git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5232 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_python.html

@@ -603,23 +603,67 @@ own scripts, send them to us and we can include them in the LAMMPS
 distribution.
 </P>
 <DIV ALIGN=center><TABLE  BORDER=1 >
-<TR><TD >trivial.py</TD><TD > read/run a LAMMPS input script via Python</TD></TR>
+<TR><TD >trivial.py</TD><TD > read/run a LAMMPS input script thru Python</TD></TR>
 <TR><TD >demo.py</TD><TD > invoke various LAMMPS library interface routines</TD></TR>
 <TR><TD >simple.py</TD><TD > mimic operation of couple/simple/simple.cpp in Python</TD></TR>
 <TR><TD >gui.py</TD><TD > GUI go/stop/temperature-slider to control LAMMPS</TD></TR>
-<TR><TD >plot.py</TD><TD > real-time temeperature plot with GnuPlot via <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A></TD></TR>
+<TR><TD >plot.py</TD><TD > real-time temeperature plot with GnuPlot via Pizza.py</TD></TR>
-<TR><TD >viz.py</TD><TD > real-time viz from GL tool in <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</A></TD></TR>
+<TR><TD >viz_tool.py</TD><TD > real-time viz via some viz package</TD></TR>
-<TR><TD >vizplotgui.py</TD><TD > combination of viz.py and plot.py and gui.py 
+<TR><TD >vizplotgui_tool.py</TD><TD > combination of viz.py and plot.py and gui.py 
 </TD></TR></TABLE></DIV>
 
+<HR>
+
+<P>For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
+with "gl" or "atomeye" or "pymol", depending on what visualization
+package you have installed.  We hope to add a VMD option soon.
+</P>
+<P>Note that for GL, you need to be able to run the Pizza.py GL tool,
+which is included in the pizza sub-directory.  See the <A HREF = "http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py doc
+pages</A> for more info:
+</P>
+
+
+<P>Note that for AtomEye, you need version 3, and their is a line in the
+scripts that specifies the path and name of the executable.  See the
+AtomEye WWW pages <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A">here</A> or <A HREF = "http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html">here</A> for more details:
+</P>
+<PRE>http://mt.seas.upenn.edu/Archive/Graphics/A
+http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html 
+</PRE>
+
+
+
+
+<P>The latter link is to AtomEye 3 which has the scriping
+capability needed by these Python scripts.
+</P>
+<P>Note that for PyMol, you need to have built and installed the
+open-source version of PyMol in your Python, so that you can import it
+from a Python script.  See the PyMol WWW pages <A HREF = "http://www.pymol.org">here</A> or
+<A HREF = "http://sourceforge.net/scm/?type=svn&group_id=4546">here</A> for more details:
+</P>
+<PRE>http://www.pymol.org
+http://sourceforge.net/scm/?type=svn&group_id=4546 
+</PRE>
+
+
+
+
+<P>The latter link is to the open-source version.
+</P>
+<HR>
+
 <P>See the python/README file for instructions on how to run them and the
 source code for individual scripts for comments about what they do.
 </P>
-
+<P>Here are screenshots of the vizplotgui_tool.py script in action for
-
+different visualization package options.  Click to see larger images:
-<P>Here's a screenshot of the vizplotgui.py script in action.  Click to
-see a larger image:
 </P>
-<CENTER><A HREF = "JPG/screenshot1.jpg"><IMG SRC = "JPG/screenshot1_small.jpg"></A>
+<A HREF = "JPG/screenshot_gl.jpg"><IMG SRC = "JPG/screenshot_gl_small.jpg"></A>
-</CENTER>
+
+<A HREF = "JPG/screenshot_atomeye.jpg"><IMG SRC = "JPG/screenshot_atomeye_small.jpg"></A>
+
+<A HREF = "JPG/screenshot_pymol.jpg"><IMG SRC = "JPG/screenshot_pymol_small.jpg"></A>
+
 </HTML>

doc/Section_python.txt

@@ -596,21 +596,61 @@ things that are possible when Python wraps LAMMPS.  If you create your
 own scripts, send them to us and we can include them in the LAMMPS
 distribution.
 
-trivial.py, read/run a LAMMPS input script via Python,
+trivial.py, read/run a LAMMPS input script thru Python,
 demo.py, invoke various LAMMPS library interface routines,
 simple.py, mimic operation of couple/simple/simple.cpp in Python,
 gui.py, GUI go/stop/temperature-slider to control LAMMPS,
-plot.py, real-time temeperature plot with GnuPlot via "Pizza.py"_pizza,
+plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
-viz.py, real-time viz from GL tool in "Pizza.py"_pizza,
+viz_tool.py, real-time viz via some viz package,
-vizplotgui.py, combination of viz.py and plot.py and gui.py :tb(c=2)
+vizplotgui_tool.py, combination of viz.py and plot.py and gui.py :tb(c=2)
+
+:line
+
+For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
+with "gl" or "atomeye" or "pymol", depending on what visualization
+package you have installed.  We hope to add a VMD option soon.
+
+Note that for GL, you need to be able to run the Pizza.py GL tool,
+which is included in the pizza sub-directory.  See the "Pizza.py doc
+pages"_pizza for more info:
+
+:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
+
+Note that for AtomEye, you need version 3, and their is a line in the
+scripts that specifies the path and name of the executable.  See the
+AtomEye WWW pages "here"_atomeye or "here"_atomeye3 for more details:
+
+http://mt.seas.upenn.edu/Archive/Graphics/A
+http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre
+
+:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
+:link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html)
+
+The latter link is to AtomEye 3 which has the scriping
+capability needed by these Python scripts.
+
+Note that for PyMol, you need to have built and installed the
+open-source version of PyMol in your Python, so that you can import it
+from a Python script.  See the PyMol WWW pages "here"_pymol or
+"here"_pymolopen for more details:
+
+http://www.pymol.org
+http://sourceforge.net/scm/?type=svn&group_id=4546 :pre
+
+:link(pymol,http://www.pymol.org)
+:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546)
+
+The latter link is to the open-source version.
+
+:line
 
 See the python/README file for instructions on how to run them and the
 source code for individual scripts for comments about what they do.
 
-:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
+Here are screenshots of the vizplotgui_tool.py script in action for
+different visualization package options.  Click to see larger images:
 
-Here's a screenshot of the vizplotgui.py script in action.  Click to
+:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg)
-see a larger image:
+:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
-
+:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
-:c,image(JPG/screenshot1_small.jpg,JPG/screenshot1.jpg)
 

doc/neb.html

@@ -136,10 +136,10 @@ The replica states will also be roughly equally spaced along the MEP
 due to the inter-replica spring force added by the <A HREF = "fix_neb.html">fix
 neb</A> command.
 </P>
-<P>In the second stage of NEB, the replica nearest the top of the barrier
+<P>In the second stage of NEB, the replica with the highest energy
 is selected and the inter-replica forces on it are converted to a
 force that drives its atom coordinates to the top or saddle point of
-the barrier, via the hill-climbing calculation described in
+the barrier, via the barrier-climbing calculation described in
 <A HREF = "#Hinkelman2">(Henkelman2)</A>.  As before, the other replicas rearrange
 themselves along the MEP so as to be roughly equally spaced.
 </P>
@@ -205,14 +205,27 @@ and restart files.
 this case), the print-out to the screen and master log.lammps file
 contains a line of output, printed once every <I>Nevery</I> timesteps.  It
 contains the timestep, the maximum force per replica, the maximum
-force per atom (in any replica), and the reaction coordinate and
+force per atom (in any replica), potential gradients in the initial,
-potential energy of each replica.  The "maximum force per replica" is
+ final, and climbing replicas, and
+the reaction coordinate and potential energy of each replica.  
+The "maximum force per replica" is
 the two-norm of the 3N-length force vector for the atoms in each
 replica, maximized across replicas, which is what the <I>ftol</I> setting
 is checking against.  In this case, N is all the atoms in each
 replica.  The "maximum force per atom" is the maximum force component
-of any atom in any replica.  The "reaction coordinate" (RC) for each
+of any atom in any replica.  The potential gradients are the two-norm
-replica is the length of the 3N-length vector of the distances between
+of the 3N-length force vector solely due to the interaction potential i.e.
+without adding in inter-replica forces. Note that inter-replica forces
+are zero in the initial and final replicas, and only affect
+the direction in the climbing replica. For this reason, the "maximum 
+force per replica" is often equal to the potential gradient in the
+climbing replica. In the first stage of NEB, there is no climbing
+replica, and so the potential gradient in the highest energy replica
+is reported, since this replica will become the climbing replica
+in the second stage of NEB.
+</P>
+<P>The "reaction coordinate" (RC) for each
+replica is the two-norm of the 3N-length vector of distances between
 its atoms and the preceding replica's atoms, added to the RC of the
 preceding replica.  The RC of the first replica = 0.0; the remaining
 RCs are normalized so that the RC of the last replica = 1.0.  In this