TransPyRend: Overview

Transportmodell in Python für den Austrag von Radionukliden aus einem Endlager / Transportmodel in Python for radionuclides in and around nuclear waste repositories.

TransPyREnd is a model for simulating the diffusion, advection, sorption and decay of radionuclides in a porous medium in one spatial dimension. A paper describing the methodology is published in “Advances in Geoscience”.

The aim for the development of TransPyREnd was to provide a flexible, modular, open-source tool to simulate radionuclide transport in the subsurface and to calculate mass and particle flux of radionuclides around a repository.

The partial differential equations that govern radionuclide transport are discretized following the finite-difference method.

Please note that the package is still under development, undergoing rigorous testing.

Concentration of radionuclides as a function of depth in a synthetic test

Concentration of radionuclides as a function of depth in a synthetic test

Getting started

  • Download the zip file or clone the repository:

    git clone https://gitlab.opengeosys.org/openworkflow/transpyrend

  • Install dependencies using Anaconda or pip:

    conda env create -f environment.yml --name rnmodel
conda activate rnmodel

# Or with a virtual environment and pip:
python -m venv .venv
source .venv/bin/activate

# Now install transpyrend into local Python environment.
# In this case also install all optional dependencies:
pip install -e .[dev,tests,docs,notebooks]

Run tests

The numerical model code was evaluated by comparing it to several analytical and semi-analytic solutions. Tests can be found in the subdirectory tests/. To run them:

python -m unittest

Run a notebook

  • Start the notebook application jupyter notebook

  • Open from the notebook/examples-directory

API documentation

There is an automatically generated html documentation done with Sphinx in the subdirectory docs/. To generate the documentation:

# With an activated conda environment (see Getting started):
conda install sphinx
pip install sphinx-autoapi myst-parser numpydoc

# OR with an activated virtual environment (see Getting started):
# Already installed via the [...,docs,...] optional dependency group

cd docs
make html
# open build/html/index.html in a browser

Build the package

# Creates tarballs and wheels in dist-directory:
python -m build

License

This work is provided under the terms of the EUPL 1.2 if not stated otherwise, see the LICENSE file. If you make use of TransPyREnd in your work, please cite our paper describing the methodology (published in “Advances in Geoscience”):

  • Behrens, C., Lujiendijk, E., Kreye, P., Panitz, F., Bjorge, M., Gelleszun, M., Renz, A., Miro, S., Rühaak, W.: TransPyREnd: a code for modelling the transport of radionuclides on geological timescales, Adv. Geosci., 58, 109-119, DOI: 10.5194/adgeo-58-109-2023

Acknowledgments

We thank the OpenGeoSys team for useful discussions, review and comparisons.

Atomic masses in TransPyREnd are taken from Nubase2020 data, for details see

  • F.G. Kondev, M. Wang, W.J. Huang, S. Naimi, and G. Audi, Chin. Phys. C45, 030001 (2021)

The implementation of the analytic solution to the Bateman equation for linear chains has been adapted from this github repository, with the copyright notice retained as required.