Reactive transport model for limestone-marl sequences

This repo was forked off Integrating-diagenetic-equations-using-Python, which is part of the Astro-turing organisation, created as part of the AstroToM ("Turing or Milankovitch") project, an OpenSSI 2021b project from the Netherlands eScience Center and Utrecht University (UU).

The diagenetic modelling efforts within AstoToM can be regarded as a precursor to this repo and to rhythmite, while LMA_utils, LHeureuxEqs and Cross-comparison are auxiliary repos.

LMA-Matlab was the first attempt to reproduce the results from L'Heureux (2018). That repo is coded in MATLAB, while the original diagenetic model from L'Heureux was written in FORTRAN.
Integrating-diagenetic-equations-using-Python was inspired by LMA-Matlab.

MindTheGap is led by dr. Emilia Jarochowska (UU).

Wide use is made of the py-pde package.

The porosity diffusion coefficient is held constant.

Installing and using

To run this code, you need git and conda or pip to install .

git clone git@github.com:MindTheGap-ERC/reactive-transport-model-for-limestone-marl-sequences.git

or

git clone https://github.com/MindTheGap-ERC/reactive-transport-model-for-limestone-marl-sequences.git

Next,

cd reactive-transport-model-for-limestone-marl-sequences
git switch release_v1.0.0
pipenv install

For the latter command you need pipenv which you can install using either pip install pipenv or conda install -c conda-forge pipenv.

Now you may be running into certain Python version requirements, i.e. the Pipfile requires a Python version that you do not have installed. For this conda can help, e.g.: conda create -n py311 python=3.11 anaconda to create a Conda Python 3.11 environment.

You can use that freshly installed Python version and possibly any additionally installed libraries - using the --site-packages argument - by executing pipenv install --python=$(conda run -n py311 which python) --site-packages --skip-lock. The latter argument - --skip-lock - may be redundant, but if your previous pipenv install failed, pipenv --rm may be needed.

After a succesful pipenv installation you should be able to execute

pipenv run python marlpde/Evolve_scenario.py

or

pipenv shell
python marlpde/Evolve_scenario.py

Results in the form of an .hdf5 file will be stored in a subdirectory of a Results directory, which will be in the root folder of the cloned repo.

Alternative: poetry

If you prefer poetry over pipenv, you may install all the dependencies and activate the environment using the command poetry install. Next, either:

poetry run python marlpde/Evolve_scenario.py

or

poetry shell
python marlpde/Evolve_scenario.py

Running tests

From the root folder, i.e. the folder you enter after cd Integrating-diagenetic-equations-using-Python, either run

pipenv run python -m pytest

or

poetry run python -m pytest

Copyright

Copyright 2023 Netherlands eScience Center and Utrecht University

Funding information

Funded by the European Union (ERC, MindTheGap, StG project no 101041077). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them.