farrell (Northwestern U)</TD></TR>
 <TR><TD >peridynamics </TD><TD > Mike Parks (Sandia)</TD></TR>
 <TR><TD >fix smd for steered MD </TD><TD > Axel Kohlmeyer (U Penn)</TD></TR>

doc/Section_intro.txt

@@ -191,6 +191,11 @@ Integrators :h4
   rRESPA hierarchical timestepping
   parallel tempering (replica exchange) :ul
 
+Diagnostics: h4
+("fix"_fix.html command, "compute"_compute.html command) 
+
+  see the various flavors of the fix and compute commands
+
 Output :h4
 ("dump"_dump.html, "restart"_restart.html commands) 
 
@@ -211,7 +216,7 @@ plotting, and visualization for LAMMPS simulations.  Pizza.py is
 written in "Python"_python and is available for download from "the
 Pizza.py WWW site"_pizza.
 
-:link(pizza,http://www.cs.sandia.gov/~sjplimp/pizza.html)
+:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
 :link(python,http://www.python.org)
 
 :line
@@ -457,6 +462,14 @@ the list.
 
 :link(sjp,http://www.cs.sandia.gov/~sjplimp)
 
+compute heat/flux for Green-Kubo : Reese Jones (Sandia), Philip Howell (Siemens), Vikas Varsney (AFRL)
+region cone : Pim Schravendijk
+fix reax/bonds : Aidan Thompson (Sandia)
+pair born/coul/long : Ahmed Ismail (Sandia)
+fix ttm : Paul Crozier (Sandia) and Carolyn Phillips (U Michigan)
+fix box/relax : Aidan Thompson and David Olmsted (Sandia)
+ReaxFF potential : Aidan Thompson (Sandia) and Hansohl Cho (MIT)
+compute cna/atom : Wan Liang (Chinese Academy of Sciences)
 Tersoff/ZBL potential : Dave Farrell (Northwestern U)
 peridynamics : Mike Parks (Sandia)
 fix smd for steered MD : Axel Kohlmeyer (U Penn)