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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8603 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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python/README
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This directory contains Python code which wraps LAMMPS as a library This directory contains Python code which wraps LAMMPS as a library
and allows the library interface to be invoked from a Python, either and allows the LAMMPS library interface to be invoked from Python,
from a script or interactively. either from a script or interactively.
Details on how to build and use this Python interface are given in 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. doc/Section_python.html.
Basically you have to extend the Python on your box to include the Basically you need to follow these 3 steps:
LAMMPS wrappers:
python setup_serial.py build # for serial LAMMPS and Python a) Add paths to environment variables in your shell script
sudo python setup_serial.py install
python setup.py build # for parallel LAMMPS and Python For example, for csh or tcsh, add something like this to ~/.cshrc:
sudo python setup.py install
but there are several issues to be aware of, as discussed in the doc setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
pages. 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 built and tested the wrappers, you can run Once you have successfully wrapped LAMMPS, you can run the Python
the Python scripts in the examples sub-directory: scripts in the examples sub-directory:
trivial.py read/run a LAMMPS input script thru Python trivial.py read/run a LAMMPS input script thru Python
demo.py invoke various LAMMPS library interface routines demo.py invoke various LAMMPS library interface routines

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python/setup.py
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#!/usr/local/bin/python
"""
setup.py file for LAMMPS with system MPICH library
"""
from distutils.core import setup, Extension
import os, glob
path = os.path.dirname(os.getcwd())
# list of src files for LAMMPS
libfiles = glob.glob("%s/src/*.cpp" % path)
lammps_library = Extension("_lammps",
sources = libfiles,
define_macros = [("MPICH_IGNORE_CXX_SEEK",1),
("LAMMPS_GZIP",1),
("FFT_NONE",1),],
# src files for LAMMPS
include_dirs = ["../src"],
# additional libs for MPICH on Linux
libraries = ["mpich","mpl","pthread"],
# where to find the MPICH lib on Linux
library_dirs = ["/usr/local/lib"],
# additional libs for MPI on Mac
# libraries = ["mpi"],
)
setup(name = "lammps",
version = "28Nov11",
author = "Steve Plimpton",
author_email = "sjplimp@sandia.gov",
url = "http://lammps.sandia.gov",
description = """LAMMPS molecular dynamics library - parallel""",
py_modules = ["lammps"],
ext_modules = [lammps_library]
)

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python/setup_serial.py
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#!/usr/local/bin/python
"""
setup_serial.py file for LAMMPS with dummy serial MPI library
"""
from distutils.core import setup, Extension
import os, glob
path = os.path.dirname(os.getcwd())
# list of src files for LAMMPS and MPI STUBS
libfiles = glob.glob("%s/src/*.cpp" % path) + \
glob.glob("%s/src/STUBS/*.c" % path)
lammps_library = Extension("_lammps_serial",
sources = libfiles,
define_macros = [("MPICH_IGNORE_CXX_SEEK",1),
("LAMMPS_GZIP",1),
("FFT_NONE",1),],
# src files for LAMMPS and MPI STUBS
include_dirs = ["../src", "../src/STUBS"]
)
setup(name = "lammps_serial",
version = "28Nov11",
author = "Steve Plimpton",
author_email = "sjplimp@sandia.gov",
url = "http://lammps.sandia.gov",
description = """LAMMPS molecular dynamics library - serial""",
py_modules = ["lammps"],
ext_modules = [lammps_library]
)