STACIE

STACIE is a Python package and algorithm that computes time integrals of autocorrelation functions. It is primarily designed for post-processing molecular dynamics simulations. However, it can also be used for more general analysis of time-correlated data. Typical applications include estimating transport properties and the uncertainty of averages over time-correlated data, as well as analyzing characteristic timescales.

All information about STACIE can be found in the documentation.

Citation

If you use STACIE in your research, please cite the following paper:

Gözdenur Toraman, Dieter Fauconnier, and Toon Verstraelen "STable AutoCorrelation Integral Estimator: Robust and Accurate Transport Properties from Molecular Dynamics Simulations" Journal of Chemical Information and Modeling 2025, 65 (19), 10445–10464, https://doi.org/10.1021/acs.jcim.5c01475, https://arxiv.org/abs/2506.20438.

@article{Toraman2025,
 author = {G\"{o}zdenur Toraman and Dieter Fauconnier and Toon Verstraelen},
 title = {STable AutoCorrelation Integral Estimator:
  Robust and Accurate Transport Properties from Molecular Dynamics Simulations},
 journal = {Journal of Chemical Information and Modeling},
 volume = {65},
 number = {19},
 pages = {10445--10464},
 year = {2025},
 month = {sep},
 url = {https://doi.org/10.1021/acs.jcim.5c01475},
 doi = {10.1021/acs.jcim.5c01475},
}

When using the Lorentz model or performing shear viscosity calculations with STACIE, please also cite the following paper:

Gözdenur Toraman, Dieter Fauconnier, and Toon Verstraelen "Reliable Viscosity Calculation from High-Pressure Equilibrium Molecular Dynamics: Case Study of 2,2,4-Trimethylhexane" Journal of Chemical Theory and Computation 2026, 22 (15), 7496–7511, https://doi.org/10.1021/acs.jctc.6c00506, https://arxiv.org/abs/2603.11247.

@article{Toraman2026,
 author = {G\"{o}zdenur Toraman and Dieter Fauconnier and Toon Verstraelen},
 title = {Reliable Viscosity Calculation from High-Pressure Equilibrium Molecular Dynamics:
  Case Study of 2,2,4-Trimethylhexane},
 journal = {Journal of Chemical Theory and Computation},
 volume = {22},
 number = {15},
 pages = {7496--7511},
 year = {2026},
 month = {jul},
 url = {https://doi.org/10.1021/acs.jctc.6c00506},
 doi = {10.1021/acs.jctc.6c00506},
}

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.

STACIE's documentation is located in the docs/ directory of its source tree and files under this directory are distributed under a choice of license: either the Creative Commons Attribution-ShareAlike 4.0 International license (CC BY-SA 4.0) or the GNU Lesser General Public License, version 3 or later (LGPL-v3+). The SPDX License Expression for the documentation is CC-BY-SA-4.0 OR LGPL-3.0-or-later.

You should have received a copy of the CC BY-SA 4.0 and LGPL-v3+ licenses along with the source code. If not, see:

• https://creativecommons.org/licenses/by-sa/4.0/
• https://www.gnu.org/licenses/

Installation

Assuming you have Python and Pip installed, the following shell command will install STACIE in your Python environment.

python -m pip install stacie

If you have a Conda environment, you can also install STACIE from the conda-forge channel:

conda install -c conda-forge stacie