98 lines
4.0 KiB
ReStructuredText
98 lines
4.0 KiB
ReStructuredText
Overview
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========
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The LAMMPS distribution includes a ``python`` directory with the Python
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code needed to run LAMMPS from Python. The ``python/lammps`` package
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contains :doc:`the "lammps" Python module <Python_module>` that wraps the
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LAMMPS C-library interface. This module makes it is possible to do the
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following either from a Python script, or interactively from a Python
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prompt:
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- create one or more instances of LAMMPS
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- invoke LAMMPS commands or read them from an input script
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- run LAMMPS incrementally
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- extract LAMMPS results
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- and modify internal LAMMPS data structures.
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From a Python script you can do this in serial or in parallel. Running
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Python interactively in parallel does not generally work, unless you
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have a version of Python that extends Python to enable multiple
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instances of Python to read what you type.
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To do all of this, you must build LAMMPS in :ref:`"shared" mode <exe>`
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and make certain that your Python interpreter can find the ``lammps``
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Python package and the LAMMPS shared library file.
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.. _ctypes: https://docs.python.org/3/library/ctypes.html
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The Python wrapper for LAMMPS uses the `ctypes <ctypes_>`_ package in
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Python, which auto-generates the interface code needed between Python
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and a set of C-style library functions. Ctypes has been part of the
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standard Python distribution since version 2.5. You can check which
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version of Python you have by simply typing "python" at a shell prompt.
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Below is an example output for Python version 3.8.5.
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.. code-block:: console
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$ python
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Python 3.8.5 (default, Aug 12 2020, 00:00:00)
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[GCC 10.2.1 20200723 (Red Hat 10.2.1-1)] on linux
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Type "help", "copyright", "credits" or "license" for more information.
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>>>
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.. warning::
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The options described in this section of the manual for using Python
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with LAMMPS currently support either Python 2 or 3. Specifically
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version 2.7 or later and 3.6 or later. Since the Python community no
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longer maintains Python 2 (see `this notice
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<https://www.python.org/doc/sunset-python-2/>`_), we recommend use of
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Python 3 with LAMMPS. While Python 2 code should continue to work,
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that is not something we can guarantee long-term. If you notice
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Python code in the LAMMPS distribution that is not compatible with
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Python 3, please contact the LAMMPS developers or submit `and issue
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on GitHub <https://github.com/lammps/lammps/issues>`_
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---------
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LAMMPS can work together with Python in three ways. First, Python can
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wrap LAMMPS through the its :doc:`library interface <Library>`, so
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that a Python script can create one or more instances of LAMMPS and
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launch one or more simulations. In Python terms, this is referred to as
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"extending" Python with a LAMMPS module.
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.. figure:: JPG/python-invoke-lammps.png
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:figclass: align-center
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Launching LAMMPS via Python
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Second, the lower-level Python interface in the :py:class:`lammps Python
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class <lammps.lammps>` can be used indirectly through the provided
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:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps
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<lammps.IPyLammps>` wrapper classes, also written in Python. These
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wrappers try to simplify the usage of LAMMPS in Python by providing a
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more object-based interface to common LAMMPS functionality. They also
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reduce the amount of code necessary to parameterize LAMMPS scripts
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through Python and make variables and computes directly accessible.
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.. figure:: JPG/pylammps-invoke-lammps.png
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:figclass: align-center
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Using the PyLammps / IPyLammps wrappers
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Third, LAMMPS can use the Python interpreter, so that a LAMMPS input
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script or styles can invoke Python code directly, and pass information
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back-and-forth between the input script and Python functions you write.
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This Python code can also call back to LAMMPS to query or change its
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attributes through the LAMMPS Python module mentioned above. In Python
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terms, this is called "embedding" Python into LAMMPS. When used in this
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mode, Python can perform script operations that the simple LAMMPS input
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script syntax can not.
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.. figure:: JPG/lammps-invoke-python.png
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:figclass: align-center
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Calling Python code from LAMMPS
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