Science Score: 67.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 4 DOI reference(s) in README -
✓Academic publication links
Links to: arxiv.org, zenodo.org -
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○Scientific vocabulary similarity
Low similarity (15.4%) to scientific vocabulary
Keywords
Repository
Stable AutoCorrelation Integral Estimator
Basic Info
- Host: GitHub
- Owner: molmod
- License: lgpl-3.0
- Language: Python
- Default Branch: main
- Homepage: https://molmod.github.io/stacie/
- Size: 20.4 MB
Statistics
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
STACIE
STACIE stands for the STable AutoCorrelation Integral Estimator. It is a Python package for post-processing molecular dynamics simulations, but it can also be used for more general analysis of time-correlated data. Typical applications include estimating transport properties, uncertainties of averages over time-correlated data, and analysis of characteristic timescales.
All information about STACIE can be found in the Documentation.
License
STACIE is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
STACIE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this program. If not, see https://www.gnu.org/licenses/.
STACIE's documentation is distributed under the Creative Commons CC BY-SA 4.0 license.
Citation
If you use STACIE in your research, please cite the following paper:
Gözdenur, T.; Fauconnier, D.; Verstraelen, T. "STable AutoCorrelation Integral Estimator (STACIE): Robust and accurate transport properties from molecular dynamics simulations" arXiv 2025, arXiv:2506.20438.
```bibtex @article{Toraman2025, title = {STable AutoCorrelation Integral Estimator (STACIE): Robust and accurate transport properties from molecular dynamics simulations}, url = {https://arxiv.org/abs/2506.20438}, doi = {10.48550/arXiv.2506.20438}, publisher = {arXiv}, author = {G\"{o}zdenur Toraman and Dieter Fauconnier and Toon Verstraelen}, year = {2025}, month = {jun} }
```
Installation
Assuming you have Python and Pip installed, the following shell command will install STACIE in your Python environment.
bash
python -m pip install stacie
Owner
- Name: Center for Molecular Modeling (CMM), Ghent University
- Login: molmod
- Kind: organization
- Location: Belgium
- Website: http://molmod.ugent.be
- Repositories: 16
- Profile: https://github.com/molmod
Technologiepark 46, 9052 Zwijnaarde, Belgium
Citation (CITATION.cff)
cff-version: 1.2.0
message: If you use this software, please cite it using these metadata.
title: STable AutoCorrelation Integral Estimator (STACIE)
type: software
url: https://molmod.github.io/stacie/
keywords:
- molecular dynamics
- post-processing
- autocorrelation integral
- time correlation
- transport properties
- characteristic timescales
- uncertainty quantification
- exponential correlation time
- integrated correlation time
- autocorrelation function
- ACF
- power spectral distribution
- PSD
- Python package
- LGPL
- open source
- scientific computing
- data analysis
- STACIE
abstract: >-
STACIE is a Python package for post-processing molecular dynamics simulations,
but it can also be used for more general analysis of time-correlated data.
Typical applications include estimating transport properties,
uncertainties of averages over time-correlated data,
and analysis of characteristic timescales.
authors:
- family-names: Gözdenur
given-names: Toraman
orcid: https://orcid.org/0000-0001-6785-333X
affiliation: >-
Labo Soete,
Ghent University,
Technologiepark-Zwijnaarde 46,
B-9052,
Ghent,
Belgium
- family-names: Verstraelen
given-names: Toon
orcid: https://orcid.org/0000-0001-9288-5608
affiliation: >-
Center for Molecular Modeling (CMM),
Ghent University,
Technologiepark-Zwijnaarde 46,
B-9052,
Zwijnaarde, Belgium
identifiers:
- type: doi
value: 10.5281/zenodo.15543903
description: Example usage of STACIE (Jupyter notebooks and trajectory data)
preferred-citation:
authors:
- family-names: Toraman
given-names: Gözdenur
- family-names: Fauconnier
given-names: Dieter
- family-names: Verstraelen
given-names: Toon
title: >-
STable AutoCorrelation Integral Estimator (STACIE):
Robust and accurate transport properties from molecular dynamics simulations
doi: 10.48550/arXiv.2506.20438
type: article
identifiers:
- description: arXiv preprint describing STACIE
type: doi
value: 10.48550/arXiv.2506.20438
license: LGPL-3.0-or-later
repository-code: https://github.com/molmod/stacie
GitHub Events
Total
- Release event: 1
- Watch event: 2
- Push event: 21
- Create event: 3
Last Year
- Release event: 1
- Watch event: 2
- Push event: 21
- Create event: 3
Packages
- Total packages: 1
-
Total downloads:
- pypi 15 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
pypi.org: stacie
STable AutoCorrelation Integral Estimator (STACIE)
- Documentation: https://molmod.github.io/stacie/
- License: lgpl-3.0
-
Latest release: 1.0.0
published 8 months ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v4 composite
- actions/setup-python v5 composite
- attrs ==25.3.0
- cattrs ==25.1.1
- matplotlib ==3.10.3
- numpy ==2.3.1
- path ==17.0.0
- scipy ==1.16.0
- attrs >=25.3.0
- cattrs >=25.1.1
- matplotlib >=3.10.3
- numpy >=2.3.1
- path ==17.0.0
- scipy >=1.16.0