reactionmechanismgenerator

Python version of the amazing Reaction Mechanism Generator (RMG).

https://github.com/reactionmechanismgenerator/rmg-py

Science Score: 77.0%

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 5 DOI reference(s) in README
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Academic publication links
Links to: acs.org
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Committers with academic emails
68 of 105 committers (64.8%) 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 (13.0%) to scientific vocabulary

Keywords

chemistry chemistry-discovery kinetics python reactions thermodynamics

Keywords from Contributors

drug-discovery

Last synced: 6 months ago · JSON representation ·

Repository

Python version of the amazing Reaction Mechanism Generator (RMG).

Basic Info

Host: GitHub
Owner: ReactionMechanismGenerator
License: other
Language: Python
Default Branch: main
Homepage: http://reactionmechanismgenerator.github.io/RMG-Py/
Size: 180 MB

Statistics

Stars: 467
Watchers: 48
Forks: 243
Open Issues: 60
Releases: 25

Topics

chemistry chemistry-discovery kinetics python reactions thermodynamics

Created over 16 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct Citation

Reaction Mechanism Generator (RMG)

Description

This repository contains the Python version of Reaction Mechanism Generator (RMG), a tool for automatically generating chemical reaction mechanisms for modeling reaction systems including pyrolysis, combustion, atmospheric science, and more.

It also includes Arkane, the package for calculating thermodynamics, high-pressure-limit rate coefficients, and pressure dependent rate coefficients from quantum chemical calculations. Arkane is compatible with a variety of ab initio quantum chemistry software programs: Gaussian, Q-Chem, Molpro, Orca, Psi4, and TeraChem.

Source Code Repository

RMG Github Repository: contains the latest source code for RMG
RMG-database Github Repository: contains source code for the latest version of the database

How to Install

You can either download the source from GitHub and compile yourself, or download the binaries from Anaconda. Please see the Download and Install page for detailed instructions.

Documentation

How to Contribute

Please see the Contributor Guidelines for details on how to contribute to RMG-Py, Arkane, or RMG-database.

How to Give Feedback

Please post any issues you may have to the issues page or email rmg_dev@mit.edu if you have questions.

Useful Links

Interactive Website: Visit this site to visualize RMG-generated models, view the databases, and perform thermodynamics and kinetics searches
Issues Page: view current issues and feature requests

Credits

Resources and References

The resources and relevant publications are listed here on the RMG-website. Please at least cite our latest publication on Reaction Mechanism Generator v3.0 and other relevant publications when publishing the results using our software.

How to cite

Please include the following citations if RMG, RMG-database, and/or Arkane were used for an academic study: - C.W. Gao, J.W. Allen, W.H. Green, R.H. West, Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms, Computer Physics Communications 2016, 203, 212-225. - M. Liu, A. Grinberg Dana, M.S. Johnson, M.J. Goldman, A. Jocher, A.M. Payne, C.A. Grambow, K. Han, N.W. Yee, E.J. Mazeau, K. Blondal, R.H. West, C.F. Goldsmith, W.H. Green, Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation, Journal of Chemical Information and Modeling 2021, 61(6), 2686-2696. - M. S. Johnson, X. Dong, A. Grinberg Dana, Y. Chung, D. Farina, R. J. Gillis, M. Liu, N. W. Yee, K. Blondal, E. Mazeau, C. A. Grambow, A. M. Payne, K. A. Spiekermann, H.-W. Pang, C. F. Goldsmith, R. H. West, W. H. Green, RMG Database for Chemical Property Prediction, Journal of Chemical Information and Modeling 2022, 62(20), 4906–4915.

License Information

RMG is a free, open-source software package (distributed under the MIT/X11 license).

Owner

Name: Reaction Mechanism Generator
Login: ReactionMechanismGenerator
Kind: organization
Email: rmg_dev@mit.edu
Location: Mostly MIT and Northeastern University, MA, USA

Website: http://reactionmechanismgenerator.github.io/
Repositories: 26
Profile: https://github.com/ReactionMechanismGenerator

Developers of Reaction Mechanism Generator and associated software.

Citation (CITATIONS.bib)

@article{RMG,
title = {{Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms}},
journal = {Computer Physics Communications},
volume = {203},
pages = {212-225},
year = {2016},
issn = {0010-4655},
doi = {https://doi.org/10.1016/j.cpc.2016.02.013},
url = {https://www.sciencedirect.com/science/article/pii/S0010465516300285},
author = {Connie W. Gao and Joshua W. Allen and William H. Green and Richard H. West},
}

@article{RMG3,
author = {Liu, Mengjie and Grinberg Dana, Alon and Johnson, Matthew S. and Goldman, Mark J. and Jocher, Agnes and Payne, A. Mark and Grambow, Colin A. and Han, Kehang and Yee, Nathan W. and Mazeau, Emily J. and Blondal, Katrin and West, Richard H. and Goldsmith, C. Franklin and Green, William H.},
title = {{Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation}},
journal = {Journal of Chemical Information and Modeling},
volume = {61},
number = {6},
pages = {2686-2696},
year = {2021},
doi = {10.1021/acs.jcim.0c01480},
}

@article{RMG_Database,
author = {Johnson, Matthew S. and Dong, Xiaorui and Grinberg Dana, Alon and Chung, Yunsie and Farina, David Jr. and Gillis, Ryan J. and Liu, Mengjie and Yee, Nathan W. and Blondal, Katrin and Mazeau, Emily and Grambow, Colin A. and Payne, A. Mark and Spiekermann, Kevin A. and Pang, Hao-Wei and Goldsmith, C. Franklin and West, Richard H. and Green, William H.},
title = {RMG Database for Chemical Property Prediction},
journal = {Journal of Chemical Information and Modeling},
volume = {62},
number = {20},
pages = {4906-4915},
year = {2022},
doi = {10.1021/acs.jcim.2c00965},
}

@article{Arkane,
author = {Dana, Alon Grinberg and Johnson, Matthew S. and Allen, Joshua W. and Sharma, Sandeep and Raman, Sumathy and Liu, Mengjie and Gao, Connie W. and Grambow, Colin A. and Goldman, Mark J. and Ranasinghe, Duminda S. and Gillis, Ryan J. and Payne, A. Mark and Li, Yi-Pei and Dong, Xiaorui and Spiekermann, Kevin A. and Wu, Haoyang and Dames, Enoch E. and Buras, Zachary J. and Vandewiele, Nick M. and Yee, Nathan W. and Merchant, Shamel S. and Buesser, Beat and Class, Caleb A. and Goldsmith, Franklin and West, Richard H. and Green, William H.},
title = {{Automated reaction kinetics and network exploration (Arkane): A statistical mechanics, thermodynamics, transition state theory, and master equation software}},
journal = {International Journal of Chemical Kinetics},
volume = {55},
number = {6},
pages = {300-323},
doi = {https://doi.org/10.1002/kin.21637},
year = {2023}
}

GitHub Events

Total

Create event: 36
Commit comment event: 7
Release event: 1
Issues event: 85
Watch event: 63
Delete event: 26
Issue comment event: 587
Push event: 330
Pull request review comment event: 97
Pull request event: 108
Pull request review event: 129
Fork event: 16

Last Year

Create event: 36
Commit comment event: 7
Release event: 1
Issues event: 85
Watch event: 63
Delete event: 26
Issue comment event: 587
Push event: 330
Pull request review comment event: 97
Pull request event: 108
Pull request review event: 129
Fork event: 16

Committers

Last synced: about 2 years ago

All Time

Total Commits: 9,653
Total Committers: 105
Avg Commits per committer: 91.933
Development Distribution Score (DDS): 0.823

Past Year

Commits: 526
Committers: 24
Avg Commits per committer: 21.917
Development Distribution Score (DDS): 0.671

Top Committers

Name	Email	Commits
Josh Allen	j**n@m**u	1,704
Connie Gao	c**g@m**u	982
Matt Johnson	m**1@g**m	750
Max Liu	m**u@m**u	720
Richard West	r**t@n**u	567
Nick Vandewiele	n**e@g**m	562
Richard West	r**t@m**u	499
alongd	a**d@m**u	434
Richard West	r**t@n**u	432
Mark Goldman	g**m@m**u	283
KEHANG	k**n@g**m	181
Jackson Burns	j**s@m**u	173
Mark Payne	a**e@m**u	168
Gregory Magoon	g**n@m**u	160
Beat Buesser	b**r@m**u	153
Nathan Yee	n**e@m**u	144
Colin Grambow	c**w@m**u	139
Pierre Bhoorasingh	p**b@g**m	138
hwpang	h**g@m**u	118
davidfarinajr	f**d@n**u	92
Belinda Slakman	s**b@h**u	83
yunsiechung	y**e@m**u	83
jwallen85	j**5@3**0	75
Michael Harper	m**r@m**u	72
Alon Grinberg Dana	a**n@t**l	69
Emily Mazeau	m**e@h**u	64
Sean Troiano	s**7@g**m	63
Kevin Spiekermann	k**r@m**u	61
Yen-Ting Wang	y**w@m**u	54
xiaoruiDong	x**i@m**u	51
and 75 more...

Committer Domains (Top 20 + Academic)

mit.edu: 39 husky.neu.edu: 9 northeastern.edu: 6 brown.edu: 3 pharos.mit.edu: 3 neu.edu: 1 technion.ac.il: 1 nick-lct-laptop.(none): 1 rmg.mit.edu: 1 gmx.de: 1 antimatter.mit.edu: 1 stossrohr.net: 1 tremily.us: 1 gitter.im: 1 ivalice.(none): 1 udel.edu: 1 campus.technion.ac.il: 1 venture.private.dns.zone: 1 g.hmc.edu: 1 openrefactory.com: 1 chem.ufl.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 158
Total pull requests: 206
Average time to close issues: 7 months
Average time to close pull requests: 5 months
Total issue authors: 66
Total pull request authors: 35
Average comments per issue: 3.51
Average comments per pull request: 8.24
Merged pull requests: 100
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 55
Pull requests: 88
Average time to close issues: about 1 month
Average time to close pull requests: 26 days
Issue authors: 28
Pull request authors: 17
Average comments per issue: 1.91
Average comments per pull request: 5.11
Merged pull requests: 39
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sevyharris (25)
rwest (16)
JacksonBurns (12)
PoojaNem (9)
liqiang4567 (8)
jonwzheng (7)
mjohnson541 (5)
OJ-0908 (4)
kirkbadger18 (3)
ChrisBNEU (3)
cassguff (3)
alongd (3)
studies9 (2)
DiegoGuajardoP (2)
123wa-zj (2)

Pull Request Authors

JacksonBurns (66)
sevyharris (34)
rwest (30)
jonwzheng (22)
alongd (14)
donerancl (13)
mjohnson541 (12)
hwpang (12)
bjkreitz (9)
ssun30 (8)
ntietje1 (6)
Nora-Khalil (5)
ChrisBNEU (5)
LekiaAnonim (4)
xiaoruiDong (4)

Top Labels

Issue Labels

stale (38) abandoned (31) bug (14) Topic: Catalysis (9) Complexity: Low (8) Good First Issue (5) Python 3.11 Transition (5) Priority: Low (4) Announcement (3) Topic: Cantera (3) Type: Testing (3) Topic: Thermo (3) Type: Bug (2) Type: Documentation (2) Type: Error (2) Topic: Chemkin (2) Status: Discussion Needed (2) Type: Risk of Error (1) Topic: Kinetics (1) Topic: Pruning (1) Topic: PDep (1) Topic: Backward Compatibility (1) Topic: Liquid (1) Topic: Installation (1) Twin RMG-database PR (1) Topic: Nitrogen (1) Type: Feature (1) Arkane (1) Complexity: High (1) Type: Question (1)

Pull Request Labels

stale (28) abandoned (28) Complexity: Low (15) Topic: Catalysis (15) Status: Ready for Review (12) Python 3.11 Transition (7) Complexity: Medium (7) Arkane (6) Type: Documentation (5) Module: Resonance (4) Topic: Installation (4) Status: WIP (3) Type: Feature (2) Priority: High (2) RMG-Py (2) Twin RMG-database PR (2) RMS (1) Priority: Low (1) Good First Issue (1) Status: Abandoned (1) Topic: Thermo (1) Type: Bug (1) Type: Code Organization (1)

Packages

Total packages: 1
Total downloads:
- pypi 6 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 1
Total maintainers: 1

pypi.org: reactionmechanismgenerator

Reaction Mechanism Generator

Homepage: http://reactionmechanismgenerator.github.io
Documentation: https://reactionmechanismgenerator.readthedocs.io/
License: other
Latest release: 0.0.0a0
published about 3 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 6 Last month

Rankings

Dependent packages count: 6.6%

Average: 18.6%

Dependent repos count: 30.6%

Maintainers (1)

JacksonBurns

Last synced: 6 months ago

Dependencies

.github/workflows/CI.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/conda_build.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/docs.yml actions

actions/checkout v2 composite
conda-incubator/setup-miniconda v2 composite

.github/workflows/stale.yml actions

actions/stale main composite

Dockerfile docker

ubuntu latest build

.github/workflows/annotate.yml actions

actions/github-script v6 composite
thollander/actions-comment-pull-request v2 composite

reactionmechanismgenerator

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Reaction Mechanism Generator (RMG)

Description

Source Code Repository

How to Install

Documentation

How to Contribute

How to Give Feedback

Useful Links

Credits

Resources and References

How to cite

License Information

Owner

Citation (CITATIONS.bib)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: reactionmechanismgenerator

Rankings

Maintainers (1)

Dependencies