A python, finite-difference implementation of the diagenetic reactive-transport model from the L'Heureux (2018) paper "Diagenetic Self-Organization and Stochastic Resonance in a Model of Limestone-Marl Sequences" https://doi.org/10.1155/2018/4968315.
This model was created as part of an attempt to reproduce the results of the L'Heureux paper, the original Fortran code used in the paper can be found at: https://github.com/astro-turing/Diagenetic_model_LHeureux_2018. A different Python implementation (https://github.com/astro-turing/Integrating-diagenetic-equations-using-Python) and a Matlab code (https://github.com/MindTheGap-ERC/LMA-Matlab) were also developed as part of this project, with each applying different numerical methods in order to understand how the results of L'Heureux (2018) can be replicated. A comparison of all the codes can be found at https://github.com/MindTheGap-ERC/Cross-comparison.
As with the original Fortran model, this code uses an upwind-scheme for the spatial derivatives in the solid phase advection equations, but instead uses a centered scheme (with optional Fiadeiro-Veronis, to match the Fortran) for the solute and porosity equations. The time evolution uses the Scipy solve_ivp function, rather than an implicit Crank-Nicholson scheme. Further details of the numerical methods and options can be found in the documentation.
The code requires python version >=3.9 and the following python packages, installable through conda or pip (except where specified):
numpyscipymatplotlibpandasnumbanumba-progress(install withpip-install numba-progress)
Charlotte Summers
Utrecht University
email: c.summers [at] uu.nl
Web page: www.uu.nl/staff/CSummers
Cedric Thieulot
Utrecht University
email: c.thieulot [at] uu.nl
Web page: www.cedricthieulot.net