lammps/python

This directory contains Python code which wraps LAMMPS as a library
and allows the library interface to be invoked from a Python, either
from a script or interactively.

Details on how to build and use this Python interface are given in
doc/Section_python.html.

Basically you have to extend the Python on your box to include the
LAMMPS wrappers:

python setup_serial.py build           # for serial LAMMPS and Python
sudo python setup_serial.py install

python setup.py build                  # for parallel LAMMPS and Python
sudo python setuppy install

but there are several issues to be aware of, as discussed in the doc
pages.

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Once you have successfully built and tested the wrappers, you can run
the Python scripts in the examples sub-directory:

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
viz_tool.py	    real-time viz via some viz package
vizplotgui_tool.py  combination of viz.py and plot.py and gui.py

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 for more info:

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 for more details:

http://mt.seas.upenn.edu/Archive/Graphics/A
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 for more details:

http://www.pymol.org
http://sourceforge.net/scm/?type=svn&group_id=4546

The latter link is to the open-source version.

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You can run a particular script in either of the following ways:

% trivial.py in.trivial
% python -i trivial.py in.trivial

The former assumes that you have changed the first line of the script
to point to the Python installed on your box.

Run the Python scripts with the following LAMMPS input scripts and
arguments:

trivial.py in.trivial
demo.py
simple.py in.simple
gui.py in.gui 100
plot.py in.plot 10 1000 thermo_temp
viz_tool.py in.viz 100 5000
vizplotgui_tool.py in.viz 100 thermo_temp

You can un-comment the Pypar calls if you want to run these in
parallel.

Each script has more documentation in the file that explains how to
use it and what it is doing.