Hydrus-1D Tutorial Book
This tutorial book provides a series of example problems for version 4.16 of HYDRUS-1D, a software package for simulating water, heat and solute movement in one-dimensional variably saturated media. The objective of this introductory HYDRUS-1D tutorial is to give HYDRUS-1D users a first hands-on experience with the HYDRUS-1D software package and to familiarize themselves with the overall organization of the HYDRUS-1D graphical user interface, including the main input and output dialog windows.
- Example problems include variably-saturated water flow in single- and multi-layered soil profiles with and without root water uptake.
- Both short- and long-term climatic boundary conditions are considered, with a focus on calculating soil water balance and groundwater recharge.
- Subsequent examples deal with basic advective-dispersive solute transport without solid-liquid interactions, as well as more advanced contaminant transport problems involving linear or non-linear equilibrium sorption reactions and chemical non-equilibrium processes described using one-site sorption kinetics.
- Physical non-equilibrium (mobile-immobile water type) solute transport is also discussed, as well as the combined effect of physical and chemical non-equilibrium effects on solute transport (i.e., a mobile-immobile type model with two-site sorption in the mobile zone).
- Two inverse modelling examples consider one-step and multi-step outflow.
- The final example is about coupled heat movement and reactive solute transport.
- Rassam, D., J. Šimůnek, D. Mallants, and M. Th. van Genuchten, The HYDRUS-1D Software Package for Simulating the One-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Media: Tutorial, CSIRO Land and Water, Adelaide, Australia, 183 pp., ISBN 978-1-4863-1001-2, 2018.
Additional Hydrus-1D Tutorials
The purpose of this tutorial is to give users hands-on experience with the Hydrus-1D software package. Several examples are given to familiarize users with the major parts and modules of Hydrus-1D (e.g., the project manager, Profile and Graphics modules), and with the main concepts and procedures of pre- and post-processing (e.g., domain design, finite element discretization, initial and boundary conditions specification, and graphical display of results).
We encourage Hydrus-1D users to provide us with additional examples (e.g., helpful classroom exercises) that they believe could be included in later versions of this tutorial, or could be discusses in more detail in one of our short courses.
The following seven examples are presented here:
- Direct Problem: Infiltration into a one-dimensional soil profile
- Inverse Problem: One-step outflow method
- Water Flow and Solute Transport in a Layered Soil Profile
- Transport of a Volatile Solute
- HP1 (Hydrus-1D – PHREEQC) Tutorials I
- HP1 (Hydrus-1D – PHREEQC) Tutorials II
- Coupled Water, Vapor and Heat Transport
- Nonequilibrium Water Flow and Solute Transport
- Modeling Salinity with the Standard and UnsatChem Modules of HYDRUS-1D
- Running the computational module of Hydrus-1D from Matlab
1. Direct Problem: Infiltration into a one-dimensional soil profile
This example represents the direct problem of infiltration into a one-meter deep loamy soil profile. The one-dimensional profile is discretized using 101 nodes. Infiltration is run for one day. Ponded infiltration is initiated with a 1-cm constant pressure head at the soil surface, while free drainage is used at the bottom of the soil profile. The example is divided into three parts: (A) first, only water flow is considered, after which (B) solute transport is added. Several other modifications are suggested in part (C). These include (1) a longer simulation time, (2) considering solute retardation, (3) using a two-layered soil profile, and (4) implementing alternative spatial discretization. Users in this example become familiar with most dialog windows of the main module, and get an introduction into using the external graphical Profile module in which one specifies initial conditions, selects observation nodes, and so on.
- Water flow
- Solute transport
- Possible additional modifications
2. Inverse Problem: One-step outflow method
This second example considers the inverse solution of a one-step outflow experiment. Data presented by Kool et al. [1985], and used in example 6 of the Hydrus-1D manual (p. 102), are used in the analysis. Three hydraulic parameters were estimated by numerical inversion of the observed cumulative outflow and the measured water content at a pressure head of -150 m. Since water exits the soil column across a ceramic plate, the flow problem involves a two-layered system. The profile, consists of a 3.95-cm long soil sample and a 0.57-cm thick ceramic plate, and is discretized using 50 nodes, of which five nodes represent the ceramic plate. Only a few nodes were used for the ceramic plate since the plate remains saturated during the entire experiment, thus causing the flow process in the plate to be linear. Outflow is initiated using a pressure head of -10 m imposed on the lower boundary. Details about this inverse problem are given in the Hydrus-1D manual.
- Water flow
3. Water Flow and Solute Transport in a Layered Soil Profile
In this tutorial with Hydrus-1D we consider water flow and the transport of tracers and adsorbing chemicals through a Podzol soil profile. The tutorial is divided into two parts. In the first part (II) only water flow is simulated, while in the second part (I) solute transport is additionally considered. Examples in the first part of this tutorial involve both steady-state and transient variably saturated flow in a 1-m deep multi-layered soil profile. Transient flow is induced by atmospheric boundary conditions. No root water uptake is considered, thus restricting the atmospheric boundary conditions to daily values of precipitation and evaporation.
In the second part of the tutorial we use the project created in the first part of the tutorial and assume that there is a spill of a chemical on the first day of simulation at the soil surface. The example is divided into three parts, each of increasing complexity.
- Tracer Transport
- Reactive Chemical Transport
- Transport of PCE and its Daughter Product
For the first run we assume that a nonreactive chemical is spilled on the soil surface. The second and third runs consider the transport of a reactive chemical and that of PCE and its degradation products, respectively. PCE degrades to sequentially form trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-DCE), trans-1,2-dichloroethylene (trans-DCE), 1,1-dichloroethylene (1,1-DCE), vinyl chloride (VC) (after Schaerlaekens et al., 1999). VC eventually degrades to ethylene (ETH) which is environmentally acceptable and does not cause direct health effects.
4. Transport of a Volatile Solute
In this computer session with Hydrus-1D we consider transport of a volatile solute that is initially injected into the homogeneous soil profile. Different treatments of the soil surface (small resistance to volatilization, high resistance, sealing of the soil surface by irrigation) are considered. The effect of the heat transport on solute transport and reactions is also evaluated. Transient flow is induced by atmospheric boundary conditions. No root water uptake is considered, thus restricting the atmospheric boundary conditions to daily values of evaporation and irrigation. The example is divided into four parts:
- Small surface resistance to volatilization
- High surface resistance (tarp) to volatilization
- Partial sealing of the soil surface by irrigation
- Effects of heat transport on solute transport and reactions.
5. HP1 (Hydrus-1D – PHREEQC) Tutorials I
Note that these examples have been developed for earlier versions of the HYDRUS-1D GUI, which required specification of initial and boundary conditions in terms of concentrations and the use of the PHREEQC GUI to prepare the PHREEEQC.in input file, i.e., prior to the release of version 4.13, in which all inputs, including the PHREEQC.in input file, are prepared directly in the HYDRUS-1D GUI.
Four tutorials have been developed to demonstrate the use of the HP1 program. These tutorials address the following processes:
- Transient Flow and Cation Exchange
- Kinetic PCE Degradation Network
- U surface complexation
- Horizontal Infiltration of Multiple Cations and Cation Exchange
The first HP1 tutorial describes leaching of Cd from an initially dry loamy soil sample of 50-cm. The adsorption process of Cd is described as cation exchange with other cations (Jacques et al., 2008). Following elements are considered: Br, Ca, Cd, Cl, K, Mg, and Na.
The second HP1 tutorial considers transport of PCE and its Daughter Product. PCE degrades to sequentially form trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-DCE), trans-1,2-dichloroethylene (trans-DCE), 1,1-dichloroethylene (1,1-DCE), and vinyl chloride (VC) (after Schaerlaekens et al., 1999). VC eventually degrades to ethylene (ETH), which is environmentally acceptable and does not cause direct health effects. This tutorial demonstrates that, unlike Hydrus-1D, HP1 can consider diverging and converging solute branches and does not need to lump all DCE species into a single constituent. The third HP1 tutorial simulates the leaching of U under saturated, steady-state flow conditions. U adsorbs on Fe-oxides in the soil profile. The following elements are considered: Ca, Cl, K, Mg, Na, U(6) and C(4). In this pH-sensitive geochemical transport problem, U adsorption is described by a non-electrostatic surface complexation model.
Finally, the fourth HP1 tutorial simulates horizontal infiltration of multiple cations (Ca, Na, and K) into the initially dry soil column. It is based vaguely on experimental data presented by Smiles and Smith [2004]. The cation exchange between particular cations is described using the Gapon Exchange equation.
6. HP1 (Hydrus-1D – PHREEQC) Tutorials II
Note that these examples have been developed for the version 4.13 (and later) of the HYDRUS-1D GUI, which allows specification of initial and boundary conditions in terms of either concentrations or solution compositions and does not require an independent use of the PHREEQC.GUI.
Four tutorials have been developed to demonstrate the use of the HP1 program. These tutorials address the following processes:
- Transport and Dissolution of Gypsum and Calcite
- Transport and Cation Exchange (a single pulse)
- Transport and Cation Exchange (multiple pulses)
- Horizontal Infiltration of Multiple Cations and Cation Exchange
The first HP1 tutorial describes infiltraton of sulfate-free water into a 50-cm long homogeneous soil column under steady-state saturated flow conditions. The reactive minerals present in the soil column are calcite and gypsum.
The second HP1 tutorial was adapted from Example 11 of the PHREEQC manual [Parkhurst and Appelo, 1999]. It simulates the chemical composition of the effluent from an 8-cm column containing a cation exchanger. The column initially contains a Na-K-NO3 solution in equilibrium with the cation exchanger. The column is flushed with three pore volumes of a CaCl2 solution. Ca, K and Na are at all times in equilibrium with the exchanger.
The third HP1 tutorial is the same as the second tutorial, except that time variable concentrations are applied at the soil surface.
Finally, the fourth HP1 tutorial simulates horizontal infiltration of multiple cations (Ca, Na, and K) into the initially dry soil column. It is based vaguely on experimental data presented by Smiles and Smith [2004]. The cation exchange between particular cations is described using the Gapon Exchange equation.
7. Coupled Water, Vapor and Heat Transport
In this Tutorial we demonstrate Hydrus-1D‘s ability to simulate to simulate coupled water, vapor, and heat transport. Water contents, total fluxes, temperatures, and concentration profiles are calculated for a 10-cm long soil sample with zero water fluxes at both the top and bottom boundaries, and with a specified temperature gradient along the sample. The example is based vaguely on experimental data presented Nasar and Horton) 1992).
Increasing temperatures from the top to the bottom of the sample cause vapor flow from the warmer bottom end toward the colder end. Water evaporates at the warmer end, flows upward as vapor and condensates at the colder end. Water contents correspondingly decrease at the warmer end, and increase at the colder bottom. As a consequence of changing water contents, a pressure head gradient develops in the sample, leading to water flow in a direction opposite to vapor flow. A steady-state is eventually reached when upward vapor flow fully balances downward liquid flow. Since water evaporates at the bottom of the sample and condensates at the top, solute becomes more concentrated near the bottom and more diluted near the top. Also, the concentration profile should eventually reach steady-state, although at a much later time, when the downward advective solute flux balances the upward diffusive flux.
8. Nonequilibrium Water Flow and Solute Transport
In this tutorial we demonstrate HYDRUS-1D‘s capacity to simulate nonequilibrium water flow and solute transport using the dual-porosity model. The dual-porosity model is demonstrated using ponded infiltration into a 60-cm deep soil profile. We assume that the water mass transfer between two pore domains is proportional to the gradient of effective saturations in the two domains. For simplicity, we consider only convective solute mass transfer between the two pore regions (i.e. no diffusive transfer), with the dispersivity again fixed at 2 cm.
9. Modeling Salinity with the Standard and UnsatChem Modules of HYDRUS-1D
In these two tutorials we demonstrate the use of the standard and UnsatChem modules of HYDRUS-1D to simulate water and solute transport using two different approaches. The first approach is based on the assumption that electric conductivity, EC (dS/m), behaves as a conservative tracer and can thus be simulated using the standard module of HYDRUS-1D. The second, much more complex approach, uses the UnsatChem module and considers the fate and transport of major ions, and their mutual reactions, such as cation exchange, precipitation/dissolution of solid phases, such as calcite and gypsum.
The two tutorials are partly based on examples listed at the HYDRUS website (Portugal), which were used to evaluate experimental data from lysimeter studies reported by Ramos et al. (2011). These examples can be freely downloaded. Selected input parameters for one year of these examples are given in the "HYDRUS Example Input.xlsx" file.
The HYDRUS-1D software package is used to simulate water movement and solute transport in two complex experiments carried out under field conditions in Alvalade and Mitra, Portugal. The experiments involved irrigating maize with synthetic saline irrigation waters blended with fresh irrigation waters. The major ion chemistry module of HYDRUS-1D was used to model water contents, the overall salinity given by the electrical conductivity of the soil solution (ECsw), the concentration of soluble cations Na+, Ca2+, Mg2+, and SAR in different experimental plots. The standard HYDRUS solute transport module was also used to simulate the overall salinity. Details about the experiment, experimental data, model input parameters, and experimental and model results are given in Ramos et al. (2011). HYDRUS-1D proved to be a powerful tool for analyzing solute concentrations related to overall soil salinity and nitrogen species.
While Ramos et al. (2011) describes experimental data for three years, the tutorials below are set up for a one year long time period.
Ramos, T. B., J. Šimůnek, M. C. Gonçalves, J. C. Martins, A. Prazeres, N. L. Castanheira, and L. S. Pereira, Field evaluation of a multicomponent solute transport model in soils irrigated with saline waters, J. of Hydrology, 407(1-4), 129-144, 2011.
10. Running the computational module of Hydrus-1D from Matlab
Stathis Diamantopoulos has prepared a tutorial demonstrating the use of Matlab to run the computational module of HYDRUS-1D. Download the text of the tutorial and the test example.
We believe that by following these examples, Hydrus-1D users will obtain the basic skills necessary to solve their own problems. We wish you all the luck and patience needed in this endeavor.