lammps/python

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 Python script or using Python 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 and in doc/Section_start.html#start_5.

Basically you need to follow these steps in the src directory:

% make g++ mode=shlib           # build for whatever machine target you wish
% make install-python           # install into site-packages folder

You can replace the last step by a one-time setting of environment
variables in your shell script.  Or you can run the python/install.py
script directly to give you more control over where the two relevant
files are installed.  See doc/Python_install.html for details.

You should then be able to launch Python and instantiate an instance
of LAMMPS:

% python
>>> from lammps import lammps
>>> lmp = lammps()

If that gives no errors, you have successfully wrapped LAMMPS with
Python.  See doc/Section_python.html#py_7 for tests you can then use
to run LAMMPS both in serial or parallel thru Python.

Note that you can also invoke Python code from within a LAMMPS input
script, using the "python" command.  See the doc/python.html doc page
for details.  The Python code you invoke can also call back to LAMMPS
using the same interface described here for wrapping LAMMPS.

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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           parallel example, mimicing examples/COUPLE/simple/simple.cpp
split.py            parallel example
mc.py               Monte Carlo energy relaxation wrapper on LAMMPS
gui.py              GUI go/stop/temperature-slider to control LAMMPS
plot.py             real-time temperature plot with GnuPlot via Pizza.py
matplotlib_plot.py  real-time temperature plot with Matplotlib 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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Each example script has more documentation in the file that explains
how to use it and what it is doing.

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 and made the script
exectable (e.g. chmod +x trivial.py).

The example scripts take the following arguments.  The in.* args are
LAMPS input scripts.

trivial.py in.trivial
demo.py
simple.py in.simple      # can run in parallel (see below)
split.py in.simple       # can run in parallel (see below)

gui.py in.gui 100
plot.py in.plot 10 1000 thermo_temp
matplotlib_plot.py in.plot 10 1000 thermo_temp
viz_tool.py in.viz 100 5000
vizplotgui_tool.py in.viz 100 thermo_temp

To run LAMMPS in parallel from Python, so something like this:

% mpirun -np P simple.py in.simple
% mpirun -np P python split.py in.simple

If you run simple.py as-is, this will invoke P instances of a
one-processor run, where both Python and LAMMPS will run on single
processors.  Each running job will read the same input file, and write
to same log.lammps file, which isn't too useful.

However, if you have the mpi4py Python package installed and uncomment mpi4py
code in simple.py, then the above commands will invoke 1 instance of a
P-processor run.  Both Python and LAMMPS will run on P processors.  The job will
read the input file and write a single log.lammps file.

The split.py script can also be run in parallel.  It uses mpi4py
version 2.0.0 (or later), which makes it possible to pass a
communicator when creating the LAMMPS object and thus run multiple
instances of LAMMPS at the same time, each on a different subset of
MPI ranks.  Or run LAMMPS on one subset and some other program on the
rest of the MPI ranks, concurrently.  See comments in the split.py
script for more details.