106 lines
4.9 KiB
ReStructuredText
106 lines
4.9 KiB
ReStructuredText
Example Python scripts that use LAMMPS
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======================================
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The python/examples directory has Python scripts which show how Python
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can run LAMMPS, grab data, change it, and put it back into LAMMPS.
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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: https://pizza.sandia.gov
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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://li.mit.edu/Archive/Graphics/A/
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http://li.mit.edu/Archive/Graphics/A3/A3.html
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.. _atomeye: http://li.mit.edu/Archive/Graphics/A/
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.. _atomeye3: http://li.mit.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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https://www.pymol.org
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https://github.com/schrodinger/pymol-open-source
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.. _pymolhome: https://www.pymol.org
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.. _pymolopen: https://github.com/schrodinger/pymol-open-source
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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:
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.. |pyex1| image:: img/screenshot_gl.jpg
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:width: 24%
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.. |pyex2| image:: img/screenshot_atomeye.jpg
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:width: 24%
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.. |pyex3| image:: img/screenshot_pymol.jpg
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:width: 24%
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.. |pyex4| image:: img/screenshot_vmd.jpg
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:width: 24%
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|pyex1| |pyex2| |pyex3| |pyex4|
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.. raw:: html
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Click to see larger versions of the images.
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