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.
To run this code, you need git
and conda
or pip
to install .
git clone [email protected]: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.
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
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 2023 Netherlands eScience Center and Utrecht University
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.