The HPx software for multicomponent reactive transport during variably-saturated flow: Recent developments and applications

Abstract HPx is a multicomponent reactive transport model which uses HYDRUS as the flow and transport solver and PHREEQC-3 as the biogeochemical solver. Some recent adaptations have significantly increased the flexibility of the software for different environmental and engineering applications. This paper gives an overview of the most significant changes of HPx, such as coupling transport properties to geochemical state variables, gas diffusion, and transport in two and three dimensions. OpenMP allows for parallel computing using shared memory. Enhancements for scripting may eventually simplify input definitions and create possibilities for defining templates for generic (sub)problems. We included a discussion of root solute uptake and colloid-affected solute transport to show that most or all of the comprehensive features of HYDRUS can be extended with geochemical information. Finally, an example is used to demonstrate how HPx, and similar reactive transport models, can be helpful in implementing different factors relevant for soil organic matter dynamics in soils. HPx offers a unique framework to couple spatial-temporal variations in water contents, temperatures, and water fluxes, with dissolved organic matter and CO2 transport, as well as bioturbation processes

Evaluation of a general model for multimodal unsaturated soil hydraulic properties

Many soils and other porous media exhibit dual- or multi-porosity type features. In a previous study (Seki et al., 2022) we presented multimodal water retention and closed-form hydraulic conductivity equations for such media. The objective of this study is to show that the proposed equations are practically useful. Specifically, dual-BC (Brooks and Corey)-CH (common head) (DBC), dual-VG (van Genuchten)-CH (DVC), and KO (Kosugi)$_1$BC$_2$-CH (KBC) models were evaluated for a broad range of soil types. The three models showed good agreement with measured water retention and hydraulic conductivity data over a wide range of pressure heads. Results were obtained by first optimizing water retention parameters and then optimizing the saturated hydraulic conductivity (K_s) and two parameters (p, q) or (p, r) in the general hydraulic conductivity equation. Although conventionally the tortuosity factor p is optimized and (q, r) fixed, sensitivity analyses showed that optimization of two parameters (p+r, qr) is required for the multimodal models. For 20 soils from the UNSODA database, the average $R^2$ for log (hydraulic conductivity) was highest (0.985) for the KBC model with r=1 and optimization of (Ks, p, q). This result was almost equivalent (0.973) to the DVC model with q=1 and optimization of (Ks, p, r); both were higher than $R^2$ for the widely used Peters model (0.956) when optimizing (Ks, p, a, $\omega$). The proposed equations are useful for practical applications while mathematically being simple and consistent.Comment: To be published in Journal of Hydrology and Hydromechanic

Closed-form hydraulic conductivity equations for multimodal unsaturated soil hydraulic properties

Closed-form expressions of the hydraulic conductivity function for linearly superposed subretention (multimodal) functions were derived for arbitrary sets of the Brooks and Corey (BC), van Genuchten (VG), and Kosugi (KO) water retention models. The generalized Mualem hydraulic conductivity model was evaluated using the mathematical approach of Priesack and Durner. Three types of modification to the multimodel were also proposed. Firstly, the derived conductivity equations can be simplified when the submodel parameters, hbi for the BC model, alpha i-1 for the VG model, and hmi for the KO model have the same (common) value (denoted as CH). Secondly, as in the case of the modified single VG and KO models, a hypothetical air-entry head near saturation can be introduced for the multimodal VG and KO models to prevent unrealistic reductions in the hydraulic conductivity near saturation when the VG n parameter approaches its lower limit of n = 1. Furthermore, the multimodal hydraulic conductivity functions become a simple sum of conductivity subfunctions when the exponent r is unity (such as for Burdine's model), which leads to independent tortuosity effects for each submodel. The models are illustrated for two soils: a highly aggregated Kumamoto Andisol and a relatively unimodal dune sand. The dual-(BC, VG, KO) and the VG(1)BC(2) models equally represented the water retention data of the Andisol, with similar hydraulic conductivity curves. The dual-BC-CH, dual-VG-CH, and VG(1)BC(2)-CH models fitted the water retention data of the dune sand well, with the hydraulic conductivity curves of the dual-porosity model being similar to those of the Fayer and Simmons (FS) model

A control volume scheme using compact integrated radial basis function stencils for solving the Richards equation

A new control volume approach is developed based on compact integrated radial basis function (CIRBF) stencils for solution of the highly nonlinear Richards equation describing transient water flow in variably saturated soils. Unlike the conventional control volume method, which is regarded as second-order accurate, the proposed approach has high-order accuracy owing to the use of a compact integrated radial basis function approximation that enables improved flux predictions. The method is used to solve the Richards equation for transient flow in 1D homogeneous and heterogeneous soil profiles. Numerical results for different boundary conditions, initial conditions and soil types are shown to be in good agreement with Warrick's semi-analytical solution and simulations using the HYDRUS-1D software package. Results obtained with the proposed method were far less dependent upon the grid spacing than the HYDRUS-1D finite element solutions

Improving wheat (Triticum aestivum L.) antioxidative defense mechanisms against salinity stress by exogenous application of potassium silicate

The primary objective of this study was to investigate the beneficial effects of seed priming and foliar spray of potassium silicate on antioxidant activities under different salinity levels, thereby potentially improving wheat growth. Seeds were soaked into solutions containing potassium silicate (K2SiO3, 1.5 mM) for 6 h, while foliar spray with K2SiO3 (4 mM) was applied at the early and the late stages of tillering. Lake Urmia water was used to prepare salinity levels of 0, 3, 5, 8, 10, 12, and 14 dS m −1. For such traits as anthocyanin, catalase, ascorbate peroxidase, guaiacol peroxidase, and superoxide dismutase activity, an initial increase was observed at lower salinity levels; higher salinities subsequently decreased these traits or they remained mostly constant. Salinity also increased phenol, malondialdehyde, hydrogen peroxide, and polyphenol oxidase, but decreased flavonoid, nitrate content, and nitrate reductase activity. Seed priming and foliar spray provided effective approaches to reduce reactive oxygen species (ROS) manifestation in wheat grown under saline conditions. The improved antioxidant defense abilities by seed priming and foliar spray alleviated the oxidative damage of proteins and lipids and improved nitrate content and nitrate reductase activity

Prediction of the absolute hydraulic conductivity function from soil water retention data

For modeling flow and transport processes in the soil-plant-atmosphere system, knowledge of the unsaturated hydraulic properties in functional form is mandatory. While much data are available for the water retention function, the hydraulic conductivity function often needs to be predicted. The classical approach is to predict the relative conductivity from the retention function and scale it with the measured saturated conductivity, Ks. In this paper we highlight the shortcomings of this approach, namely, that measured Ks values are often highly uncertain and biased, resulting in poor predictions of the unsaturated conductivity function. We propose to reformulate the unsaturated hydraulic conductivity function by replacing the soil-specific Ks as a scaling factor with a generally applicable effective saturated tortuosity parameter τs and predicting total conductivity using only the water retention curve. Using four different unimodal expressions for the water retention curve, a soil-independent general value for τs was derived by fitting the new formulation to 12 data sets containing the relevant information. τs was found to be approximately 0.1. Testing of the new prediction scheme with independent data showed a mean error between the fully predicted conductivity functions and measured data of less than half an order of magnitude. The new scheme can be used when insufficient or no conductivity data are available. The model also helps to predict the saturated conductivity of the soil matrix alone and thus to distinguish between the macropore conductivity and the soil matrix conductivity

Field-scale assessment of the unsaturated hydraulic properties of residual soils in southeastern Brazil

Field tests were carried out to estimate effective unsaturated soil hydraulic properties of layered residual soils in Rio de Janeiro, southeastern Brazil. Data of this type are important for understanding the initiation of rainstorm-induced soil landslides, which often occur in the state of Rio de Janeiro as well as other areas having similar geologic settings and climate conditions. Tests were carried out using a simplified field approach, referred to as the Monitored Infiltration Test, which requires only a tensiometer to measure pressure heads below the wetting front, triggered by flow from a Mariotte bottle which maintains a constant pressure at the top edge of the soil profile. The data can then be analyzed by numerical inversion using the HYDRUS-2D software package. The test is relatively fast since no steady-state flow conditions are needed, and versatile since the test can be carried out quickly on steep slopes with the help of a manual auger. Soil water retention and the unsaturated hydraulic conductivity functions were obtained for a range of young, mature and saprolitic residual soils. The effective hydraulic properties of the distinct residual soil layers can be quite large, reflecting a need to provide a careful analysis of field-scale hydraulic heterogeneity in geotechnical analyses

A modeling framework to quantify the effects of compaction on soil water retention and infiltration

The water retention curve (WRC) of arable soils from the southeastern United States at different levels of compaction (no compaction, and 10 and 20% increases in soil bulk density) was estimated using the van Genuchten-Mualem (VG) model. The VG water retention parameters of the noncompacted soils were obtained first by fitting measured soil hydraulic data. To construct the WRC of the compacted soils, gravimetric values of the permanent wilting point (theta(gw), 1,500 kPa) and the residual (theta(gr)) water content were assumed to remain unchanged with compaction. The VG parameter alpha and exponent eta after compaction were estimated using two approaches. In Approach 1, alpha and eta were estimated from saturation, the permanent wilting point, and the residual water content. In Approach 2, the value of eta was assumed to remain unchanged with compaction, which allowed alpha to be estimated immediately from the VG equation. Approach 2 was found to give slightly better agreement with measured data than Approach 1. The effect of compaction on the saturated hydraulic conductivity (K-s) was predicted using semitheoretical approaches and the VG-WRC function. HYDRUS-1D was further used to simulate vertical infiltration into a single-layered soil profile to determine the impact of compaction on the infiltration characteristics of the soils used in our analyses. Results showed that a 10-20% increase in soil bulk density, due to compaction, reduced cumulative infiltration (I-c) at time T = T-final (steady-state) by 55-82%, and the available water storage capacity by 3-49%, depending upon soil type

Impacts of Mineralogy on Petrophysical Properties

Because of their extreme heterogeneity at multiple scales, carbonate rocks present a great challenge for studying and managing oil reservoirs. Depositional processes and diagenetic alterations of carbonates may have produced very complex pore structures and, consequently, variable fluid storage and flow properties of hydrocarbon reservoirs. To understand the impact of mineralogy on the pore system, we analyzed four carbonate rock samples (coquinas) from the Morro do Chaves Formation in Brazil. For this study, we used thin sections and XRD for their mineralogical characterization, together with routine core analysis, NMR, MICP and microCT for the petrophysical characterizations. The samples revealed very similar porosity values but considerably different permeabilities. Samples with a relatively high quartz content (terrigenous material) generally had lower permeabilities, mostly caused by more mineral fragmentation. Samples with little or no quartz in turn exhibited high permeabilities due to less fragmentation and more diagenetic actions (e.g., dissolution of shells). Results confirm that carbonate minerals are very susceptible to diagenesis, leading to modifications in their pore body and pore throat sizes, and creating pores classified as moldic and vug pores, or even clogging them. For one of the samples, we acquired detailed pore skeleton information based on microCT images to obtain a more complete understanding of its structural characteristics

HYPROP measurements of the unsaturated hydraulic properties of a carbonate rock sample.

The unsaturated hydraulic properties provide important theoretical and practical information about fluid flow in soils and rocks for a range of soil, environmental and engineering applications. In this study we used the evaporation (HYPROP) and chilled-mirror dew point (WP4C) methods to estimate the water retention and unsaturated hydraulic conductivity curves of an Indiana Limestone carbonate rock sample. The obtained data were analyzed in terms of unimodal and bimodal VG (van Genuchten, 1980) and PDI (Peters et al., 2015) type functions. Bimodal functions were found to produce excellent descriptions for the unsaturated hydraulic data we measured, slightly better than the standard unimodal formulations. For our particular test using an Indiana Limestone rock sample, we did not find much improvement when accounting for film and corner flow using the PDI formulation, relative to the VG model. As far as we know, this is the first time the HYPROP methodology was applied to a rock sample