TReacLab: An object-oriented implementation of non-intrusive splitting methods to couple independent transport and geochemical software

Abstract

Cochepin. TReacLab: An object-oriented implementation of non-intrusive splitting methods to couple independent transport and geochemical software. Computers Geosciences, Elsevier, 2017, 109, pp.281-294 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Reactive transport modeling contributes to understand geophysical and geochemical processes 9 in subsurface environments. Operator splitting methods have been proposed as non-intrusive 10 coupling techniques that optimize the use of existing chemistry and transport codes. In this 11 spirit, we propose a coupler relying on external geochemical and transport codes with 12 appropriate operator segmentation that enables possible developments of additional splitting 13 methods. We provide an object-oriented implementation in TReacLab developed in the 14 MATLAB environment in a free open source frame with an accessible repository. TReacLab 15 contains classical coupling methods, template interfaces and calling functions for two 16 classical transport and reactive software (PHREEQC and COMSOL). It is tested on four 17 classical benchmarks with homogeneous and heterogeneous reactions at equilibrium or 18 kinetically-controlled. We show that full decoupling to the implementation level has a cost in 19 terms of accuracy compared to more integrated and optimized codes. Use of non-intrusive 20 implementations like TReacLab are still justified for coupling independent transport and 21 chemical software at a minimal development effort but should be systematically and carefully 22 assessed. M A N U S C R I P T A C C E P T E D ACCEPTED MANUSCRIPT

Nernst‐Planck‐based Description of Transport, Coulombic Interactions, and Geochemical Reactions in Porous Media: Modeling Approach and Benchmark Experiments

“…Notable examples are the modules IPhreeqc (Charlton & Parkhurst, 2011) and PhreeqcRM (Parkhurst & Wissmeier, 2015) that have been released to favor the interface of the widely used geochemical package PHREEQC (Parkhurst & Appelo 2013) with other simulators (e.g., He et al, 2015;Kolditz et al, 2012;Korrani et al, 2015;Muniruzzaman & Rolle, 2016). Different initiatives have proposed to adopt the IPhreeqc and PhreeqcRM modules to use the PHREEQC capabilities as reaction engine for the multipurpose finite element code COMSOL Multiphysics V R (e.g., Jara et al, 2017;Masi et al, 2017;Nardi et al, 2014;Wissmeier & Barry, 2011).…”

Modeling electrokinetic transport and biogeochemical reactions in porous media: A multidimensional Nernst–Planck–Poisson approach with PHREEQC coupling

“…In EK systems the current applied at the electrodes also creates different redox conditions at the electrodes' surfaces. The resulting competitive electrolysis reactions at the electrodes will be influenced by their reduction potentials, in which the reaction with the (Jara et al, 2017;Masi et al, 2017;Jang et al 2017;Nardi et al, 2014;Rolle et al, 2018;Wissmeier and Barry, 2009), in particular after the release of the modules IPhreeqc (Charlton and Parkhurst, 2011) and PhreeqcRM (Parkhurst and Wissmeier, 2015) The transport equations are solved considering the concentrations of the charged species in the system and the electric potential as unknows. The system of equations is then given by the system of the Nernst-Planck based governing transport equations (Eq.…”

Multicomponent Ionic Transport Modeling in Physically and Electrostatically Heterogeneous Porous Media With PhreeqcRM Coupling for Geochemical Reactions

“…Furthermore, the presented multicomponent ionic transport code (MMIT-Clay) is coupled with PHREEQC (Parkhurst & Appelo, 2013), taking advantage of the capabilities of linking this geochemical simulator with transport codes (Charlton & Parkhurst, 2011;He et al, 2015;Nardi et al, 2014;Parkhurst & Wissmeier, 2015;Wissmeier & Barry, 2011;Muniruzzaman & Rolle, 2016). MMIT-Clay utilizes the PhreeqcRM module (Parkhurst & Wissmeier, 2015), which allows great flexibility and a multipurpose framework to access all the PHREEQC's reaction capabilities (e.g., Healy et al, 2018;Jara et al, 2017;Rolle et al, 2018). At the end of the advective and dispersive transport within a time step (Δt), the concentration vector of all the species (primary and secondary species from aqueous speciation) is passed to PhreeqcRM to perform reaction calculations (i.e., any other reactions excluding Donnan and/or interlayer processes), which are done by considering a batch reactor in each cell of the simulation domain containing user-defined reactive processes of interest.…”