reaction-network

Reaction Network is a Python package for predicting likely inorganic chemical reaction pathways using graph theoretical methods. Project led by @mattmcdermott (formerly at Berkeley Lab).

https://github.com/materialsproject/reaction-network

Science Score: 67.0%

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

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 2 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
2 of 8 committers (25.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (18.2%) to scientific vocabulary

Keywords

chemistry materials-science python reaction-network reactions simulation

Keywords from Contributors

materials materials-informatics interactive workflows mesh interpretability sequences generic projection optim

Last synced: 6 months ago · JSON representation ·

Repository

Reaction Network is a Python package for predicting likely inorganic chemical reaction pathways using graph theoretical methods. Project led by @mattmcdermott (formerly at Berkeley Lab).

Basic Info

Host: GitHub
Owner: materialsproject
License: other
Language: Python
Default Branch: main
Homepage: https://materialsproject.github.io/reaction-network/
Size: 73.5 MB

Statistics

Stars: 114
Watchers: 3
Forks: 24
Open Issues: 6
Releases: 36

Topics

chemistry materials-science python reaction-network reactions simulation

Created over 6 years ago · Last pushed about 1 year ago

Metadata Files

Readme Changelog Contributing License Code of conduct Citation

README.md

Reaction Network (rxn_network) is a Python package for synthesis planning and predicting chemical reaction pathways in inorganic materials synthesis.

Installation

We recommend installing the latest release using pip:

properties pip install -U reaction-network

The package will then be installed under the name rxn_network. The Materials Project API is not installed by default; to install it, run: pip install -U mp-api.

For developers, you can clone the repository and install the package in editable mode by running pip install -e . in the root directory.

Note As of version 7.0 and beyond, the reaction-network package no longer uses graph-tool. All network functionality is now implemented using rustworkx. This means it is no longer required to complete any extra installation.

Tutorials

The examples folder contains two (2) demonstration notebooks:

1_enumerators.ipynb: how to enumerate reactions from a set of entries; running enumerators using jobflow
2_networks.ipynb: how to build reaction networks from a list of enumerators and entries; how to perform pathfinding to recommend balanced reaction pathways; running reaction network analysis using jobflow

Citation

If you use this code in your work, please consider citing the following paper (see CITATION.bib):

McDermott, M. J., Dwaraknath, S. S., and Persson, K. A. (2021). A graph-based network for predicting chemical reaction pathways in solid-state materials synthesis. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23339-x

Acknowledgements

This work was supported as part of GENESIS: A Next Generation Synthesis Center, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award Number DE-SC0019212.

Learn more about the GENESIS EFRC here: https://www.stonybrook.edu/genesis/

Owner

Name: Materials Project
Login: materialsproject
Kind: organization
Email: feedback@materialsproject.org
Location: 1 Cyclotron Rd, Berkeley CA 94720

Website: https://www.materialsproject.org
Repositories: 51
Profile: https://github.com/materialsproject

Citation (CITATION.bib)

@article{McDermott2021,
  title = {A Graph-Based Network for Predicting Chemical Reaction Pathways in Solid-State Materials Synthesis},
  author = {McDermott, Matthew J. and Dwaraknath, Shyam S. and Persson, Kristin A.},
  year = {2021},
  month = may,
  journal = {Nature Communications},
  volume = {12},
  number = {1},
  pages = {3097},
  publisher = {{Nature Publishing Group}},
  issn = {2041-1723},
  doi = {10.1038/s41467-021-23339-x},
  langid = {english},
}

@article{McDermott2023,
  title = {Assessing {{Thermodynamic Selectivity}} of {{Solid-State Reactions}} for the {{Predictive Synthesis}} of {{Inorganic Materials}}},
  author = {McDermott, Matthew J. and McBride, Brennan C. and Regier, Corlyn E. and Tran, Gia Thinh and Chen, Yu and Corrao, Adam A. and Gallant, Max C. and Kamm, Gabrielle E. and Bartel, Christopher J. and Chapman, Karena W. and Khalifah, Peter G. and Ceder, Gerbrand and Neilson, James R. and Persson, Kristin A.},
  year = {2023},
  month = oct,
  journal = {ACS Central Science},
  publisher = {{American Chemical Society}},
  issn = {2374-7943},
  doi = {10.1021/acscentsci.3c01051},
  url = {https://doi.org/10.1021/acscentsci.3c01051},
  urldate = {2023-10-16}
}

GitHub Events

Total

Create event: 3
Issues event: 3
Release event: 3
Watch event: 28
Issue comment event: 3
Push event: 12
Pull request event: 6
Fork event: 5

Last Year

Create event: 3
Issues event: 3
Release event: 3
Watch event: 28
Issue comment event: 3
Push event: 12
Pull request event: 6
Fork event: 5

Committers

Last synced: 9 months ago

All Time

Total Commits: 970
Total Committers: 8
Avg Commits per committer: 121.25
Development Distribution Score (DDS): 0.107

Past Year

Commits: 26
Committers: 1
Avg Commits per committer: 26.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Matthew McDermott	m**t@b**u	866
dependabot[bot]	4****]	53
Shyam D	s**d@l**v	44
Rajat	2****t	2
Max Gallant	m**2@g**m	2
Janosh Riebesell	j**l@g**m	1
materialsproject	f**k@m**g	1
Matthew McDermott	m**4@g**u	1

Committer Domains (Top 20 + Academic)

gadi-login-06.gadi.nci.org.au: 1 materialsproject.org: 1 lbl.gov: 1 berkeley.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 14
Total pull requests: 104
Average time to close issues: 24 days
Average time to close pull requests: 19 days
Total issue authors: 7
Total pull request authors: 4
Average comments per issue: 3.0
Average comments per pull request: 1.03
Merged pull requests: 31
Bot issues: 0
Bot pull requests: 73

Past Year

Issues: 3
Pull requests: 8
Average time to close issues: N/A
Average time to close pull requests: 18 minutes
Issue authors: 2
Pull request authors: 2
Average comments per issue: 0.33
Average comments per pull request: 0.0
Merged pull requests: 6
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

amalie-trewartha (2)
MShirazAhmad (2)
Imhaenoo (2)
ancarnevali (2)
wangxuan1586 (2)
mattmcdermott (2)
CLRom (1)

Pull Request Authors

dependabot[bot] (69)
mattmcdermott (33)
mcgalcode (3)
R1j1t (1)

Top Labels

Issue Labels

bug (2) enhancement (1) help wanted (1)

Pull Request Labels

dependencies (69) release:patch (19) release:minor (6) release:major (2) bug (1)

Packages

Total packages: 1
Total downloads:
- pypi 164 last-month

Total dependent packages: 0
Total dependent repositories: 2
Total versions: 28
Total maintainers: 2

pypi.org: reaction-network

Reaction-network is a Python package for synthesis planning and predicting chemical reaction pathways in inorganic materials synthesis.

Documentation: https://reaction-network.readthedocs.io/
License: modified BSD
Latest release: 8.3.0
published almost 2 years ago

Versions: 28
Dependent Packages: 0
Dependent Repositories: 2
Downloads: 164 Last month

Rankings

Dependent packages count: 10.0%

Dependent repos count: 11.6%

Average: 14.3%

Downloads: 21.4%

Maintainers (2)

shyamd mattmcdermott

Last synced: 6 months ago

Dependencies

.github/workflows/post-process.yml actions

ridedott/merge-me-action v2 composite
rymndhng/release-on-push-action v0.27.0 composite

.github/workflows/release.yml actions

actions/checkout v2.4.0 composite
actions/checkout v3 composite
actions/setup-python v4.3.0 composite
ad-m/github-push-action master composite
charmixer/auto-changelog-action v1 composite
peaceiris/actions-gh-pages v3.9.0 composite
pypa/gh-action-pypi-publish v1.5.1 composite

.github/workflows/testing.yml actions

actions/checkout v3 composite
actions/setup-python v4.3.0 composite
codecov/codecov-action v3.1.1 composite

pyproject.toml pypi

jobflow >=0.1.8
mp-api >=0.30.0
numba >=0.56.1
pymatgen >=2022.8.23
ray >=2.0.0
rustworkx >=0.12.0