Merge branch 'master' of github.com:materialsproject/pymatgen

README.md

@@ -20,32 +20,38 @@ 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` and `Structure` objects.
-2. Extensive input/output support, including support for [VASP](https://cms.mpi.univie.ac.at/vasp), [ABINIT](https://abinit.org), CIF, Gaussian, XYZ, and many other file formats.
+2. Extensive input/output support, including support for [VASP](https://cms.mpi.univie.ac.at/vasp), [ABINIT](https://abinit.org), [CIF](https://wikipedia.org/wiki/Crystallographic_Information_File), [Gaussian](https://gaussian.com), [XYZ](https://wikipedia.org/wiki/XYZ_file_format), 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 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](https://pymatgen.org)
-- Bug reports or feature requests: Please submit a [GitHub Issue](https://github.com/materialsproject/pymatgen/issues).
-- Code contributions via [pull requests](https://github.com/materialsproject/pymatgen/pulls) are welcome.
-- For help with usage that is unrelated to bugs or feature requests, please use the `pymatgen` [MatSci page](https://discuss.matsci.org/c/pymatgen).
-- [`matgenb`](https://github.com/materialsvirtuallab/matgenb#introduction) provides some Jupyter notebooks demonstrating functionality.
+- [Official documentation][`pymatgen` docs]
+- 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 `pymatgen` [MatSci forum](https://matsci.org/pymatgen) or open a [GitHub discussion].
+- [`matgenb`](https://github.com/materialsvirtuallab/matgenb#introduction) provides some example Jupyter notebooks that demonstrate how to use `pymatgen` functionality.
 - Follow us on [Twitter](https://twitter.com/pymatgen) to get news and tips.
 
-## Why use pymatgen?
+[pull request]: https://github.com/materialsproject/pymatgen/pulls
+[github issue]: https://github.com/materialsproject/pymatgen/issues
+[github discussion]: https://github.com/materialsproject/pymatgen/discussions
+
+## Why use `pymatgen`?
 
 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 Github Actions for continuous integration, which ensures that every new code passes a comprehensive suite of unit tests.
 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.
+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 fast. 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.
-6. **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](https://pymatgen.org/contributing) and [add-ons page](https://pymatgen.org/addons) for details and examples.
+6. **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](https://pymatgen.org/contributing) and [add-ons page](https://pymatgen.org/addons) for details and examples.
 
 ## Installation
 
-The version at the [Python Package Index (PyPI)](https://pypi.org/project/pymatgen) is always the latest stable release that is relatively bug-free and can be installed via `pip`:
+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`:
+
+[pypi]: https://pypi.org/project/pymatgen
 
 ```sh
 pip install pymatgen
@@ -57,15 +63,15 @@ If you'd like to use the latest unreleased changes on the main branch, you can i
 pip install -U git+https://github.com/materialsproject/pymatgen
 ```
 
-The minimum Python version is 3.8. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` page]).
+The minimum Python version is 3.8. Some extra functionality (e.g., generation of POTCARs) does require additional setup (see the [`pymatgen` docs]).
 
 ## Change Log
 
 Please check [GitHub releases](https://github.com/materialsproject/pymatgen/releases) and [commit history](https://github.com/materialsproject/pymatgen/commits/master) for the latest changes. A legacy changelog is still up at <https://pymatgen.org/change_log>.
 
 ## Using pymatgen
 
-Please refer to the official [`pymatgen` page] for tutorials and examples.
+Please refer to the official [`pymatgen` docs] for tutorials and examples.
 
 ## How to cite pymatgen
 
@@ -78,7 +84,7 @@ If you use `pymatgen` in your research, please consider citing the following wor
 > Analysis.* Computational Materials Science, 2013, 68, 314-319.
 > [doi:10.1016/j.commatsci.2012.10.028](https://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](https://pymatgen.org) on how to cite them.
+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
 
@@ -102,7 +108,7 @@ The [`pymatgen` development team] is the set of all contributors to the `pymatge
 
 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.
 
-[`pymatgen` page]: https://pymatgen.org
+[`pymatgen` docs]: https://pymatgen.org
 [materials project]: https://materialsproject.org
 [`pymatgen` development team]: https://pymatgen.org/team
 [materials virtual lab]: https://materialsvirtuallab.org