Python Materials Genomics (pymatgen) is a robust materials analysis code that defines classes for structures and molecules with support for many electronic structure codes. It powers the Materials Project.
OTHER License
Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis. These are some of the main features:
Element
, Site
, Molecule
and Structure
objects.Pymatgen is free to use. However, we also welcome your help to improve this library by making your contributions. These contributions can be in the form of additional tools or modules you develop, or feature requests and bug reports. The following are resources for pymatgen
:
pymatgen
MatSci forum or open a GitHub discussion.matgenb
provides some example Jupyter notebooks that demonstrate how to use pymatgen
functionality.pymatgen
?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.pymatgen
have been optimized by vectorizing in numpy
/scipy
. This means that coordinate manipulations are fast. Pymatgen also comes with a complete system for handling periodic boundary conditions.pymatgen
's functionality even further. Check out the contributing page and add-ons page for details and examples.The version at the Python Package Index PyPI is always the latest stable release that is relatively bug-free and can be installed via pip
:
pip install pymatgen
If you'd like to use the latest unreleased changes on the main branch, you can install directly from GitHub:
pip install -U git+https://github.com/materialsproject/pymatgen
The minimum Python version is 3.10. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the pymatgen
docs).
See GitHub releases, docs/CHANGES.md
or commit history in increasing order of details.
Please refer to the official pymatgen
docs for tutorials and examples.
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
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 the pymatgen
docs on how to cite them.
pymatgen
paperIf you are a long-standing pymatgen
contributor and would like to be involved in working on an updated pymatgen
publication,
please fill out this co-author registration form or contact @shyuep, @mkhorton and @janosh with questions.
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.
Shyue Ping Ong (@shyuep) of the Materials Virtual Lab started Pymatgen in 2011 and is still the project lead. Janosh Riebesell (@janosh) and Matthew Horton (@mkhorton) are co-maintainers.
The pymatgen
development team is the set of all contributors to the pymatgen
project, including all subprojects.
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.