Submitted as: model description paper
03 Jun 2022
Submitted as: model description paper | 03 Jun 2022
Status: this preprint is currently under review for the journal GMD.

P3D-BRNS v1.0.0: A Three-dimensional, Multiphase, Multicomponent, Pore-scale Reactive Transport Modelling Package for Simulating Biogeochemical Processes in Subsurface Environments

Amir Golparvar1, Matthias Kästner2, and Martin Thullner1 Amir Golparvar et al.
  • 1UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Leipzig, Germany
  • 2UFZ - Helmholtz Centre for Environmental Research, Department Environmental Biotechnology, Leipzig, Germany

Abstract. The porous microenvironment of soil offers various environmental functions which are governed by physical and reactive processes. Understanding reactive transport processes in porous media is essential for many natural systems (soils, aquifers, aquatic sediments or subsurface reservoirs) or technological processes (water treatment, or ceramic and fuel cell technologies). In particular, in the vadose zone of the terrestrial subsurface the spatially and temporally varying saturation of the aqueous and the gas phase leads to systems that involve complex flow and transport processes as well as reactive transformations of chemical compounds in the porous material. To describe these interacting processes and their dynamics at the pore scale requires a well-suited modelling framework accounting for the proper description of all relevant processes at a high spatial resolution. Here we present P3D-BRNS as a new open-source modelling toolbox harnessing the core libraries of OpenFOAM and coupled externally to the Biogeochemical Reaction Network Simulator (BRNS). The native OpenFOAM Volume of Fluid solver is extended to have an improved representation of the fluid-fluid interface. The solvers are further developed to couple the reaction module which can be tailored for a specific reactive transport simulation. P3D-RBNS is benchmarked against three different flow and reactive transport processes; 1) fluid-fluid configuration in a capillary corner, 2) mass transfer across the fluid-fluid interface and 3) microbial growth with a high degree of accuracy. Our model allows for simulation of the spatio-temporal distribution of all bio-chemical species in the porous structure (obtained from µ-CT images), for conditions that are commonly found in the laboratory and environmental systems. With our coupled computational model, we provide a reliable and efficient tool for simulating multiphase, reactive transport in porous media.

Amir Golparvar et al.

Status: open (until 07 Sep 2022)

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Amir Golparvar et al.

Model code and software

P3D-BRNS Amir Golparvar

Amir Golparvar et al.


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Short summary
Coupled reaction-transport modeling is an established and highly beneficial method for studying natural and synthetic porous material with applications ranging from industrial processes to natural decompositions in terrestrial environments. Up to now, a framework that explicitly considers the porous structure (e.g., from µ-CT images), for modeling the transport of reactive species is missing. We presented a model that overcomes this limitation and represents a novel numerical simulation toolbox.