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This is the first step for moving the documentation format from *.txt to the *.rst format. In the last years we've been automatically converting txt files from Steve's markup into RST to generate the documentation pages via Sphinx. The decision has now been made to fully migrate to RST and avoid the conversion in the future. This will enable us to fully use RST and Sphinx to improve the documentation. For the intermediate period, while there are still pending PRs with documentation changes, we will keep both source files and update the RST files accordingly.
117 lines
4.9 KiB
ReStructuredText
117 lines
4.9 KiB
ReStructuredText
Example Python scripts that use LAMMPS
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======================================
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These are the Python scripts included as demos in the python/examples
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directory of the LAMMPS distribution, to illustrate the kinds of
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things that are possible when Python wraps LAMMPS. If you create your
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own scripts, send them to us and we can include them in the LAMMPS
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distribution.
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+----------------------------------------------------------------+--------------------------------------------------+
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| trivial.py | read/run a LAMMPS input script through Python |
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+----------------------------------------------------------------+--------------------------------------------------+
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| demo.py | invoke various LAMMPS library interface routines |
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+----------------------------------------------------------------+--------------------------------------------------+
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| simple.py | run in parallel |
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+----------------------------------------------------------------+--------------------------------------------------+
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| similar to examples/COUPLE/simple/simple.cpp | split.py |
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+----------------------------------------------------------------+--------------------------------------------------+
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| same as simple.py but running in parallel on a subset of procs | gui.py |
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+----------------------------------------------------------------+--------------------------------------------------+
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| GUI go/stop/temperature-slider to control LAMMPS | plot.py |
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+----------------------------------------------------------------+--------------------------------------------------+
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| real-time temperature plot with GnuPlot via Pizza.py | viz\_tool.py |
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+----------------------------------------------------------------+--------------------------------------------------+
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| real-time viz via some viz package | vizplotgui\_tool.py |
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+----------------------------------------------------------------+--------------------------------------------------+
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| combination of viz\_tool.py and plot.py and gui.py | |
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+----------------------------------------------------------------+--------------------------------------------------+
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----------
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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" or "vmd", depending on what
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visualization package you have installed.
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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 pages <pizza_>`_ for more info:
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.. _pizza: http://www.sandia.gov/~sjplimp/pizza.html
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Note that for AtomEye, you need version 3, and there is a line in the
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scripts that specifies the path and name of the executable. See the
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AtomEye WWW pages `here <atomeye_>`_ or `here <atomeye3_>`_ for more details:
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.. parsed-literal::
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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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.. _atomeye: http://mt.seas.upenn.edu/Archive/Graphics/A
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.. _atomeye3: http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html
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The latter link is to AtomEye 3 which has the scripting
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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 `here <pymolhome_>`_ or
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`here <pymolopen_>`_ for more details:
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.. parsed-literal::
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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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.. _pymolhome: http://www.pymol.org
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.. _pymolopen: 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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Note that for VMD, you need a fairly current version (1.8.7 works for
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me) and there are some lines in the pizza/vmd.py script for 4 PIZZA
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variables that have to match the VMD installation on your system.
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----------
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See the python/README file for instructions on how to run them and the
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source code for individual scripts for comments about what they do.
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Here are screenshots of the vizplotgui\_tool.py script in action for
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different visualization package options. Click to see larger images:
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.. image:: JPG/screenshot_gl_small.jpg
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:target: JPG/screenshot_gl.jpg
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.. image:: JPG/screenshot_atomeye_small.jpg
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:target: JPG/screenshot_atomeye.jpg
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.. image:: JPG/screenshot_pymol_small.jpg
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:target: JPG/screenshot_pymol.jpg
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.. image:: JPG/screenshot_vmd_small.jpg
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:target: JPG/screenshot_vmd.jpg
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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