matgenb.materialsvirtuallab.orgmatgenb | Materials Science Jupyter

Notebooks matgenb Materials Science Jupyter Notebooks View On GitHub This project is maintained by materialsvirtuallab navigation Search 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 Option 1: Google Colab You can easily run all the notebooks via Google Colab . Option 2: BinderHub One of the best ways to get a feel of the functionality is to run it yourself using BinderHub. Click on the icon below to start a BinderHub instance where you can explore the notebooks, make any changes to the code to see the changes in output. Contributing Fork this repo and clone. git clone git@github.com:your_github_username/matgenb cd matgenb Write a new notebook in the notebooks folder. cd notebooks jupyter notebook 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 instructure 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 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. 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 . In the root folder of the repo, convert the jupyter notebooks to html. jupyter nbconvert to html notebooks/ * .ipynb output-dir docs/_posts Commit and push. git add . git commit -a -m "Describe your contribution" git push Submit a pull request from Github. Notebooks Aug 26, 2021 Magnetic structure generation as input for initial dft calculations May 12, 2021 Explanation of corrections Jul 15, 2020 How to plot a fermi surface Mar 11, 2019 Interface reactions Jan 11, 2019 How to plot and evaluate output files from lobster Jan 4, 2019 How to use boltztrap2 interface Jan 4, 2019 How to use boltztra2 interface Nov 6, 2018 Dopant suggestions using pymatgen Sep 25, 2018 Structure prediction using pymatgen and the materials api Jul 24, 2018 Adsorption on solid surfaces Mar 14, 2018 Plotting cohp from lobster Mar 9, 2018 Computing the reaction diagram between two compounds Jan 1, 2018 Chemenv how to automatically identify coordination environments in a structure Dec 15, 2017 Plotting a pourbaix diagram Sep 3, 2017 Analyze and plot band structures May 11, 2017 Running jupyter notebook on clusters Apr 14, 2017 Inputs and analysis of vasp runs Apr 3, 2017 Slab generation and wulff shape Mar 2, 2017 Getting data from materials project Sep 25, 2016 Plotting phonon bandstructure and dos Jan 1, 2013 Units Jan 1, 2013 Plotting the electronic structure of fe Jan 1, 2013 Plotting and analyzing a phase diagram using the materials api Jan 1, 2013 Ordering disordered structures Jan 1, 2013 Molecule Jan 1, 2013 Getting crystal structures from online sources Jan 1, 2013 Explanation of corrections Jan 1, 2013 Calculating xrd patterns Jan 1, 2013 Calculating reaction energies with the materials api Jan 1, 2013 Basic functionality Jan 1, 2013 Bandstructure of nio subscribe via RSS Hosted on GitHub Pages using the...