pysisyphus
Python suite for optimization of stationary points on ground- and excited states PES and determination of reaction paths.
Science Score: 77.0%
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 -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: wiley.com, zenodo.org -
✓Committers with academic emails
3 of 14 committers (21.4%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.4%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Python suite for optimization of stationary points on ground- and excited states PES and determination of reaction paths.
Basic Info
Statistics
- Stars: 118
- Watchers: 9
- Forks: 46
- Open Issues: 58
- Releases: 38
Topics
Metadata Files
README.md
As of November 2024 I'm no longer in academia. I've no longer access to commerical/closed-source codes like Gaussian or Turbomole, nor to paywalled scientific papers. Consider pysisyphus to be unmaintained.
Use at your own risk.
pysisyphus is a software-suite for the exploration of potential energy surfaces in ground-
and excited states. It implements several methods to search for stationary points
(minima and first order saddle points) and the calculation of minimum energy paths by means
of IRC and Chain of States methods like Nudged Elastic Band and Growing String.
Furthermore it provides tools to easily analyze & modify geometries (aligning, translating, interpolating, ...) and to visualize the calculation results.
Required energies, gradients and hessians are calculated by calling external quantum chemistry codes. Alternatively pysisyphus can also be used as a library to implement custom quantum chemistry workflows.
Further information can be found in the Open Access pysisyphus paper.
Documentation
Please have a look at the documentation.
Example
Fully internal coordinate transition state search for the famous alanine dipeptide isomerization reaction, using the xtb calculator and the growing string method.
Contribute
If any problems arise, please open an issue and I'll see if I can help if my time permits it. Contributions are welcome, so feel free to submit a PR.
Owner
- Name: Johannes Steinmetzer
- Login: eljost
- Kind: user
- Location: Jena, Germany
- Repositories: 6
- Profile: https://github.com/eljost
PhD in Theoretical Chemistry. :badger:
Citation (Citation.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Steinmetzer
given-names: Johannes
orcid: https://orcid.org/0000-0003-2493-6893
title: pysisyphus
version: 0.7.1
license: GPLv3
commit: 78a2a11a171efacfca7b1cf6fd11d9bd5d6a8a52
doi: 10.5281/zenodo.5172406
preferred-citation:
type: article
title: "pysisyphus: Exploring potential energy surfaces in ground and excited states"
authors:
- family-names: Steinmetzer
given-names: Johannes
orcid: https://orcid.org/0000-0003-2493-6893
- family-names: Kupfer
given-names: Stephan
orcid: https://orcid.org/0000-0002-6428-7528
- family-names: Gräfe
given-names: Stefanie
orcid: https://orcid.org/0000-0002-1747-5809
month: 8
year: 2020
doi: 10.1002/qua.26390
publisher: Wiley
journal: "International Journal of Quantum Chemistry"
date-released: 2021-08-09
GitHub Events
Total
- Create event: 5
- Release event: 1
- Issues event: 4
- Watch event: 17
- Delete event: 5
- Issue comment event: 23
- Push event: 47
- Pull request event: 19
- Pull request review event: 1
- Pull request review comment event: 1
- Fork event: 7
Last Year
- Create event: 5
- Release event: 1
- Issues event: 4
- Watch event: 17
- Delete event: 5
- Issue comment event: 23
- Push event: 47
- Pull request event: 19
- Pull request review event: 1
- Pull request review comment event: 1
- Fork event: 7
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 4,893
- Total Committers: 14
- Avg Commits per committer: 349.5
- Development Distribution Score (DDS): 0.523
Top Committers
| Name | Commits | |
|---|---|---|
| Johannes Steinmetzer | j****r@u****e | 2,335 |
| Johannes Steinmetzer | j****8@a****m | 2,235 |
| Johannes Steinmetzer | j****m@p****e | 164 |
| Phillip Seeber | p****r@g****m | 62 |
| Phillip Seeber | p****r@u****e | 58 |
| dachs_desktop | d****s@d****m | 9 |
| dependabot[bot] | 4****]@u****m | 7 |
| Wanja Schulze | w****u@p****m | 6 |
| Greg | b****1@g****m | 6 |
| Phillip Seeber | p****r@g****e | 3 |
| carpx | c****x@b****n | 3 |
| Greg Jones | g****s@c****u | 3 |
| LGTM Migrator | l****r@u****m | 1 |
| Jianyi | m****9@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 71
- Total pull requests: 115
- Average time to close issues: 4 months
- Average time to close pull requests: 20 days
- Total issue authors: 32
- Total pull request authors: 13
- Average comments per issue: 1.87
- Average comments per pull request: 1.43
- Merged pull requests: 102
- Bot issues: 0
- Bot pull requests: 50
Past Year
- Issues: 4
- Pull requests: 19
- Average time to close issues: 3 months
- Average time to close pull requests: 30 days
- Issue authors: 4
- Pull request authors: 6
- Average comments per issue: 0.25
- Average comments per pull request: 2.11
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 10
Top Authors
Issue Authors
- eljost (27)
- Kr0n0ss (5)
- ptrab (3)
- RaphaelRobidas (3)
- sheepforce (2)
- sespic (2)
- timcypresswong (2)
- O2-AC (2)
- Amingeo (1)
- EmotionalSupportBurrito (1)
- fredauski (1)
- sunghwan-choi (1)
- danstine (1)
- hccc317 (1)
- chburger (1)
Pull Request Authors
- dependabot[bot] (63)
- eljost (26)
- sheepforce (23)
- bapride11 (6)
- xjf729 (3)
- wangenau (3)
- henryw7 (2)
- Marclie (2)
- greghjones (2)
- cvsik (1)
- lgtm-com[bot] (1)
- RaphaelRobidas (1)
- computerscienceiscool (1)
- ptrab (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 275 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 42
- Total maintainers: 1
pypi.org: pysisyphus
Python suite for exploring potential energy surfaces.
- Homepage: https://github.com/eljost/pysisyphus
- Documentation: https://pysisyphus.readthedocs.io/
- License: GNU General Public License v3 (GPLv3)
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Latest release: 0.7.6
published over 3 years ago