pyCADMium
pyCADMium: Chemical Atoms in Diatomic Molecules. A prolate spheroidal Python module for embedding calculations - Published in JOSS (2022)
Science Score: 98.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README and JOSS metadata -
✓Academic publication links
Links to: joss.theoj.org -
✓Committers with academic emails
3 of 7 committers (42.9%) from academic institutions -
✓Institutional organization owner
Organization wasserman-group has institutional domain (purdue.edu) -
✓JOSS paper metadata
Published in Journal of Open Source Software
Scientific Fields
Repository
Solve the Kohn-Sham equations on a prolate spheroidal grid.
Basic Info
- Host: GitHub
- Owner: wasserman-group
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://wasserman-group.github.io/pyCADMium/
- Size: 5.84 MB
Statistics
- Stars: 9
- Watchers: 0
- Forks: 7
- Open Issues: 1
- Releases: 2
Metadata Files
README.md
- Prolate spheroidal coordinates grid-based code that solves a cylindrical problem semi-analytically.
- Calculations of atoms and diatomic molecules in real space.
- Kohn-Sham DFT calculations using density functional approximations by interfacing with libxc.
- Density-to-potential inversion calculations.
- Fragment-based calculations using partition-DFT.
Getting started:
- Clone and install from this repository.
- If installing in Windows, we recommend the use of WSL.
git clone https://github.com/wasserman-group/CADMium.git
cd CADMium
pip install .
pylibxc must be installed as well.
pip install pylibxc2
- Alternative, one can install libxc through conda and install pylibxc manually.
conda install -c conda-forge libxc
wget http://www.tddft.org/programs/libxc/down.php?file=5.0.0/libxc-5.0.0.tar.gz # Replace with most recent libxc download link
tar -xf libxc-5.0.0.tar.gz # Replace with name of downloaded file
cd libxc-5.0.0 # Replace with name of downloaded file
python setup.py install
- Proceed to test your pyCADMium installation.
Within the pyCADMium/tests/ folder run:
pytest .This will run a set of tests dedicated to ensure that your code is fully functional. Be wary of warnings, but don't fret on them if present.
Community Guideliness
- If any unexpected error occurs, please contact us at: victorandscience@gmail.com.
- Any comment, suggestion or change is welcomed as an issue or a pull request.
Tutorials:
Learn how to use CADMium with these examples.
Copyright
Copyright (c) 2020, Wasserman Group
Acknowledgements
Victor H. Chavez was supported by a fellowship from The Molecular Sciences Software Institute under NSF grant OAC-1547580.
Project based on the MolSSI Cookiecutter.
Owner
- Name: Wasserman Group
- Login: wasserman-group
- Kind: organization
- Location: United States of America
- Website: purdue.edu/dft
- Twitter: AdamWassermanR
- Repositories: 6
- Profile: https://github.com/wasserman-group
JOSS Publication
pyCADMium: Chemical Atoms in Diatomic Molecules. A prolate spheroidal Python module for embedding calculations
Authors
Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
Gridspace, Los Angeles, California, USA
Department of Chemistry, Purdue University, West Lafayette, Indiana, USA, Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana, USA
Editor
Lucy Whalley
Tags
partition density functional theory computational chemistry density functional theory embedding methodsGitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Victor H. Chavez | g****5@p****u | 217 |
| Victor Hugo | 5****z | 36 |
| Raghu | 6****3 | 3 |
| Daniel S. Katz | d****z@i****g | 2 |
| taylor-a-barnes | t****s@g****m | 1 |
| Lucy Whalley | l****y@n****k | 1 |
| root | r****t@Q****n | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 1
- Total pull requests: 11
- Average time to close issues: 2 months
- Average time to close pull requests: 1 day
- Total issue authors: 1
- Total pull request authors: 6
- Average comments per issue: 4.0
- Average comments per pull request: 0.27
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- srmnitc (1)
Pull Request Authors
- VHchavez (6)
- raghurama123 (1)
- lgtm-com[bot] (1)
- taylor-a-barnes (1)
- danielskatz (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v1 composite
- codecov/codecov-action v1 composite
- actions/checkout v2 composite
- actions/upload-artifact v1 composite
- openjournals/openjournals-draft-action master composite
- numpy *
- pydantic *
- pytest *
- scipy *
- setuptools *
- wheel *