HYDRUS Description
HYDRUS is a Microsoft Windows based modeling environment for the analysis of water flow and solute transport in variably saturated porous media. The software package includes computational finite element models for simulating the one-, two-, and three-dimensional movement of water, heat, and multiple solutes in variably saturated media. The model includes a parameter optimization algorithm for inverse estimation of a variety of soil hydraulic and/or solute transport parameters (only for the standard modules). The model is supported by an interactive graphics-based interface for data-preprocessing, generation of structured and unstructured finite element mesh, and graphic presentation of the results. The program can be extended with a number of special add-on modules. HYDRUS version 5 was released in April 2022 and it merges two previously independent software packages HYDRUS-1D (version 4, for one-dimensional applications) and HYDRUS (2D/3D) (version 3, for two- and three-dimensional applications).
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HYDRUS Editions / Levels
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HYDRUS is distributed in multiple different versions (Editions / Levels) so that users may acquire only that segment of the software that is most appropriate for their application. Users can select software limited to one-dimensional applications (the 1D-Standard Level), general two-dimensional applications (the 2D-Standard Level, which corresponds with former Hydrus-2D with MeshGen-2D) or for both two- and three-dimensional applications (i.e., 3D-Standard or 3D-Professional). Users can also opt for relatively simple (two-dimensional rectangular geometries – 2D-Lite [which corresponds with former Hydrus-2D without MeshGen-2D] or three-dimensional hexahedral geometries – 3D-Lite) or more complex geometries (i.e., 2D-Standard for general two-dimensional geometries, 3D-Standard for problems that can be defined using the general two-dimensional base and a layered third dimension, or 3D-Professional for applications with general three-dimensional geometries). Users may upgrade to higher Levels from lower Levels, as well as from lower versions (e.g., version 1.x) to higher versions (e.g., version 2 (and higher - in the future)).
Standard Computational Models
The HYDRUS program is a finite element model for simulating the one-, two-, and three-dimensional movement of water, heat, and multiple solutes in variably saturated media. The HYDRUS program numerically solves the Richards equation for saturated-unsaturated water flow and convection-dispersion type equations for heat and solute transport. The flow equation incorporates a sink term to account for water uptake by plant roots. The heat transport equation considers movement by conduction as well as convection with flowing water. The governing convection-dispersion solute transport equations are written in a very general form by including provisions for nonlinear nonequilibrium reactions between the solid and liquid phases, and linear equilibrium reaction between the liquid and gaseous phases. Hence, both adsorbed and volatile solutes, such as pesticides, can be considered. The solute transport equations also incorporate the effects of zero-order production, first-order degradation independent of other solutes, and first-order decay/production reactions that provide the required coupling between the solutes involved in the sequential first-order chain. The transport models also account for convection and dispersion in the liquid phase, as well as diffusion in the gas phase, thus permitting the model to simulate solute transport simultaneously in both the liquid and gaseous phases. At present, HYDRUS considers up to fifteen solutes, which can either be coupled in a unidirectional chain or move independently of each other. Physical nonequilibrium solute transport can be accounted for by assuming a two-region, dual porosity type formulation, which partitions the liquid phase into mobile and immobile regions. Attachment/detachment theory, including the filtration theory, is included to simulate transport of viruses, colloids, and/or bacteria.
The program may be used to analyze water and solute movement in unsaturated, partially saturated, or fully saturated porous media. HYDRUS can handle flow domains delineated by irregular boundaries. The flow region itself may be composed of nonuniform soils having an arbitrary degree of local anisotropy. Flow and transport can occur in the vertical plane, the horizontal plane, a three-dimensional region exhibiting radial symmetry about a vertical axis, or in a three-dimensional region.
The water flow part of the model can deal with (constant or time-varying) prescribed head and flux boundaries, as well as boundaries controlled by atmospheric conditions. Soil surface boundary conditions may change during the simulation from prescribed flux to prescribed head type conditions (and vice versa). The code can also handle a seepage face boundary, through which water leaves the saturated part of the flow domain, and free drainage boundary conditions. Nodal drains are represented by a simple relationship derived from analog experiments.
For solute transport, the code supports both (constant and varying) prescribed concentration (Dirichlet or first-type) and concentration flux (Cauchy or third-type) boundaries. The dispersion tensor includes a term reflecting the effects of molecular diffusion and tortuosity.
The unsaturated soil hydraulic properties are described using van Genuchten [1980], Brooks and Corey [1964], Durner [1994], Kosugi [1995], and modified van Genuchten type analytical functions. Modifications were made to improve the description of hydraulic properties near saturation. The HYDRUS code incorporates hysteresis by using the empirical model introduced by Scott et al. [1983] and Kool and Parker [1987]. This model assumes that drying scanning curves are scaled from the main drying curve, and wetting scanning curves from the main wetting curve. As an alternative, we also incorporated the hysteresis model of Lenhard et al. [1991] and Lenhard and Parker [1992], which eliminates pumping by keeping track of historical reversal points, into HYDRUS. HYDRUS also implements a scaling procedure to approximate hydraulic variability in a given soil profile by means of a set of linear scaling transformations that relate the individual soil hydraulic characteristics to those of a reference soil.
The governing equations are solved numerically using a Galerkin type linear finite element method applied to a network of triangular elements. Integration in time is achieved using an implicit (backwards) finite difference scheme for both saturated and unsaturated conditions. The resulting equations are solved in an iterative fashion, by linearization and subsequent Gaussian elimination for banded matrices, a conjugate gradient method for symmetric matrices, or the ORTHOMIN method for asymmetric matrices. Additional measures are taken to improve solution efficiency in transient problems, including automatic time step adjustment and ensuring that the Courant and Peclet numbers do not exceed preset levels. The water content term is evaluated using the mass-conservative method proposed by Celia et al. (1990). To minimize numerical oscillations upstream weighing is included as an option for solving the transport equation.
In addition, HYDRUS implements a Marquardt-Levenberg type parameter estimation technique for the inverse estimation of selected soil hydraulic and/or solute transport and reaction parameters from measured transient or steady-state flow and/or transport data (only for the standard modules). The procedure permits several unknown parameters to be estimated from observed water contents, pressure heads, concentrations, and/or instantaneous or cumulative boundary fluxes (e.g., infiltration or outflow data). Additional retention or hydraulic conductivity data, as well as a penalty function for constraining the optimized parameters to remain in some feasible region (Bayesian estimation), can be included in the parameter estimation procedure.
Reasons for using HYDRUS models:
- The HYDRUS software has been developed by leading (award winning) scientists in the field of vadose zone hydrology (Rien van Genuchten and Jirka Simunek). Note that both of them are Fellows of AGU (American Geophysical Union), AAAS (American Association for Advancement of Science, SSSA (Soil Science Society of America) and ASA (American Society of Agronomy), which are the highest awards given by these respective societies. Both these scientists are one of the most widely cited researchers in their field of science, having an h-index of 66 and 56 (in 2018), respectively, and tens of thousands of citations (both according to Web of Knowledge). Always at the cutting edge of the most recent developments in vadose zone hydrology.
- The HYDRUS software is considered to be a standard tool in both research and industrial applications. The two manuscripts describing the history of the development, recent applications and latest developments:
Šimůnek, J., M. Th. van Genuchten, and M. Šejna, Recent developments and applications of the HYDRUS computer software packages, Vadose Zone Journal, 15(7), pp. 25, doi: 10.2136/vzj2016.04.0033, 2016. (Hot paper according to Web of Knowledge (ISI))
Šimůnek, J., M. Th. van Genuchten, and M. Šejna, Development and applications of the HYDRUS and STANMOD software packages, and related codes, Vadose Zone Journal, doi:10.2136/VZJ2007.0077, Special Issue “Vadose Zone Modeling”, 7(2), 587-600, 2008. (Highly cited paper according to Web of Knowledge (ISI))
According to the Web of Knowledge (ISI), the “Highly Cited” or “Hot” manuscripts are manuscripts that has received enough citations to place them in the top of either 1% or 0.1% of papers in their field, respectively. - The HYDRUS software is used by thousands of users around the world (over ten thousand of downloads in 2017 alone, and many more before and since then), including leading research institutions, regulatory agencies, and consulting companies.
- The HYDRUS software has been used in thousands of successful applications published in peer-reviewed journal articles (1D, 2D, and 3D). There exist many successful examples of HYDRUS verifications and validations.
- There are hundreds of resolved problems in the HYDRUS public library of projects (1D, 2D, and 3D), from which HYDRUS users can learn how to use HYDRUS in their particular applications.
- The HYDRUS software is easy to use and learn as there are the many free 1D and 2D, and 3D tutorials. Both HYDRUS developers are organizing short courses organized around the world. Also see the recently released HYDRUS textbook and HYDRUS Tutorial eBook.
- There are thousands of registered users in HYDRUS discussion forums allowing them to share their experience and learn from others.
- The HYDRUS software has been linked to other widely used programs in their respective fields of applications (e.g., MODFLOW, PHREEQC, Wetland Module, DSSAT, and Rosetta).
- No other software for subsurface hydrology can match any of these accomplishments.
Main References:
- Šimůnek, J., M. Šejna, and M. Th. van Genuchten, New Features of the Version 3 of the HYDRUS (2D/3D) Computer Software Package, Journal of Hydrology and Hydromechanics, 66(2), 133-142, doi: 10.1515/johh-2017-0050, 2018.
- Šimůnek, J., M. Th. van Genuchten, and M. Šejna, Recent developments and applications of the HYDRUS computer software packages, Vadose Zone Journal, 15(7), pp. 25, doi: 10.2136/vzj2016.04.0033, 2016. (Hot paper according to Web of Knowledge (ISI))
- Šimůnek, J., D. Jacques, G. Langergraber, S. A. Bradford, miroslav-sejna M. Šejna, and M. Th. van Genuchten, Numerical modeling of contaminant transport with HYDRUS and its specialized modules, Invited paper for the Special Issue "Water Management in Changing Environment", Editor M. S. Mohan Kumar, Journal of the Indian Institute of Science, 93(2) 265-284, ISSN: 0970-4140 Coden-JIISAD, 2013.
- Šimůnek, J., M. Th. van Genuchten, and M. Šejna, HYDRUS: Model use, calibration and validation, Special issue on Standard/Engineering Procedures for Model Calibration and Validation, Transactions of the ASABE, 55(4), 1261-1274, 2012.
- Šimůnek, J., M. Th. van Genuchten, and M. Šejna, Development and applications of the HYDRUS and STANMOD software packages, and related codes, Vadose Zone Journal, doi:10.2136/VZJ2007.0077, Special Issue “Vadose Zone Modeling”, 7(2), 587-600, 2008. Download PDF (2MB). (Highly cited paper according to Web of Knowledge (ISI))
- Šimůnek, J. and M. Th. van Genuchten, Modeling nonequilibrium flow and transport with HYDRUS, Vadose Zone Journal, doi:10.2136/VZJ2007.0074, Special Issue “Vadose Zone Modeling”, 7(2), 782-797, 2008. Download PDF (2MB).
- Jacques, D., J. Šimůnek, D. Mallants, and M. Th. van Genuchten, Modeling coupled hydrological and chemical processes: Long-term uranium transport following mineral phosphorus fertilization, Vadose Zone Journal, doi:10.2136/VZJ2007.0084, Special Issue “Vadose Zone Modeling”, 7(2), 698-711, 2008.Download PDF (2MB).
Manuals:
- Šimůnek, J., M. Šejna, G. Brunetti, and M. Th. van Genuchten, The HYDRUS Software Package for Simulating the One-, Two, and Three-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably Saturated Media, Technical Manual I, Hydrus 1D, Version 5.0, PC Progress, Prague, Czech Republic, 334p., 2022. (PDF 3.9MB)
- Šimůnek, J., M. Th. van Genuchten, and M. Šejna, The HYDRUS Software Package for Simulating One-, Two-, and Three-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Porous Media, Technical Manual II, Hydrus 2D/3D. Version 5.0, PC Progress, Prague, Czech Republic, 283 p., 2022. (PDF 3.6MB)
- Šejna, M., J. Šimůnek, and M. Th. van Genuchten, The HYDRUS Software Package for Simulating One-, Two- and Three-Dimensional Movement of Water, Heat, and Multiple Solutes in Variably-Saturated Porous Media, User Manual, Version 5.0, PC Progress, Prague, Czech Republic, 348 p., 2022. (PDF 9.6MB)
- Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The C-Ride Module for HYDRUS-1D Simulating One-Dimensional Colloid-Facilitated Solute Transport in Variably-Saturated Porous Media, Version 2.0, PC Progress, Prague, Czech Republic, 45 pp., 2022. (PDF, 0.8 MB)
- Brunetti, G., J. Šimůnek, R. Kodešova, and M. Šejna, The Dynamic Plant Uptake Module for HYDRUS Simulating the Translocation and Transformation of Neutral Compounds in the Soil-Plant Continuum, Version 1.0, PC Progress, Prague, Czech Republic, 29 pp., 2022. (PDF, 1.3 MB)
- Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The UNSATCHEM Module for HYDRUS (2D/3D) Simulating Two- and Three-Dimensional Movement of and Reactions Between Major Ions in Soils, Version 3.0, PC Progress, Prague, Czech Republic, 54 pp., 2022. (PDF, 1.1 MB)
- Brunetti, G., J. Šimůnek, and M. Šejna, The Furrow Module for HYDRUS (2D/3D) Simulating Water Flow and Solute Transport in a Pseudo-Three-Dimensional Furrow Irrigation System, Version 1.0, PC Progress, Prague, Czech Republic, 43 pp., 2019 (Version 2.0, 2022).
- Šimůnek, J., D. Jacques, M. Šejna, and M. Th. van Genuchten, The HP2 Program for HYDRUS (2D/3D): A Coupled Code for Simulating Two-Dimensional Variably-Saturated Water Flow, Heat Transport, and Biogeochemistry in Porous Media, Version 1.0, PC Progress, Prague, Czech Republic, 78 pp., 2012. (pdf 2.0MB)
- Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The C-Ride Module for HYDRUS (2D/3D) Simulating Two-Dimensional Colloid-Facilitated Solute Transport in Variably-Saturated Porous Media, Version 1.0, PC Progress, Prague, Czech Republic, 45 pp., 2012. (pdf 0.75MB)
- Šimůnek, J., M. Šejna, and M. Th. van Genuchten, The DualPerm Module for HYDRUS (2D/3D) Simulating Two-Dimensional Water Movement and Solute Transport in Dual-Permeability Porous Media, Version 1.0, PC Progress, Prague, Czech Republic, 32 pp., 2012. (pdf 0.6MB)
- Langergraber, G., and J. Šimůnek, The HYDRUS Wetlands Module, Version 2, HYDRUS Software Series 4, Department of Environmental Sciences, University of California Riverside, Riverside, CA, 56 pp., 2011. (PDF 1.4MB)
- Jacques, D., and J. Šimůnek, Notes on HP1 – a software package for simulating variably-saturated water flow, heat transport, solute transport and biogeochemistry in porous media, HP1 Version 2.2, SCK•CEN-BLG-1068, Waste and Disposal, SCK•CEN, Mol, Belgium, 113 pp., 2010.
- Šimůnek, J., M. Šejna, H. Saito, M. Sakai, and M. Th. van Genuchten, The Hydrus-1D Software Package for Simulating the Movement of Water, Heat, and Multiple Solutes in Variably Saturated Media, Version 4.0, HYDRUS Software Series 3, Department of Environmental Sciences, University of California Riverside, Riverside, California, USA, pp. 315, 2008.
- Langergraber, G., and J. Šimůnek, The Multi-component Reactive Transport Module CW2D for Constructed Wetlands for the HYDRUS Software Package, Manual – Version 1.0, HYDRUS Software Series 2, Department of Environmental Sciences, University of California Riverside, Riverside, CA, 72 pp., 2006.
Graphical User Interface
A Microsoft Windows based Graphical User Interface (GUI) manages the inputs required to run HYDRUS, as well as grid design and editing, parameter allocation, problem execution, and visualization of results. The program includes a set of controls that allows the user to build a flow and transport model, and to perform graphical analyses on the fly. Both input and output can be examined using spatial or cross-sectional views and line graphs. The main program unit of the HYDRUS Graphical User Interface defines the overall computational environment of the system. This main module controls execution of the program and determines which other optional tools are necessary for a particular application. The module contains a project manager and both the pre-processing and post-processing units. The pre-processing unit includes specification of all necessary parameters to successfully run the HYDRUS FORTRAN codes, grid generators for relatively simple rectangular and hexahedral transport domains, a grid generator for unstructured finite element meshes for complex two- and three-dimensional domains, a small catalog of soil hydraulic properties, and a Rosetta Lite program for generating soil hydraulic properties from soil textural data.
Automatic FE-Mesh Generation
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Data preprocessing involves specification of the two-dimensional flow region having an arbitrary continuous shape bounded by polylines, arcs, and splines, discretization of domain boundaries, and subsequent generation of an unstructured finite element mesh. HYDRUS (Standard Levels) comes with an optional mesh generation program, Meshgen, which generates an unstructured finite element mesh for two-dimensional domains. This program, based on the Delaunay triangulation, is seamlessly integrated into the HYDRUS environment. In the absence of the Meshgen program, the HYDRUS GUI provides an option for automatic construction of simple, structured grids (Lite Levels). The third dimension is developed in both the Lite and Standard levels by adding specified number of layers of equal or different thicknesses. HYDRUS 3D-Professional comes with a tree-dimensional mesh generation programs (GENEX and T3D), which generate an unstructured finite element mesh for general three-dimensional domains.
Post-Processing
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Output graphics include 2D contours (isolines or color spectra) in spatial or cross-sectional view for heads, water contents, velocities, concentrations, and temperatures. Output also includes velocity vector plots, color edges, color points, animation of graphic displays for sequential time-steps, and line-graphs for selected boundary or internal sections. The post-processing unit also includes simple x-y graphics for a graphical presentation of soil hydraulic properties, as well as such output as distributions versus time of a particular variable at selected observation points, and actual or cumulative water and solute fluxes across boundaries of a particular type. Areas of interest can be zoomed in on, and the vertical scale can be enlarged for cross-sectional views. The mesh can be displayed with boundaries, and numbering of triangles, edges and points. Observation points can be added anywhere in the grid. Viewing of grid and/or spatially distributed results (for pressure heads, water contents, velocities, concentrations, and temperatures) is facilitated using high resolution color or gray scales. An extensive and context-sensitive online Help is part of the interface.
Domain and FE-Mesh Sections
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To simplify the work with complex transport geometries, these can be divided into simpler parts, called Sections. Only these simpler parts can then be displayed in the View Window, while the remaining parts can be hidden. Two types of sections exist: those for geometric objects and those for the FE-Mesh. Multiple Sections can be displayed simultaneously. Undesired (to be displayed) parts of the transport domain can be cut off and hidden from the View window using various commands.
System Requirements
Applies to the latest version HYDRUS 5.x. Please note that older versions of HYDRUS (versions 1.x - 3.x) are no longer maintained and may be incompatible with the latest Windows operating systems.
Minimum System Requirements:
- Operating Systems:
- Windows 11 (64-bit)
- Windows 10 (64-bit)
- Windows 8 (64-bit)
- X64 CPU with 2 GHz
- 2 GB RAM
- 10 GB total hard disk capacity with about 500 MB reserved for installation
- Graphic card with a resolution of 1280 x 800 pixels
Recommended System Configuration:
To use HYDRUS comfortably for calculations of 3D models, we recommend the following system requirements:
- Operating System Windows 11 (64-bit)
- CPU: 4-core or better. The single-core performance is more important than the number of cores.
- RAM: 16 GB or better
- 500 GB hard disk capacity
- Graphics: resolution 1920x1200 or better, a good graphic card with OpenGL support - ATI/NVIDIA