Articles | Volume 56
Adv. Geosci., 56, 33–43, 2021
https://doi.org/10.5194/adgeo-56-33-2021
Adv. Geosci., 56, 33–43, 2021
https://doi.org/10.5194/adgeo-56-33-2021

  05 Oct 2021

05 Oct 2021

Geochemical and reactive transport modelling in R with the RedModRphree package

Geochemical and reactive transport modelling in R with the RedModRphree package
Marco De Lucia1 and Michael Kühn1,2 Marco De Lucia and Michael Kühn
  • 1GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany
  • 2University of Potsdam, Institute of Geosciences, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany

Correspondence: Marco De Lucia (delucia@gfz-potsdam.de)

Abstract

Advances in computing and experimental capabilities in the research of water-rock-interactions require geoscientists to routinely combine laboratory data and models to produce new knowledge. Data science is hence a more and more pervasive instrument for geochemists, which in turn demands flexible and easy to learn software adaptable to their specific needs. The GNU R language and programming environment has established itself as de facto standard language for statistics and machine learning, enjoying increasing diffusion in many applied scientific fields such as bioinformatics, chemometrics and ecological modelling. The availability of excellent third party extensions as well as its advanced graphical and numerical capabilities make R an ideal platform for comprehensive geochemical data analysis, experiment evaluation and modelling.

We introduce the open source RedModRphree extension package, which leverages the R interface to the established PHREEQC geochemical simulator. The aim of RedModRphree is to provide the user with an easy-to-use, high-level interface to program algorithms involving geochemical models: parameter calibration, error and sensitivity analysis, thermodynamical database manipulation, up to CPU-intensive parallel coupled reactive transport models. Among the out-of-the-box features included in RedModRphree, we highlight the computation and visualization of Pourbaix (Eh-pH) diagrams using full speciation as computed by PHREEQC and the implementation of 1D advective reactive transport supporting the use of surrogate models replacing expensive equation-based calculations.

1 Introduction

GNU R (R Core Team2021) is an open source software environment and programming language originally developed for statistical computing and graphics as new implementation of the closed source S language. Its expressive and elegant syntax combines elements of object-oriented and functional languages and is perfectly suited to represent computational problems in an extremely concise way. R's comprehensive numerical capabilities and its collaborative development nature has attracted a large user base over the years, leading to its establishment as de facto standard language in many areas of mathematics, statistics and machine learning, and as one of the most successful open source projects overall. R is more and more extending its ecosystem to different applied sciences, including geosciences, where the language's core strengths and its extremely large toolbox of user contributed extension packages benefit the daily work of students, academics and professionals alike. At the moment of writing, over 17750 user-contributed extension packages have been submitted to the official repository called Comprehensive R Archive Network (CRAN). Indices of these packages, termed “Task Views” (Zeileis2005, 2021), are provided by domain experts to offer guidance in navigating such an ample landscape by organizing them under specific topics. For example, the Task View Chemometrics and Computational Physics (Mullen2021) lists over 80 packages covering many aspects of data analysis relevant for chemistry and physics experiments, and the simulation of physico-chemico systems; furthermore, it points to other related Task Views of obvious interest such as Differential Equations and Multivariate Analysis.

https://adgeo.copernicus.org/articles/56/33/2021/adgeo-56-33-2021-l01

Listing 1R code used to obtain the git version of RedModRphree.

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Listing 2Code snippet illustrating the manipulation of an exemplary input script to compute calcite solubility in a 0.1 molal NaCl solution.

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Specifically for geochemistry, the CHNOSZ package (Dick2019) allows for thermodynamic calculations in aqueous geochemistry and geobiochemistry based on the Helgeson-Kirkham-Flowers (HKF) equations (Johnson et al.1992), extending the capabilities of the well known SUPCRT92 software. Furthermore, an interface to the established geochemical simulator PHREEQC (Appelo et al.2013; Parkhurst and Appelo2013) for the R language is available on CRAN as package phreeqc (Charlton and Parkhurst2011, note the lowercase writing adopted in this paper to distinguish it from PHREEQC itself). However, this interface only exposes the Application Programming Interface (API) of PHREEQC to R, and does not provide utility functions to quickly setup new models or in general to program algorithms involving geochemical calculations.

The freely available extension package RedModRphree, introduced with this contribution, aims at fulfilling this need. Its goal is to enhance the user experience by streamlining repetitive tasks connected with the utilization of PHREEQC for computing-intensive tasks, leveraging at the same time the software infrastructure offered by the R environment. RedModRphree supersedes a discontinued package called Rphree (https://rphree.r-forge.r-project.org/, last access: 30 September 2021 De Lucia and Kühn2013), which involved modifications of PHREEQC's source code at c level. The availability of the phreeqc extension package (Charlton and Parkhurst2011), on par with each new PHREEQC's release made this approach superfluous.

New functionalities and applications have been added to RedModRphree over the years. In particular, the package version 0.3.6 includes a novel implementation of Pourbaix diagrams computation following the suggestions of Kölling et al. (2000), which will be explained and demonstrated in Sect. 3.1. Advective one-dimensional reactive transport simulations which can use surrogates to speedup lengthy PHREEQC calculation are discussed in Sect. 3.2. Before diving into these applications, however, in the next section we provide a general overview of RedModRphree, its logic and its fundamentals illustrated with code examples.

https://adgeo.copernicus.org/articles/56/33/2021/adgeo-56-33-2021-l03

Listing 3Exemplary usage of the Distribute function to create input scripts “distributing” varying values of a given property, in this case calcite solubility as function of temperature in 16 steps from 25 to 100 C.

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Listing 4Running the simulation with phreeqc functions.

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2 Methods

2.1 Package description

PHREEQC itself operates by interpreting input scripts written in its own syntax, and outputting the results either as formatted text or as data tables. Thus, the primary need for a high-level interface to the chemical engine is offering comfortable mechanisms to create, manipulate and check the input scripts and to parse the structured text outputs. Much of RedModRphree code is hence related to text manipulation.

Several programmatic design choices were made in the development of RedModRphree:

  • the user is assumed to be familiar with PHREEQC and its syntax. The package does not hide it under own classes or abstractions, and instead only provides functions to manipulate input scripts and obtain calculations' results back into the R runtime;

  • minimal number of external dependencies, meaning that code is in standard R for maximum portability, maintenance and ease of installation;

  • code is platform-independent, however development and testing are mainly focused on POSIX operating systems such as Linux.

The current RedModRphree version 0.3.6 supports PHREEQC keywords EQUILIBRIUM_PHASES and KINETICS. Support of further options such as surface complexation, solid solutions and isotope is planned for future versions.

2.2 Basic usage demonstration

RedModRphree version 0.3.6, which is the version considered in this paper, can be downloaded from Zenodo (https://doi.org/10.5281/zenodo.5046427) or by anonymous download from the git server of GFZ. The commands given in Listing 1 install it along with the required dependencies.

RedModRphree provides utility functions to manipulate input scripts, which are represented in R as character vectors whose elements correspond to a line of a PHREEQC input script. The current RedModRphree version does not support line continuation (i.e., logical lines splitted across different actual text lines), so the user must be aware of this convention.

The fundamental input manipulations are provided by the functions AddProp and RepSol. The first adds to a base script a property such as a concentration or an equilibrium mineral and should be called explicitly for each new property added. Listing 2 illustrates its use leveraging the pipe operator %>% for code clarity, which must be enabled explicitly since it is not loaded by the package itself. When calling AddProp, the user must specify to which logical block the new property belongs as per standard PHREEQC syntax. This can be one of tot (a property belonging under the SOLUTION keyword, e.g. pH, temperature or total element concentrations), pphases (a mineral or a gas at equilibrium, from the conventional name “pure phases” used in PHREEQC; the package always adopts the PURE alternative keyword to EQUILIBRIUM_PHASES) or kin (for KINETICS blocks). RepSol repeats a template script a specified amount of times.

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Listing 5Parse a PHREEQC output with the ReadOut function.

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Listing 6Generate a SELECTED_OUTPUT block from an already calculated simulation parsed by the ReadOut function.

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Listing 7Using the generated SELECTED_OUTPUT block with function RunPQC.

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The next step is to use this basic template script to create meaningful calculations. The fundamental mechanism provided by RedModRphree is the function Distribute (and its variant DistributeKin which deals specifically with kinetic blocks). In Listing 3 is demonstrated how to create an input script which computes the solubility of calcite as function of temperature, varying it between 25 and 100 C.

By inspecting the new simT input buffer, it becomes clear that the initial template script was repeated 16 times, each with a different value of temperature. The new script can then be run with phreeqc-provided functions.

The results of these PHREEQC calculations are stored as text buffer in the out variable 4, using its standard format. RedModRphree provides functions to parse such output and obtain the numerical values as R objects (function ReadOut, Listing 5). In particular, ReadOut returns a list where each element is one simulation in the output buffer, and each simulation itself is a set of tabular data (specifically, data.frames in R) corresponding to the logical blocks in the output file. These logical blocks are named desc (some descriptive parameters about the calculated solutions such as pe, pH and ionic strength), tot (total elements concentrations), SI (saturation indices of minerals), pphases (equilibrium minerals) and species (concentration of dissolved species).

It is possible to transform back such a list to a valid PHREEQC input using the function InputFromList. Another way to obtain the needed results from PHREEQC is by specifying a SELECTED_OUTPUT or USER_PUNCH. When such blocks are specified, a data.frame containing the numerical values is directly returned to R from phreeqc. A simple mechanism to generate a SELECTED_OUTPUT block from a parsed simulation is provided by function FormSelectedOutput (Listing 6).

res2 is the resulting table containing all the variables included in the SELECTED_OUTPUT block.

2.3 Parallel computations

R offers an easy way to parallelize computing-intensive tasks. In RedModRphree this capability is leveraged making use of the extension packages foreach and doParallel. In particular the RunPQC function offers the option of parallel computing, however in this case it expects as input a list of input scripts which represent the tasks to be parallelized. A simple example of parallel computation of 320 simulations on 4 CPUs is given in listing 8.

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Listing 8Example of parallel execution with function RunPQC.

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The res3 variable contains the selected output corresponding to the 320 rows of the df data.frame. R offers many options to visualize three-dimensional data. Listing 9 gives an example of interactive visualization using the plotly package (Plotly Technologies2015). The resulting picture is interactive and opens in a browser. A screenshot is given in Fig. 1.

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Listing 93D visualization of the computed solubility of calcite as function of temperature and NaCl salinity using package plotly.

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Figure 1Screenshot of the interactive visualization of the results of the calcite solubility as function of T and salinity computed with Listing 8.

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Figure 2Pourbaix diagrams of copper across aqueous and solid species, using the llnl.dat thermodynamical database. Since at each point of the diagram all equilibrium activities are considered, the boundaries between predominance regions are no longer straight lines but curves. The interpretation of these diagrams requires expert knowledge. For example, kinetic limitation would prevent precipitation of delafossite from aqueous phase at 25 (John et al.2016).

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2.4 Additional resources: demos and documentation

The previous sections showcase a simple working session with the package. These functions are the fundamental building blocks needed to quickly create complex calculations, and can be easily leveraged to efficiently implement algorithms involving geochemical models, such as reactive transport simulations. The package includes further utilities to deal with KINETICS blocks and to parse and manipulate thermodynamical databases, which are not covered in this manuscript, and for which the reader is referred to the package documentation and demo.

RedModRphree ships with functions' documentation, usage examples and with a set of demos which illustrate in more detail different use cases not covered in this manuscript (Listing 10). The code of the included demos is commented and intended as additional documentation.

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Listing 10Commands to list all functions and demos and run one.

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In particular, several demos focus on the use of pre-trained emulators or surrogates instead of more computationally expensive PHREEQC calculations in 1D advective reactive transport simulations (De Lucia and Kühn2021). Surrogates are machine learning regressors able to reproduce a multivariate output as function of multivariate input. They must be trained in advance on a set of PHREEQC simulations, and can then be plugged-in in coupled reactive transport simulations for speedup. More details concerning the reactive transport capabilities of RedModRphree are given in Sect. 3.2.

3 Applications

3.1 Pourbaix diagrams

Pourbaix or Eh-pH diagrams were first introduced by the Belgian chemist Marcel Pourbaix in 1945. They are standard phase diagrams with electrochemical potential (Eh or pe) and pH as axes, and are a valuable tool in electrochemistry, material science and in general in aqueous chemistry and geochemistry (Huang2016; Hennig et al.2020), since they synthetically summarize the thermodynamically stable phases (i.e., at chemical equilibrium) of an aqueous electrochemical system. Since they are based on thermodynamics, like all phase diagrams, they do not account for reaction rates or kinetic effects. Classically, the boundaries between predominant chemical species (aqueous ions in solution or solid phases) are straight lines computed directly by evaluating Nernst and Law of Mass Action equations and imposing a condition of equality between two species' activities. Such approach is for example employed by the CHNOSZ package (Dick2019). However, beside potential and pH, the equilibrium activities depend also upon temperature, pressure, and, crucially, on the activities of all other dissolved species in the considered system. This makes the classical approach illicit from a rigorous standpoint (Kölling et al.2000). In particular, the predominance region for a given species should be defined as the locus of points in the diagram where its activity is larger than the activities of all other species. The borders between regions would not result in straight lines anymore, but curves.

PHREEQC offers the capability to calculate the speciation of a solution in its entirety; and using RedModRphree it is simple to achieve a more realistic predominance diagram as suggested by Kölling et al. (2000). This has been implemented in the Pourbaix function, which performs the computations and visualizes the diagram in a convenient way. The user provides a base script describing the solution and defines at which levels of pe and pH the speciation must be calculated; the function computes all combinations of these levels in a dense grid, restricted to the stability region of water, approximated by the limiting boundaries for release of molecular hydrogen and oxygen respectively (Eqs. 1, 2), not considering the effect of temperature.

(1)pe=0-pHrelease of free hydrogen(2)pe=20.75-pHrelease of free oxygen

The corresponding simulations are computed in parallel if the procs argument is larger than one. Then from the results for each simulation point, the mineral with largest positive saturation index is extracted, or, if none has positive SI, the largest activity of all the dissolved species. Once all the data are collected, the whole parameter space is displayed assigning a different colour for each phase. Each region is labelled with the brute formula of the represented species, written in italic font under their name for the minerals. Optionally the function restricts the diagram only to phases or species containing one element, specified by the element argument. If left unspecified, then all computed saturation indices and activities are considered in the diagram. The current version of Pourbaix() does not support the inclusion of pure phases at equilibrium with the system, such as partial pressure of CO2(g). Furthermore, no check is performed whether the resulting equilibrated solutions have a different pH or pe than the values specified in the input for each simulation point. Frequent numerical instabilities and non-convergence of simulations happen near the boundaries of the water stability region, in particular for large pe values. Since no error control mechanism is implemented in the current RedModRphree version, the user is recommended to restrict the range of pe and pH and to try different resolutions of the calculation grid.

Figure 2 (Listing 11) displays the Pourbaix diagram for copper speciation in a solution containing Na, Cl, Ca and Fe, on a 101×101 grid for a total of 8239 simulations inside the water stability region, which computes in under three seconds employing two CPUs.

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Listing 11R code used to obtain Fig. 2, which represents the equilibrium speciation of 10−3 moles of copper in 1 kg of water in presence of total dissolved Ca, Cl, Na and Fe concentrations as indicated in the picture.

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Specifying aqonly=TRUE restricts the diagram to aqueous species only. In this case, the user can specify a specific valence state for the element argument, for example with element='Fe(2)'. This option is only reliable for aqueous species since the valence state of an element in minerals is not readily obtainable by parsing the stoichiometric equations in a PHREEQC database. Finally, the user can specify a list of species or phases to be excluded from the diagram, enumerating them using the argument suppress.

A Pourbaix diagram is a synthetic way to highlight discrepancies in different thermodynamic databases, indicating the need for a closer inspection of the applied databases and/or more experimental data to support them. Figure 3 (Listing 12) showcases the aqueous speciation of iron computed by evaluating the same base solution with the phreeqc.dat and llnl.dat databases. It is apparent that the stability region of ferric oxyhydroxide FeIII(OH)3 is quite different following the two databases.

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Figure 3Pourbaix diagrams of aqueous iron speciation at 25 C and p=01:00 atm using two different thermodynamic databases: (a) phreeqc.dat and (b) llnl.dat.

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Listing 12R code used to obtain Figure 3.

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Figure 4Profiles of variables across a 1D domain resulting from kinetic reactive transport simulations computed with the ReactTranspBalanceKin function and PHREEQC's ADVECTION keyword respectively, for validation. A MgCl2 solution is injected from the left inlet of the domain which is initially at equilibrium with calcite, triggering the transient precipitation of Dolomite. Displayed are the relevant total dissolved concentrations and amounts of minerals (scale on the left y-axis) and pH (in gray, right y-axis) after 30 coupling iterations. The code used to produce this picture is included in the package as demo-validate.

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A major advantage of a Pourbaix diagram computed in this way is that it can be applied to “real” solutions of any complexity, not being restricted to pure systems of 4 or 5 components as in the classical approach. Furthermore, it is straightforward to implement the same kind of calculations as result of kinetic simulations, thus removing the last limitation shared with the classical diagrams. In facts, in most natural systems even if a mineral is thermodynamically the most favoured in a specific diagram region, other minerals with lower saturation index but faster kinetics may be the phases actually formed (Kölling et al.2000).

3.2 1D reactive transport using surrogate models

A further application provided by RedModRphree pertains to 1D reactive transport models. The functions ReactTranspBalanceEq and ReactTranspBalanceKin implement, for equilibrium minerals and kinetics respectively, a sequential non-iterative coupling between transport and chemistry similar to the PHREEQC's ADVECTION keyword, however disregarding heat transport and changes in porosity and hence assuming stationary Darcy flow. In particular, these functions transport total elements concentrations – a valid assumption in case of pure advection – and the proton and electron activities instead of total H, total O and charge imbalance, as done by PHREEQC internally (Parkhurst and Wissmeier2015). Figure 4 shows a visual validation of this simplified advection approach by comparing the results of a reactive transport benchmark on a one-dimensional grid with 50 elements computed once with PHREEQC's ADVECTION and once with ReactTranspBalanceKin. The whole computation is included in RedModRphree as demo-validate). In the benchmark, a MgCl2 solution is injected at the left inlet in a medium initially at equilibrium with calcite. This reactive solution triggers the dissolution of calcite and the transient precipitation of dolomite. All reactions involving minerals are kinetically controlled with a Lasaga rate law (Palandri and Kharaka2004). After 30 iterations with fixed time step of 999 s, the variables' profiles across the domain resulting from the two simulations are perfectly superposable, up to some negligible error imputable to truncation of floating point numbers occurring when passing from PHREEQC's c++ domain and R, which happens through strings.

Furthermore, the above mentioned functions implement an acceleration technique which at each iteration minimizes the chemical evaluations by identifying grid elements with nearly equal geochemical problems (De Lucia and Kühn2013). This is achieved by compressing the matrix used to represent the governing variables for the whole grid (one row per grid element, one column per concentration). This option is fully automatic and can be activated by setting argument reduce=TRUE. It achieves important speedups for initially homogeneous systems. Moreover, the simulations are again internally parallelized when argument procs is larger than one. The users are referred to the specific functions documentation for more usage details.

The main motivation for the development of these reactive transport functions was investigating the substitution of equation-based numerical solution of the chemical sub-process with a pre-trained statistical surrogate for computational speedup (Jatnieks et al.2016; De Lucia et al.2017; De Lucia and Kühn2021, which points to more advanced numerical experiments than those included as demo into the package). The user can activate this capability by providing a named list containing the trained regressors and an R function which uses them to perform the surrogate geochemistry calculations. This surrogate function is then called after each advective step, and its predictions are checked for plausibility by computing mass balances. The predictions trespassing a user-imposed threshold are rejected and in their place PHREEQC simulations are run instead. This process is repeated at each transport-chemistry iteration.

Five of RedModRphree's demos extensively illustrate the usage of its reactive transport capability. demo-validate, demo-equilibrium and demo-kinetics are simulations using only PHREEQC; demo-eq-surr-RF and demo-kin-surr-RF use Random Forests as surrogates for the equilibrium and kinetic version of the same reactive transport problem.

4 Conclusions

The richness of high-quality third-party applications, the large number of users and the overall maturity and stability of its code base make R an attractive computing platform for geoscientists and in particular for geochemists.

The free and open source RedModRphree package offers high-level programming utilities and out-of-the-box applications to enhance users' productivity when working with PHREEQC geochemical models. The utility functions provided by RedModRphree help to rapidly perform many parallelized calculations and collect the corresponding results as required, e.g., in sensitivity and uncertainty analyses, thus profiting from the excellence of the R ecosystem in that area and its graphics capabilities for visualization.

The RedModRphree version 0.3.6 offers novel applications of general interest for geochemists, in particular the calculation of Pourbaix diagrams based on the actual full speciation of complex aqueous systems. It is a valuable computational tool which overcomes some limitations of classical stability diagrams. Further development will aim at including kinetic control of reactions, three-dimensional stability diagrams, and having different variables as one of the axes, for example partial pressure of CO2(g).

The package release is meant to attract users and foster collaborative development in order to increase both the coverage of PHREEQC functionalities and number and scope of provided applications.

Code availability

RedModRphree is released under LGPL v2.1 license. A copy of the 0.3.6 version of the package has been stored on Zenodo at https://doi.org/10.5281/zenodo.5046427 (De Lucia2021). Until the process of inclusion into the Comprehensive R Archive Network (CRAN) is completed, development versions can be installed from https://git.gfz-potsdam.de/delucia/RedModRphree, last access: 30 September 2021.

Author contributions

MDL shaped the research, performed analyses, programming and wrote the manuscript. MK helped providing funding, shaping the research, and revised the manuscript.

Competing interests

The contact author has declared that neither they nor their co-author has any competing interests.

Disclaimer

Publisher’s note: Copernicus Publications remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Special issue statement

This article is part of the special issue “European Geosciences Union General Assembly 2021, EGU Division Energy, Resources & Environment (ERE)”. It is a result of the EGU General Assembly 2021, 19–30 April 2021.

Acknowledgements

The authors gratefully acknowledge Helge Moog and an anonymous reviewer for their suggestions which greatily improved the manuscript.

Financial support

This research has been supported by the Helmholtz Association in the framework of the project “Reduced Complexity Models – Explore advanced data science techniques to create models of reduced complexity” (grant no. ZT-I-0010).

The article processing charges for this open-access publication were covered by the Helmholtz Centre Potsdam – GFZ German Research Centre for Geosciences.

Review statement

This paper was edited by Sonja Martens and reviewed by Helge Moog and one anonymous referee.

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Short summary
RedModRphree is an R extension package to leverage the PHREEQC engine for geochemical models, providing convenience functions to efficiently setup computations and program algorithms involving geochemical models. Version 0.3.6 ships with a novel implementation of Pourbaix (potential/pH) diagram computation which considers the full speciation of the solution at each diagram point.