Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. It is currently the core analysis code powering the Materials Project (https://www.materialsproject.org).
Project description
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Pymatgen (Python Materials Genomics) is a robust, open-source Python library
for materials analysis. These are some of the main features:
1. Highly flexible classes for the representation of Element, Site, Molecule,
Structure objects.
2. Extensive input/output support, including support for VASP
(http://cms.mpi.univie.ac.at/vasp/), ABINIT (http://www.abinit.org/), CIF,
Gaussian, XYZ, and many other file formats.
3. Powerful analysis tools, including generation of phase diagrams, Pourbaix
diagrams, diffusion analyses, reactions, etc.
4. Electronic structure analyses, such as density of states and band structure.
5. Integration with the Materials Project REST API.
Pymatgen is free to use. However, we also welcome your help to improve this
library by making your own contributions. These contributions can be in the
form of additional tools or modules you develop, or feature requests and bug
reports. Please report any bugs and issues at pymatgen's `Github page
<https://github.com/materialsproject/pymatgen>`_. If you wish to be notified
of pymatgen releases, you may become a member of `pymatgen's Google Groups page
<https://groups.google.com/forum/?fromgroups#!forum/pymatgen/>`_.
Why use pymatgen?
=================
There are many materials analysis codes out there, both commerical and free,
but pymatgen offer several advantages:
1. **It is (fairly) robust.** Pymatgen is used by thousands of researchers,
and is the analysis code powering the `Materials Project`_. The analysis it
produces survives rigorous scrutiny every single day. Bugs tend to be
found and corrected quickly. Pymatgen also uses
`CircleCI <https://circleci.com>`_ and `Appveyor <https://www.appveyor.com/>`_
for continuous integration on the Linux and Windows platforms,
respectively, which ensures that every commit passes a comprehensive suite
of unittests. The coverage of the unittests can be seen at
`here <coverage/index.html>`_.
2. **It is well documented.** A fairly comprehensive documentation has been
written to help you get to grips with it quickly.
3. **It is open.** You are free to use and contribute to pymatgen. It also means
that pymatgen is continuously being improved. We will attribute any code you
contribute to any publication you specify. Contributing to pymatgen means
your research becomes more visible, which translates to greater impact.
4. **It is fast.** Many of the core numerical methods in pymatgen have been
optimized by vectorizing in numpy/scipy. This means that coordinate
manipulations are extremely fast and are in fact comparable to codes
written in other languages. Pymatgen also comes with a complete system for
handling periodic boundary conditions.
5. **It will be around.** Pymatgen is not a pet research project. It is used in
the well-established Materials Project. It is also actively being developed
and maintained by the `Materials Virtual Lab`_, the ABINIT group and many
other research groups.
With effect from version 3.0, pymatgen now supports both Python 2.7 as well
as Python 3.x. All developers must ensure that their code passes the
unittests on both Py2.7 and 3.x.
Getting pymatgen
================
Before installing pymatgen, you may need to first install a few critical
dependencies manually. Please refer to the official `pymatgen page`_ for
installation details and requirements, including instructions for the
bleeding edge developmental version. For people who are absolutely new to
Python packages, it is highly recommended you do the installation using
conda, which will make things a lot easier, especially on Windows. Visit
`materials.sh <http://materials.sh>`_ for instructions on how to use the
matsci channel to install pymatgen and other packages.
The version at the Python Package Index (PyPI) is always the latest stable
release that is relatively bug-free. The easiest way to install pymatgen on
any system is to use pip::
pip install pymatgen
Wheels for Mac (Python 2.7 and 3.5) and Windows (Python 3.5) have been built
for convenience.
Some extra functionality (e.g., generation of POTCARs) do require additional
setup (please see the `pymatgen page`_).
Change Log
==========
The latest change log is available `here <http://pymatgen.org/change_log>`_.
Using pymatgen
==============
Please refer to the official `pymatgen page`_ for tutorials and examples.
How to cite pymatgen
====================
If you use pymatgen in your research, please consider citing the following
work:
Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier,
Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A.
Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
Open-Source Python Library for Materials Analysis.* Computational
Materials Science, 2013, 68, 314-319. `doi:10.1016/j.commatsci.2012.10.028
<http://dx.doi.org/10.1016/j.commatsci.2012.10.028>`_
In addition, some of pymatgen's functionality is based on scientific advances
/ principles developed by the computational materials scientists in our team.
Please refer to `pymatgen's documentation <http://pymatgen.org/>`_ on how to
cite them.
License
=======
Pymatgen is released under the MIT License. The terms of the license are as
follows::
The MIT License (MIT)
Copyright (c) 2011-2012 MIT & LBNL
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
the Software, and to permit persons to whom the Software is furnished to do so,
subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
About the Pymatgen Development Team
===================================
Shyue Ping Ong of the `Materials Virtual Lab`_ started Pymatgen in 2011, and is
still the project lead.
The Pymatgen Development Team is the set of all contributors to the
pymatgen project, including all subprojects.
Our Copyright Policy
====================
Pymatgen uses a shared copyright model. Each contributor maintains copyright
over their contributions to pymatgen. But, it is important to note that these
contributions are typically only changes to the repositories. Thus, the
pymatgen source code, in its entirety is not the copyright of any
single person or institution. Instead, it is the collective copyright of the
entire pymatgen Development Team. If individual contributors want to maintain a
record of what changes/contributions they have specific copyright on, they
should indicate their copyright in the commit message of the change, when
they commit the change to one of the pymatgen repositories.
With this in mind, the following banner should be used in any source code file
to indicate the copyright and license terms::
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
.. _`pymatgen page` : http://www.pymatgen.org
.. _`Materials Project` : https://www.materialsproject.org
.. _`Materials Virtual Lab`: http://www.materialsvirtuallab.org
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