only support Python version 3.6 or later. Update and correct docs and README
This commit is contained in:
Axel Kohlmeyer
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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 Python script or using Python interactively.
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This directory contains the LAMMPS Python module that allows the LAMMPS
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C library interface to be invoked from Python, either from a Python
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script or using Python 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 and in doc/Section_start.html#start_5.
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https://docs.lammps.org/Build_basics.html#exe
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and
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https://docs.lammps.org/Python_install.html
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Basically you need to follow these steps in the src directory:
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Basically you need to use the flag -D BUILD_SHARED_LIBS=ON when
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configuring LAMMPS with CMake and then in the build folder use the
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command % cmake --build . --target install-python
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or for the legacy GNU build system execute these steps in the src folder:
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% make g++ mode=shlib # build for whatever machine target you wish
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% make install-python # install into site-packages folder
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You can replace the last step by a one-time setting of environment
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variables in your shell script. Or you can run the python/install.py
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script directly to give you more control over where the two relevant
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files are installed. See doc/Python_install.html for details.
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variables in your shell environment. Or you can run the
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python/install.py script directly to give you more control over where
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the two relevant files are installed. See
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https://docs.lammps.org/Python_install.html for details.
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You should then be able to launch Python and instantiate an instance
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of LAMMPS:
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@ -24,39 +31,41 @@ of LAMMPS:
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>>> lmp = lammps()
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If that gives no errors, you have successfully wrapped LAMMPS with
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Python. See doc/Section_python.html#py_7 for tests you can then use
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to run LAMMPS both in serial or parallel thru Python.
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Python. See https://docs.lammps.org/Python_launch.html for examples how
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to run LAMMPS both in serial or parallel from Python.
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Note that you can also invoke Python code from within a LAMMPS input
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script, using the "python" command. See the doc/python.html doc page
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for details. The Python code you invoke can also call back to LAMMPS
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using the same interface described here for wrapping LAMMPS.
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script, using the "python" command. See the
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https://docs.lammps.org/python.html doc page for details. The Python
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code you invoke can also call back to LAMMPS using the same interface
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described here for wrapping LAMMPS.
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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 parallel example, mimicing examples/COUPLE/simple/simple.cpp
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split.py parallel example
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mc.py Monte Carlo energy relaxation wrapper on LAMMPS
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gui.py GUI go/stop/temperature-slider to control LAMMPS
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plot.py real-time temperature plot with GnuPlot via Pizza.py
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matplotlib_plot.py real-time temperature plot with Matplotlib 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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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 parallel example, mimicing examples/COUPLE/simple/simple.cpp
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split.py parallel example
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mc.py Monte Carlo energy relaxation wrapper on LAMMPS
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gui.py GUI go/stop/temperature-slider to control LAMMPS
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plot.py real-time temperature plot with GnuPlot via Pizza.py
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matplotlib_plot.py real-time temperature plot with Matplotlib 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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For the viz_<tool>.py and vizplotgui_<tool>.py commands, replace
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"<tool>" with "gl" or "atomeye" or "pymol", depending on what
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visualization package you have installed. We hope to add a VMD option
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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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https://lammps.github.io/pizza/
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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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@ -115,17 +124,14 @@ one-processor run, where both Python and LAMMPS will run on single
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processors. Each running job will read the same input file, and write
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to same log.lammps file, which isn't too useful.
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However, if you have the mpi4py Python package installed and uncomment mpi4py
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code in simple.py, then the above commands will invoke 1 instance of a
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P-processor run. Both Python and LAMMPS will run on P processors. The job will
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read the input file and write a single log.lammps file.
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The split.py script can also be run in parallel. It uses mpi4py
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version 2.0.0 (or later), which makes it possible to pass a
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communicator when creating the LAMMPS object and thus run multiple
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instances of LAMMPS at the same time, each on a different subset of
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MPI ranks. Or run LAMMPS on one subset and some other program on the
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rest of the MPI ranks, concurrently. See comments in the split.py
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script for more details.
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However, if you have the mpi4py Python package installed and uncomment
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mpi4py code in simple.py, then the above commands will invoke 1 instance
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of a P-processor run. Both Python and LAMMPS will run on P processors.
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The job will read the input file and write a single log.lammps file.
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The split.py script can also be run in parallel. It uses mpi4py version
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2.0.0 (or later), which makes it possible to pass a communicator when
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creating the LAMMPS object and thus run multiple instances of LAMMPS at
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the same time, each on a different subset of MPI ranks. Or run LAMMPS
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on one subset and some other program on the rest of the MPI ranks,
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concurrently. See comments in the split.py script for more details.
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