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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.
-------------------------------------------------------------------
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.
-------------------------------------------------------------------
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.
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