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Example Trajectory Data and Jupyter Notebooks Showing How to Compute Various Properties with STACIE

Toraman, Gözdenur; Verstraelen, Toon

Publisher
Zenodo
DOI
10.5281/zenodo.17582172
Repository
zenodo.org
Language
en

Abstract

This archive contains (i) Jupyter notebooks with examples of how to use STACIE. (ii) The output files needed to execute the example notebooks. Detailed descriptions and input files with which trajectories can be reproduced are provided in STACIE's Git repository: https://github.com/molmod/stacie/. Instructions for running the examples can be found in the README.pdf file included in this archive. All files in this dataset 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 data set. If not, see: https://creativecommons.org/licenses/by-sa/4.0/ https://www.gnu.org/licenses/

Full text

Example Trajectory Data and JupyterNotebooks Showing How to ComputeVarious Properties with STACIEGözdenur Toraman† and Toon Verstraelen✶¶† Soete Laboratory, Ghent University, Technologiepark-Zwijnaarde 46, 9052 Ghent, Belgium¶ Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052,Ghent, Belgium✶E-mail: [email protected]UsageTo run the example notebooks, you need to:1.Install STACIE and Jupyter Labpip install stacie jupyterlab 2.Download and unpack the archive with notebooks and trajectory data.unzip examples.zip 3.Finally, you should be able to start Jupyter Lab and run the notebooks.jupyter lab Overview of included filesSome Jupyter notebooks generate data and then analyze it, while others directly analyze existing data.1.Examples that do not need existing trajectory data:•minimal.ipynb: Minimal example of how to use STACIE, with detailed description of outputs.•error_mean.ipynb: Uncertainty of the mean of time-correlated data•applicability.ipynb: Applicability of the Lorentz model•surface_diffusion.ipynb: Diffusion of an argon atom on a surface2.Examples that analyze existing molecular dynamics trajectory data:•lj_shear_viscosity.ipynb: Shear viscosity of a Lennard-Jones fluid•lj_bulk_viscosity.ipynb: Bulk viscosity of a Lennard-Jones fluid•lj_thermal_conductivity.ipynb: Thermal conductivity of a Lennard-Jones fluid•molten_salt.ipynb: Ionic electrical conductivity of a molten salt systemThis second set of notebooks use MD data from the following sources:•lammps_lj3d: LAMMPS simulations of Lennard-Jones 3D systems•openmm_salt: OpenMM simulations of molten salt systems3.Examples analyzing data from external sources:•cloud-cover.ipynb: Correlation time analysis of cloud cover data from Open-MeteoRevision historyv1.1.0 (2025-11-11)Include cloud cover example data and notebook. v1.0.2 (2025-10-18)Switch to choice of license CC-BY-SA-4.0 OR LGPL-3.0-or-later.v1.0.1 (2025-10-03)Bugfix release: add missing nvt_thermo.txt files to the lammps_lj3d data.v1.0.0 (2025-06-26)Initial release of the STACIE example data and notebooks.