The HP2 Programfor

HYDRUS (2D/3D)
A Coupled Code for Simulating Two-Dimensional VariablySaturated Water Flow, Head Transport, Solute Transportand Biogeochemistry in Porous Media(HYDRUS + PHREEQC + 2D)
Version 1.0

Jirka Šimůnek1, Diederik Jacques2, Miroslav Šejna3, and Martinus Th. van Genuchten4
September 2012
1

Department of Environmental Sciences
University of California Riverside
Riverside, CA, 92521, USA

2

Performance Assessments, Belgian Nuclear Research Institute SCK•CEN,
BE-2400 Mol, Belgium
3

PC Progress, Ltd.
Prague, Czech Republic
4

Department of Mechanical Engineering
Federal University of Rio de Janeiro
Rio de Janeiro, Brazil© 2012 J. Šimůnek and M. Šejna. All rights reserved.

2

Table of Contents
Table of Contents................................................................................................................................. 3
List of Figures ...................................................................................................................................... 5
List of Tables ........................................................................................................................................ 6
Abstract ................................................................................................................................................ 7
1. Introduction ..............................................................................................................................92. Running HP2 from the HYDRUS (2D/3D) Graphical User Interface ............................... 11
2.1.

Preprocessing and Input Data ..................................................................................112.1.1.

Main Processes .............................................................................................112.1.2.

Solute Transport - General Information .......................................................122.1.3.

HP2/3 Components and Database Pathway .................................................122.1.3.1. Thermodynamic Databases ............................................................13
2.1.3.2. Components....................................................................................142.1.4.

PH2/3 Definitions ..........................................................................................142.1.4.1. Additions to Thermodynamic Database ..........................................15
2.1.4.2. Definitions of Solution Compositions ..............................................16
2.1.4.3. Geochemical Model .......................................................................172.1.4.4. Additional Output...........................................................................172.2.

2.1.5.

Solute Transport Parameters ........................................................................20

2.1.6.

Solute Reaction Parameters ..........................................................................21

2.1.7.

Initial and Boundary Conditions ..................................................................20

2.1.8.

HP2 Print and Punch Controls .....................................................................20

Post-Processing...........................................................................................................25
2.2.1.

Results – Graphical Display .........................................................................25

2.2.2.

Results – Other Information..........................................................................25

3. Example Problems .................................................................................................................27
4. Step-by-Step Instructions for Selected Examples ...............................................................29
4.1.

4.2.

Example 1: Transport and Cation Exchange (Single Pulse) ....................................29
4.1.1.

Problem Definition........................................................................................30

4.1.2.

Input ..............................................................................................................30

4.1.3.

Output ...........................................................................................................36

Example 2: Transport and Cation Exchange (Multiple Pulses)...............................37

3

4.3.

4.4.

4.5.

4.2.1.

Problem Definition........................................................................................37

4.2.2.

Input ..............................................................................................................37

4.2.3.

Output ...........................................................................................................39

Example 3: Transport and Dissolution of Gypsum and Calcite ............................40
4.3.1.

Problem Definition........................................................................................40

4.3.2.

Input ..............................................................................................................40

4.3.3.

Output ...........................................................................................................44

Example 4: Furrow Irrigation with Cation Exchange..............................................48
4.4.1.

Problem Definition........................................................................................49

4.4.2.

Input ..............................................................................................................50

4.4.3.

Output ...........................................................................................................56

Example 5: Leaching of the Uranium Tailings ........................................................59
4.5.1.

Problem Definition........................................................................................59

4.5.2.

Input ..............................................................................................................61

4.5.3.

Output ...........................................................................................................73

References .....................................................................................................................................774

List of Figures
Figure 1.

The Main Processes dialog window. .......................................................................11

Figure 2.

The Solute Transport dialog window. .....................................................................12

Figure 3.

The HP2/3 Components and Database Pathway dialog window. ...........................13

Figure 4.

The HP2/3 Definitions dialog window (with a displayed Database Viewer). ........15

Figure 5.

The HP2 Definitions - Additions to Thermodynamic Database dialog window. .....16

Figure 6.

The HP2 Definitions - Definitions of Solution Compositions dialog window. ......17

Figure 7.

The HP2 Definitions - Geochemical Model dialog window. ..................................18

Figure 8.

The HP2 Definitions - Additional Output dialog window. .....................................19

Figure 9.

The Solute Transport Parameters dialog window. ..................................................20

Figure 10.

The Reaction Parameters for Solute -1 dialog window. ..........................................21

Figure 11.

The "Initial Conditions" part of Data Tab of the Navigator Bar for the HP2 module.
.................................................................................................................................22

Figure 12.

The HP2-related part of the Time-Variable Boundary Conditions dialog window.22

Figure 13.

The HP2- Print and Punch Controls dialog window. ..............................................23

Figure 14.

The "Results - Graphical Display" part of Data Tab of the Navigator Bar for the
HP2 module. ............................................................................................................25

Figure 15.

Outflow concentrations of Cl, Ca, Na and K for the single-pulse cation exchange
example. ..................................................................................................................36

Figure 16.

Time series of K concentrations at four depths for the multiple-pulse cationexchange example. ..................................................................................................39

Figure 17.

Outflow concentrations for the multiple-pulse cation exchange example. .............39

Figure 18.

Vertical profiles of pH (top left), total aqueous C concentration (top right), total
aqueous Ca concentration (middle left), total aqueous S concentration (middle
right), the amount of gypsum (bottom left) and the amount of calcite (bottom right)
at selected print times during dissolution of calcite and gypsum.. ..........................47

Figure 19.

Time series of pH (top left), total aqueous C concentration (top right), total
aqueous Ca concentration (middle left), total aqueous S concentration (middle
right), the amount of gypsum (bottom left) and the amount of calcite (bottom right)
at selected depths (observation nodes) during dissolution of calcite and gypsum.. 48

Figure 20.

Schematic representation and finite element mesh of the flow domain for the furrow
rrigation system for example 4. ................................................................................49

Figure 21.

Pressure head (cm) profiles at times: a) 0.1, b) 0.5, c) 1, and d) 2 days for example 4.
.................................................................................................................................56

Figure 22.

Chloride concentration profiles (mol L-1) at times: a) 0.1, b) 1, c) 3, and d) 5 days forexample 4. ................................................................................................................57

5

Figure 23.

Sodium concentration profiles (mol L-1) at times: a) 0.5, b) 1, c) 3, and d) 5 days forexample 4. ................................................................................................................57

Figure 24.

Exchangeable concentrations of sodium (mol kg-1) profiles at times: a) 0.5, b) 1, c)
3, and d) 5 days for example 4. ................................................................................58

Figure 25.

Description for the Uranium Tailing Problem [Yeh and Tripathi, 1991]................59

Figure 26.

The steady-state pressure head (cm) (top) and flux (cm/d) (bottom) profiles for theTailing Pile Leaching example. ...............................................................................74

Figure 27.

Uranium concentration profiles at time 0 (top), 250 (middle), and 500 d (bottom)
for Tailing Pile Leaching example. .........................................................................74

Figure 28.

pH (top), calcite (mol/L) (middle), and gypsum (mol/L) (bottom) profiles after
1000 d for the Tailing Pile Leaching example. .......................................................75

List of Tables
Table 1.

Soil specific solute transport parameters... ..................................................................20

Table 2.

List of test examples for the HP2 module.. ..................................................................27

Table 3.

Reaction network for the uranium tailing problem... ...................................................60

Table 4.

Initial and boundary compositions of recharge water and pore water in the tailings
and regions outside of the tailing for the uranium tailing problem..............................61

6

AbstractŠimůnek, 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.
This user manual documents the HP2 program that resulted from coupling Hydrus (its twodimensional part) with the PHREEQC geochemical code [Parkhurst and Appelo, 1999] tocreate this new comprehensive simulation tool (HP2 - acronym for HYDRUS-PHREEQC-2D),
corresponding to a similar one-dimensional module HP1 [Jacques and Šimůnek, 2005; Jacqueset al., 2006; Šimůnek et al., 2006, 2008). HP2 has, apart from the dimensionality (2D), thesame capabilities as HP1. HP2 contains modules simulating (1) transient water flow, (2) thetransport of multiple components, (3) mixed equilibrium/kinetic biogeochemical reactions, and(4) heat transport in two-dimensional variably-saturated porous media (soils). HP2 is thus asignificant expansion of the individual HYDRUS-2D and PHREEQC programs by preserving
most of their original features. The code still uses the Richards equation for simulating twodimensional variably-saturated water flow and advection-dispersion type equations for heat andsolute transport. However, the loosely coupled program can simulate also a broad range of lowtemperature biogeochemical reactions in water, the vadose zone and in ground water systems,
including interactions with minerals, gases, exchangers and sorption surfaces based onthermodynamic equilibrium, kinetic, or mixed equilibrium-kinetic reactions. HP2 (similarly asHP1) uses the operator-splitting approach with no iterations during one time step (a noniterative sequential modeling approach).
The HP2 code is fully incorporated into the HYDRUS (2D/3D) software package, and hence isinstalled automatically, together with selected examples, when one obtains HYDRUS (2D/3D)
and HP2 licenses and downloads HYDRUS from the Hydrus website.
The purpose of this report is to documents the HP2 program for the HYDRUS (2D/3D) software
package [Šimůnek et al., 2011; Šejna et al., 2011] simulating two-dimensional variably-saturated
water flow, heat transport, solute transport, and biogeochemistry. The HP2 module, as well as thedescription of the module in this report, is largely based on the earlier one-dimensional HP1 module
Jacques and Šimůnek [2005, 2010]. One can find additional useful information, especially related
to biogeochemical reactions, in the PHREEQC [Parkhurst and Appelo, 1999] and HP1 [Jacquesand Šimůnek, 2005, 2010] manuals. The report serves as both a Technical Manual and a User
Manual, as well as a reference document of the Graphical User Interface of HP2 related parts ofthe HYDRUS software package.

7

DISCLAIMER
The HP2 module was developed as a supplemental module of the HYDRUS (2D/3D) software
package to simulate the water flow, heat transport, solute transport, and biogeochemical reactions
in soils and groundwater. The software has been verified against selected test cases. However, nowarranty is given that the program is completely error-free. If you do encounter problems with thecode, find errors, or have suggestions for improvement, please contact the senior author at
Jirka Šimůnek
Tel/Fax: 1-951-827-7854
Email: jiri.simunek@ucr.edu

8

1. Introduction
This user manual documents the HP2 program that resulted from coupling Hydrus (its twodimensional part) with the PHREEQC geochemical code [Parkhurst and Appelo, 1999] tocreate this new comprehensive simulation tool (HP2 - acronym for HYDRUS-PHREEQC-2D),
corresponding to a similar one-dimensional module HP1 [Jacques and Šimůnek, 2005; Jacqueset al., 2006; Šimůnek et al., 2006, 2008). HP2 has, apart from the dimensionality (2D), thesame capabilities as HP1. HP2 contains modules simulating (1) transient water flow, (2) thetransport of multiple components, (3) mixed equilibrium/kinetic biogeochemical reactions, and(4) heat transport in two-dimensional variably-saturated porous media (soils). HP2 is thus asignificant expansion of the individual HYDRUS-2D and PHREEQC programs by preserving
most of their original features. The code still uses the Richards equation for simulating twodimensional variably-saturated water flow and advection-dispersion type equations for heat andsolute transport. However, the loosely coupled program can simulate also a broad range of lowtemperature biogeochemical reactions in water, the vadose zone and in ground water systems,
including interactions with minerals, gases, exchangers and sorption surfaces based onthermodynamic equilibrium, kinetic, or mixed equilibrium-kinetic reactions. HP2 (similarly asHP1) uses the operator-splitting approach with no iterations during one time step (a noniterative sequential modeling approach). Jacques et al. [2006] evaluated the accuracy of theoperator-splitting approach for a kinetic reaction network (i.e., sequential and parallel kinetic
degradation reactions) by comparing HP1 with an analytical solution for TCE-degradation, as
well as for mixed equilibrium and kinetic reactions involving different flow conditions (steadystate and transient).
Jacques and Šimůnek [2005], Šimůnek et al. [2006], Jacques et al. [2008ab], demonstrated theversatility of HP1 on several examples, which included a) the transport of heavy metals (Zn2+,
Pb2+, and Cd2+) subject to multiple cation exchange reactions, b) transport with mineraldissolution of amorphous SiO2 and gibbsite (Al(OH)3), c) heavy metal transport in a medium
with a pH-dependent cation exchange complex, d) infiltration of a hyperalkaline solution in aclay sample (this example considers kinetic precipitation-dissolution of kaolinite, illite, quartz,
calcite, dolomite, gypsum, hydrotalcite, and sepiolite), e) long-term transient flow and transportof major cations (Na+, K+, Ca2+, and Mg2+) and heavy metals (Cd2+, Zn2+, and Pb2+) in a soil
profile, f) cadmium leaching in acid sandy soils, g) radionuclide transport, and h) long term
uranium migration in agricultural field soils following mineral P-fertilization. Most of theseexamples have been rerun using HP2, which verified correct implementation of various
components of the coupled program.
The HP2 code is fully incorporated into the HYDRUS (2D/3D) software package, and hence isinstalled automatically, together with selected examples, when one obtains HYDRUS (2D/3D)
and HP2 licenses and downloads HYDRUS from the Hydrus website.
The main purpose of this report is to document a two-dimensional numerical module HP2 thatincorporates flow and transport processes, as well as biogeochemical reactions in variablysaturated porous media. HP2 was developed specifically for the HYDRUS (2D/3D) software
package [Šimůnek et al., 2011; Šejna et al., 2011]. The general conceptual basis of the module is9discussed in detail in reports of Jacques and Šimůnek [2005, 2010], and restated here for multidimensional systems.
The documentation in this report focuses mostly on implementation of the HP2 module into
HYDRUS (2D/3D). All processes related to variably-saturated water flow, heat transport, andsolute transport are described in detail in the HYDRUS (2D/3D) documentation [Šimůnek et al.,2011], and will not be repeated here. Similarly, processes and reactions related to biogeochemical
reactions are described in detail in the PHREEQC [Parkhurst and Apello, 1998] and HP1 [Jacquesand Šimůnek, 2005, 2010] manuals.
The HP2 module may be used to analyze water flow, solute movement, and biogeochemical
reactions in unsaturated, partially saturated, or fully saturated porous media. HP2 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 verticalplane, the horizontal plane, or in a three-dimensional region exhibiting radial symmetry about avertical axis. The water flow part of the model considers prescribed head and flux boundaries, aswell as boundaries controlled by atmospheric conditions.
The governing flow and transport equations are solved numerically using standard Galerkin-typelinear finite element schemes. The HP2 module is fully supported by the HYDRUS (2D/3D)
graphical user interface [Šejna et al., 2011]. Applications of the HP2 module are demonstrated
later in this report on several examples.

102. Running HP2 from the HYDRUS (2D/3D) Graphical User Interface
The HP2 code is fully incorporated into the HYDRUS (2D/3D) software package, and hence isinstalled automatically, together with selected examples, when one obtains HYDRUS (2D/3D)
and HP2 licenses and downloads HYDRUS from the Hydrus website. The documentation in thisreport focuses mostly on implementation of the HP2 module into HYDRUS (2D/3D). All processes
related to geometry design, finite element discretization, variably-saturated water flow, heattransport, solute transport, initial and boundary conditions are described in detail in the HYDRUS(2D/3D) documentation [Šimůnek et al., 2011; Šejan et al., 2011], and will not be repeated here.
Similarly, processes and reactions related to biogeochemical reactions are described in detail in the
PHREEQC [Parkhurst and Apello, 1998] and HP1 [Jacques and Šimůnek, 2005, 2010] manuals.
2.1. Preprocessing and Input Data
HP2 projects are managed in the same way as other HYDRUS (2D/3D) projects using the
Project Manager. The Project Manager is used to manage data of existing projects, and tolocate, open, delete, copy, or rename projects. A new HP2 project is created in the same as anyother HYDRUS (2D/3D) project, i.e., using the button "New" in the Project Manager. Since allother inputs, i.e., domain design, FE discretization, water flow and heat transport, are the same as
in standard HYDRUS (2D/3D) projects, only parts related specifically to HP2 are discussed
below.
2.1.1. Main Processes
The HP2 module is activated in the Main Processes window (Fig. 1) by selecting the Solute
Transport check box and the HP2 (Hydrus + Phreeqc) radio button.

Figure 1. The Main Processes dialog window.

112.1.2. Solute Transport - General Information
When the HP2 module is used, basic information needed for defining solute transport problem isentered in the Solute Transport dialog window displayed in Figure 2. Once the HP2 module isselected in the Main Processes window, large parts of the Solute Transport dialog window aredisabled, since they are not relevant to HP2. However, a user can still select the Space and Time
Weighting Schemes, and the Stability Criterion, which constraints the temporal discretization(see the HYDRUS Technical Manual). A user has to specify the Number of Solutes (i.e., main
HP2 components) and can select the tortuosity model (either Millington and Quirk [ 1961] or
Moldrup [1997, 2000] models can be used). Note that also Mass Units are disabled, sinceconcentrations are entered using PHREEQC conventions (i.e., many different types of units canbe used, such as mol/l, mmol/L, mg/L, µg/L, ppm, etc), and results are reported in mol/L (withthe assumption that 1 L water = 1 kg water).

Figure 2. The Solute Transport dialog window.

2.1.3.

HP2/3 Components and Database Pathway

The next window that appears is the HP2/3 Components and Database Pathway window (Fig.
3).

12Figure 3. The HP2/3 Components and Database Pathway dialog window.
Note that the option to specify initial and boundary conditions In Concentrations is disabled
and only Solution Compositions can be used for this purpose (In Solution Composition). Also,
the check box Create PHREEQC.IN file using HYDRUS GUI is selected by default. Although
the PHREEQC.In file can be created outside of the HYDRUS GUI (e.g., using specialized
PHREEQC GUIs), we do not recommend to do it that way. Both these options, as well as theformat of the structured phreeqc.in file, are discussed in detail by Jacques and Šimůnek [2010].
When the option In Solution Composition is selected together with the option Create
PHREEQC.IN file using HYDRUS GUI, then:• the phreeqc.in file (the file with the definition of the geochemical model) is a structured
file, which is created and can be modified using the HP2 Definitions dialog window (Fig.
4)• the composition of the initial and boundary solutions has to be defined in phreeqc.in
using specific solution composition numbers• the temporal variation of the boundary solutions is defined in the HYDRUS GUI by
specifying the solution composition number corresponding to the solution composition
number defined in phreeqc.in• the spatial distribution of the initial solutions is defined in the HYDRUS GUI by
specifying the solution composition number in the soil domain corresponding to thesolution composition number defined in phreeqc.in

2.1.3.1. Thermodynamic Databases
In the HP2/3 Components and Database Pathway window, users have to select thethermodynamic database to be used with HP2 calculations (Path to Folder with Thermodynamic
Databases; Fig. 2). Thermodynamic databases contain definitions of various chemical species
and thermodynamic constants for various chemical reactions, and related information (e.g.,temperature dependence, ion activity model, etc). Using the "Browse" button, it is possible to13

locate and select a thermodynamic database. Note that the format of the thermodynamic data inthe database must follow the conventions of PHREEQC (see PHREEQC-2 manual, Parkhurst
and Appelo, 1999). A number of thermodynamic databases (e.g., phreeqc.dat, wateq4f.dat,
minteq.dat, llnl.dat, ex15.dat, and others, typically included in the PHREEQC-2 program) areinstalled with HYDRUS into the ThermodynamicDB folder. Users can create and use their own
database files.
2.1.3.2. Components
The element names of components have to be listed in the Components column in the HP2/3
Components and Database Pathway dialog window. The number of components is specified in
the Solute Transport - General Information dialog window (Fig. 2).
Components must start with a capital letter and must be present as element_name in the
SOLUTION_MASTER_SPECIES keyword block of the thermodynamic database or in thephreeqc.in input file (which can be defined in the GUI in the editor Addition to the
Thermodynamic Database of the HP2/3 Definitions dialog window, Fig. 4). Three special
components are:
• Total_O: a component related to O(-2) that sums up all O(-2) in the aqueous species
except in H2O. It is recommended to include this component in each project.
• Total_H: a component related to H(1) that sums up all H(1) in the aqueous species
except in H2O. It is recommended to include this component in each project.
• Charge: a component related to the charge of the aqueous phase. This component
should be used when a non-electrical surface complexation model involving charged
species is used. In the non-electrical surface complexation model, positive or negative
charges on the surface are not compensated. Therefore the aqueous phase also has anegative or positive charge. Note that the complete system (surface + aqueous phase) ischarge balanced.
Each redox state of redox-sensitive components has to be defined as a component. Without avalence state, a redox-sensitive component will not be recognized. Thus, while Fe is not a valid
component, Fe(2) and Fe(3) are. HP2 will issue a warning when a component is present in the
aqueous phase during the geochemical calculations (with PHREEQC), but is not transported (i.e.,
when it is not defined as a component in the HP2/3 Components and Database Pathway dialog
windows; Fig. 3).
2.1.4. HP2/3 Definitions
The phreeqc.in file can be modified by users using the text editors in the HP2/3 Definitions
dialog window (Fig. 4). The HP2/3 Definitions dialog window has five pages that can beselected in the top left corner (List of Pages). The first four pages are four text editors using
which one can edit:(1) Additions to the Thermodynamic Database (section 2.1.4.1.),
14

(2) Definitions of Solution Compositions (section 2.1.4.2.),(3) Geochemical Model (section 2.1.4.3.), and(4) Additional Output (section 2.1.4.4.)
The fifth page (5 - Database Viewer) displays the selected database (e.g., PHREEQC.DAT) (Fig.
4).

Figure 4. The HP2/3 Definitions dialog window (with a displayed Database Viewer).
The section Keywords (double-click to insert) (bottom left part) offers the most commonlyused PHREEQC Keywords that are used in the four PHREEQC editors. The Keywords arehierarchically organized in a tree-like structure in seven main groups: Solution Definition,
Geochemical Model, Output, Chemical/Physical Reaction, Database, Advanced, andMiscellaneous. A single click opens a particular tree subsection, a double click copies theselected keyword to the Editor Window.

2.1.4.1. Additions to Thermodynamic Database
Additional thermodynamic definitions can be added to the phreeqc.in file (not to thethermodynamic database file itsel) using the editor Additions to Thermodynamic Database in
the HP2/3 Definitions dialog window (Fig. 4). Typical PHREEQC data blocks used here are(found under the Database group of the Keywords):••

SOLUTION_MASTER_SPECIESSOLUTION_SPECIES

15

•
•
•
•
•
•

PHASESEXCHANGE_MASTER_SPECIESEXCHANGE_SPECIESSURFACE_MASTER_SPECIESSURFACE_SPECIESRATESUsers are referred to the PHREEQC-2 manual [Parkhurst and Appelo, 1999] for the conventions
used for the input of thermodynamic data. An example of "Additions to Thermodynamic
Database" is shown in Figure 5, in which three SOLUTION_MASTER_SPECIES (U, S, and P),
7 SOLUTION_SPECIES (PO43-, SO42-, UO22+, CaPO4-, CaHPO4, (UO2)(OH)+, and (UO2)2(OH)22+, and 2 PHASES (gypsum and calcite) are defined.

Figure 5. The HP2 Definitions - Additions to Thermodynamic Database dialog window.
2.1.4.2. Definitions of Solution Compositions
Compositions of the initial and boundary solutions are defined using the editor Definitions of
Solution Compositions (Fig. 6) in the HP2/3 Definitions dialog window. Typical PHREEQC
data blocks are SOLUTION and SOLUTION_SPREAD. The solution number refers to thesolution composition numbers of the initial and boundary solutions defined in the Hydrus GUI.
A following solution composition numbering is used throughout this manual:

16

•
•
•

Numbers 1001 – 2000: to define initial solutions for the mobile water phase.
Numbers 2001 – 3000: to define initial solutions for the immobile water phase.
Numbers 3001 – 4000: to define boundary solutions

Note that these numbers should all be larger than the maximum number of FE nodes. Thus if thenumber of FE nodes is 10,000, numbers higher than 10,000 should be used to define the solution
compositions otherwise these elements will be linked to a specific FE node.
The initial conditions (spatial distribution of solution composition) are then defined directly
using the solution composition numbers. Similarly, boundary conditions are defined using thesolution composition numbers.
An example of a solution composition defined using concentrations of various components (i.e.,
Ca, C, U, P, S, and Fe) and in equilibrium with two phases (i.e., gypsum and calcite) is shown in
Figure 6.

Figure 6. The HP2 Definitions - Definitions of Solution Compositions dialog window.

2.1.4.3. Geochemical Model
The definition of the geochemical model is done using the editor Geochemical Model (Fig. 7) inthe HP2/3 Definitions dialog window and it typically involves the following PHREEQC data
blocks:

17

•
•
•
•
•

EXCHANGE
EQUILIBRIUM_PHASESSURFACEKINETICSSOLID_SOLUTIONSThe numbering of geochemical keywords must either refer to the node numbers, such as
EXCHANGE 1-102

or to a particular material as defined using the HYDRUS GUI, such as
EXCHANGE 1001

-material 1
While in the former case, if the material distribution is changed, the user must change thenumbering of the geochemical model as well, in the latter case, there is no need for that. Notethat the exchanger number for the latter case should again be larger than the number of FE nodes.
Figure 7 shows an example of the Geochemical Model, in which a pure phase assemblage withthree minerals (gypsum, calcite, and O2) are defined in nodes 1 through 202 using the data block
EQUILIBRIUM_PHASES. Cation exchange sites (EXCHANGE) with the cation exchange capacity X of
0.0011 mol/kg and with exchange sites in equilibrium with the solution composition 1001 aredefined are also defined.

Figure 7. The HP2 Definitions - Geochemical Model dialog window.

18

Additionally, the following two lines
reactive_transport-dimension 2
indicating to the PHREEQC part of the computational module that the application is twodimensional, should be written into this window. These two lines could be written to any part of
the PHREEQC.in file, but we recommend to place them here.
Using the commands at the bottom of the window (Add: Exchange, Surface, Equilibrium Phases,
and Kinetics), one can enter the Keyword for a particular process and a template, guiding users
how to define a particular process.
2.1.4.4. Additional Output
The user can define additional output using the editor Additional Output (Fig. 8) in the HP2/3
Definitions dialog window by using the PHREEQC data blocks SELECTED_OUTPUT and
USER_PUNCH.
Standard output in HP2 is limited to the concentration of the components. In addition, dependingon the options selected in the HP2/3 – Print and Punch Control dialog window (Fig. 13), a
number of output files is created. HP2 specific output files (with the file name variable.hpo)
have the same binary structure as other HYDRUS output files, such as h.out or concx.out and canbe displayed using the GUI. Example shown in Figure 8 requests output for two mineral phases
calcite and gypsum, and Na+ and Ca2+ concentrations at the cation exchange site X.

Figure 8. The HP2 Definitions - Additional Output dialog window.
192.1.5. Solute Transport Parameters
The standard structure of HYDRUS input parameters is preserved also for the HP2 transportmodule. The input parameters for individual components are described below. Figure 9 shows
the Solute Transport Parameters dialog window, in which both soil-specific and solutespecific (identified by their component names) transport parameters are specified. Note that themolecular diffusion coefficient in the liquid (Diffus.W.) and gas (Diffus.G.) phases [LT-2] are theonly solute-specific parameters. Fig. 13). A standard definition of a HP2 transport problem
requires equal molecular diffusion coefficients for all components (see Jacques and Šimůnek,2005). However, when a project is defined with no equilibrium aqueous complexation reactions
and charged species, different molecular diffusion coefficients can be used.

Figure 9. The Solute Transport Parameters dialog window.
Table 1. Soil specific solute transport parameters.
Parameter Notation
Description
3
Bulk. D.
Bulk
density[M/L]ρ
Disp.L.
Longitudinal dispersivity [L]λL
Disp.T.
Transverse dispersivity [L]λT
Mass Tr.
Mass transfer coefficient describing the rate of exchange between theαmobile and immobile water contents [T-1]. This parameters is used only
when the dual-porosity solute transport model is used. Set equal to zero
when this model is not used.
ThImob.
Immobile water content when the dual-porosity solute transport modelθimis used. Set equal to zero when this model is not used.

20

2.1.6. Solute Reaction Parameters
All reaction parameters are specified in the PHREEQC.in input file (using PHREEQC specifictext editors) and thus the Reaction Parameters dialog window (Fig. 10) is not used to specify
the reaction parameters (that part of the window is disabled), but only to assign Solution
Compositions to boundaries with constant water flow boundary conditions. Solution
Compositions assigned to boundaries with time-variable water flow boundary conditions are
given in the Variable Boundary Conditions window. Solution composition 3001 is used as theboundary condition in the example shown in Figure 10.

Figure 10. The Reaction Parameters for Solute -1 dialog window.

212.1.7. Initial and Boundary Conditions
Solution composition numbers (e.g., 1001) defined in Definitions of Solution Compositions
window (Fig. 6) are used to assign different solution compositions to different parts of thetransport domain as initial conditions (Fig. 11), similarly as other initial conditions. Solution
composition numbers used to assign solute transport initial conditions must correspond to thesolution composition numbers defined in phreeqc.in.

Figure 11. The "Initial Conditions" part of Data Tab of the Navigator Bar for the HP2 module.
Solution composition numbers (e.g., 1001) defined in Definitions of Solution Compositions
window (Fig. 6) are similarly used to assign different solution compositions to different
boundaries as boundary conditions. For boundaries with constant water flow conditions, solution
composition numbers are specified in the Reaction Parameters dialog window (Fig. 10). For
boundaries with time-variable water flow conditions, solution composition numbers are specified
in the Time Variable Boundary Conditions dialog window (Fig. 12).

Figure 12. The HP2-related part of the Time-Variable Boundary Conditions dialog window.

222.1.8. HP2 Print and Punch Controls
The HP2 Print and Punch Controls dialog window (Fig. 13) allows users to specify variables(i.e., water, temperature, pH, pe, ionic strength, alkalinity, charge balance, and percent error),times (Print Times), and locations (Observation Nodes), for which output should be provided.
The information in this dialog should be self-explanatory. More information is provided in thehelp file and in the user manual of the HP1 program [Jacques and Simunek, 2010].

Figure 13. The HP2 Print and Punch Controls dialog window.

23

24

2.2.

Post-Processing

2.2.1. Results – Graphical Display
The output for the HP2 module is similar as the output for the standard HYDRUS module and forstandard variables, such as pressure head, water contents, and so on. Multiple variables can bedisplayed in the View window (Figure 14). Main components defined in the HP2/3 Components
and Database Pathway window (Fig. 3), variables selected in the HP2 Print and Punch
Controls dialog window (Fig. 12), and variables specified in the Additional Output (Fig. 8) of
the HP2/3 Definitions dialog window (Fig. 4) can be displayed this way.
Figure 14 below shows the "Results - Graphical Display" part of Data Tab of the Navigator Bar
for the Leaching of the Uranium Tailings example given below (Section 4.5). From the HP2variables, first seven are the main components (Total_H, Total_O, Ca, C, U, P, S, and Fe)
defined in the HP2/3 Components and Database Pathway window (Fig. 3), the next two (pHand pe) are variables selected in the HP2 Print and Punch Controls dialog window (Fig. 12),and finally the last four (calcite, gypsum, ratherfordine and siderite) are mineral phases specified
in the Additional Output (Fig. 8) of the HP2/3 Definitions dialog window.

Figure 14. The "Results - Graphical Display" part of Data Tab of the Navigator Bar for the HP2
module.
2.2.2. Results – Other Information
The content of the PHREEQC.out output file is described in detail in the PHREEQC user manual[Parkhurst and Appelo, 1999].

25

26

3. Example Problems
The HP2 module supplements the standard HYDRUS program, which includes variably-saturated
water flow and solute transport model, and thus the water flow, solute transport and colloids
transport parts of the model have been tested earlier. Therefore, verification and test examples
presented in this section concentrate on the demonstration of the new features of the model.
Table 2 shows selected two-dimensional examples that can be downloaded from the HYDRUS(HP2) website. Some of these examples are discussed in detail in the HP1 manuals [Jacques andŠimůnek, 2005, 2010]. Others are described in detail in Section 4 together with detailed step-bystep instructions how to develop them using the HYDRUS GUI. We will be continuously
expanding this list of examples and tutorials, depending on users needs and interests.
Table 2. List of test examples for the HP2 module.
Name

Flow+

Description

Verification examples that can be downloaded from the HYDRUS website
2D-EQCL
2D-NEQCL

SS
SS

2D-TransCl
2D-TransCla
2D-STAds

T
TSS

2D-STDecaySS

2D-SeasonChain

T

2D-CatExch
2D-MinDis
2D-MCatExch

SSSS

Physical equilibrium transport of chloride (verification problem 1)
Physical nonequilibrium transport of chloride (verification problem
1)
Transient physical nonequilibrium transport (verification problem 2)
Transient equilibrium transport (verification problem 2)
Steady state transport of a nonlinearly adsorbing contaminant(verification problem 3)
Steady state transport of a nonlinearly adsorbing and decaying
contaminant (verification problem 4)First-order decay chain of nonlinearly adsorbing contaminants
during unsteady flow (verification problem 5)
Transport with multiple cation exchange (verification problem 6)
Transport with mineral dissolution
Heavy metal transport in a medium with a pH-dependent cationexchange complex

Verification examples that are described below in this report and that can also be
downloaded from the HYDRUS website
2D-CEC-1
SS
Example 1: Transport and Cation Exchange (Single Pulse)
2D-CEC-1
SS
Example 2: Transport and Cation Exchange (Multiple Pulses)
2D-HP1-1
SS
Example 3: Transport and Dissolution of Gypsum and Calcite
2D-CEC-Furrow
T
Example 4: Furrow Irrigation with cation Exchange
UTailing
T
Example 5: Leaching of the Uranium Tailings+
SS - steady-state water flow, T - transient water flow

27

28

4. Step-by-Step Instructions for Selected HP2 Examples
The purpose of these examples is to documents how to use the version 1.0 of HP2. The following
tutorials are described in this report:
1.
2.
3.
4.
5.

Example 1: Transport and Cation Exchange (Single Pulse)
Example 2: Transport and Cation Exchange (Multiple Pulses)
Example 3: Transport and Dissolution of Gypsum and Calcite
Example 4: Furrow Irrigation with cation Exchange
Example 5: Leaching of the Uranium Tailings

While the first three examples involve one-dimensional steady-state water flow, examples 4 and5 involve transient two-dimensional water flow. Cation exchange is the main chemical process inexamples 1, 2, and 4. Precipitation/dissolution reactions are the main chemical processes inexamples 3 and 5. Each of these examples can be easily further modified to include additional
chemical processes. Only simple structural FE-Meshes are used in all examples.

29

4.1. Example 1: Transport and Cation Exchange (Single Pulse)
4.1.1.

Problem Definition

This example is adapted from Example 11 of the PHREEQC manual [Parkhurst and Appelo,1999] and is also used in the HP1 manual [Jacques and Simunek, 2010]. The chemicalcomposition of the effluent from an 8-cm column containing a cation exchanger is simulated inthis example. The column initially contains a Na-K-NO3 solution in equilibrium with the cationexchanger. The column is flushed with three pore volumes of a CaCl2 solution. Ca, K and Na areat all times in equilibrium with the exchanger. The simulation is run for one day; the fluid flux
density is equal to 24 cm/d (0.00027777 cm/s).
The column is discretized vertically into 40 finite elements and horizontally into two columns(i.e., 82 nodes). The example assumes that the same solution is initially associated with eachnode. This is, in general, not necessary and different solutions can be defined for each node. The
solution, however, must be specified for each node. The exchanger can be defined also for eachnode, but it does not have to be (this depends on the specific conceptual geochemical model for a
project). In this example we use the same exchanger composition at all nodes.
The initial Na-K-NO3 solution is made by using 1 x 10-3 M NaNO3 and 2 x 10-4 M KNO3 M. The
inflowing CaCl2 solution has a concentration of 6 x 10-4 M. Both solutions were prepared underoxidizing conditions (in equilibrium with the partial pressure of oxygen in the atmosphere). The
amount of exchange sites (X) is 1.1 meq/1 dm³ soil. The log K constants for the exchange
reactions are defined in the PHREEQC.dat database and do not have to be therefore specified at
the input.
This project is available in the Project Group ‘2D_Tests’ and is named 2D-CEC-1. In thisexample, only the outflow concentrations of Cl, Ca, Na, and K are of interest.
4.1.2.

Input

Project Manager (File->Project Manager)
Button "New"New Project (or File->New)
Name: 2D-CEC-1
Description: Transport and Cation Exchange, single pulse
Working Directory: Temporary – exists only when the project is open
Button "Next"
Domain Type and Units (Edit->Domain Geometry->Domain Type and Units)
Type of Geometry: 2D - Simple
2D-Domain Options: 2D - Vertical Plane XZ
Units: cm
Initial Workspace: X-Min=0, X-Max=1, Z-Min=0, Z-Max=8 cm
Button "Next"

30

Regular Domain Definition (Edit->Domain Geometry->Simple Domain)
Dimensions: Lx = 1 cm, Lz = 8 cm, Slope α = 0
Button "Next"
Main Processes (Edit->Flow and Transport Parameters->Main Processes)
Uncheck "Water Flow" (Note: this is a steady-state water flow)
Check "Solute Transport"
Button "Next"
Time Information (Edit->Flow and Transport Parameters->Time Information)
Time Units:
Seconds
Final Time:
86400 (s)Initial Time Step:
180 (s)Minimum Time Step: 180 (s)Maximum Time Step: 180 (s) (Note: we use the constant time step to have the same
conditions as in the original comparable PHREEQC
calculations; in general, there is no need to have constanttime steps in HP2).
Button "Next"
Output Information (Edit->Flow and Transport Parameters->Output Information)
Print Options:
Check T-Level Information
Check Screen Output
Check Press Enter at the End
Print Times: Count: 12
UpdateDefault
Button "Next"
HP2/3 – Print and Punch Controls
Button "Next
Water Flow - Iteration Criteria (Edit->Flow and Transport Parameters->Water Flow
Parameters->Iteration Criteria)
Leave default values except:
Lower Time Step Multiplication Factor: 1 (Note: the constant time step)
Button "Next"
Water Flow - Soil Hydraulic Model (Edit->Flow and Transport Parameters->Water Flow
Parameters->Hydraulic Properties Model)
Leave default values as follows:
Radio button - van Genuchten-Mualem
Radio button - No hysteresis
Button "Next"

31

Water Flow - Soil Hydraulic Parameters (Edit->Flow and Transport Parameters->Water Flow
Parameters->Soil Hydraulic Parameters)
Catalog of Soil Hydraulic Properties: Loam
Qs:
1 (Note: to have the same conditions as in the original comparable PHREEQC
calculations)Ks:
0.00027777 (cm/s)
Button "Next"
Solute Transport – General Info (Edit->Flow and Transport Parameters->Solute TransportParameters->General Information)
Number of Solutes: 7
Select “HP2 (HYDRUS+PHREEQC)”
Button "Next"
Solute Transport – HP2/3 Components and Database Pathway
Database Pathway: Leave the default PHREEQC database and default path
Add seven components: Total_O, Total_H, Na, K, Ca, Cl, N(5)
Leave the checkbox on: "Create the PHREEQC.IN file Using HYDRUS GUI"
Leave the radio button on: In Solution Composition
Button "Next"
Solute Transport – HP2/3 Definitions
Definitions of Solution Composition
Define the initial condition 1001:• K-Na-N(5) solution• use pH to charge balance the solution• Adapt the concentration of O(0) to be in equilibrium with the partialpressure of oxygen in the atmosphere
Define the boundary condition 3001:• Ca-Cl solution• Use pH to charge balance the solution• Adapt the concentration of O(0) to be in equilibrium with the partialpressure of oxygen in the atmosphere
Solution 1001 Initial condition-units mmol/kgw
pH 7 charge
Na 1
K 0.2
N(5) 1.2
O(0) 1 O2(g) -0.68
Solution 3001 Boundary solution-units mmol/kgw

32

pH 7 charge
Ca 0.6
Cl 1.2O(0) 1 O2(g) -0.68

Geochemical Model
Define for each node (82 nodes) the geochemical model, i.e., the cation exchange
assemblage X (0.0011 moles/1000 cm³) and equilibrate it with the initial solution(solution 1001). Note that since no equilibrium constants for cation exchange are
specified, they are taken from the PHREEQC.dat database. Additionally, indicate
to PHREEQC, that this is a two-dimensional project.
EXCHANGE 1-82 @Layer 1@
X 0.0011-equilibrate with solution 1001
reactive_transport-dimension 2

Button "OK"
Additional Output
Since output is required only for the total concentrations and such output isavailable in the automatically generated file obs_node.out, there is no need todefine additional output. If we want to have spatial profiles of cation exchange
concentrations, then we can use the following command:
selected_output-molalities NaX KX CaX2

Button "Next"
Solute Transport - Solute Transport Parameters (Edit->Flow and Transport Parameters>Solute Transport Parameters->Solute Transport Parameters)
Leave default values
Bulk Density = 1.5 cm3/g
Longitudinal Dispersivity, Disp.L = 0.2 cm
Transverse Dispersivity, Disp.T = 0.02 cm
Molecular Diffusion Coefficient for Liquid Phase, Diffus.W.=0
Button "Next"
Solute Transport - Reaction Parameters (Edit->Flow and Transport Parameters->Solute
Transport Parameters->Solute Reaction Parameters)
Boundary Condition: cBnd1=3001 (the solution composition number for the upperboundary condition)
Button "Next"

33

Rectangular Domain Spatial Discretization (Edit->FE-Mesh->FE-Mesh Parameters)
Horizontal Discretization in X
Count = 1
Entries in the x column: 0, 1
Horizontal Discretization in Z
Count = 41
Default Entries in the z column
Button "Next"

Default Domain Properties (Edit->Domain Properties->Default Domain Properties)
Set Code on the first and last row to 1.
Set the initial pressure head, h, for all nodes equal to zero.
Set the temperature, Temp, to 25.
Set the solution concentration, sc, to 1001.
Button "Next"

34

Observation Nodes
Click on the Domain Properties Tab under the View Window.
On the Navigator Bar click on Domain Properties – Observation Nodes (or Insert>Domain Properties->Observation Nodes).
Click on the Insert Observation Node () command on the Edit Bar
and insert one observation nodes in the very bottom left node.
Run Calculations
Click the Calculate Current Project command (>Calculate Current Project)(Execution time on 3 GHz PC – 7 s)

) on the Toolbar (or Calculation-

Note: This exercise will produce following warnings: "Master species N(3) is present in solution
n but is not transported.". The same warning occurs for N(0). N(3) and N(0) are two secondary
master species from the primary master species N. Only the secondary master species N(5) was
defined as a component to be transported (Solute Transport – HP2 Components). HP2, however,checks if all components, which are present during the geochemical calculations, are defined in
the transport model. If not, a warning message is generated. In our example, the concentrationsof the components N(0) and N(3) are very low under the prevailing oxidizing conditions.
Therefore, they can be neglected in the transport problem. If you want to avoid these warnings,
you have to either include N(0) and N(3) as components to be transported or define an alternative
using
primary
masterspecies
representing
nitrate
(such
as
Nit-)
SOLUTION_MASTER_SPECIES and SOLUTION_SPECIES.

35

4.1.3. Output
When the program finishes, explore the output files. Display results for “Observation Points”.
Figure below can be created using the Observation Points (All Concentration) information(information from the obs_nod.out output file).
0.0014

Concentration [mol/kg]

0.00120.001
Cl0.0008Ca
Na

0.0006K
0.00040.0002

0
0

14400

28800

43200

57600

72000

86400

Time [s]Figure 15. Outflow concentrations of Cl, Ca, Na and K for the single-pulse cation exchange
example.
The results for this example are shown in Figure 15. The concentrations of node 41 (the lastnode) are plotted against time. Chloride is a conservative solute and arrives in the effluent at
about one pore volume. The sodium initially present in the column exchanges with the incoming
calcium and is eluted as long as the exchanger contains sodium. The midpoint of the
breakthrough curve for sodium occurs at about 1.5 pore volumes. Because potassium exchanges
more strongly than sodium (larger log K in the exchange reaction; note that log K for individual
pairs of cations are defined in the database and therefore did not have to be specified), potassium
is released after sodium. Finally, when all of the potassium has been released, the concentrationof calcium increases to a steady-state value equal to the concentration of the applied solution.

36

4.2. Example 2: Transport and Cation Exchange (Multiple Pulses)
This project is available in the Project Group ‘2D_Tests’ and is named 2D-CEC-2.
4.2.1. Problem Definition
This example is the same as Example 1, except that time variable concentrations are applied at
the soil surface. The following sequence of pulses is applied at the top boundary:0 – 8 hr: 6 x 10-4 M CaCl2
8 – 18 hr: 5 x 10-6 M CaCl2, 1 x 10-3 M NaNO3, and 2 x 10-4 M KNO3
18 – 38 hr: 6 x 10-4 M CaCl2
38 – 60 hr: 5 x 10-6 M CaCl2, 1 x 10-3 M NaNO3, and 8 x 10-4 M KNO3
4.2.2.

Input

Project Manager (File->Project Manager)
Click on 2D-CEC-1
Button "Copy"
New Name: 2D-CEC-2
Description: Transport and Cation Exchange, multiple pulses
Button "OK", "Open"Time Information (Edit->Flow and Transport Parameters->Time Information)
Time Units:
hours
Final Time:60 (h)
Initial Time Step:
0.1 (h)Minimum Time Step: 0.1 (h)Maximum Time Step: 0.1 (h)Check Time-Variable Boundary Conditions
Number of Time-Variable Boundary Records:
4
Button "Next"
Output Information (Edit->Flow and Transport Parameters->Output Information)
Number of Print Times: 12
Default
Button "Next"
HP2/3 – Print and Punch Controls
Button "Next"
Solute Transport – General Info (Edit->Flow and Transport Parameters->Solute TransportParameters->General Information)
Button "Next"
Solute Transport – HP2 Components and Database Pathway

37

Button "Next"
Solute Transport – HP2/3 Definitions
Definitions of Solution Composition
Add additional solution compositions for boundary conditions with numbers 3002
and 3003.
Solution 3002 Boundary solution-units mmol/kgw
ph 7 charge
Na 1
K 0.2
N(5) 1.2
Ca 5E-3
Cl 1E-2
O(0) 1 O2(g) -0.68
Solution 3003 Boundary solution-units mmol/kgw
ph 7 charge
Na 1
K 0.8
N(5) 1.8
Ca 5E-3
Cl 1E-2
O(0) 1 O2(g) -0.68

Button "OK"
Button "Next"
Time-Variable Boundary Conditions (Edit->Flow and Transport Parameters->Variable
Boundary Conditions)Fill in the time, and the solution composition numbers for the top boundary
Time
8
18
38
60

cValue1
3001
3002
3001
3003

Observation Nodes
Click on the Domain Properties Tab under the View Window.
On the Navigator Bar click on Domain Properties – Observation Nodes (or Insert>Domain Properties->Observation Nodes).
Click on the Insert Observation Node () command on the Edit Bar
and insert observation nodes on the left column at depths of 2, 4, 6, and 8 cm.
Run Calculations
38

Click the Calculate Current Project command (>Calculate Current Project)(Execution time on 3 GHz PC – 7 s)

) on the Toolbar (or Calculation-

4.2.3. Output
Figure 16 gives the K concentration at different depths in the profile. Figure 17 shows theoutflow concentration. The first pulse is identical to the single pulse project. Then additional
solute pulses of different solution compositions will restart the cation exchange processdepending on the incoming solution composition.

Figure 16. Time series of K concentrations at four depths for the multiple-pulse cation exchange
example.

Figure 17. Outflow concentrations for the multiple-pulse cation exchange example.

39

4.3. Example 3: Transport and Dissolution of Gypsum and Calcite
This project is available in the Project Group ‘2D_Tests’ and is named 2D-HP1-1.
4.3.1. Problem Definition
Sulfate-free water is infiltrated in a 50-cm long homogeneous soil column under steady-state
saturated flow conditions. The reactive minerals present in the soil column are calcite (CaCO3)
and gypsum (CaSO4.2H2O), both at a concentration of 2.176 x 10-2 mmol/kg soil.
Physical properties of the soil column are as follows: the porosity of 0.35, the saturated hydraulicconductivity of 10 cm/day, the bulk density of 1.8 g/cm³, and the dispersivity of 1 cm.
The input solution contains 1 mM CaCl2 and is in equilibrium with the atmospheric partialpressure of oxygen and carbon dioxide. The initial soil solution is in equilibrium with thereactive minerals and with the atmospheric partial pressure of oxygen. As a result of theseequilibria, the initial soil solution contains only Ca and oxidized components of S and C.
Calculate the movement of dissolution fronts of calcite and gypsum over a period of 2.5 days.
4.3.2. Input
Project Manager (File->Project Manager)
Button "New"New Project (or File->New)
Name: 2D-HP1-1
Description: "Dissolution of calcite and gypsum in the soil profile"Working Directory: Temporary – exists only when the project is open
Button Next"
Domain Type and Units (Edit->Domain Geometry->Domain Type and Units)
Type of Geometry: 2D - Simple
2D-Domain Options: 2D - Vertical Plane XZ
Units: cm
Initial Workspace: X-Min=0, X-Max=1, Z-Min=0, Z-Max=5 cm
Button "Next"
Regular Domain Definition (Edit->Domain Geometry->Simple Domain)
Dimensions: Lx = 1 cm, Lz = 50 cm, Slope α = 0
Button "Next"
Main Processes (Edit->Flow and Transport Parameters->Main Processes)
Uncheck "Water Flow" (Note: this is a steady-state water flow)
Check "Solute Transport"
Button "Next"

40

Time Information (Edit->Flow and Transport Parameters->Time Information)
Time Units: Days
Final Time: 2.5 (d)Initial Time Step: .001 (d)Maximum Time Step: 0.05
Button "Next"
Output Information (Edit->Flow and Transport Parameters->Output Information)
Print Options:
Uncheck T-Level Information
Check Interval Output
Time Interval: 0.025
Check Screen Output
Check Press Enter at the End
Print Times: Count: 5
UpdateDefault
Button "Next"
HP2/3 – Print and Punch Controls
Check: "Make GNUplot Templates"
This allows easy visualization of time series and profile data for variables, which aredefined in the SELECTED_OUTPUT section below in this dialog window and also
defined later in the Additional Output part of the Solute Transport – HP2
Definitions dialog.
Button "Next"
Water Flow – Iteration Criteria (Edit->Flow and Transport Parameters->Water Flow
Parameters->Iteration Criteria)
Leave default values
Button "Next"
Water Flow – Soil Hydraulic Model (Edit->Flow and Transport Parameters->Water Flow
Parameters->Hydraulic Properties Model)
Leave default values as follows:
Radio button - van Genuchten-Mualem
Button "Next"
Water Flow - Soil Hydraulic Parameters (Edit->Flow and Transport Parameters->Water Flow
Parameters->Soil Hydraulic Parameters)
Catalog of Soil Hydraulic Properties: Loam
Qs: 0.35
Ks: 10 (cm/d)
Button "Next"

41

Solute Transport – General Info (Edit->Flow and Transport Parameters->Solute TransportParameters->General Information)
Number of Solutes: 6
Select “HP2 (HYDRUS+PHREEQC)”
Button "Next"
Solute Transport – HP1 Components and Database Pathway
Database Pathway: Leave the default PHREEQC database and default path
Six Components: Total_O, Total_H, Ca, C(4), Cl, S(6)Note: Redox sensitive components should be entered with the secondary master species,
i.e., with their valence state between brackets. The primary master species of a redox
sensitive component, i.e., the element name without a valence state, is not recognized as acomponent to be transported. Therefore, the primary master species C cannot be entered
here; one has to enter either C(4) or C(-4). Also S is not allowed; one has to enter either
S(6) or S(-2). Note that the HYDRUS GUI will not check if a correct master species isentered. Because the redox potential is high in this example (a high partial pressure ofoxygen), the secondary master species C(-4) and S(-2) are not considered.
Check: "Create PHREEQC.IN file using HYDRUS GUI"
Button "Next"
Solute Transport – HP2/3 Definitions
Definitions of Solution Composition
Define the initial condition, i.e., the solution composition of water in the soilcolumn, with the identifier 1001:• Pure water• Bring it in equilibrium with gypsum, calcite, and O(0), to be in
equilibrium with the partial pressure of oxygen in the atmosphere
Define the boundary condition, i.e., the solution composition of water entering thesoil column, with the identifier 3001:• Ca-Cl solution• Use pH to obtain the charge balance of the solution• Adapt the concentration of O(0) and C(4) to be in equilibrium with theatmospheric partial pressure of oxygen and carbon dioxide, respectively
solution 1001
equilibrium_phases 1001
gypsumcalciteO2(g) -0.68
save solution 1001
end
solution 3001

42

-units mmol/kgw
pH 7 charge
Cl 2
Ca 1
O(0) 1 O2(g) -0.68
C(4) 1 CO2(g) -3.5

Button "OK"Geochemical Model
Define for each node the geochemical model. Note that the initial amount of amineral must be defined as mol/1 dm³ soil (i.e., 2.176 x 10-5 mol/kg soil * 1.8
kg/1 dm³). Additionally, indicate to PHREEQC, that this is a two-dimensional
project.
Equilibrium_phases 1-101
gypsum 0 3.9E-5
calcite 0 3.9E-5
O2(g) -0.68
reactive_transport-dimension 2

Button "OK"
Additional Output
Define the additional output to be written to selected output files.
selected_output-totals Ca Mg Cl S C-equilibrium_phases gypsum calcite

Button "OK"
Button "Next"
Solute Transport - Solute Transport Parameters (Edit->Flow and Transport Parameters>Solute Transport Parameters->Solute Transport Parameters)
Bulk D. = 1.8 (g/cm³)
Longitudinal Dispersivity, Disp.L = 1 cm
Transverse Dispersivity, Disp.T = 0.1 cm
Molecular Diffusion Coefficient for Liquid Phase, Diffus.W.=0
Button "Next"
Solute Transport - Reaction Parameters (Edit->Flow and Transport Parameters->Solute
Transport Parameters->Solute Reaction Parameters)
Boundary Condition: cBnd1=3001 (the solution composition number for the upperboundary condition)

43

Button "Next"
Rectangular Domain Spatial Discretization (Edit->FE-Mesh->FE-Mesh Parameters)
Horizontal Discretization in X
Count = 1
Entries in the x column: 0, 1
Horizontal Discretization in Z
Count = 101
Default Entries in the z column
Button "Next"
Default Domain Properties (Edit->Domain Properties->Default Domain Properties)
Set Code on the first and last row to 1.
Set the initial pressure head, h, for all nodes equal to zero.
Set the temperature, Temp, to 25.
Set the solution concentration, sc, to 1001.
Button "Next"
Observation Nodes
Click on the Domain Properties Tab under the View Window.
On the Navigator Bar click on Domain Properties – Observation Nodes (or Insert>Domain Properties->Observation Nodes).
Click on the Insert Observation Node () command on the Edit Bar
and insert observation nodes at a depth increment of 10 cm.
Run Calculations
Click the Calculate Current Project command (>Calculate Current Project)(Execution time on 3 GHz PC – 5 s)

) on the Toolbar (or Calculation-

4.3.3. Output
The standard HYDRUS output can be viewed using commands in the Results part of theNavigator Bar. Only the total concentrations of the components, which were defined in“Solute Transport – HP2 Components”, at the observation nodes can be viewed using
the HYDRUS-GUI.
HP2 creates a number of additional output files in the project folder. The path to the project
folder is displayed in the Project Manager:
File -> Project Information
Path: Gives the path to the project group folder. The path can be copied into the Windows
Explorer to locate all project files.
.

44Following HP2 output files are created for the HP2-1 project:
Createdfiles.out

An ASCII text file containing a list of all files created by HP2 (inaddition to the output files created by the HYDRUS module ofHP2);
Phreeqc.out
An ASCII text file, which is the standard output file created by the
PHREEQC-module in HP2 and can be viewed via the GUI:
Results->HP2 Text Output…
or via the Project Navigator bar
H3D2_2D_HP2-1.hse An ASCII text file, tab-delimited, that includes a selected output of
all geochemical calculations in HP2 carried out before actual
transport calculations. Inspection of this file can be done with any
spreadsheet, such as MS Excel;
obs_nod_chem41.out
obs_nod_chem81.out
obs_nod_chem121.out
obs_nod_chem161.out
obs_nod_chem201.out A series of ASCII files, tab-delimited, with the selected output forthe defined observation nodes (41, 81, 121, 161, and 201) at
specific times (every 0.025 days). Numerical values can be seen by
opening this file in a spreadsheet, such as Excel. A single plot oftime series at five observation nodes can be generated for eachgeochemical variable with the ts_*.plt files using the GNUPLOT
graphical program (see below);
ts_pH.plt
An ASCII file containing command line instructions to generate aplot of pH (or pe, or other variables) using GNUPLOT;
ts_pe.plt
ts_tot_Ca.plt
An ASCII file containing command line instructions to generate aplot with total concentrations of Ca (or Cl, S and C) using
GNUPLOT;
ts_tot_Cl.plt
ts_tot_S.plt
ts_tot_C.plt
ts_eq_gypsum.plt
An ASCII file containing command line instructions to generate aplot with the amount of the minerals gypsum (or calcite) with
GNUPLOT;
ts_eq_calcite.plt
ts_d_eq_gypsum.plt An ASCII file containing command line instructions to generate aplot with the change in amount of the minerals gypsum (or calcite)with GNUPLOT;
ts_d_eq_calcite.plt
To view these various plots, the GNUPLOT code needs to be installed on your computer.
GNUPLOT is freeware software that can be downloaded from http://www.gnuplot.info/. Notethat GNUPLOT (the wgnuplot.exe program for the Windows OS) is usually, after being
downloaded, in the gnuplot\bin folder and does not require any additional special installation.

45

After opening the Windows version of GNUPLOT by clicking on wgnuplot.exe, a plot can bedirectly generated by carrying out these commands:
File->OpenBrowse to the project folder
Open the template file of interest (*.plt)
The figure can be adapted using line commands (see tutorials on the internet). After adaptations,the command lines can be saved to be used later on. If you have trouble with the display of fonts,
it is possible that the terminal on your computer is set incorrectly. In such case, type at the
GNUPlot prompt:
Gnuplot> set terminal "Windows"
The default terminal for the plots should be Window. We illustrate here only how a plot can betransferred to another terminal:
Set terminal emf
Set output "name.emf"
Replot
Set terminal window
ReplotA name.emf file is created in the project directory.
Figure 18 shows vertical profiles of pH, total aqueous C concentration, total aqueous Caconcentration, total aqueous S concentration, the amount of gypsum and the amount of calcite atselected print times during dissolution of calcite and gypsum. Figure 19 shows the time series ofpH, total aqueous C concentration, total aqueous Ca concentration, total aqueous S concentration,
the amount of gypsum and the amount of calcite at selected observation nodes during dissolutionof calcite and gypsum.

460Distance (cm)

-10

-20

-30

-40

-50
5.5

6.5

6

7.5
pH

8

8.5

9.5

9

2.00 days
2.50 days

1.00 days
1.50 days

0

0

-10

-10

Distance (cm)Distance (cm)

0 days0.50 days

7

-20

-30

-40

-30

-40

-50

-50
0

0.016

0.012
0.008
0.004
Total concentration of Ca (mol/kg water)
0 days0.50 days

1.00 days
1.50 days

0

2.00 days
2.50 days

0

0

-10

-10

-20

-30

-40

0.016

0.012
0.008
0.004
Total concentration of S (mol/kg water)
0 days0.50 days

Distance (cm)Distance (cm)-20

1.00 days
1.50 days

2.00 days
2.50 days

-20

-30

-40

-50

-50
0

3e-0052e-0051e-005
gypsum (mol/1000 cm³ of soil)
0 days0.50 days

1.00 days
1.50 days

4e-0052.00 days
2.50 days0

1e-0050 days0.50 days

4e-0053e-0052e-005
calcite (mol/1000 cm³ of soil)
1.00 days
1.50 days

5e-0052.00 days
2.50 days

Figure 18. Vertical profiles of pH (top left), total aqueous C concentration (top right), total
aqueous Ca concentration (middle left), total aqueous S concentration (middle right), theamount of gypsum (bottom left) and the amount of calcite (bottom right) at selected print times
during dissolution of calcite and gypsum.

47

Total concentration of C (mol/kg water)

9.5
9
8.5

pH

8
7.5
7
6.5
6
5.5
0

0.5

1
1.5
Time (days)

0.008

0.004

0
1
1.5
Time (days)-10.0 cm
-20.0 cm
-30.0 cm

2e-0051e-005
0

2

0.5

1
1.5
Time (days)2

2.5-40.0 cm
-50.0 cm

0.016

0.012

0.008

0.004

0
0

2.5

0.5

1
1.5
Time (days)-10.0 cm
-20.0 cm
-30.0 cm

-40.0 cm
-50.0 cm2

2.5

-40.0 cm
-50.0 cm

5e-005

calcite (mol/1000 cm³ of soil)

4e-005

gypsum (mol/1000 cm³ of soil)

3e-005-10.0 cm
-20.0 cm
-30.0 cm

0.012

0.5

4e-005-40.0 cm
-50.0 cm0.016

05e-005

2.5

Total concentration of S (mol/kg water)

Total concentration of Ca (mol/kg water)-10.0 cm
-20.0 cm
-30.0 cm2

6e-0053e-0052e-0051e-0054e-0053e-0052e-0051e-0050

00

0.5-10.0 cm
-20.0 cm
-30.0 cm1.5
1Time (days)

2

2.5

0

0.5

-10.0 cm
-20.0 cm
-30.0 cm

-40.0 cm
-50.0 cm1
1.5Time (days)2

2.5-40.0 cm
-50.0 cm

Figure 19. Time series of pH (top left), total aqueous C concentration (top right), total aqueous
Ca concentration (middle left), total aqueous S concentration (middle right), the amount of
gypsum (bottom left) and the amount of calcite (bottom right) at selected depths (observation
nodes) during dissolution of calcite and gypsum.

48

4.4. Example 4: Furrow Irrigation with Cation Exchange
4.4.1.

Problem Definition

A furrow irrigation problem, similar to the one used in the UNSATCHEM manual, was used tosimulate two-dimensional infiltration of gypsum saturated water into a sodic soil. The example thus
simulates sodic soil reclamation problem and demonstrates the cation exchange feature of HP2. The
schematic representation of the flow domain for the considered furrow irrigation together with thefinite element mesh is presented in Figure 20. It is assumed that every other furrow is flooded withwater and that the water level in the irrigated furrow is kept constant at a level of 6 cm. Due tosymmetry, it is necessary to carry out the simulation only for the domain between the axis of twoneighboring furrows. Free drainage is used as the bottom boundary condition and zero flux is
considered on the rest of the boundary. The initial pressure head condition is -200 cm and the soil
hydraulic properties for silt are used.

15

15

40

15

15

15

85

100 cm100 cmFigure 20. Schematic representation and finite element mesh of the flow domain for the furrow
irrigation system for example 4.

49

The calculation was run at a constant temperature of 25 oC. The bulk density of the soil was taken as
1.4 g cm-3 and molecular diffusion as 2 cm2day-1. Longitudinal and transverse dispersivities wereequal to 2 and 0.2 cm, respectively.
The solution composition of the water initially present in the soil profile is that of the following
highly sodic water: CaT=1.0 MgT=0.0, NaT=5.0, KT=0.0, SO4T=3.5, ClT=0.0 mmol L-1. The cationexchange capacity is equal to 7.143 mmol kg-1 (10 mmol dm-3) and is divided between exchangeablecalcium and sodium (it is equilibrated with the solution). The solution composition of the irrigationwater was almost gypsum saturated: CaT=16.3, MgT=0.0, NaT=4.4, KT=0.0, ClT=5.0, SO4T=16.0
mmolL-1. As a consequence of the reactions of the irrigation water with the exchanger composition,
cation exchange was the dominant chemical processes in the soil profile. Cation exchange is treatedas an instantaneous process in the model.

4.4.2. Input
Project Manager (File->Project Manager)
Button "New"New Project (or File->New)
Name: 2D-CEC-Furrow
Description: HP2 Test: Furrow Irrigation, Transport and Cation Exchange
Working Directory: Temporary – exists only when the project is open
Button "Next"
Domain Type and Units (Edit->Domain Geometry->Domain Type and Units)
Type of Geometry: 2D - Simple
2D-Domain Options: 2D - Vertical Plane XZ
Units: cm
Initial Workspace: X-Min=0, X-Max=100, Z-Min=0, Z-Max=100 cm
Button "Next"
Regular Domain Definition (Edit->Domain Geometry->Simple Domain)
Dimensions: Lx = 100 cm, Lz = 100 cm, Slope α = 0
Button "Next"
Main Processes (Edit->Flow and Transport Parameters->Main Processes)
Check "Water Flow" (Note: this is transient water flow)
Check "Solute Transport"
Check “HP2”
Button "Next"
Time Information (Edit->Flow and Transport Parameters->Time Information)
Time Units:
Days
Final Time:
5 (d)Initial Time Step:
0.0005 (d)50Minimum Time Step: 1e-05 (d)Maximum Time Step: 5 (d)Button "Next"
Output Information (Edit->Flow and Transport Parameters->Output Information)
Print Options:
Check T-Level Information
Check Screen Output
Check Press Enter at the End
Print Times: Count: 8
Print Times: 0.05, 0.1, 0.25, 0.5, 1, 2, 3, 5 (d)Button "Next"
HP2/3 – Print and Punch Controls
Number of Warnings: 5
Button "Next
Water Flow - Iteration Criteria (Edit->Flow and Transport Parameters->Water Flow
Parameters->Iteration Criteria)
Leave default values
Button "Next"
Water Flow - Soil Hydraulic Model (Edit->Flow and Transport Parameters->Water Flow
Parameters->Hydraulic Properties Model)
Leave default values as follows:
Radio button - van Genuchten-Mualem
Radio button - No hysteresis
Button "Next"
Water Flow - Soil Hydraulic Parameters (Edit->Flow and Transport Parameters->Water Flow
Parameters->Soil Hydraulic Parameters)
Catalog of Soil Hydraulic Properties: Silt
Button "Next"
Solute Transport – General Info (Edit->Flow and Transport Parameters->Solute TransportParameters->General Information)
Number of Solutes: 8
Button "Next"
Solute Transport – HP2/3 Components and Database Pathway
Database Pathway: Leave the default PHREEQC database and default path
Add seven components: Total_O, Total_H, Ca, Mg, Na, K, Cl, S(6)Leave the checkbox on: "Create the PHREEQC.IN file Using HYDRUS GUI"
Leave the radio button on: In Solution Composition
Button "Next"

51

Solute Transport – HP2/3 Definitions
Select Definitions of Solution Composition
Define the initial condition 1501:• Ca-Na-SO4 solution• use pH to charge balance the solution• Adapt the concentration of O(0) to be in equilibrium with the partialpressure of oxygen in the atmosphere
Define the boundary condition 3001:• Ca-Na-Cl-SO4 solution• Use pH to charge balance the solution• Adapt the concentration of O(0) to be in equilibrium with the partialpressure of oxygen in the atmosphere
Solution 1501 Initial condition-units mmol/kgw
pH 7 charge
Na 5.0Ca 1.0Cl 0.0S(6) 3.5
O(0) 1 O2(g) -0.68
Solution 3001 Boundary solution-units mmol/kgw
pH 7 charge
Ca 16.3
Na 4.4
Cl 5.0S(6) 16.0
O(0) 1 O2(g) -0.68

Select Geochemical Model
Define for each node (1170 nodes) the geochemical model, i.e., the cationexchange assemblage X (0.01 moles/dm³) and equilibrate it with the initialsolution (solution 1501). Note that since no equilibrium constants for cationexchange are specified, they are taken from the PHREEQC.dat database.
EXCHANGE 1-1170
X 0.01-equilibrate with solution 1501

Additionally, you may indicate to PHREEQC, that this is a two-dimensional
project. However, this information will be added by default in GUI, if not
specified manually.

52

reactive_transport-dimension 2

Select Additional Output
Define the additional output to be written to selected output files.
selected_output-equilibrium_phases gypsum calcite-molalities NaX CaX2

Button "Next"
Solute Transport - Solute Transport Parameters (Edit->Flow and Transport Parameters>Solute Transport Parameters->Solute Transport Parameters)
Leave default values
Bulk Density = 1.4 cm3/g
Longitudinal Dispersivity, Disp.L = 2 cm
Transverse Dispersivity, Disp.T = 0.2 cm
Molecular Diffusion Coefficient for Liquid Phase, Diffus.W.=2 cm2/d (for allcomponents)
Button "Next"
Solute Transport - Reaction Parameters (Edit->Flow and Transport Parameters->Solute
Transport Parameters->Solute Reaction Parameters)
Boundary Condition: cBnd1=3001 (the solution composition number for the upperboundary condition)
Button "Next"
Rectangular Domain Spatial Discretization (Edit->FE-Mesh->FE-Mesh Parameters)
Horizontal Discretization in X
Count = 45
Entries in the x column: 0, 3, 6, 9, 12, 15, 16.5, 18, 19.5, 21, 22.5, 24, 25.5, 27,
28.5, 30, 32, 34, 36.5, 39, 42, 46, 50, 54, 58, 61, 63.5, 66, 68, 70, 71.5, 73, 74.5,
76, 77.5, 79, 80.5, 82, 83.5, 85, 88, 91, 94, 97, 100
Entries in the dz column: -15, -15, -15, -15, -15, -15, -13.5, -12, -10.5, -9, -7.5, -6,-4.5, -3, -1.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1.5, -3, -4.5, -6, -7.5, -9, -10.5,-12, -13.5, -15, -15, -15, -15, -15, -15
Horizontal Discretization in Z
Count = 26
Entries in z column: 100, 99, 97.5, 95.5, 93, 90, 87, 84, 81, 78, 75, 72, 69, 66, 62,
58, 54, 50, 45, 40, 34, 28, 21, 14, 7, 0
Button "Next"

53

Default Domain Properties (Edit->Domain Properties->Default Domain Properties)
Set Code on the last row to -6 (free drainage).
Set the initial pressure head, h, for all nodes equal to -200.
Set the temperature, Temp, to 25.
Set the solution concentration, sc, to 1501.
Button "Next"

54

Water Flow Boundary Conditions (Edit->Boundary Conditions->Water
Click on the Boundary Conditions Tab under the View Window.

Flow)a) Click on Zoom by Rectangle ( ) at the Toolbar (or View-> Zoom by Rectangle) andzoom on the left furrow.
Select Constant Head () from the Edit Bar, select bottom of the left
furrow and 4 nodes on the side, specify 6 cm with Equilibrium from the lowest locatednodal point.
b) Click on View All ( ) at the Toolbar (or View->View All).
Select Free Drainage () from the Edit Bar, and select the entire bottom of
the transport domain.
c) On the Navigator Bar double click on Solute Transport) and check that "-1" (or "+1") is
Click on Display codes on the Edit Bar (displayed in the furrow. This means that solution composition 1 will be applied with theirrigation water.
Uncheck "Display Codes" again.
Observation Nodes
Click on the Domain Properties Tab under the View Window.
On the Navigator Bar click on Domain Properties – Observation Nodes (or Insert->Domain
Properties->Observation Nodes).
Click on the Insert command on the Edit Bar and specify 5 points arbitrarily in the transportdomain between the furrow and the bottom of the transport domain.
Save
55

Save the project using the Save command () on the Toolbar (or File->Save).

Run Calculations
Click the Calculate Current Project command (Current Project)) on the Toolbar (or Calculation->Calculate

4.4.3. Output
Figure 21 shows the pressure head profiles for four different times. The distribution of chloride
concentrations (a tracer) is shown on Figure 22.

Figure 21. Pressure head (cm) profiles at times: a) 0.1, b) 0.5, c) 1, and d) 2 days for example 4.

56

Figure 22. Chloride concentration profiles (mol L-1) at times: a) 0.1, b) 1, c) 3, and d) 5 days forexample 4.

Figure 23. Sodium concentration profiles (mol L-1) at times: a) 0.5, b) 1, c) 3, and d) 5 days forexample 4.

57

Figures 23 and 24 present the liquid phase and exchangeable concentrations of sodium, respectively.
The exchange phase concentrations reflect the changes in aqueous Na and Ca concentration. Notethe significant lagging of the exchanger front to both the water and tracer front. Also due to the highnonlinearity of Na-Ca exchange, the concentration and exchange fronts are very sharp, in contrast to
the more diffuse tracer fronts. After 5 days less than 25% of the profile has been reclaimed to
exchangeable sodium percentage less than 15 (which has been the criteria defining the designation
sodic soil). The selected cation exchange capacity of 10 mmol kg-1 is relatively low. Selection of ahigher exchange capacity and associated hydraulic properties of a finer textured soil would enhanceboth the time required for infiltration, as well as quantity of water required for reclamation.

Figure 24. Exchangeable concentrations of sodium (mol kgw-1) profiles at times: a) 0.5, b) 1, c) 3,
and d) 5 days for example 4.

58

4.5. Example 5: Leaching of the Uranium Tailings
4.5.1. Problem Definition
This problem was inspired by, and is a modification of (to make it more realistic), a problem
reported by Yeh and Tripathi [1991]. The problem considers the release and migration of
uranium from a simplified uranium mill tailings pile towards a river. The schematic of thetransport domain is shown in Figure 25. The mill tailings pile is located adjacent to a surface thatslopes down to a river. The medium has the hydraulic properties of a loam with the saturated
hydraulic conductivity of KS = 3.78 m/day.
Cauchy Flow
= 0.139 dm/day
Mill Tailing
Pile

Infiltration Rate
= 0.0139 dm/day
Dirichlet Flow
Nodes

240 dmPumping Well

39 dm
1,050 dm

Figure 25 Problem Description for the Uranium Tailing Problem [Yeh and Tripathi, 1991].
The horizontal bottom of the region is impermeable. The vertical left-edge has the Dirichletboundary condition (Variable Head 1) with a groundwater table 12 m above the bottom of thetransport domain (exactly in the middle of the boundary). The top boundary (except for the milltailing pile and the river) has a flux boundary condition (Variable Flux 2) with a net rainfall rateof 0.139 cm/day. The horizontal region on the top of the mill tailings pile is a Cauchy flowboundary (Variable Flux 3) with an infiltration rate of 1.39 cm/day. The nodes on the verticalline on the right side and the nodes on the river bottom have the Dirichlet boundary condition(Variable Head 1) reflecting the position of water in the river (4.5 m above the bottom of thetransport domain). A hypothetical pumping well with a withdrawal rate of 271.58 cm2/day islocated at (x, z) = (400, 100). The region is discretized using a structural FE mesh with 1564
elements and 852 nodes.
Table 3 lists chemical reactions and their thermodynamic equilibrium constants considered inthis example. For reactive hydrogeochemical transport, the problem consists of eightcomponents: Total H, Total O, Ca, C, uranium, sulfate, phosphate, and Fe. A total of 35 species
and 14 minerals is defined for the problem; redox reactions were not considered. Table 3 lists
chemical reactions involved in this example.

59

Table 3. Reaction network for the uranium tailing problem.
Reaction

No

Log K

H2O ⇔ H+ + OHCa2+ + CO32- ⇔ CaCO3 (aq)Ca2+ + H+ + CO32- ⇔ CaHCO3+
Ca2+ + SO42- ⇔ CaSO4 (aq)Ca2+ + 2H+ + PO43- ⇔ CaH2PO4+
Ca2+ + PO43- ⇔ CaPO4Ca2+ + H+ + PO43- ⇔ CaHPO4 (aq)Ca2+ + H2O ⇔ H+ + CaOH+
Fe2+ + SO42- ⇔ FeSO4 (aq)Fe2+ + H2O ⇔ H+ + FeOH+
Fe2+ + 2H2O ⇔ 2H+ + Fe(OH)2 (aq)Fe2+ + 3H2O ⇔ 3H+ + Fe(OH)3Fe2+ + 4H2O ⇔ 4H+ + Fe(OH)42UO22+ + H2O ⇔ H+ + (UO2)(OH)+
2UO22+ + 2H2O ⇔ 2H+ + (UO2)2(OH)22+
3UO22+ + 4H2O ⇔ 4H+ + (UO2)3(OH)42+
3UO22+ + 5H2O ⇔ 5H+ + (UO2)3(OH)5+
4UO22+ + 7H2O ⇔ 7H+ + (UO2)4(OH)7+
3UO22+ + 7H2O ⇔ 7H+ + (UO2)3(OH)7UO22+ + CO32- ⇔ (UO2)(CO3)(aq)
UO22+ + 2CO32- ⇔ (UO2)(CO3)22UO22+ + 3CO32- ⇔ (UO2)(CO3)34-

(R1)
(R2)
(R3)
(R4)
(R5)
(R6)
(R7)
(R8)
(R9)
(R10)
(R11)
(R12)
(R13)
(R14)
(R15)
(R16)
(R17)
(R18)
(R19)
(R20)
(R21)
(R22)

-14.00
3.22
11.43
2.31
20.96
6.46
15.08
-12.582.20-9.50-20.57-31.00-43.00-5.30-5.68-11.88-15.82-21.90-28.34
9.65
17.08
21.70

2UO22+ + CO32- + 3H2O ⇔ 3H+ + (UO2)2(CO3)(OH)3UO22+ + SO42- ⇔ (UO2)(SO4) (aq)UO22+ + 2SO42- ⇔ (UO2)(SO4)222H+ + UO22+ + PO43- ⇔ H2(UO2)(PO4)+
3H+ + UO22+ + PO43- ⇔ H3(UO2)(PO4)2+
Ca2+ + 4H+ + UO22+ + 2PO43- ⇔ CaH4(UO2)(PO4)22+
Ca2+ + 5H+ + UO22+ + 2PO43- ⇔ CaH5(UO2)(PO4)23+
H+ + CO32- ⇔ HCO32H+ + CO32- ⇔ H2CO3(aq)H+ + SO42- ⇔ HSO4-

(R23)
(R24)
(R25)
(R26)
(R27)
(R28)
(R29)
(R30)
(R31)
(R32)

-1.18
2.95
4.00
23.20
22.90
45.24
46.00
10.32
16.67
1.99

Aqueous Complexation Reactions60

H+ + PO43- ⇔ HPO422H+ + PO43- ⇔ H2PO43H+ + PO43- ⇔ H3PO4
Precipitation-Dissolution Reactions

(R33)
(R34)
(R35)

12.35
19.55
21.74

Ca2+ + SO42- ⇔ CaSO4(s)Ca2+ + CO32- ⇔ CaCO3(s)5Ca2+ + 3PO43- + H2O ⇔ H+ + Ca5(OH)(PO4)3(s)Fe2+ + CO32- ⇔ FeCO3(s)Ca2+ + 2UO22+ + 2PO43- ⇔ Ca(UO2)2(PO4)2(s)4Ca2+ + H+ + 3PO43- ⇔ Ca4H(PO4)3(s)Ca2+ + H+ + PO43- ⇔ CaH(PO4)(s)Ca2+ + 2H2O ⇔ 2H+ + Ca(OH)2(s)3Fe2+ + 2PO43- ⇔ Fe3(PO4)2(s)Fe2+ + 2H2O ⇔ 2H+ + Fe(OH)2(s)UO22+ + 2H2O ⇔ 2H+ + (UO2)(OH)2(s)UO22+ + CO32- ⇔ (UO2)(CO3)(s)Fe2+ + 2UO22+ + 2PO43- ⇔ Fe(UO2)2(PO4)2 (s)H+ + UO22+ + PO43- ⇔ H(UO2)(PO4)(s)

(R36)
(R37)
(R38)
(R39)
(R40)
(R41)
(R42)

4.62
8.48
40.47
10.50
48.61
48.20
19.30

(R43)
(R44)
(R45)
(R46)
(R47)
(R48)
(R49)

-21.9033.30-12.10
-5.40
14.11
46.00
25.00

The composition of the pore water in the tailings, pore water outside of the tailing pile and therecharge water are given in Table 4. Cauchy boundary conditions are considered on all
boundaries where boundary conditions are specified. A total of 1000 days was simulated.
Table 4. Initial and boundary compositions of recharge water and pore water in the tailings
and regions outside of the tailing for the uranium tailing problem.
Species
Ca2+
CO32UO22+
PO43SO42H+
Fe2+

Inside the Tailing
1.0 x 10-2
1.0 x 10-2
5.0 x 10-4
1.0 x 10-6
2.0 x 10-1
2.0 x 10-1
3.5 x 10-2

Outside the Tailing
1.0 x 10-2
1.5 x 10-3
1.0 x 10-7
1.0 x 10-6
2.0 x 10-2
1.0 x 10-3
1.0 x 10-7

61

Recharge Water
1.0 x 10-3
1.5 x 10-3
1.0 x 10-8
1.0 x 10-6
1.0 x 0-41.ox 10-3
1.0x 10-7

4.5.2. Input
Project Manager (File->Project Manager)
Button "New"New Project (or File->New)
Name: UTailing
Description: " Mille Tailing Pile - transient water flow and reactive transport"
Working Directory: Temporary – exists only when the project is open
Button Next"
Domain Type and Units (Edit->Domain Geometry->Domain Type and Units)
Type of Geometry: 2D - Simple
2D-Domain Options: 2D - Vertical Plane XZ
Units: cm
Initial Workspace: X-Min=0, X-Max=10,500, Z-Min=0, Z-Max=2,400 cm
Button "Next"
Regular Domain Definition (Edit->Domain Geometry->Simple Domain)
Dimensions: Lx = 10,500 cm, Lz = 2,400 cm, Slope α = 0
Button "Next"
Main Processes (Edit->Flow and Transport Parameters->Main Processes)
Check "Water Flow"
Check "Solute Transport"
Check “HP2”
Button "Next"
Time Information (Edit->Flow and Transport Parameters->Time Information)
Time Units: Days
Final Time: 1,000 (d)Initial Time Step: 0.0001 (d)Minimum Time Step: 0.00001 (d)Maximum Time Step: 500 (d)Check Time-Variable Boundary Conditions
Number of Time-Variable Boundary Records: 2
Button "Next"
Output Information (Edit->Flow and Transport Parameters->Output Information)
Print Options:
Uncheck T-Level Information
Check Interval Output
Time Interval: 1 (d)Check Screen Output
Check Press Enter at the End
Print Times: Count: 20

62

UpdateDefault
Button "Next"
HP2/3 – Print and Punch Controls
Check: "Make GNUplot Templates"
This allows easy visualization of time series and profile data for variables, which aredefined in the SELECTED_OUTPUT section below in this dialog window and also
defined later in the Additional Output part of the Solute Transport – HP2
Definitions dialog.
Button "Next"
Water Flow – Iteration Criteria (Edit->Flow and Transport Parameters->Water Flow
Parameters->Iteration Criteria)
Leave default values
Button "Next"
Water Flow – Soil Hydraulic Model (Edit->Flow and Transport Parameters->Water Flow
Parameters->Hydraulic Properties Model)
Leave default values as follows:
Radio button - van Genuchten-Mualem
No Hysteresis
Button "Next"
Water Flow - Soil Hydraulic Parameters (Edit->Flow and Transport Parameters->Water Flow
Parameters->Soil Hydraulic Parameters)
Number of Materials: 2
Catalog of Soil Hydraulic Properties: Loam (both lines)
Name 1: Loam
Name 2: Mill Tailing Pile
Ks: 378 (cm/d) for both materials
Button "Next"
Solute Transport – General Info (Edit->Flow and Transport Parameters->Solute TransportParameters->General Information)
Number of Solutes: 8
Button "Next"
Solute Transport – HP1 Components and Database Pathway
Database Pathway: Create an empty database, which only defines a few obliged mastercomponents, such as Alkalinity, C, E, H, H(0), H(1), O, O(-2), O(0), H+, e-, H2O, andCO3-2 (see below) (Database Empty)
Six Components: Total_O, Total_H, Ca, C, U, P, S, Fe
Check: "Create PHREEQC.IN file using HYDRUS GUI"
Button "Next"

63

Database for the UTailing example:
SOLUTION_MASTER_SPECIES
Alkalinity CO3-2
1.0
C
CO3-2
2.0
E
e0.0
H
H+
-1.
H(0)
H2
0.0
H(1)
H+
-1.
O
H2O
0.0
O(-2)
H2O
0.0
O(0)
O2
0.0
SOLUTION_SPECIES
H+ = H+
log_k
0.0-gamma9.0
0.0
e- = elog_k
0.0
H2O = H2O
log_k
0.0
CO3-2 = CO3-2
log_k
0.0
-gamma 5.4
0.0
2 H+ + 2 e- = H2
log_k
-3.15
delta_h -1.759 kcal
2H2O = O2 + 4H+ + 4elog_k-86.08delta_h 134.79 kca

50.05
61.0173
0.0
1.008
1.008
1.008
16.00
18.01616.00

50.05
12.0111
0.0
1.008

16.00

Solute Transport – HP2/3 Definitions
Select Additions to Thermodynamic Database
SOLUTION_MASTER_SPECIES
Fe
Fe+2
Ca
Ca+2
U
UO2+2
S
SO4-2
P
PO4-3

0
0
0.0
0.0
2.0

SOLUTION_SPECIES
Ca+2 = Ca+2
log_k
0.0
Fe+2 = Fe+2
log_k
0.0
PO4-3 = PO4-3
log_k
0.0
SO4-2 = SO4-2
log_k
0.0
UO2+2 = UO2+2
log_k
0.0
CO3-2 + Ca+2 = CaCO3
log_k
3.22
CO3-2 + Ca+2 + H+ = CaHCO3+
log_k
11.43
Fe+2 + H2O = FeOH+ + H+
log_k
-9.5
Ca+2 + SO4-2 = CaSO4
log_k
2.31
Ca+2 + 2H+ + PO4-3 = CaH2PO4+

64

55.84740.08
238.0290
96.061630.9738

55.84740.08
238.0290
32.06430.9738log_k
20.96
Ca+2 + PO4-3 = CaPO4log_k
6.46
Ca+2 + H+ + PO4-3 = CaHPO4
log_k
15.08
Fe+2 + SO4-2 = FeSO4
log_k
2.2
Fe+2 + 2H2O = Fe(OH)2 + 2H+
log_k-20.57
Fe+2 + 3H2O = Fe(OH)3- + 3H+
log_k
-31
Fe+2 + 4H2O = Fe(OH)4-2 + 4H+
log_k
-43
H2O + UO2+2 = (UO2)(OH)+ + H+
log_k
-5.3
2H2O + 2UO2+2 = (UO2)2(OH)2+2 + 2H+
log_k
-5.68
4H2O + 3UO2+2 = (UO2)3(OH)4+2 + 4H+
log_k-11.88
5H2O + 3UO2+2 = (UO2)3(OH)5+ + 5H+
log_k-15.82
7H2O + 4UO2+2 = (UO2)4(OH)7+ + 7H+
log_k
-21.9
7H2O + 3UO2+2 = (UO2)3(OH)7- + 7H+
log_k-28.43CO3-2 + UO2+2 = (UO2)(CO3)
log_k
9.65
2CO3-2 + UO2+2 = (UO2)(CO3)2-2
log_k
17.08
3CO3-2 + UO2+2 = (UO2)(CO3)3-4
log_k
21.7
2UO2+2 + CO3-2 + 3H2O =(UO2)2(CO3)(OH)3- + 3H+
log_k
-1.18
UO2+2 + SO4-2 =(UO2)(SO4)
log_k
2.95
UO2+2 + 2SO4-2 = (UO2)(SO4)2-2
log_k
4
2H+ + UO2+2 + PO4-3 = H2(UO2)(PO4)+
log_k
23.2
3H+ + UO2+2 + PO4-3 = H3(UO2)(PO4)+2
log_k
22.9
Ca+2 + 4H+ + UO2+2 + 2PO4-3 =CaH4(UO2)(PO4)2+2
log_k
45.24
Ca+2 + 5H+ + UO2+2 + 2PO4-3 =CaH5(UO2)(PO4)2+3
log_k
46
H+ + CO3-2 =HCO3log_k
10.32
2H+ + CO3-2 =
H2CO3
log_k
16.67
H+ + SO4-2 =HSO4log_k
1.99
H+ + PO4-3 =HPO4-2
log_k
12.35

PHASES
gypsumCaSO4 = Ca+2 +
log_k
-4.62
calciteCaCO3 = Ca+2 +
log_k
-8.48
Hydroxyapatite

SO4-2

CO3-2

65

Ca5(OH)(PO4)3 + H+
= 5Ca+2 + 3PO4-3 +log_k-40.47
Siderite
FeCO3 = Fe+2 + CO3-2
log_k
-10.5
Autunite
Ca(UO2)2(PO4)2 = Ca+2 + 2UO2+2 + 2PO4-3
log_k-48.61
Ca4H(PO4)3
Ca4H(PO4)3 = 4Ca+2 + H+ + 3PO4-3
log_k
-48.2
CaH(PO4)
CaH(PO4) = Ca+2 + H+ + PO4-3
log_k
-19.5
Portlandite
Ca(OH)2 + 2H+ = Ca+2 + 2H2O
log_k
21.9
Vivianite
Fe3(PO4)2 = 3Fe+2 + 2PO4-3
log_k
-33.3
Fe(OH)2
Fe(OH)2 + 2H+ = Fe+2 + 2H2O
log_k
12.1
beta-Schoepite
UO2(OH)2 + 2H+ = UO2+2 + 2H2O
log_k
5.4
Rutherfordine
UO2CO3 = UO2+2 + CO3-2
log_k-14.11
Bassetite
Fe(UO2)2(PO4)2 = Fe+2 + 2UO2+2 + 2PO4-3
log_k
-46
H(UO2)(PO4)
H(UO2)(PO4) = H+ + UO2+2 + PO4-3
log_k
-25
O2(g)
O2 = O2log_k-2.960delta_h -1.844 kcal
H2(g)H2 = H2
log_k-3.150delta_h -1.759 kcal

H2O

Select Definitions of Solution Composition
Define the initial condition, i.e., the solution composition of water in the soil, with
the identifier 1001:• Bring it in equilibrium with gypsum, calcite, and O(0), to be in
equilibrium with the partial pressure of oxygen in the atmosphere
Define the initial condition, i.e., the solution composition of water in the minetailing, with the identifier 1002:• pH 2.3• Bring it in equilibrium with O(0), to be in equilibrium with the partialpressure of oxygen in the atmosphere• Bring it in equilibrium with gypsum and calcite

66

•High level of U (=5e-4 mol/kgw)

Define the boundary condition, i.e., the solution composition of water entering thesoil column, with the identifier 3001:• Ca-Cl solution• Use pH to obtain the charge balance of the solution• Adapt the concentration of O(0) and C(4) to be in equilibrium with theatmospheric partial pressure of oxygen and carbon dioxide, respectively
solution 1001 soil
-temp 25
-units mol/kgw-pH 2 charge
Ca 1E-2 calcite
C 1.5E-3
U 1E-7
P 1E-6
S 2E-1 gypsum
Fe 1E-7
O(0) 1 O2(g) -0.68 # O(0) initially in equilibrium with a partialpressure of oxygen of 10^-0.68 atm
end
solution 1002 mine tailing-temp 25
-units mol/kgw-pH 2.3
Ca 1E-2 charge
C 1E-2
U 5E-4
P 1E-6
S 2E-1
Fe 3.5E-2
O(0) 1 O2(g) -0.68 # O(0) initially in equilibrium with a partialpressure of oxygen of 10^-0.68 atm
equilibrium_phases 1002
gypsum 0 3.7E-3
calcite 0 0
save solution 1002
end
solution 3001 boundary condition-temp 25
-units mol/kgw-pH 7 charge
Ca 1E-3
C 1.5E-3
U 1E-8
P 1E-6
S 1E-4Fe 1E-7

Select Geochemical Model
Define for each node the geochemical model. Note that the initial amount of amineral must be defined as mol/1 dm³ soil. There is calcite (4.7e-4 mol/dm³ soil)67

in the soil and gypsum (3.7e-3 mol/dm³ soil) in the waste zone. Many othermineral phases (see their names below) are allowed to precipitate. Additionally,
indicate to PHREEQC, that this is a two-dimensional project (added by default).
equilibrium_phases 1001 soil
-material 1
calcite
0 4.7E-4
gypsum0 0
Autunite 0 0
Bassetite 0 0
Ca4H(PO4)3 0 0
CaH(PO4) 0 0
Fe(OH)2
0 0
Hydroxyapatite 0 0
Portlandite 0 0
Rutherfordine 0 0
Siderite 0 0
Vivianite 0 0
H(UO2)(PO4) 0 0
beta-Schoepite 0 0
equilibrium_phases 1002 waste zone
-material 2
calcite0 0
gypsum
0 3.7E-3
Autunite 0 0
Bassetite 0 0
Ca4H(PO4)3 0 0
CaH(PO4) 0 0
Fe(OH)2
0 0
Hydroxyapatite 0 0
Portlandite 0 0
Rutherfordine 0 0
Siderite 0 0
Vivianite 0 0
H(UO2)(PO4) 0 0
beta-Schoepite 0 0

Select Additional Output
Define the additional output to be written to selected output files.
selected_output-equilibrium_phases

calcite gypsum
Siderite

Rutherfordine

Button "Next"
Solute Transport - Solute Transport Parameters (Edit->Flow and Transport Parameters>Solute Transport Parameters->Solute Transport Parameters)
Bulk D. = 1.5 (g/cm³)
Longitudinal Dispersivity, Disp.L = 250 cm
Transverse Dispersivity, Disp.T = 25 cm
Molecular Diffusion Coefficient for Liquid Phase, Diffus.W.=068

Button "Next"
Time-Variable Boundary Conditions* (Edit->Flow and Transport Parameters->Solute
Transport Parameters->Variable Boundary Conditions)

Button "Next"*

Why are we using Time-Variable Boundary Conditions, when the fluxes and concentrations are constant in time?
HYDRUS reports actual and cumulative water (and solute fluxes) for different boundary parts with different typesof boundary conditions. If we select everywhere Constant BC, then we would get only one total flux integrated overall boundary parts. By using different boundary types, HYDRUS will report various fluxes for different boundaryparts.

Rectangular Domain Spatial Discretization (Edit->FE-Mesh->FE-Mesh Parameters)
Horizontal Discretization in X
Count = 55
Horizontal Discretization in Z
Count = 16x[cm]:

0, 250, 500, 750, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2750, 3000, 3250, 3500,
3750, 4000, 4250, 4500, 4750, 5000, 5200, 5400, 5600, 5800, 6000, 6200, 6400, 6600,
6800, 7000, 7200, 7400, 7550, 7700, 7850, 8000, 8150, 8300, 8450, 8600, 8750, 8900,
9050, 9200, 9350, 9500, 9625, 9750, 9875, 10000, 10125, 10250, 10375, 10500
dz[cm]: 19*0, -35, -70, -140, -210, -310, -410, -535, -660, -770, -880, -1005, -1130, -1190, 1250, -1295, -1340, -1370, -1400, -1430, -1460, -1490, -1520, -1550, -1580, -1610, 1640, -1670, -1700, -1730, -1760, -1785, -1810, -1830, -1850, -1865, -1880
z[cm]: 2400, 2350, 2300, 2200, 2100, 2000, 1900, 1800, 1650, 1500, 1250, 1000, 750, 500,
250, 0
Button "OK"69

Click on the FE-Mesh Tab under the View Window.
Zoom on the right side of the transport domain)
From the Tool Bar select the command Select by Rhomboid ((or Edit->Select->Select by Rhomboid)
Select the 6 elements vertically from the top and 4 element horizontally from the right.
On the Navigator Bar click on Remove Selected Elements () to
get the domain as shown below.

70Material Distribution
Click on the Domain Properties Tab under the View Window.
On the Navigator Bar click on Domain Properties – Material Distribution (or Insert>Domain Properties->Material Distribution).
On the Edit Bar select Material 2 (Mill Tailing) and assign it as shown below

Nodal Recharge
On the Navigator Bar click on Domain Properties – Nodal Recharge (or Insert->Domain
Properties->Nodal Recharge).
Double Click on the node with coordinates x=4,000 cm and z=1,000 cm.
In the Edit Nodal Recharge window set Value to -271.58 cm2/d.
Subregions
On the Navigator Bar click on Domain Properties – Subregions (or Insert->Domain
Properties->Subregions).
Click on Set Subregions = Materials (Edit bar)On the Edit Bar select Subregion 2 (Mill Tailing) and assign it in the same part of thedomain as Material 2.
Observation Nodes
On the Navigator Bar click on Domain Properties – Observation Nodes (or Insert>Domain Properties->Observation Nodes).
Click on the Insert Observation Node () command on the Edit Bar
and insert observation nodes at similar locations as shown below.

Initial Conditions
Click on the Initial Conditions under the View Window.
On the Navigator Bar click on Pressure Head.
Select the entire transport domain

71

From the Edit Bar select the command Set Pressure Head IC (Insert->Initial Condition->Pressure Head/Water Content)
In the Water Flow Initial Condition window :Check Equilibrium from the lowest located nodal point
Check Slope in X-direction
Set the slope to -4.4o
Set Bottom Pressure Head Value to 1,200 cm

On the Navigator Bar click on Solution Composition.
Assigned the Solution Compositions as follows

Boundary Conditions
Click on the Boundary Conditions under the View Window.
72

) (or

On the Navigator Bar click on Water Flow.
Assign BC as follows:

On the Navigator Bar click on Solute Transport.
Assign Third-Type BC with the following pointers as shown below:

Run Calculations
Click the Calculate Current Project command (>Calculate Current Project)(Execution time on 3 GHz PC – 468 s)) on the Toolbar (or Calculation-

4.5.3. Output
The steady-state pressure heads and velocity fields are depicted in Figure 26. Uranium
concentration profiles are shown in Figure 27. pH , calcite, and gypsum profiles are shown in
Figure 28.

73

Figure 26. The steady-state pressure head (cm) (top) and flux (cm/d) (bottom) profiles for theTailing Pile Leaching example.

Figure 27. Uranium concentration profiles at time 0 (top), 250 (middle), and 500 (bottom) d for
Tailing Pile Leaching example.

74

Figure 28. pH (top), calcite (mol/L) (middle), and gypsum (mol/L) (bottom) profiles after 1000 d
for the Tailing Pile Leaching example.

75

76

References
Jacques, D., and J. Šimůnek, User Manual of the Multicomponent Variably-Saturated Flow andTransport Model HP1, Description, Verification and Examples, Version 1.0, SCK•CEN-BLG998, Waste and Disposal, SCK•CEN, Mol, Belgium, 79 pp., 2005.
Jacques, D., J. Šimůnek, D. Mallants, and M. Th. van Genuchten, Operator-splitting errors incoupled reactive transport codes for transient variably saturated flow and contaminanttransport in layered soil profiles, J. Contam. Hydrology, 88, 197-218, 2006.
Jacques, D., J. Šimůnek, D. Mallants, and M. Th. van Genuchten, Modeling coupledhydrological and chemical processes: Long-term uranium transport following mineralphosphorus fertilization, Vadose Zone Journal, 7(2), 698-711, 2008.
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