Python Materials Genomics is a robust materials analysis code that defines core object representations for structures
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Project description
Pymatgen (Python Materials Genomics) is a robust, open-source Python library for materials analysis. These are some of the main features:
- Highly flexible classes for the representation of
Element,Site,MoleculeandStructureobjects. - Extensive input/output support, including support for VASP, ABINIT, CIF, Gaussian, XYZ, and many other file formats.
- Powerful analysis tools, including generation of phase diagrams, Pourbaix diagrams, diffusion analyses, reactions, etc.
- Electronic structure analyses, such as density of states and band structure.
- 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 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:
- Official documentation
- Bug reports or feature requests: Please submit a GitHub issue.
- Code contributions via pull request are welcome.
- For questions that are not bugs or feature requests, please use the
pymatgenMatSci forum or open a GitHub discussion. matgenbprovides some example Jupyter notebooks that demonstrate how to usepymatgenfunctionality.
Why use pymatgen?
- 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 Github Actions for continuous integration, which ensures that every new code passes a comprehensive suite of unit tests.
- It is well documented. A fairly comprehensive documentation has been written to help you get to grips with it quickly.
- It is open. You are free to use and contribute to
pymatgen. It also means thatpymatgenis continuously being improved. We will attribute any code you contribute to any publication you specify. Contributing topymatgenmeans your research becomes more visible, which translates to greater impact. - It is fast. Many of the core numerical methods in
pymatgenhave been optimized by vectorizing innumpy/scipy. This means that coordinate manipulations are fast. Pymatgen also comes with a complete system for handling periodic boundary conditions. - 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.
- A growing ecosystem of developers and add-ons. Pymatgen has contributions from materials scientists all over
the world. We also now have an architecture to support add-ons that expand
pymatgen's functionality even further. Check out the contributing page and add-ons page for details and examples.
Installation
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
Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the pymatgen docs).
Change Log
See GitHub releases, docs/CHANGES.md or commit history in increasing order of details.
Using pymatgen
Please refer to the official pymatgen docs for tutorials and examples. Dr Anubhav Jain (@computron) has also created
a series of tutorials and YouTube videos, which is a good resource, especially for beginners.
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
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.
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 (@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.
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.
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