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

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64
doc/Section_python.html
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@ -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 >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 >vizplotgui.py</TD><TD > combination of viz.py and plot.py and gui.py
<TR><TD >plot.py</TD><TD > real-time temeperature plot with GnuPlot via Pizza.py</TD></TR>
<TR><TD >viz_tool.py</TD><TD > real-time viz via some viz package</TD></TR>
<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's a screenshot of the vizplotgui.py script in action. Click to
see a larger image:
<P>Here are screenshots of the vizplotgui_tool.py script in action for
different visualization package options. Click to see larger images:
</P>
<CENTER><A HREF = "JPG/screenshot1.jpg"><IMG SRC = "JPG/screenshot1_small.jpg"></A>
</CENTER>
<A HREF = "JPG/screenshot_gl.jpg"><IMG SRC = "JPG/screenshot_gl_small.jpg"></A>
<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>

58
doc/Section_python.txt
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@ -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,
viz.py, real-time viz from GL tool in "Pizza.py"_pizza,
vizplotgui.py, combination of viz.py and plot.py and gui.py :tb(c=2)
plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
viz_tool.py, real-time viz via some viz package,
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
see a larger image:
:c,image(JPG/screenshot1_small.jpg,JPG/screenshot1.jpg)
:image(JPG/screenshot_gl_small.jpg,JPG/screenshot_gl.jpg)
:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)

25
doc/neb.html
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@ -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
potential energy of each replica. The "maximum force per replica" is
force per atom (in any replica), potential gradients in the initial,
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
replica is the length of the 3N-length vector of the distances between
of any atom in any replica. The potential gradients are the two-norm
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