Operator-splitting errors in coupled reactive transport codes for transient variably saturated flow and contaminant transport in layered soil profiles

Reactive transport model for bentonites in COMSOL multiphysics: Benchmark and validation exercise

At present, the deep geological repository concept for spent nuclear fuel is considered the most reliable and safe technique for the permanent disposal of this type of waste. One of the many safety elements used is an engineered barrier made of compacted bentonite. This material allows the encapsulated waste to be isolated from the host rock. Therefore, there is great interest in a detailed study of the behavior of bentonites to different changes in the composition of the surrounding groundwater. In this context, this work presents a new reactive transport model for bentonites implemented in the COMSOL Multiphysics platform. The model contemplates a non-simplistic geochemical system composed of 42 species and 4 minerals. Reactive transport involves the diffusive-dispersive-advective processes defined by the Nernst Planck equations for two overlapping modeling levels (macro- and microstructural) to simulate the behavior of double-porosity media. The uniqueness of this model is that the system of equations used to calculate the chemical speciation problem and the advective-diffusive-dispersive transport can be integrally solved in COMSOL. The model has been satisfactorily verified and validated using the benchmark exercise consisting of the simulation of the multicomponent advective-diffusive column experiment conducted on a compacted bentonite core extracted from a field experiment (LOT project) in the Äspö Hardrock laboratory (Sweden).

A worksheet-based tool to implement reactive transport models in COMSOL Multiphysics

The increasing needs for modelling of reactive transport phenomena in different areas of environmental modelling have led to the development of many numerical codes. However, many of them suffer from a lack of flexibility, which hinders the adaptation of the codes to new problems. Moreover, in many cases, changes can be done by a very reduced group of people, and often by a single person, the main developer. Implementation platforms based on multiphysics modelling removes these barriers, although until now within that programming environments has been only possible the coupling of geochemical codes to transport equations using operator splitting techniques. This paper presents the EE4MGM tool, a MS Excel worksheet, provided in supplementary material, for the edition and complete implementation of reactive transport models in COMSOL. The tool automatically generates the code needed to solve the desired reactive transport problem by selecting only which species make up the geochemical system. This way, the numerical model will be completely adapted to the idealisation to be applied, being able to choose easily and effortlessly from a wide range of different levels of conceptual complexity. The organization of data input and the equation libraries obtained for the implementation in the multiphysics COMSOL environment are first described. Afterwards, two examples, in one and two-dimensional domains, to check the utility of the tool are presented.

A hydro-thermal-geochemical modeling framework to simulate reactive transport in a waste coal area under amended and non-amended conditions

Acid mine drainage (AMD) is a major cause of water quality deterioration across watersheds where acidic coal refuse (CR) piles are located. The oxidation of pyrite (the most common sulfide mineral), found in many of the CR piles, releases major ions, such as Fe²⁺, Fe³⁺, SO42−, and H⁺ into the environment. Bauxite residue (BR), commonly called alkaline clay (AC), a highly alkaline byproduct of the alumina refining process, can be combined with coal mine refuse to reduce and potentially eliminate the AMD problem associated with waste coal piles. A new hydro-thermal-geochemical model is developed in this study to simulate the reactive transport processes in AMD-treated areas. First, the model is tested at the experimental plots located within a CR pile in Greene County, Pennsylvania (USA), where two of the plots are used to show the impact of BR on CR piles. Then, the model capabilities are tested at a mine-impacted watershed in Indiana County, Pennsylvania (USA). In general, the model not only captures the patterns of both soil moisture, soil temperature and chemical concentrations at plots scales but it is also successfully implemented at a watershed scale. In conclusion, this study shows encouraging results regarding the AMD remediation simulation at different spatial scales.

The effects of irrigation and fertilization on the migration and transformation processes of main chemical components in the soil profile

Understanding the changes in chemical composition of soil plays an important role in effective control of irrigation and fertilization in agricultural productions, which further protects the groundwater quality and predicts its evolution. Field trials were conducted from 2014 to 2016 to investigate the impacts of irrigation and fertilization on mineral composition transformation in the soil profile. Based on HYDRUS-HP1 and Visual MINTEQ, this paper simulated and computed the migration and transformation of chemical components during the irrigation and fertilization in the vadose zone soil of Jinghuiqu district. The results showed that when the nitrogen fertilizer entered the soil, the urea was hydrolyzed to NH₄⁺ and it was nitrified as NO₂^-, which caused pH value to drop around the first 4 days after irrigation, and rise slightly on the 12th day. Due to the fact that soil belongs to calcareous soil, concentration of CaCO₃ and other carbonates (Mg or Na in sodic soils) could buffer the soil pH well above 8.5. Thus, on the 30th day of the post-irrigation the pH reached the same level as it was before irrigation. The change in pH resulted in the main ions reacting, dissolving and precipitating simultaneously in the soil profile. The concentrations of Ca²⁺, Mg²⁺ and HCO₃^- had significant correlations with the increasing ammonia nitrogen hydrolyzed from urea, and this process is accompanied with the saturation index of minerals and the main ion content changing. At the same time, the varying temperature action on pH of the soil was higher in summer than that in winter. Thus, the irrigation, fertilization and temperature had affected pH and main chemical components in the soil.

Enhanced electrokinetic remediation of polluted soils by anolyte pH conditioning

In the treatment of a polluted soil, the pH has a strong impact on the development of different physicochemical processes as precipitation/dissolution, adsorption/desorption or ionic exchange. In addition, the pH determines the chemical speciation of the compounds present in the system and, consequently, it conditions the transport processes by which those compounds will move. This question has aroused great interest in the development of pH control technologies coupled to soil remediation processes. In electrokinetic remediation processes, pH has usually been controlled by catholyte pH conditioning with acid solutions, applied to cases of heavy metals pollution. However, this method is not effective with pollutants that can be dissociated in anionic species. In this context, this paper presents a study of the electrokinetic remediation of soils polluted with 2,4-Dichlorophenoxyacetic acid, a common polar pesticide, enhanced with an anolyte pH conditioning strategy. A numerical study is proposed to evaluate the effectiveness of the strategy. Several numerical tests have been carried out for NaOH solutions with different concentrations as pH conditioning fluid. The results show that the anolyte pH conditioning strategy makes it possible to control the pH of the soil and, consequently, the chemical speciation of pollutant species. Thus, it is possible to achieve an important flux of pesticide into the anolyte compartment (electro-migration of anionic species and diffusive transport of acid species). This way, it possible to maximise the pesticide accumulation in this compartment, allowing a much more effective removal of pollutants from the soil than without the anolyte pH conditioning strategy.

CRootBox: a structural-functional modelling framework for root systems

Background and Aims

Root architecture development determines the sites in soil where roots provide input of carbon and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architecture models have been widely used and been further developed into functional-structural models that simulate the fate of water and solutes in the soil-root system. The root architecture model CRootBox presented here is a flexible framework to model root architecture and its interactions with static and dynamic soil environments.

Methods

CRootBox is a C++-based root architecture model with Python binding, so that CRootBox can be included via a shared library into any Python code. Output formats include VTP, DGF, RSML and a plain text file containing coordinates of root nodes. Furthermore, a database of published root architecture parameters was created. The capabilities of CRootBox for the unconfined growth of single root systems, as well as the different parameter sets, are highlighted in a freely available web application.

Key results

The capabilities of CRootBox are demonstrated through five different cases: (1) free growth of individual root systems; (2) growth of root systems in containers as a way to mimic experimental setups; (3) field-scale simulation; (4) root growth as affected by heterogeneous, static soil conditions; and (5) coupling CRootBox with code from the book Soil physics with Python to dynamically compute water flow in soil, root water uptake and water flow inside roots.

Conclusions

CRootBox is a fast and flexible functional-structural root model that is based on state-of-the-art computational science methods. Its aim is to facilitate modelling of root responses to environmental conditions as well as the impact of roots on soil. In the future, this approach will be extended to the above-ground part of the plant.

A reactive transport model for mercury fate in contaminated soil--sensitivity analysis

We present a sensitivity analysis of a reactive transport model of mercury (Hg) fate in contaminated soil systems. The one-dimensional model, presented in Leterme et al. (2014), couples water flow in variably saturated conditions with Hg physico-chemical reactions. The sensitivity of Hg leaching and volatilisation to parameter uncertainty is examined using the elementary effect method. A test case is built using a hypothetical 1-m depth sandy soil and a 50-year time series of daily precipitation and evapotranspiration. Hg anthropogenic contamination is simulated in the topsoil by separately considering three different sources: cinnabar, non-aqueous phase liquid and aqueous mercuric chloride. The model sensitivity to a set of 13 input parameters is assessed, using three different model outputs (volatilized Hg, leached Hg, Hg still present in the contaminated soil horizon). Results show that dissolved organic matter (DOM) concentration in soil solution and the binding constant to DOM thiol groups are critical parameters, as well as parameters related to Hg sorption to humic and fulvic acids in solid organic matter. Initial Hg concentration is also identified as a sensitive parameter. The sensitivity analysis also brings out non-monotonic model behaviour for certain parameters.

A reactive transport model for mercury fate in soil--application to different anthropogenic pollution sources

Soil systems are a common receptor of anthropogenic mercury (Hg) contamination. Soils play an important role in the containment or dispersion of pollution to surface water, groundwater or the atmosphere. A one-dimensional model for simulating Hg fate and transport for variably saturated and transient flow conditions is presented. The model is developed using the HP1 code, which couples HYDRUS-1D for the water flow and solute transport to PHREEQC for geochemical reactions. The main processes included are Hg aqueous speciation and complexation, sorption to soil organic matter, dissolution of cinnabar and liquid Hg, and Hg reduction and volatilization. Processes such as atmospheric wet and dry deposition, vegetation litter fall and uptake are neglected because they are less relevant in the case of high Hg concentrations resulting from anthropogenic activities. A test case is presented, assuming a hypothetical sandy soil profile and a simulation time frame of 50 years of daily atmospheric inputs. Mercury fate and transport are simulated for three different sources of Hg (cinnabar, residual liquid mercury or aqueous mercuric chloride), as well as for combinations of these sources. Results are presented and discussed with focus on Hg volatilization to the atmosphere, Hg leaching at the bottom of the soil profile and the remaining Hg in or below the initially contaminated soil layer. In the test case, Hg volatilization was negligible because the reduction of Hg(2+) to Hg(0) was inhibited by the low concentration of dissolved Hg. Hg leaching was mainly caused by complexation of Hg(2+) with thiol groups of dissolved organic matter, because in the geochemical model used, this reaction only had a higher equilibrium constant than the sorption reactions. Immobilization of Hg in the initially polluted horizon was enhanced by Hg(2+) sorption onto humic and fulvic acids (which are more abundant than thiols). Potential benefits of the model for risk management and remediation of contaminated sites are discussed.

Inverse optimization of hydraulic, solute transport, and cation exchange parameters using HP1 and UCODE to simulate cation exchange

Reactive transport modeling is a powerful tool to evaluate systems with complex geochemical relations. However, parameters are not always directly measurable. This study represents one of the first attempts to obtain hydrologic, transport and geochemical parameters from an experimental dataset involving transient unsaturated water flow and solute transport, using an automatic inverse optimization (or calibration) algorithm. The data come from previously published, controlled laboratory experiments on the transport of major cations (Na, K, Mg, Ca) during water absorption into horizontal soil columns that were terminated at different times. Experimental data consisted of the depth profiles of water contents (θ), Cl concentrations, and total aqueous and sorbed concentrations of major cations. The dataset was used to optimize several parameters using the reactive transport model, HP1 and the generic optimization code, UCODE. Although the soil hydraulic and solute transport parameters were also optimized, the study focused mainly on the geochemical parameters because the soil columns were constructed from disturbed soil. The cation exchange capacity and the cation exchange coefficients for two exchange models (Gapon and Rothmund-Kornfeld) were optimized. The results suggest that both calibrated models satisfactorily described the experimental data, although the Rothmund-Kornfeld model fit was slightly better. However, information content and surface response analyses indicated that parameters of the Gapon model are well identifiable, whereas those of the Rothmund-Kornfeld model were strongly correlated. The calibrated geochemical parameters were validated using an independent dataset. In agreement with the identifiability analysis, the Gapon approach was better than the Rothmund-Kornfeld model at calculating the observed concentrations of major cations in the soil solution and on the exchange sites.

Dynamic sorption of ammonium by sandy soil in fixed bed columns: Evaluation of equilibrium and non-equilibrium transport processes

The release of excess nitrogen-containing compounds into groundwater is a major concern in aquifer recharge by the Soil Aquifer Treatment (SAT) process. Ammonium (NH(4)(+)) is one of the most nocive and common nitrogen compounds in wastewaters. In order to assess the risk of wastewater use for aquifer recharge, NH(4)(+)adsorption onto Souhil wadi soil sampled from the SAT pilot plant (Nabeul, Tunisia) was studied using laboratory columns experiments. Several experiments were conducted using aqueous synthetic solutions under different aqueous ammonium concentrations and flow rates. Furthermore, a real wastewater solution was used to test the effect of competitive cations contents on NH(4)(+) adsorption. Afterwards, the Hydrus-1D model was used in inverse mode to simulate the ammonium transport through the Souhil wadi soil. For the synthetic solutions, the adsorbed ammonium amount varied from 1 to 30.7 mg kg(-1) for aqueous ammonium concentrations between 4.9 and 36.4 mg L(-1). The linear isotherm model was found to be the most suitable for describing this adsorption. The flow rate decrease from 45 to 15 mL min(-1) induced an increase in the ammonium adsorption capacity by 49%. Indeed, the lesser the flow rate is, the longer the residence time and the higher the exchange between the aqueous solution and soil matrix. The use of wastewater instead of aqueous synthetic solution decreased about 7 times the Souhil wadi adsorption capacity of ammonium because of its relatively high concentrations of competitive ions such as calcium and magnesium. The use of the Hydrus-1D model showed that the chemical non-equilibrium model was the best to simulate the ammonium transport through the laboratory soil columns.