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radicalpy

An intuitive open-source framework specific to radical pair spin dynamics.

https://github.com/spin-chemistry-labs/radicalpy

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary

Keywords

radical-pair simulation spin-dynamics

Scientific Fields

Mathematics Computer Science - 84% confidence
Artificial Intelligence and Machine Learning Computer Science - 83% confidence
Last synced: 4 months ago · JSON representation ·

Repository

An intuitive open-source framework specific to radical pair spin dynamics.

Basic Info
Statistics
  • Stars: 13
  • Watchers: 2
  • Forks: 1
  • Open Issues: 57
  • Releases: 28
Topics
radical-pair simulation spin-dynamics
Created over 3 years ago · Last pushed 4 months ago
Metadata Files
Readme License Citation

README.md

Documentation Status

IMPORTANT NOTICE

MANUAL INTERVENTION REQUIRED. We had some large files in the GitHub history, and to delete them, we needed to do a git push --force. As a consequence, if you've cloned the repo, and try git pull, you'll get an error about divergent branches (or something similar). What you need to do is:

git fetch --all # download the repo with full history from github git reset origin/main # or origin/<THE_BRANCH_YOU'RE_ON>

Git will reset your local history, to match the force-pushed history from GitHub.

OR IF YOU'RE NOT SURE YOU CAN ALWAYS DELETE AND CLONE AGAIN!

RadicalPy: a toolbox for radical pair spin dynamics

RadicalPy in an intuitive (object-oriented) open-source Python framework specific to radical pair spin dynamics.

To get started take a look at the quick start guide or the examples.

The package is still under development. Basic functionality is implemented, documentation is sparse, testing partial.

If you would like to contact us, please visit the Spin Chemistry Community Discord server.

Installation

Install simply using pip:

pip install radicalpy

Citation (CITATION.bib) 

@article{antill2024radicalpy,
  title = {{{RadicalPy}}: {{A Tool}} for {{Spin Dynamics Simulations}}},
  shorttitle = {{{RadicalPy}}},
  author = {Antill, Lewis M. and Vatai, Emil},
  year = {2024},
  month = oct,
  journal = {Journal of Chemical Theory and Computation},
  publisher = {American Chemical Society},
  issn = {1549-9618},
  doi = {10.1021/acs.jctc.4c00887},
  urldate = {2024-11-09},
  abstract = {Radical pairs (electron--hole pairs, polaron pairs) are transient reaction intermediates that are found and exploited in all areas of science, from the hard realm of physics in the form of organic semiconductors, spintronics, quantum computing, and solar cells to the soft domain of chemistry and biology under the guise of chemical reactions in solution, biomimetic systems, and quantum biology. Quantitative analysis of radical pair phenomena has historically been successful by a few select groups. With this in mind, we present an intuitive open-source framework in the Python programming language that provides classical, semiclassical, and quantum simulation methodologies. A radical pair kinetic rate equation solver, Monte Carlo-based spin dephasing rate estimations, and molecule database functionalities are implemented. We introduce the kine-quantum method, a new approach that amalgamates classical rate equations, semiclassical, and quantum techniques. This method resolves the prohibitively large memory requirement issues of quantum approaches while achieving higher accuracy, and it also offers wavelength-resolved simulations, producing time- and wavelength-resolved magnetic field effect simulations. Model examples illustrate the versatility and ease of use of the software, including the new approach applied to the magnetosensitive absorption and fluorescence of flavin adenine dinucleotide photochemistry, spin--spin interaction estimation from molecular dynamics simulations on radical pairs inside reverse micelles, radical pair anisotropy inside proteins, and triplet exciton pairs in anthracene crystals. The intuitive interface also allows this software to be used as a teaching or learning aid for those interested in the field of spin chemistry. Furthermore, the software aims to be modular and extensible, with the aim to standardize how spin dynamics simulations are performed.},
  file = {/home/vatai/Sync/zotero-data/pdfs/my_pub/Antill and Vatai - 2024 - RadicalPy A Tool for Spin Dynamics Simulations.pdf}
}

GitHub Events

Total
  • Create event: 9
  • Release event: 2
  • Issues event: 11
  • Watch event: 6
  • Delete event: 5
  • Member event: 1
  • Issue comment event: 8
  • Push event: 44
  • Pull request event: 10
Last Year
  • Create event: 9
  • Release event: 2
  • Issues event: 11
  • Watch event: 6
  • Delete event: 5
  • Member event: 1
  • Issue comment event: 8
  • Push event: 44
  • Pull request event: 10

Issues and Pull Requests

Last synced: 4 months ago

All Time
  • Total issues: 105
  • Total pull requests: 69
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.39
  • Average comments per pull request: 0.17
  • Merged pull requests: 59
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 7
  • Average time to close issues: 5 months
  • Average time to close pull requests: 3 days
  • Issue authors: 2
  • Pull request authors: 3
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.14
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • vatai (86)
  • lmantill (19)
Pull Request Authors
  • vatai (51)
  • lmantill (16)
  • KenHino (2)
Top Labels
Issue Labels
enhancement (26) documentation (13) feature (8) bug (5) performance (3) help wanted (2) simulation (1) question (1)
Pull Request Labels
enhancement (3) feature (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 395 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 42
  • Total maintainers: 2
pypi.org: radicalpy

RadicalPy: a toolbox for radical pair spin dynamics

  • Versions: 42
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 395 Last month
Rankings
Dependent packages count: 10.1%
Downloads: 12.6%
Average: 17.7%
Dependent repos count: 21.6%
Stargazers count: 21.6%
Forks count: 22.7%
Maintainers (2)
antill vatai
Last synced: 4 months ago

Dependencies

.github/workflows/publish-to-pypi.yml actions
  • actions/checkout master composite
  • actions/setup-python v1 composite
  • pypa/gh-action-pypi-publish release/v1 composite
.github/workflows/run-tests.yml actions
  • actions/checkout master composite
  • actions/setup-python v4 composite
requirements.txt pypi
  • matplotlib *
  • numpy *
  • scikit-learn *
  • scipy *
.github/workflows/add-to-project.yml actions
  • actions/add-to-project v0.4.0 composite
pyproject.toml pypi