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Created PyLammps documentation

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Based on material presented during MD Workshop at Temple University in
August 2016.
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Richard Berger
2016-11-18 23:58:57 -07:00
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doc/src/Section_python.txt
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11. Python interface to LAMMPS :h3
LAMMPS can work together with Python in two ways. First, Python can
LAMMPS can work together with Python in three ways. First, Python can
wrap LAMMPS through the "LAMMPS library
interface"_Section_howto.html#howto_19, so that a Python script can
create one or more instances of LAMMPS and launch one or more
simulations. In Python lingo, this is "extending" Python with LAMMPS.
Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
Second, the low-level Python interface can be used indirectly through the
PyLammps and IPyLammps wrapper classes in Python. These wrappers try to
simplify the usage of LAMMPS in Python by providing an object-based interface
to common LAMMPS functionality. It also reduces the amount of code necessary to
parameterize LAMMPS scripts through Python and makes variables and computes
directly accessible. See "PyLammps interface"_#py_9 for more details.
Third, LAMMPS can use the Python interpreter, so that a LAMMPS input
script can invoke Python code, and pass information back-and-forth
between the input script and Python functions you write. The Python
code can also callback to LAMMPS to query or change its attributes.
In Python lingo, this is "embedding" Python in LAMMPS.
This section describes how to do both.
This section describes how to use these three approaches.
11.1 "Overview of running LAMMPS from Python"_#py_1
11.2 "Overview of using Python from a LAMMPS script"_#py_2
@ -29,7 +36,8 @@ This section describes how to do both.
11.5 "Extending Python with MPI to run in parallel"_#py_5
11.6 "Testing the Python-LAMMPS interface"_#py_6
11.7 "Using LAMMPS from Python"_#py_7
11.8 "Example Python scripts that use LAMMPS"_#py_8 :ul
11.8 "Example Python scripts that use LAMMPS"_#py_8
11.9 "PyLammps interface"_#py_9 :ul
If you are not familiar with it, "Python"_http://www.python.org is a
powerful scripting and programming language which can essentially do
@ -824,3 +832,7 @@ different visualization package options. Click to see larger images:
:image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
:image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
:image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
11.9 PyLammps interface :link(py_9),h4
Please see the "PyLammps Tutorial"_tutorial_pylammps.html.