A library of BASIC scripts of reaction rates for geochemical modeling using phreeqc

Highlights

• Compiled reaction kinetics data in the literature for 102 mineral phases.

• A library of BASIC scripts that can be used with PHREEQC.

• Tested different rate laws for feldspar dissolution in reaction path modeling.

Abstract

Rate equations and kinetic parameters for about 100 minerals were programmed into a library of callable Basic language scripts for the geochemical modeling program Phreeqc (version 3.5.0) to facilitate the application of kinetics in geochemical modeling. For most minerals, the following general equation is used: $r_{net}=S_A\sum _j{A}_j{e}^{-E_{a,j}/RT}\prod _i{a_{i,j}^{ni}(1-{\Omega }^{p_j})}^{q_j}$

where r_net stands for the net dissolution rate of a mineral phase (mol kgw⁻¹ s⁻¹); j the jth reaction mechanism; S_A the surface area per unit water mass (m² kgw⁻¹); A_j the Arrhenius pre-exponential factor (mol m⁻² s⁻¹); E_a,j the apparent reaction activation energy (J mol⁻¹); R the universal gas constant (8.31446 J mol⁻¹ K⁻¹); T the temperature (K); a_i the activity of aqueous species i; Ω the mineral saturation quotient. p_j and q_j are empirical fitting parameters. j stands for the specific mechanisms of reaction. Other forms of rate equations and associated parameters programmed in the library include parallel mechanisms, Langmuir adsorption isotherm, and empirical rate equations that apply to a specific reaction mechanism or geochemical system. A separate file of PHASEs, which define the chemical stoichiometry of the phases, dissolution reactions, and equilibrium constants of the dissolution reactions, is also provided. PHREEQC requires that the names in PHASES and RATES blocks match with each other.

The Basic language scripts can also be used as templates for writing other rate equations which users might wish to use. To illustrate the application of the script library, we simulated the reaction path of albite dissolution at 25 °C and 1 bar, using three rate equations and compared the results. The script and phase library and supporting materials can be downloaded from https://github.com/HydrogeoIU/PHREEQC-Kinetic-Library and doi.org/10.5967/41gq-yr13.

Introduction

In the last three decades, a large number of laboratory experiments have produced mineral dissolution rates in a wide range of temperatures, pH, and solution chemistry (see reviews by Brantley et al., 2008, pp. 151–210; Marini, 2007, pp. 211–266; Palandri and Kharaka, 2004; Schott et al., 2009). As a result, applications of reaction kinetics to water-rock interaction have also grown significantly in such fields as carbon dioxide sequestration (e.g., Knauss et al., 2005; Liu et al., 2011, 2012; Lu et al., 2011, 2013; 2015; Tutolo et al., 2015; White et al., 2005; Wilkin and DiGiulio, 2010; Xu et al., 2007; Xu et al., 2010; Zhang et al., 2013; Zhang et al., 2015; Zhang et al., 2016), diagenetic processes (Jones and Xiao, 2005, 2006; Lu and Cantrell, 2016; Roy et al., 2011; Whitaker and Xiao, 2010), geothermal systems (Dobson et al., 2004; Giambalvo et al., 2002; Spycher et al., 2003; Wanner et al., 2014; Xu and Pruess, 2001; Xu et al., 2004), and weathering (Maher et al., 2009; Perez-Fodich and Derry, 2019). Furthermore, advances in geochemical modeling software development have made application of kinetics to geochemical models much easier (Parkhurst and Appelo, 2013). Using thermodynamic data (e.g., equilibrium constants and activity coefficient models) and kinetic parameters (e.g., rate constants and activation energy), mineral dissolution and precipitation processes can be quantified with geochemical modeling software (e.g., EQ3/6: Wolery, 1992; Phreeqc: Parkhurst and Appelo, 1999, 2013; ToughReact: Xu et al., 2006, 2011; Crunchflow, Steefel et al., 2015).

Among the many geochemical simulation programs, the software package Phreeqc — a computer program for simulating aqueous speciation, reaction path, and 1-D reactive transport (Charlton and Parkhurst, 2011; Parkhurst and Appelo, 2013) — has gained popularity. This is partly because the program allows the user to describe the rate equations via BASIC scripts. These scripts are then run with the program along with other parts of input files and databases for kinetic model simulations. For example, Zhu et al. (2010) constructed a reaction path model for feldspar dissolution and secondary mineral precipitation in batch systems with their own Phreeqc database and kinetics scripts. Geochemical models of fluid-rock interaction have evolved from equilibrium only to kinetic approaches, thus addressing geochemical reactions on a real time scale (Zhu, 2009).

However, the databases that accompany the Phreeqc package only contain limited rate equations. Much of the kinetics data needed for geochemical modeling is scattered in the literature. Proper assembly of the kinetic data needed for modeling, such as preparing the codes for kinetic scripts and assembling other necessary parts for kinetic calculation, is an intimidating task for many users. To facilitate the use of kinetics in geochemical modeling, we collected the rate equations and kinetic parameters from the literature and compiled them into a library of scripts for Phreeqc. These BASIC language data blocks can be readily copied into input files or databases.

It is beyond the scope of this study to evaluate kinetic experiments and compile them into an internally consistent kinetic database. In fact, we took the kinetic parameters from the literature directly as they are and programmed them in easy-to-use formats. In this sense, users must be very careful about the conditions of these kinetic parameters are applicable. These conditions include the temperature, pH, solution chemistry, and saturation states. As they are in the original sources, the kinetic parameters for most minerals in this library were derived from dissolution experiments at far-from-equilibrium conditions. Extrapolation of them to near-equilibrium and precipitation conditions need careful verification. Users must be aware of this and other assumptions when applying this kinetic library to systems beyond the experimental conditions in the original studies.

The resulting library contains kinetic data for approximately 100 minerals. We understand that to derive a comprehensive and self-consistent kinetic rate database is a daunting task, and this library represents only the first effort in a long, multiphase project. The script and phase library and supporting materials can be downloaded from https://github.com/HydrogeoIU/PHREEQC-Kinetic-Library and doi.org/10.5967/41gq-yr13. The library of scripts are also included in an online version of Phreeqc, which can be accessed at the corresponding author's Indiana University web site www.hydrogeochem.earth.indiana.edu.