README.md

Visit the Github Pages for a nicely formatted HTML page and notebook search functionality.

Introduction

This repo is started by the Materials Virtual Lab as a useful collection of Jupyter notebooks that demonstrate the utilization of open-source codes for the study of materials science.

We frequently get requests (from students, postdocs, collaborators, or just general users) for example codes that demonstrate various capabilities in the open-source software we maintain and contribute to, such as the Materials Project software stack comprising Python Materials Genomics (pymatgen), Custodian, and Fireworks. This repo is a start at building a more sustainable path towards sharing of code examples.

It is not limited to the codes we develop - any use of open source software for materials analysis is welcome. Also, anyone is welcome to contribute.

Running the examples from a browser

2013-01-01-Basic functionality
2013-01-01-Calculating Reaction Energies with the Materials API
2013-01-01-Calculating XRD patterns
2013-01-01-Getting crystal structures from online sources
2013-01-01-Ordering Disordered Structures
2013-01-01-Plotting and Analyzing a Phase Diagram using the Materials API
2013-01-01-Plotting the electronic structure of Fe
2016-09-08-Data-driven First Principles Methods for the Study and Design of
2016-09-08-Data-driven First Principles Methods for the Study
2016-09-08-Data-driven First Principles Methods for the Study
2016-09-25-Plotting phonon bandstructure and dos
2017-03-02-Getting data from Materials Project
2017-04-03-Slab generation and Wulff shape
2017-04-14-Inputs and Analysis of VASP runs
2017-05-11-Running Jupyter Notebook on clusters
2017-09-03-Analyze and plot band structures
2017-12-15-Plotting a Pourbaix Diagram
2018-01-01-ChemEnv - How to automatically identify coordination environments in a structure
2018-03-09-Computing the Reaction Diagram between Two Compounds
2018-03-14-Plotting COHP from LOBSTER
2018-07-24-Adsorption on solid surfaces
2018-09-25-Structure Prediction using Pymatgen and the Materials API
2018-11-6-Dopant suggestions using Pymatgen
2019-01-04-How to use Boltztrap2 interface
2019-01-11-How to plot and evaluate output files from Lobster
2019-03-11-Interface Reactions
2020-07-15-How to plot a Fermi surface
2021-08-26-Magnetic Structure Generation as Input for Initial DFT Calculations
2021-5-12-Explanation of Corrections
2022-07-23 Interactive Crystal Toolkit Structure Viewer
2024-06-27 Charge Density Difference

Contributing

1. Fork this repo and clone.

   git clone git@github.com:<your_github_username>/matgenb
   cd matgenb

2. Write a new notebook in the notebooks folder.

   cd notebooks
   jupyter notebook

3. Notebooks should be well-documented and simple. The idea here is to be pedagogical. A newcomer to the software (with the right materials science background) should be able to follow the logic without too much difficulty. Feel free to add authorship and contact information, as well as works to cite and acknowledge your contributions. In view that scientific codes tend to be continuously being updated, please put in a list of the key pinned dependencies so that other users can install the exact version of software to run the notebook if needed. The best practice is to put a section that provides a commented out pip install command that can be used in Google Colab. For example,

   # Uncomment the subsequent lines in this cell to install dependencies for Google Colab.
   # !pip install pymatgen==2022.2.27

4. Ideally, please update notebooks as needed to use more modern versions of the codes, and you may update the date of the notebook as needed.

5. Notebooks should be placed in the notebooks folder, and the name should start with the date in YYYY-MM-DD-<intuitive title> format. See existing examples. Remember to add it to the above table too.

6. In the root folder of the repo, convert the jupyter notebooks to html.

   jupyter nbconvert --to html notebooks/*.ipynb --output-dir docs/_posts

7. Commit and push.

   git add .
   git commit -a -m "Describe your contribution"
   git push

8. Submit a pull request from Github.