12.9. Example Python scripts that use LAMMPS

These are the Python scripts included as demos in the python/examples directory of the LAMMPS distribution, to illustrate the kinds of 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 thru Python
demo.py invoke various LAMMPS library interface routines
simple.py run in parallel
similar to examples/COUPLE/simple/simple.cpp split.py
same as simple.py but running in parallel on a subset of procs gui.py
GUI go/stop/temperature-slider to control LAMMPS plot.py
real-time temperature plot with GnuPlot via Pizza.py viz_tool.py
real-time viz via some viz package vizplotgui_tool.py
combination of viz_tool.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” or “vmd”, depending on what visualization package you have installed.

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:

Note that for AtomEye, you need version 3, and there is a line in the scripts that specifies the path and name of the executable. See the AtomEye WWW pages here or here 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 scripting 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 or here 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.

Note that for VMD, you need a fairly current version (1.8.7 works for me) and there are some lines in the pizza/vmd.py script for 4 PIZZA variables that have to match the VMD installation on your system.


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.

Here are screenshots of the vizplotgui_tool.py script in action for different visualization package options. Click to see larger images:

_images/screenshot_gl_small.jpg _images/screenshot_atomeye_small.jpg _images/screenshot_pymol_small.jpg _images/screenshot_vmd_small.jpg