BioReactPy: An open-source software for simulation of microbial-mediated reactive processes in porous media

Abstract

This paper provides a new open-source software, named BioReactPy, for simulation of microbial-mediated coupled processes of flow and reactive transport in porous media. The software is based on the micro-continuum approach, and geochemistry is handled in a fully coupled manner with biomass-nutrient growth treated with Monod equation in a single integrated framework, without dependencies on third party packages. The distinguishing features of the software, its design principles, and formulation of multiphysics problems and discretizations are discussed. Validation of the Python implementation using several established benchmarks for flow, reactive transport, and biomass growth is presented. The flexibility of the framework is then illustrated by simulations of highly non-linearly coupled flow and microbial reactive transport at conditions relevant to carbon mineralization for CO${}_2$ storage. All results can be reproduced by openly available simulation scripts.