110 lines
3.7 KiB
Plaintext
110 lines
3.7 KiB
Plaintext
This directory contains Python code which wraps LAMMPS as a library
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and allows the LAMMPS library interface to be invoked from Python,
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either from a script or interactively.
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Details on the Python interface to LAMMPS and how to build LAMMPS as a
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shared library for use with Python are given in
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doc/Section_python.html.
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Basically you need to follow these 3 steps:
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a) Add paths to environment variables in your shell script
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For example, for csh or tcsh, add something like this to ~/.cshrc:
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setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
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setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
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setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src/STUBS
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The latter is only necessary if you will use the MPI stubs library
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instead of an MPI installed on your machine.
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b) Build LAMMPS as a dynamic library, including dynamic versions of
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any libraries it includes for the packages you have installed,
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e.g. STUBS, MPI, FFTW, JPEG, package libs.
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From the src directory:
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% make makeshlib
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% make -f Makefile.shlib g++
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If successful, this results in the file src/liblmp_g++.so
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c) Launch Python and import the LAMMPS wrapper
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% python
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>>> from lammps import lammps
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>>> lmp = lammps()
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If that gives no errors, you have succesfully wrapped LAMMPS with
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Python.
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-------------------------------------------------------------------
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Once you have successfully wrapped LAMMPS, you can run the Python
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scripts in the examples sub-directory:
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trivial.py read/run a LAMMPS input script thru Python
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demo.py invoke various LAMMPS library interface routines
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simple.py mimic operation of couple/simple/simple.cpp in Python
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gui.py GUI go/stop/temperature-slider to control LAMMPS
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plot.py real-time temeperature plot with GnuPlot via Pizza.py
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viz_tool.py real-time viz via some viz package
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vizplotgui_tool.py combination of viz.py and plot.py and gui.py
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For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
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with "gl" or "atomeye" or "pymol", depending on what visualization
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package you have installed. We hope to add a VMD option soon.
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Note that for GL, you need to be able to run the Pizza.py GL tool,
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which is included in the pizza sub-directory. See the Pizza.py doc
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pages for more info:
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http://www.sandia.gov/~sjplimp/pizza.html
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Note that for AtomEye, you need version 3, and their is a line in the
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scripts that specifies the path and name of the executable. See
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the AtomEye WWW pages for more details:
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http://mt.seas.upenn.edu/Archive/Graphics/A
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http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
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The latter link is to AtomEye 3 which has the scriping
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capability needed by these Python scripts.
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Note that for PyMol, you need to have built and installed the
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open-source version of PyMol in your Python, so that you can import it
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from a Python script. See the PyMol WWW pages for more details:
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http://www.pymol.org
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http://sourceforge.net/scm/?type=svn&group_id=4546
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The latter link is to the open-source version.
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-------------------------------------------------------------------
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You can run a particular script in either of the following ways:
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% trivial.py in.trivial
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% python -i trivial.py in.trivial
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The former assumes that you have changed the first line of the script
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to point to the Python installed on your box.
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Run the Python scripts with the following LAMMPS input scripts and
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arguments:
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trivial.py in.trivial
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demo.py
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simple.py in.simple
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gui.py in.gui 100
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plot.py in.plot 10 1000 thermo_temp
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viz_tool.py in.viz 100 5000
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vizplotgui_tool.py in.viz 100 thermo_temp
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You can un-comment the Pypar calls if you want to run these in
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parallel.
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Each script has more documentation in the file that explains how to
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use it and what it is doing.
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