add links to ctypes, ipython, and jupyter

See the :doc:`Python library <Python_library>` doc page for a

description of the Python interface to LAMMPS, which wraps the C-style

interface from a shared library through the ctypes python module.

interface from a shared library through the `ctypes python module <ctypes_>`_.

See the sample codes in examples/COUPLE/simple for examples of C++ and

C and Fortran codes that invoke LAMMPS through its library interface.

Other examples in the COUPLE directory use coupling ideas discussed on

the :doc:`Howto couple <Howto_couple>` doc page.

.. _ctypes: https://docs.python.org/3/library/ctypes.html

Overview

--------

PyLammps is a Python wrapper class which can be created on its own or

use an existing lammps Python object.  It creates a simpler,

Python-like interface to common LAMMPS functionality, in contrast to

the lammps.py wrapper on the C-style LAMMPS library interface which is

written using Python ctypes.  The lammps.py wrapper is discussed on

the :doc:`Python library <Python_library>` doc page.

Unlike the flat ctypes interface, PyLammps exposes a discoverable API.

It no longer requires knowledge of the underlying C++ code

implementation.  Finally, the IPyLammps wrapper builds on top of

PyLammps and adds some additional features for IPython integration

into IPython notebooks, e.g. for embedded visualization output from

dump/image.

``PyLammps`` is a Python wrapper class for LAMMPS which can be created

on its own or use an existing lammps Python object.  It creates a simpler,

more "pythonic" interface to common LAMMPS functionality, in contrast to

the ``lammps.py`` wrapper for the C-style LAMMPS library interface which

is written using `Python ctypes <ctypes_>`_.  The ``lammps.py`` wrapper

is discussed on the :doc:`Python library <Python_library>` doc page.

Unlike the flat ``ctypes`` interface, PyLammps exposes a discoverable

API.  It no longer requires knowledge of the underlying C++ code

implementation.  Finally, the ``IPyLammps`` wrapper builds on top of

``PyLammps`` and adds some additional features for

`IPython integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_,

e.g. for embedded visualization output from :doc:`dump style image <dump_image>`.

.. _ctypes: https://docs.python.org/3/library/ctypes.html

.. _ipython: https://ipython.org/

.. _jupyter: https://jupyter.org/

Comparison of lammps and PyLammps interfaces

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

lammps.lammps

"""""""""""""

* uses C-Types

* uses ``ctypes``

* direct memory access to native C++ data

* provides functions to send and receive data to LAMMPS

* requires knowledge of how LAMMPS internally works (C pointers, etc)

lammps.PyLammps

"""""""""""""""

* higher-level abstraction built on top of original C-Types interface

* higher-level abstraction built on top of original ctypes interface

* manipulation of Python objects

* communication with LAMMPS is hidden from API user

* shorter, more concise Python