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 from GL tool in Pizza.py 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

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 AtomEye 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.

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.