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Crystal Toolkit is an interactive web app that allows you to import, view, analyze and transform crystal structures and molecules, including a suite of reusable web components to make your own materials science web apps. Project led by @mkhorton.

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Crystal Toolkit

Citations

You can read more about Crystal Toolkit in our preprint, available here.

A citation.cff file is available or a BibTeX citation is as follows:

@article{horton2023crystal,
  title={Crystal Toolkit: A Web App Framework to Improve Usability and Accessibility of Materials Science Research Algorithms},
  author={Horton, Matthew and Shen, Jimmy-Xuan and Burns, Jordan and Cohen, Orion and Chabbey, Fran{\c{c}}ois and Ganose, Alex M and Guha, Rishabh and Huck, Patrick and Li, Hamming Howard and McDermott, Matthew and others},
  journal={arXiv preprint arXiv:2302.06147},
  year={2023}
}

If you use Crystal Toolkit, either for your own web apps, or by incorporating images generated by Crystal Toolkit in your work, please make sure to cite it appropriately! Citations are a good way to recognize the contributions of the Crystal Toolkit developers, and allow us to see how it has been used by the community.

Interested in contributing?

A current list of new contributor issues can be seen here. If you would like a new-contributor issue assigned, get in touch with project maintainers!

Status

Tests Visual Regression Test Status Docker Build Status Release pre-commit.ci status arXiv link

Installation

pip install crystal-toolkit

Documentation

Documentation can be found at docs.crystaltoolkit.org.

Example Apps

Description        
bandstructure.py
Demonstrates capabilities of the BandstructureAndDosComponent component
Launch Codespace
basic_hello_structure.py
Uses StructureMoleculeComponent to show a simple pymatgen structure
Launch Codespace
basic_hello_structure_interactive.py
Adds a button to the basic_hello_structure.py to toggle between two structures interactively
Launch Codespace
basic_hello_world.py
Bare-bones example showing how to render the text "Hello scientist!" in Dash app
Launch Codespace
diffraction.py
Demonstrates capabilities of the XRayDiffractionComponent component
Launch Codespace
diffraction_dynamic.py
Adds a button to diffraction.py to load a new structure on the fly
Launch Codespace
diffraction_empty.py
Shows XRayDiffractionComponent can be mounted without a passing structure
Launch Codespace
kwarg_inputs.py
Shows off boolean input (aka toggle), matrix input and slider input components
Launch Codespace
phase_diagram.py
Combines MPRester.get_entries_in_chemsys() and the PhaseDiagram component to plot the Li-O-Co convex hull
Launch Codespace
pourbaix.py
Combines MPRester.get_pourbaix_entries() and the PourbaixDiagramComponent to plot the Fe-CO Pourbaix diagram
Launch Codespace
structure.py
Show cases multiple layout options for the StructureMoleculeComponent
Launch Codespace
structure_magnetic.py
Plots a structure with magnetic moments
Launch Codespace
matbench_dielectric_structure_on_hover.py
Creates a scatter plot hooked up to a StructureMoleculeComponent and DataTable that show the structure and highlight the table row corresponding to the hovered scatter point.
Launch Codespace
matbench_dielectric_datatable_xrd.py
Renders a DataTable hooked up to a StructureMoleculeComponent and XRayDiffractionComponent so that hovering a table row will show the corresponding structure and its XRD pattern.
Launch Codespace
transformations.py
Combines StructureMoleculeComponent and AllTransformationsComponent to apply interactive structure transformations
Launch Codespace
transformations_minimal.py
Shows how to restrict the types of allowed transformations
Launch Codespace
write_structure_screenshot_to_file.py
Shows to save interactive structure views as image files
Launch Codespace

Team and Contribution Policy

The Crystal Toolkit Development Team includes:

New contributors are welcome, please see our Code of Conduct. If you are a new contributor please modify this README in your Pull Request to add your name to the list.

Future of This Repository

The Crystal Toolkit repository is home of an object-oriented Python framework for rendering materials science data based on the schema employed by the Materials Project.

The custom Plotly Dash components that power Crystal Toolkit are now maintained in a separate repository for ease of development, as well as the custom React components. These components were formerly included in the Crystal Toolkit repo, and are still considered part of Crystal Toolkit in spirit.

There are some important issues still to be resolved, as well as general improvements to documentation and test suite planned. Some currently-private code is also planned to be re-incorporated into the public Crystal Toolkit repo.

Acknowledgements

Thank you to all the authors and maintainers of the libraries Crystal Toolkit depends upon, and in particular pymatgen for crystallographic analysis and Dash from Plotly for their web app framework.

Thank you to the NERSC Spin service for hosting the app and for their technical support.

Contact

Please contact @mkhorton with any queries or add an issue on the GitHub Issues page.

About

Crystal Toolkit is an interactive web app that allows you to import, view, analyze and transform crystal structures and molecules, including a suite of reusable web components to make your own materials science web apps. Project led by @mkhorton.

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