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

Details on the Python interface to LAMMPS and how to build LAMMPS as a shared library for use with Python are given in doc/Section_python.html.

Basically you need to follow these 3 steps:

a) Add paths to environment variables in your shell script

For example, for csh or tcsh, add something like this to ~/.cshrc:

setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src/STUBS

The latter is only necessary if you will use the MPI stubs library instead of an MPI installed on your machine.

b) Build LAMMPS as a dynamic library, including dynamic versions of any libraries it includes for the packages you have installed, e.g. STUBS, MPI, FFTW, JPEG, package libs.

From the src directory:

% make makeshlib % make -f Makefile.shlib g++

If successful, this results in the file src/liblmp_g++.so

c) Launch Python and import the LAMMPS wrapper

% python

from lammps import lammps lmp = lammps()

If that gives no errors, you have succesfully wrapped LAMMPS with Python.

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Once you have successfully wrapped LAMMPS, 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.