OPEN REPORTSCK•CEN-BLG-1068
09/DJa/P-129

Notes on HP1 – a software package
for simulating variably-saturated
water flow, heat transport, solutetransport, and biogeochemistry inporous media

HP1 Version 2.2

Diederik Jacques and Jiri Šimůnek1
1

Department of Environmental Sciences
University of Riverside
Riverside, CA, USA
Jiri.Simunek@ucr.edu

January, 2010

SCK•CEN
Boeretang 200
BE-2400 Mol
Belgium

IPA/PAS

OPEN REPORT OF THE BELGIAN NUCLEAR RESEARCH CENTRESCK•CEN-BLG-1068
09/DJa/P-129

Notes on HP1 – a software package forsimulating variably-saturated water
flow, heat transport, solute transport,
and biogeochemistry in porous media

HP1 Version 2.2

Diederik Jacques and Jiri Šimůnek1
1

Department of Environmental Sciences
University of Riverside
Riverside, CA, USA
Jiri.Simunek@ucr.edu

January, 2010
Status: Unclassified
ISSN 1379-2407

SCK•CEN
Boeretang 200
BE-2400 Mol
Belgium

IPA/PAS© SCK•CEN
Studiecentrum voor Kernenergie
Centre d’étude de l’énergie Nucléaire
Boeretang 200
BE-2400 Mol
Belgium
Phone +32 14 33 21 11
Fax +32 14 31 50 21
http://www.sckcen.beContact:
Knowledge Centre
library@sckcen.be
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All property rights and copyright are reserved. Any communication or reproduction of this document, andany communication or use of its content without explicit authorization is prohibited. Any infringement tothis rule is illegal and entitles to claim damages from the infringer, without prejudice to any other right incase of granting a patent or registration in the field of intellectual property.
SCK•CEN, Studiecentrum voor Kernenergie/Centre d'Etude de l'Energie Nucléaire
Stichting van Openbaar Nut – Fondation d'Utilité Publique - Foundation of Public Utility
Registered Office: Avenue Herrmann Debroux 40 – BE-1160 BRUSSEL
Operational Office: Boeretang 200 – BE-2400 MOL

v

Table of contents
1
2Introduction .............................................................................................................................1
Running HP1 from the HYDRUS-1D Graphical User Interface ............................................2
2.1
Differences Between Version 2.2.002 of HP1 (HYDRUS-1D Version 4.13) and Older
Versions of HP1 and HYDRUS-1D............................................................................................2
2.2
Manage HP1 Projects ......................................................................................................3
2.3
Create a New Project.......................................................................................................3
2.4
Define the Physical Part of a Project...............................................................................3
2.5
Define the Thermodynamic Database .............................................................................4
2.6
Define Components.........................................................................................................4
2.7
Create the phreeqc.in File................................................................................................5
2.7.1
Options to create and modify the phreeqc.in file ....................................................5
2.7.2
Structured phreeqc.in File .......................................................................................6
2.7.3
Modify the Structured phreeqc.in File ....................................................................82.7.4
Define Additions to the Thermodynamic Database ................................................82.7.5
Define the Composition of Initial and Boundary Solutions....................................92.7.6
Define the Geochemical Model...............................................................................92.7.7
Define the Output ..................................................................................................10
2.8
Define the Spatial Distribution of the Initial Solutions and Temporal VariationS of theBoundary Solutions ...................................................................................................................10
2.9
Control Output...............................................................................................................11
2.9.1
Punch Times and Locations ..................................................................................112.9.2
Selected Output .....................................................................................................13
2.9.3
Print Options .........................................................................................................13
2.9.4
PHREEQC Dump..................................................................................................13
2.9.5
HP1 Output Files with Geochemical Information.................................................13
2.10 Create Templates to Produce Graphs with GNUPLOT ................................................15
2.11 Running a HP1 Project..................................................................................................16
2.12 Looking at Selected Numerical Results ........................................................................16
2.13 Help File........................................................................................................................16
3
Examples Installed with HP1 ................................................................................................18
3.1
EqCl: Physical Equilibrium Transport of Cl for Steady-State Flow Conditions ..........18
3.2
NEQCL: Physical Nonequilibrium Transport of Cl for Steady-State Flow Conditions18
3.3
TRANSCL: Physical Nonequilibrium Transport of Chloride for Transient Flow
Conditions .................................................................................................................................19
3.4
STADS: Transport of nonlinearly adsorbed contaminant for steady-state flow
conditions ..................................................................................................................................20
3.5
STDECAY: Transport of Nonlinearly Adsorbing Contaminant with First-Order Decay
for Steady-State Flow Conditions .............................................................................................21
3.6
SEASONCHAIN: First-Order Decay Chain of Nonlinearly Adsorbing Contaminants
During Unsteady Flow ..............................................................................................................22
3.7
CATEXCH: Transport of Heavy Metals Subject to Multiple Cation Exchange ..........23
3.8
MINDIS: Transport with Mineral Dissolution..............................................................27
3.9
MCATEXCH: Transport of Heavy Metals in a Porous Medium with a pH-Dependent
Cation Exchange Complex........................................................................................................28
4
Step-By-Step Instructions for Selected Examples ................................................................32
4.1
Dissolution of Gypsum and Calcite ..............................................................................32
4.1.1
Problem Definition................................................................................................32
4.1.2
Input ......................................................................................................................32
4.1.3
Output....................................................................................................................35

vi

4.1.4
Overview of Selected Results: Profile Data..........................................................38
4.1.5
Overview of Selected Results: Time Series ..........................................................39
4.2
Dissolution of Gypsum and Calcite and Transport of Cd .............................................40
4.2.1
Problem Definition................................................................................................40
4.2.2
Input ......................................................................................................................40
4.2.3
Output....................................................................................................................42
4.3
Dissolution of gypsum and calcite and transport of Cd – the effect of higher Cl
concentrations on the Cd mobility ............................................................................................43
4.3.1
Problem Definition................................................................................................43
4.3.2
Input ......................................................................................................................43
4.3.3
Output....................................................................................................................44
4.4
Transport and Cation Exchange (Single Pulse).............................................................46
4.4.1
Problem Definition................................................................................................46
4.4.2
Input ......................................................................................................................46
4.4.3
Output....................................................................................................................49
4.5
Transport and Cation Exchange (Multiple Pulses) .......................................................51
4.5.1
Problem Definition................................................................................................51
4.5.2
Input ......................................................................................................................51
4.5.3
Output....................................................................................................................53
4.6
Transport of Cations and Heavy Metals in a Multi-Layered Soil .................................54
4.6.1
Background ...........................................................................................................54
4.6.2
Problem Definition................................................................................................54
4.6.3
Cation Exchange Capacities..................................................................................56
4.6.4
Input ......................................................................................................................56
4.6.5
Output....................................................................................................................62
4.7
Horizontal Infiltration of Multiple Cations and Cation Exchange................................64
4.7.1
Problem Definition................................................................................................64
4.7.2
Definition of the Geochemical Model and its Parameters ....................................64
4.7.3
Input ......................................................................................................................66
4.7.4
Output....................................................................................................................69
4.8 U Transport and Surface Complexation........................................................................72
4.8.1
Problem definition.................................................................................................72
4.8.2
Calculation of the Size of the Surface Sorption Site.............................................72
4.8.3
Input ......................................................................................................................73
4.8.4
Output....................................................................................................................76
4.9
First-Order Kinetic PCE Degradation Network ............................................................77
4.9.1
Background ...........................................................................................................77
4.9.2
Problem Definition................................................................................................78
4.9.3
Input ......................................................................................................................78
4.9.4
Output....................................................................................................................83
4.10 First-Order Kinetic PCE Degradation Network: Leaching of Initial PCE Source........85
4.10.1
Background and Problem Definition.....................................................................85
4.10.2
Input ......................................................................................................................85
4.10.3
Output....................................................................................................................87
4.11 First-Order Kinetic PCE Degradation Network: Initial Source Trapped in Immobile
Water Phase...............................................................................................................................89
4.11.1
Problem Definition................................................................................................89
4.11.2
Input ......................................................................................................................89
4.11.3
Output....................................................................................................................90
4.12 Coupled Nta Degradation and Biomass Growth ...........................................................92
4.12.1
Background ...........................................................................................................92

vii

5

4.12.2
Problem Definition................................................................................................92
4.12.3
Input ......................................................................................................................93
4.12.4
Output....................................................................................................................96
References .............................................................................................................................98

viii

ix

ABSTRACT
Jacques, D., and J. Šimůnek, 2010. Notes HP1– a software for simulating variably-saturated
water flow, heat transport, solute transport, and biogeochemistry in porous media. Version 2.2.
SCK•CEN, Mol, Belgium, BLG-1068.
HP1 is a comprehensive modeling tool in terms of processes and reactions for simulating
reactive transport and biogeochemical processes in variably-saturated porous media. HP1 resultsfrom coupling the water and solute transport model HYDRUS-1D (Šimůnek et al., 2009a) and
PHREEQC-2 (Parkhurst and Appelo, 1999). This note provides an overview of how to set up
and execute a HP1 project using version 2.2.002 of HP1 and version 4.13 of the graphical userinterface (GUI) of HYDRUS-1D.
Version 2.2 of HP1 is embedded in the graphical interface of version 4.13 of HYDRUS-1D. The
graphical user interface of HYDRUS-1D (H1D GUI) provides support to the HP1 code in orderto• Manage HP1 projects using the Project Manager• Create new HP1 projects• Define the physical part (water flow, solute transport, heat transport)• Define the thermodynamic database• Define the components for the transport problem• Create the phreeqc.in input fileo Define additions to the thermodynamic databaseo Define the composition of the initial and boundary solutions
o Define the geochemical modelo Define the output• Define the spatial distribution of the initial solutions and the temporal variation of theboundary solutions• Control output• Create templates to produce graphs with GNUPLOT• Run HP1 projects• Display selected numerical results• Display the help file
A large part of this note are step-by-step instructions for selected examples involving mineraldissolution and precipitation, cation exchange, surface complexation and kinetic degradation
networks. The implementation of variably-saturated flow conditions, changing boundary
conditions, a layered soil profile or immobile water is also illustrated.

Keywords
HP1, reactive transport model, variably-saturated water flow, multicomponent solute transport,heat transport, biogeochemical processes, numerical model, HYDRUS-1D

x

Warranty
The software has been verified against selected test cases. However, no warranty is given that the
program is completely error-free. If you do encounter problems with the code, find errors, or
have suggestions for improvement, please contact one of the authors at:
Diederik Jacques
Tel: +32-14-333209
Fax: +32-14-323553
Email: djacques@skcen.be
Jirka Šimůnek
Tel: 1-951-827-7854
Fax: 1-951-827-3993
Email: jiri.simunek@ucr.edu

xi

LIST OF TABLES
Table 1 Hydrological, transport, and reaction parameters for the example SEASONCHAIN............................... 22
Table 2 Initial and inflow concentrations for the example CATEXCH................................................................... 24
Table 3 pH and solution concentrations used in the simulation (µmol l-1). ............................................................ 29
Table 4 Soil hydraulic properties and cation exchange capacities of five soil layers (Seuntjens, 2000). ............... 29
Table 5 Overview of aqueous equilibrium reactions and corresponding equilibrium constants (data fromphreeqc.dat database, Parkhurst and Appelo, 1999). ...................................................................................... 29
Table 6 Log K parameters for multi-site exchange complex.................................................................................... 30
Table 7 Soil hydraulic and other properties of six soil horizons (from Seuntjens, 2000). ...................................... 55
Table 8 Initial pH and concentration for 9 components. ......................................................................................... 55
Table 9 Definition of parameters and their values for the PCE biodegradation problem (from Case 1 and 2 in
Sun et al., 2004). Rate parameters are for a reference temperature of 20°C. ................................................ 78

xii

xiii

LIST OF FIGURES
Figure 1 - Time series of Cl at two depths for the example EQCL.
18
Figure 2 - Time series of Cl at two depths for the example NEQCL.
19
Figure 3 – Time series of Cl concentrations in the mobile phase at four depths for the example TRANSCL. 20
Figure 4 – Profile plots of Cl concentrations in the mobile phase (left) and immobile phase (right) at selected
times for the example TRANSCL.
20
Figure 5 – Profiles of Pola concentrations for the example STADS.
21
Figure 6 – Profiles of Pola concentrations for the example STDECAY.
21
Figure 7 – Profile plots of Conta, Contb and Contc concentrations at selected times for the example
SEASONCHAIN.
23
Figure 8 – Time series of pH (top left), total concentrations of Ca (top right), Cd (bottom left), and Zn(bottom right) at four depths for the example CATEXCH.
24
Figure 9 – Time series of molalities of sorbed K (top left), Ca (top right), Cd (bottom left), and Zn (bottom
right) at four depths for the example CATEXCH.
25
Figure 10 – Profiles of pH (top left), Ca (top right), Cd (bottom left), and Zn (bottom right) at selected times
for the example CATEXCH.
26
Figure 11 – Profiles of molalities of sorbed K (top left), Ca (top right), Cd (bottom left), and Zn (bottom right)
at selected times for the example CATEXCH.
27
Figure 12 – Profiles of pH (top), total Si (middle left) and Al (middle right) concentrations, and amounts ofamorf SiO2 (bottom left) and gibbsite (bottom right) at selected times for the example MINDIS.
28
Figure 13 – Outflow curves of pH (left) and Cd (right) for the example MCATEXCH.
30
Figure 14 – Profiles of pH (top left), Cd (top right), the fraction of deprotonated cation exchange sites (bottom
left), and the fraction of cation exchange sites with Cd (bottom right) at selected times for the example
MCATEXCH.
31
Figure 15 – 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 theamount of calcite (bottom right) at selected print times during dissolution of calcite and gypsum.
38
Figure 16 – Time series of pH (top left), total aqueous C concentration (top right), total aqueous Caconcentration (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.
39
Figure 17 – Profiles of total aqueous Cd (top left), the amount of otavite (top right), and the percentage of Cd
in solution (bottom) at selected print times during dissolution of calcite and gypsum and Cd transport.
42
Figure 18 – Comparison between a simulation when a solution with a low Cl concentration enters the system(described in paragraph 4.2, left figures) and a simulation when a solution with a high Cl concentrationenters the system after 1 day (described in paragraph 4.3, right figures) for time series of Cd
concentrations at different depths (top figures) and profiles of the amount of otavite (bottom figures). 44
Figure 19 – Time series of Cl at selected depths (observation nodes) for the example described in section 4.3.
45
Figure 20 – Outflow concentrations of Cl, Ca, Na, and K for the single-pulse cation exchange example.
50
Figure 21 – Time series of K concentrations at four depths for the multiple-pulse cation exchange example. 53
Figure 22 – Outflow concentrations for the multiple-pulse cation exchange example.
54
Figure 23 – Time series of Cl (top left), Ca (top right), and Cd (bottom) concentrations at selected depths(observation nodes) for the example described in section 4.6.
63
Figure 24 – Profiles of water content (top left), and total aqueous concentrations of Cl, Na, K, Ca and Mg atselected print times during horizontal infiltration of multiple cations (the example is described in
section 4.7).
70
Figure 25 – Profiles of sorbed concentrations of Na, K, Ca, and Mg at selected print times during horizontal
infiltration of multiple cations (the example is described in section 4.7).
71
Figure 26 – Profiles of aqueous concentration of U for the example described in section 4.8.
76
Figure 27 – Perchloroethylene (PCE) degradation pathway. (Figure from Schaerlaekens et al., 1999).
77
Figure 28 – Degradation pathway of PCE using first-order rate constants.
78
Figure 29 – Time series of Dcecis (left) and Vc (righ ) at selected depths (observation nodes) for the example
described in section 4.9.
83
Figure 30 – Profiles of Tce (left) and Eth (righ ) at selected print times for the example described inparagraph 4.9.
84
Figure 31 – Outflow curves for the example described in section 4.9.
84
Figure 32 – Profiles of the solid phase PCE_lq (left) and the aqueous concentrations of Pce (right) at selected
print times for the example described in section 4.10.
87

xiv

Figure 33 – Outflow concentrations for the example described in section 4.10.
88
Figure 34 – Profiles of the solid phase PCE_lq (top), aqueous concentrations of Pce in the mobile (right) andimmobile (right) water phases at selected print times for the example described in section 4.11.
91
Figure 35 – Outflow concentrations for the example described in section 4.11.
91
Figure 36 – Time series of Nta concentrations and biomass at selected depths (observation nodes) for theexample described in section 4.12.
96
Figure 37 – Profiles of Nta concentrations and biomass at selected print times for the example described in
section 4.12.
97

1

1 Introduction
HP1 is a comprehensive modeling tool in terms of processes and reactions for simulating
reactive transport and biogeochemical processes in variably-saturated porous media. HP1 resultsfrom coupling the water and solute transport model HYDRUS-1D (Šimůnek et al., 2009a) and
PHREEQC-2 (Parkhurst and Appelo, 1999). The combined code contains modules simulating(1) transient water flow in variably-saturated media, (2) transport of multiple components, (3)mixed equilibrium/kinetic biogeochemical reactions, and (4) heat transport. HP1 is a significant
expansion of the individual HYDRUS-1D and PHREEQC programs by combining, andpreserving, most of the features and capabilities of the two codes into a single numericalsimulator. The code uses the Richards equation for variably-saturated flow and advectiondispersion type equations for heat and solute transport. The program can also simulate a broad
range of low-temperature biogeochemical reactions in water, the vadose zone and in groundwater systems, including interactions with minerals, gases, exchangers, and sorption surfaces,
based on thermodynamic equilibrium, kinetics, or mixed equilibrium-kinetic reactions. Various
applications of HP1 were presented by Jacques and Šimůnek (2005), Jacques et al. (2006,
2008a,b) and Šimůnek et al. (2006, 2009b).
The first version of HP1 was released in November 2004 and is described in Jacques andŠimůnek (2005). The HP1 version 2.2.002 (released November 2009) is different with respect tofollowing points, amongst others:
•
•
•
•
•
•
•

includes the computational module of version 4.0 of HYDRUS-1D
includes version 2.15.0-2697 of PHREEQC-2
is based on the source code of the HYDRUS-1D computational module rewritten in
double precisionconsiders new components Total_O, Total_H, and Charge to allow simulations of redox
processes and surface complexation
allows initial concentrations of components to be zerodefines solution compositions using solution composition numbers
is fully integrated in the graphical user interface of version 4.13 of HYDRUS-1D.

This note provides an overview of how to set up and execute a HP1 project using version 2.2.002
of HP1 and version 4.13 of the graphical user interface (GUI) of HYDRUS-1D. Chapter 2
describes how an HP1 project is created, modified, and executed using GUI of HYDRUS-1D.
Chapter 3 shows the implementation of the verification examples from the first manual (Jacquesand Šimůnek, 2005) using version 2.2 of HP1. Chapter 4 describes a number of simple HP1
projects and gives step-by-step instructions for their implementation using HP1.

22 Running HP1 from the HYDRUS-1D Graphical User Interface
HP1, version 2.2.002 (released 31.10.2009), is embedded in version 4.13 of HYDRUS-1D(released 31.10.2009). The graphical user interface of HYDRUS-1D (H1D GUI) provides
support to the HP1 code in order to
•
•
•
•
•
•

•
•
•
•
•
•

Manage HP1 projects using the Project Manager
Create new HP1 projects
Define the physical part (water flow, solute transport, heat transport)
Define the thermodynamic database
Define the components for the transport problem
Create the phreeqc.in input fileo Define additions to the thermodynamic databaseo Define the composition of the initial and boundary solutions
o Define the geochemical modelo Define the output
Define the spatial distribution of the initial solutions and the temporal variation of theboundary solutions
Control output
Create templates to produce graphs with GNUPLOTRun HP1 projects
Display selected numerical results
Display the help file

In chapter 4, a number of step-by-step examples are given to illustrate the implementation andexecution of a HP1 project using the H1D GUI. A short description of the provided support isgiven in this chapter.
2.1
Differences Between Version 2.2.002 of HP1 (HYDRUS-1D Version 4.13) and Older
Versions of HP1 and HYDRUS-1D
Previous releases of HP1 were less embedded in the H1D GUI. No H1D GUI support wasavailable for the geochemical part of HP1 projects of versions 1.0 and 2.0. Users had to prepare
the HP1 input files species.in and phreeqc.in in an ASCII text editor or graphical user interface
for PHREEQC and saved them in the project directory. In addition, a path.dat file was needed to
identify the project directory. HP1 itself was executed from the Windows Explorer or theCommand Prompt. Detailed instructions were given in the HP1 manual (Jacques and Šimůnek,2005).
Starting with version 4.0 of HYDRUS-1D, the H1D GUI provided more support to HP1. One
additional pre-processing menu allowed one to define the thermodynamic database and thecomponents, i.e., the species.in file was automatically created by the H1D GUI. In addition, HP1
projects were managed by the Project Manager and HP1 was executed from the H1D GUI. LaterHYDRUS-1D versions (starting with version 4.06) also included an option to create a templateof the phreeqc.in file, but editing of this file was still done outside of the H1D GUI.

3

In version 4.13 of HYDRUS-1D, the user can create a HP1 project using the H1D GUI without
the need to use any external programs. The GUI of version 4.13 of HYDRUS-1D allows one tocreate a structured phreeqc.in file, which can be defined and/or modified using the H1D GUI(see paragraph 2.7). Note that projects created with previous versions of HP1 or HYDRUS-1D
can be opened and executed with the GUI of version 4.13 of HYDRUS-1D. Furthermore, theuser can still create the phreeqc.in file in an ASCII text editor or graphical user interface of
PHREEQC.
Another major difference between version 2.2.002 of HP1 and its older versions is the possibility
to define the composition of the initial and boundary solutions in the phreeqc.in file. However,the spatial distribution of the initial solutions and the temporal variations of the boundary
solutions are defined using the H1D GUI. In previous releases of HP1, initial solutions were
defined only in the phreeqc.in file, whereas boundary solutions were defined via the H1D GUI.
Version 2.2.002 of HP1 defines solutions in terms of solution composition numbers instead ofconcentrations. Solution composition numbers are used to define the spatial distribution of theinitial solutions and the temporal variations of the boundary solutions in the H1D GUI.
Concentrations of the components of a solution composition are defined in the phreeqc.in file.
2.2

Manage HP1 Projects

HP1 projects are managed in the same way as HYDRUS-1D projects using the Project Manager.
The Project Manager is used to manage data of existing projects, and to locate, open, delete,copy, or rename projects.
2.3

Create a New Project

A new HP1 project is created using the button "New" in the Project Manager. After defining a
name and a description of a project, the Main Process dialog window allows users to select the
HP1 model from available solute transport models:

2.4

Define the Physical Part of a Project

The physical part of a HP1 project (water flow, solute transport and heat transport) is definedusing the H1D GUI in the same way as for HYDRUS-1D projects. Depending on the choice of
selected processes, models, and options, a number of pre-processing menus will be displayed.

4

Options, which are not available in HP1, are disabled in the H1D GUI. The main difference
between HYDRUS-1D and HP1 projects is that the Solute Transport - Solution Reaction
Parameters dialog window, which is not needed in HP1, is replaced by the HP1 Definitions
dialog window.
2.5

Define the Thermodynamic Database

The definition of the thermodynamic database is in the HP1 Components and Database
Pathway dialog window. Using the "Browse" button, it is possible to select a thermodynamic
database. Note that the format of the thermodynamic data in the database must follow theconventions of PHREEQC (see PHREEQC-2 manual, Parkhurst and Appelo, 1999). A numberof thermodynamic databases is installed with HYDRUS-1D.
2.6

Define Components

The element names of components are defined in the HP1 Components and Database Pathway
dialog window. The number of components is specified in the Solute Transport - General
Information dialog window.
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 H1D GUI in the editor Addition to thethermodynamic database of the HP1 Definitions dialog window, see paragraph 2.7.4). 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 isused. In the non-electrical surface complexation model, positive or negative charges on
the surface are not compensated. Therefore the aqueous phase also has a negative or
positive charge. Note that the complete system (surface + aqueous phase) is chargebalanced.
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. HP1 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 HP1 Components and Database Pathway
dialog windows).

5

2.7

Create the phreeqc.in File

2.7.1 Options to create and modify the phreeqc.in file
The H1D GUI allows for three options to create the phreeqc.in file:•••

Create and modify the phreeqc.in file using the H1D GUI
Create the phreeqc.in file using the H1D GUI and modify it using an ASCII text editor or
the PHREEQC graphical user interface
Create and modify the phreeqc.in file using an ASCII text editor or the PHREEQC
graphical user interface

The selection of this option is done in the HP1 Components and Database Pathway dialog
window.

When the option "Create PHREEQC.IN file using HYDRUS GUI" is not selected, thephreeqc.in file has to be created and modified outside the H1D GUI:•

When the option "In Concentrations" is selected, the approach of specifying initial andboundary conditions as described in Jacques and Šimůnek (2005) has to be followed.
This implies that:• the phreeqc.in file has to be created and modified outside the H1D GUI,
• the composition of the boundary solutions has to be defined within the H1D GUI• the initial conditions and their spatial distributions have to be defined in thephreeqc.in file•

When the option "In Solution Compositions" is selected without the option "Create
PHREEQC.IN file using HYDRUS GUI", only solution composition numbers aredefined in the H1D GUI. Therefore:• the phreeqc.in file has to be created and modified outside the H1D GUI• the composition of the boundary solutions has to be defined in phreeqc.in using
specific solution composition numbers

6••

the temporal variation of the boundary solution is defined in the H1D GUI by
specifying the solution composition number corresponding to the solution
composition number defined in phreeqc.in
the initial conditions and their spatial distribution have to be defined in thephreeqc.in file

When the option "In Solution Composition" is selected together with the option "Create
PHREEQC.IN file using HYDRUS GUI", then:
•
•
•
•
•

the phreeqc.in file is a structured file, which is created and can be modified using the
HP1 Definitions dialog window and the H1D GUI.
the composition of the boundary solutions has to be defined in phreeqc.in using specificsolution composition numbers
the temporal variation of the boundary solutions is defined in the H1D GUI by specifying
the solution composition number corresponding to the solution composition number
defined in phreeqc.in
the initial solutions are defined in the phreeqc.in file using specific solution composition
numbers
the spatial distribution of the initial solutions is defined in the H1D GUI by specifying thesolution composition number in the soil profile corresponding to the solution composition
number defined in phreeqc.in

Note that the phreeqc.in file is automatically updated when changes are made in initial settings
in the H1D GUI (e.g., different material distributions, initial water contents, or spatial
distribution of initial solutions), but only for initial distribution of the solutions and the initialwater content.
Alternatively, the phreeqc.in file can be first created and saved using the H1D GUI when theoption "Create PHREEQC.IN file using HYDRUS GUI" is selected. The option “Create
PHREEQC.IN file using HYDRUS GUI" can then be deselected. The phreeqc.in file will not be
automatically updated any longer by the H1D GUI and can be modified outside the H1D GUI.
2.7.2 Structured phreeqc.in File

The structured phreeqc.in file consists of seven blocks. Each block starts with the identifier#HP1BEGIN and ends with the identifier #HP1END. The seven blocks are written in thissequence:
GENERAL

This block contains general information, such as the path to the
database, the project folder, a number of soil layers andcorresponding node numbers, and the project title. All thisinformation, except the last one, is saved as comments (i.e., withthe # sign in front). This block is automatically updated by the
HYDRUS GUI when the project is saved.

DATABASE

This block contains additions to the thermodynamic databasetypically defined using the following PHREEQC data blocks:
SOLUTION_MASTER_SPECIES,
SOLUTION_SPECIES,

7

PHASES,EXCHANGE_MASTER_SPECIES,
EXCHANGE_SPECIES,
SURFACE_MASTER_SPECIES,
SURFACE_SPECIES and RATES. The content is defined in theeditor Additions to Thermodynamic Database of the Solute
Transort – HP1 Definition dialog window.
OUTPUT

This block consists of two parts. The first part starts with the
PHREEQC keyword SELECTED_OUTPUT, followed by the
information defined in the HP1 – Print and Punch Controls
dialog window. This block is automatically updated by the
HYDRUS GUI when the project is saved. The second part contains
additional specifications to be written to the output files and istypically defined using the following PHREEQC data blocks:
USER_PUNCH, USER_PRINT, and SELECTED_OUTPUT. The
content is defined in the editor Additional Output of the Solute
Transport – HP1 Definitions dialog window.

SOLUTIONDEFINITION

This block contains the definitions of the initial solutions andboundary solutions. The latter is only read from the phreeqc.in
input file when the radio button In Solution Compositions in the
Solute Transport – HP1 Components dialog window is selected.
The content is defined in the editor Definitions of Solution
Composition of the Solute Transport – HP1 Definitions dialog
window.

INITIAL

This block contains definitions of the initial solutions for eachnode. The block starts with an END keyword. For each node, bothfor the mobile and immobile aqueous phases, a MIX – SAVE
statement is included with the following format: MIX
solution_number; solution_composition water_content; SAVESOLUTION solution_number; END, where solution_number is thesolution number (equal to the node number for the mobile aqueous
phase and to the node number + N for the immobile aqueous phase,where N is the number of nodes), solution_composition is thesolution composition number as defined in the H1D GUI (SoilProfile – Summary Soil Profile – Summary dialog window), andwater_content is the initial water content as defined in the H1D
GUI (either as the initial water content or calculated from the initialpressure head and soil retention parameters). This block is
automatically updated by the H1D GUI when the project is saved.

GEOCHEMICALThis block contains the definition of the geochemical model
typically using the following PHREEQC data blocks:
EQUILIBRIUM_PHASES,EXCHANGE,
SURFACE,KINETICS, and SOLID_SOLUTIONS. The content is defined in
the editor Geochemical Model of the Solute Transport – HP1
Definitions dialog window.

TRANSPORT

This block contains the keywords END, followed by PRINT with
the identifiers –reset and -warnings as defined in the HP1 – Print

8

and Punch Controls dialog window, and the keyword
TRANSPORT with –cells to define the number of nodes(information from the H1D GUI) and print-, punch- and dumprelated identifiers as defined in the HP1 – Print and Punch
Controls dialog window. All relevant identifiers for the
TRANSPORT keyword are defined using the H1D GUI. This block
is automatically updated by the H1D GUI when the project issaved.

2.7.3 Modify the Structured phreeqc.in File
The user can modify the phreeqc.in file using the four editors in the HP1 definitions dialog
window:

2.7.4 Define Additions to the Thermodynamic Database
Additional thermodynamic definitions are added to the phreeqc.in file (not to the thermodynamic
database file) using the editor Additions to Thermodynamic Database in the HP1 Definitions
dialog window. Typical PHREEQC data blocks used here are:
• SOLUTION_MASTER_SPECIES• SOLUTION_SPECIES• PHASES• EXCHANGE_MASTER_SPECIES• EXCHANGE_SPECIES• SURFACE_MASTER_SPECIES• SURFACE_SPECIES• RATES
Users are referred to the PHREEQC-2 manual (Parkhurst and Appelo, 1999) for the conventions
used for the input of thermodynamic data.

92.7.5 Define the Composition of Initial and Boundary Solutions
Compositions of the initial and boundary solutions are defined using the editor Definitions of
Solution Compositions in the HP1 Definitions dialog window. Typical PHREEQC data blocks
are SOLUTION and SOLUTION_SPREAD. The solution number refers to the solution
composition numbers of the initial and boundary solutions defined in the H1D GUI.
The following solution composition numbering is used throughout this manual:••••

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 upper boundary solutions
Numbers 4001 – 5000: to define lower boundary solutions

The link between the initial solution composition numbers and the spatial distribution is definedin the Soil Profile – Summary dialog window.
The link between the boundary solution composition numbers and the boundary conditions isdefined in the Solute Transport – Boundary condition dialog window or the Variable
Boundary Conditions dialog window.
2.7.6 Define the Geochemical Model
The definition of the geochemical model is done using the editor Geochemical Model in the HP1Definitions dialog window and it typically involves the following PHREEQC data blocks:• EXCHANGE• EQUILIBRIUM_PHASES• SURFACE• KINETICS• SOLID_SOLUTIONSThere is currently no automatic link between the definition of different materials in the H1D GUI
and the chemical heterogeneity in the geochemical model. Thus, numbering of geochemical
keywords must refer to the node numbers. If the material distribution is changed in the H1D
GUI, the user must change the numbering of the geochemical model using the editor
Geochemcial Model in the HP1 Definitions dialog window.
When the user defines a material distribution in the H1D GUI, a template of it withcorresponding node numbers is incorporated in the text editor when he clicks the "Add" buttonof the corresponding geochemical model. Note that this template is not automatically updated
when the material distribution or number of nodes are changed.
The numbering of the geochemical model is• 1 to number of nodes for the mobile water phase• number of nodes + 1 to 2 * number of nodes for the immobile water phase10

2.7.7 Define the Output
The user can define additional output using the editor Additional output in the HP1 Definitions
dialog window by using the PHREEQC data blocks SELECTED_OUTPUT and USER_PUNCH.
Depending on the options selected in the HP1 – Print and Punch Control dialog window, anumber of output files is created.
HP1 specific output files have the same structure as the "selected output" files of PHREEQC.
They are tab-delineated and can be opened using ASCII text editors or EXCELL.
2.8
Define the Spatial Distribution of the Initial Solutions and Temporal VariationS of
the Boundary Solutions
The following methods are available to define the spatial distribution of the initial solutions:•

Using the Soil Profile – Graphical Editor module. After selecting
Condition -> Initial Conditions -> Concentration
Concentration number: 1
Edit Conditiona range of nodes can be selected and a solution composition number can be assigned forthe mobile water phase. To assign a solution composition number for the immobile waterphase:
Condition -> Initial Conditions -> Sorbed Concentration
Concentration number: 1
Edit Condition•

Via the Soil Profile – Summary dialog window. Solution composition numbers aredefined in the column "Cnc. Comp." for the mobile water phase and in the column "Im.
C. Comp." for the immobile water phase.

In case of a constant boundary condition, the boundary condition is assigned in the Solute
Transport – Boundary Conditions dialog window by specifying the solution composition
number. Solution composition numbers 3001 and 4001 are specified in the example below:

11

In case of time variable boundary conditions, the boundary condition is assigned in the Variable
Boundary Conditions dialog window. For example:

2.9

Control Output

The H1D GUI allows users to specify times and locations, for which output variables are to beprinted into output files. This is defined in the HP1 Print and Punch Controls dialog window:

2.9.1 Punch Times and Locations
The Punch Times and Locations section defines how variables selected by in the PHREEQC data
blocks SELECTED_OUTPUT and USER_PUNCH are to be printed. Depending on the choice of
the user, data is written in a series of ASCII files with tab-delimited columns.

12

If the option "Controlled by HYDRUS" is checked, punch times and locations (i.e., observation
nodes) are defined using the H1D GUI:•Time series at observation points:o Locations of the observation points are defined in the "Soil Profile – Graphical
Editor" module, which can be selected from the pre-processing menu:
Conditions -> Observation Points
Inserto Print times are defined in the Print Times dialog window:
Print Options -> T-level information; and/or
Print Options -> Print at Regular Time Interval•Profiles at specific times:o Print times are defined in the Print Times dialog window:
Print Times
Number of Print Times
Select Print Times

Depending on the options selected by the user, a number of output files is created:••"Observ. Nodes Printed to Different Files": Time series for different observation nodes
are printed into different files"Mobile and Immobile Cells in Different Files": Time series and profile data for themobile and immobile water phases are printed into different files.

Following files are created:
•
•

•

•

If both options are uncheckedo Obs_node_chem.out for the time serieso Node_inf_chem.out for the profile data
If "Observ. Nodes Printed to Different Files" is checked:o Obs_node_chemx.out for the time series for the observation point with a node
number x. One file is created for each observation pointo Node_inf_chem.out for the profile data
If "Mobile and Immobile Cells in Different Files" is checked:o Obs_node_chem_m.out for the time series of the mobile water phaseo Obs_node_chem_im.out for the time series of the immobile water phaseo Node_inf_chem_m.out for the profile data of the mobile water phaseo Node_inf_chem_im.out for the profile data of the immobile water phaseIf both options are checkedo Obs_node_chemxm.out for the time series of the mobile water phase for theobservation point with a node number x. One file is created for each observation
point.
o Obs_node_chemxim.out for the time series of the immobile water phase for theobservation point with a node number x. One file is created for each observation
point.

13o Node_inf_chem_m.out for the profile data of the mobile water phaseo Node_inf_chem_im.out for the profile data of the immobile water phase
If "controlled by PHREEQC" is checked, the user can defined a series of punch cells (e.g., "1 2 525", or "1-5 25") and a punch frequency. The punch frequency indicates the number of time
steps between printing of data. All data are printed in a single output file. The user specifies thename of the output file in the File name text box of the Selected Output section.
2.9.2 Selected Output
This submenu allows specifying a number of output variables to be written to the selected output
files. Additional variables can be specified using the PHREEQC data blocks
SELECTED_OUTPUT and USER_PUNCH in the editor Additional Output of the HP1Definitions dialog window. It is not needed to specify a file name in the editor Additional
Output.
2.9.3 Print Options
This submenu allows specifying the print times and locations to write geochemical information
to the standard PHREEQC text output file phreeqc.out.
Print locations can be linked to the HYDRUS observation points specified in the Soil Profile –Graphical Editor module using the option "HYDRUS Observation Nodes". Alternatively, aseries of node numbers can be defined.
Print times can be linked to the specified print options in the Print Options dialog window.
Alternatively, a print frequency can be defined.
2.9.4 PHREEQC Dump
The dump files created by PHREEQC give a complete geochemical state for all nodes at a given
time step. It is formatted as a PHREEQC input file and can thus be used to restart a HP1
calculation after failure (some adaptations may be necessary). More information is given in the
PHREEQC manual.
There are options to link the times when a dump file should be created to the print times definedin the Print Options dialog window.
2.9.5 HP1 Output Files with Geochemical Information

Following output files are created by HP1 (in addition to the output files created by the regularroutines of the HYDRUS program):• Phreeqc.out: the standard text output file of PHREEQC. This file contains information ondifferent calculations steps, warnings, and a full description of the geochemical

14

calculations. The amount of information written to the phreeqc.out file can be controlledusing the PHREEQC data block PRINT. Specific user-defined output in the phreeqc.out
output file can be defined using the PHREEQC data block USER_PRINT. When theradio button No Printing in phreeqc.out is selected in the HP1 – Print and Punch
Controls dialog window, the output is generated only during the initialization of the
project (i.e., for the PHREEQC commands defined in the blocks GENERAL to
GEOCHEMICAL in the Phreeqc.in Input File), but not during the TRANSPORT
calculations. This option is recommended because, otherwise, an enormous amount of
output will be generated during the transport calculations. The running time will also
increase when all the geochemical information is written into phreeqc.out.
• Selected output file (xxx.hse): The name of the selected output file is defined in the File
Name text box of the HP1 – Print and Punch Controls dialog window. Information,
which is printed into this file is: status, solution number, time, depth, options selected in
the Selected Output section of the HP1 – Print and Punch Controls dialog window, andoptions the user defines using the PHREEQC data block SELECTED_OUTPUT in the
text editor Additional Output of the Solute Transport – HP1 Definitions dialog window.
When the user selects only the option that punch times and locations are controlled by
HYDRUS (see the HP1 – Print and Punch Controls dialog window), the selected
output file contains only information for the initial PHREEQC calculations, i.e., the
PHREEQC calculations before the TRANSPORT keyword. Geochemical information
during the transport calculations is saved in output files described below. When the user
selects the option that punch times and locations are controlled by PHREEQC (see theHP1 – Print and Punch Controls dialog window), geochemical information during thetransport calculations is also printed in the selected output file for the locations and times
defined in the text editors Punch Cells and Punch Frequency in the HP1 – Print
Information dialog window.
• Obs_node_chem.out,
obs_node_chemx.out,
obs_nod_chem_m.out,
obs_nod_chem_im.out, obs_node_chem_mx.out, and obs_node_chem_imx.out: These arefiles containing time series of the geochemical variables at the observation nodes definedin the Soil Profile – Graphical Editor module. The content is identical to the selected
output file, but information is only written during the transport calculations. The exact
names of the files created depend on the options the user selected in the HP1 – Print andPunch Controls dialog window (see paragraph 2.9.1).
• Nod_inf_chem.out, nod_inf_chem_m.out, and nod_inf_chem_im.out: These are files
containing profile information of the geochemical variables for the Print Times defined in
the Print Information dialog window. The content is identical to the selected output file,
but information is only written during the transport calculations. The exact names of thefiles created depend on the options the user selected in the HP1 – Print and Punch
Controls dialog window (see paragraph 2.9.1).
• Phreeqc.dmp: This is a file which contains complete geochemical conditions at a specifictime (as defined in the HP1 – Print and Punch Controls dialog window). This file canbe used to start a new simulation. Note that the dump file was created for transport
simulations with PHREEQC, and thus some modifications for the use with HP1 may beneeded.
• Phreeqc.log: This file contains information about each calculation. The information
includes the number of iterations in revising the initial estimates of the master unknowns,

15

the number of Newton-Raphson iterations, and the iteration at which any infeasible
solution was encountered while solving the system of nonlinear equations (An infeasible
solution occurs if no solution to the equality and inequality constraints can be found.). At
each iteration, the identity of any species that exceeds 30 mol (an unreasonably large
number) is written to the log file and noted as an "overflow". Any basis switches arenoted in the log file. The phreeqc.log file is created when the identifier –logfile is true
under the PHREEQC data block KNOBS.
2.10

Create Templates to Produce Graphs with GNUPLOT

If the options "Observ. Nodes Printed to Different Files" and "Mobile and Immobile Cells in
Different Files" are checked in the HP1 - Print and Punch Controls dialog window, the user
can also check the option "Make GNUplot Tempates" in the same dialog window. HP1 creates aseries of templates *.plt, two for each variable printed in the selected output files. Thesevariables are specified in the Selected Output section of the HP1 - Print and Punch Controls
dialog window and using the PHREEQC data block SELECTED_OUTPUT and USER_PUNCH in
phreeqc.in or the editor Additional output in the HP1 Definitions dialog window.
The name of the template file can consists of up to four parts, separated by an underscore:• pd or ts: These two template files are made for each variable.
o The file, which begins with "pd", contains information to produce depth profilesof a particular variable at selected times. The times are specified as the Print
Times in the Print Information dialog window.
o The file, which begins with "ts", contains information to produces time series of aparticular variable at selected observation points. The observation points aredefined in the Soil Profile – Graphical Editor module. The times are defined in
the Print Options of the Print Information dialog window.
• Type of a variable:o Name of the variable: pH, pe, Temperature, Total alkalinity, Ionic strength, massof water, Electrical balance, Percent error on electrical balance,o Type of the variable: tot: total aqueous concentration (-totals in SELECTED_OUTPUT) mol: molality (-molalities in SELECTED_OUTPUT) act: activity (-activities in SELECTED_OUTPUT) eq: amount of an equilibrium phase [mol/1000 cm³] (-equilibrium_phases
in SELECTED_OUTPUT)
 d_eq: change in amount of an equilibrium phase [mol/1000 cm³/time] unit(-equilibruim_phases in SELECTED_OUTPUT) si: saturation index of an equilibrium phase (-saturation_indices in
SELECTED_OUTPUT) kin: amount of a kinetic reactant [mol/1000 cm³] (-kinetics in
SELECTED_OUTPUT) d_kin: change in amount of a kinetic reactant [mol/1000 cm³/time] (kinetics in SELECTED_OUTPUT)
 ss: amount of a component in a solid solution [mol/1000 cm³] (solid_solutioins in SELECTED_OUTPUT)
 iso: isotopes (-isotopes in SELECTED_OUTPUT) calc: value of a calculated variable (-calculate_value in
SELECTED_OUTPUT)

16



•
•

user: values of the punch variables in the PHREEQC USER_PUNCH data
block
Name of a variable (e.g., Ca in case –totals, or Ca+2 in case of –molalities)m, im: m indicates values in the mobile water phase, im indicates values in the immobile
water phase.

A specific format of the headings in the PHREEQC data block USER_PUNCH can be used forappropriate definitions of texts at axes in the GNUPLOT templates. An underscore (“_”) istranslated to a space and the symbol “@” separates the name of a variable from its unit. Thus, forthe heading Total_Cd@µmol_per_kgw, the corresponding text in the GNUPLOT template is"Total Cd (µmol per kgw)".
To view a plot, the GNUPLOT code should be installed on the computer. GNUPLOT is freeware
software and can be downloaded from http://www.gnuplot.info/.
After opening the window version of GNUPLOT, wgnuplot.exe, a plot can be directly generatedby:File -> OpenBrowse to project directory
Open the template file of interest (*.plt)
The figure can be adapted using line commands (see tutorials of GNUPLOT on the internet).
After adaptations, the command lines can be saved to be used later on.
2.11

Running a HP1 ProjectA HP1 project is saved and executed as a regular HYDRUS-1D project. After saving input data,
all output files *.out are deleted. Output files with other extensions are not deleted. Note that the*.plt files are overwritten whenever input data are saved, as long as the option "Make GNUplot
Templates" in the HP1 Print and Punch Controls dialog window is checked.
2.12

Looking at Selected Numerical Results

After execution of the HP1 code, output variables related to the physical part of the project canbe inspected using the post-processing menus in the H1D GUI. The post-processing menu shows
only the total concentration of the components. Concentrations are always in moles/1000 cm³.
The user has to go to the project directory to look at the output of the geochemical variables. Partof the data can be visualized using GNUPLOT if GNUPLOT templates are generated.
2.13

Help File

The help file of the H1D GUI contains some information on HP1 and on the PHREEQC
keywords, identifiers and BASIC statements for the phreeqc.in file. Only some basic information
is included in the help file. The user is referred to the PHREEQC manual (Parkhurst and Appelo,

171999) for a full description of the PHREEQC keywords, identifiers and BASIC statements. Not
all keywords are yet documented in the help file of version 4.13 of HYDRUS-1D.

18

3 Examples Installed with HP1
These examples are the verification examples that were described in the manual of HP1, version
1.0 (Jacques and Šimůnek, 2005). Details on these examples and the corresponding HP1 input
are given in Jacques and Šimůnek (2005) and are not repeated here. Graphs given below weregenerated using the GNUPLOT software, based on the GNUPLOT templates generated with
HP11. Note that some figures differ from those in the manual of HP1, version 1.0 (Jacques andŠimůnek, 2005), because the temperature in the simulations reported here was 25ºC, whereas itwas 20ºC in the manual of version 1.0 of HP1.
3.1

EqCl: Physical Equilibrium Transport of Cl for Steady-State Flow Conditions2This problem simulates the transport of chloride (a geochemically inert tracer) during saturated
steady-state flow in a 20-cm long soil column. The saturated hydraulic conductivity Ks is 1 cm d1and the saturated water content is 0.5 cm3cm-3. The dispersivity is 8 cm. Initially, no Cl ispresent in the soil column. The Cl concentration in the percolating water is 1 mmol/kgw.
Simulated time series of Cl at two depths are shown in Figure 1.
Total concentration of Cl (mol/kg water)

0.001
0.00090.00080.00070.00060.00050.00040.00030.00020.000100

10-10.0 cm20
30
Time (days)

40

50-20.0 cm

Figure 1 - Time series of Cl at two depths for the example EQCL.

3.2
NEQCL: Physical Nonequilibrium Transport of Cl for Steady-State Flow
Conditions 3
This problem simulates the transport of chloride (a geochemically inert tracer) during saturated
steady-state flow in a 20-cm long soil column. The saturated hydraulic conductivity Ks is 1 cm d1and the saturated water content is 0.5 cm3cm-3. The dispersivity is 8 cm; the immobile watercontent (θim) is 0.1 cm3cm-3; and the first-order exchange coefficient (ω) is 0.01 d-1. Initially, no
Cl is present in the soil column. The Cl concentration in the percolating water is 1 mmol/kgw.
Simulated time series of Cl at two depths are shown in Figure 2.
1

Small changes in the GNUPLOT graphs presented here were made compared to the HP1 generated templates inorder to improve the layout for this report. Changes are related only to line colors, thickness, and text sizes. Thesechanges are easily done using the command line definition of GNUPLOT.
2
Verification problem 1 in Jacques and Šimůnek (2005).
3
Verification problem 1 in Jacques and Šimůnek (2005).

19

Total concentration of Cl (mol/kg water)

0.001
0.00090.00080.00070.00060.00050.00040.00030.00020.0001
0
0

10

20
30
Time (days)-10.0 cm

40

50

-20.0 cm

Figure 2 - Time series of Cl at two depths for the example NEQCL.

3.3
TRANSCL: Physical Nonequilibrium Transport of Chloride for Transient Flow
Conditions4This problem simulates the transport of chloride through a 1-m deep soil profile subject to atransient upper boundary condition given by daily values of precipitation and evaporation over a
300-d period. Physical nonequilibrium (i.e., the presence of immobile water in the soil profile)
was considered in this problem. The soil hydraulic properties are typical for a loamy soil (θr =0.078 cm3cm-3, θs = 0.43 cm3cm-3, α = 0.036 cm-1, n = 1.56, and Ks = 24.96 cm d-1, from Carsel
and Parish, 1988). Solute transport parameters were as follows: a dispersivity DL of 8 cm, animmobile water content θim of 0.05 cm3cm-3, and a first-order exchange coefficient ω of 0.0125
d-1. Precipitation and evaporation rates were typical for the Campine region in Belgium. The soil
profile was discretized into 100 elements of 1 cm each. Chloride was applied during the first 53
days of the simulation with a concentration of 0.1 mmol l-1. Time series of Cl outflow
concentrations and concentration profiles are shown in Figure 3 and Figure 4, respectively.

4

Similar to Verification problem 2 in Jacques and Šimůnek (2005).

Total concentration of Cl (mol/kg water)

20

6e-0055e-0054e-0053e-0052e-0051e-005
0
0

50

100

150
200
Time (days)-25.0 cm
-50.0 cm250

300

-75.0 cm-100.0 cm

Figure 3 – Time series of Cl concentrations in the mobile phase at four
depths for the example TRANSCL.
0 days10.00 days
30.00 days
50.00 days
100.00 days
200.00 days
300.00 days

Distance (cm)

-20

-40

-60

0

0 days10.00 days
30.00 days
50.00 days
100.00 days
200.00 days
300.00 days

-20

Distance (cm)

0

-40

-60

-80

-80

-100

-100
0
5e-0050.00010.00015
Total concentration of Cl (mol/kg water)

0
5e-0050.00010.00015
Total concentration of Cl (mol/kg water)

Figure 4 – Profile plots of Cl concentrations in the mobile phase (left) and immobile phase (right) atselected times for the example TRANSCL.

3.4
STADS: Transport of nonlinearly adsorbed contaminant for steady-state flow
conditions5
In this problem, saturated steady-state water flow and single-component transport of anonlinearly adsorbing contaminant (Pola) through a soil column of 1-m length for a period of1000 d are considered. Transport and reactive parameters are as followed: the saturated hydraulicconductivity Ks = 1 cm d-1, the saturated water content = 0.5 cm3 cm-3, the dispersivity = 1 cm,
the bulk density = 1.5 g cm-³, the Freundlich distribution coefficient = 5 cm³ g-1, and theFreundlich exponent is 0.8. Initially, no contaminant is present in the soil. The contaminantconcentration in the percolating water is 1 mol/kgw. Profiles of Pola concentrations are shown in
Figure 5.
5

Verification problem 3 in Jacques and Šimůnek (2005).

21

0

0 days
250.00 days
500.00 days
750.00 days
1000.00 days

Distance (cm)

-20

-40

-60

-80

-100
0
0.2
0.4
0.6
0.8
1
Total concentration of Pola (mol/kg water)

Figure 5 – Profiles of Pola concentrations for the example STADS.

3.5
STDECAY: Transport of Nonlinearly Adsorbing Contaminant with First-Order
Decay for Steady-State Flow Conditions6
In this problem, saturated steady-state water flow and single-component transport of anonlinearly adsorbing, first-order decaying contaminant (Pola) through a soil column of 1-m
length for a period of 1000 d are considered. Transport and reactive parameters are as followed:
the saturated hydraulic conductivity Ks = 1 cm d-1, the saturated water content = 0.5 cm3 cm-3,
the dispersivity = 1 cm, the bulk density = 1.5 g cm-³, the Freundlich distribution coefficient = 5
cm³ g-1, the Freundlich exponent is 0.8, and the first-order decay constant is 0.02 d-1.7 Initially,
no contaminant is present in the soil. The contaminant concentration in the percolating water is 1
mol/kgw. Profiles of Pola concentrations are shown in Figure 6.
0

0 days
250.00 days
500.00 days
750.00 days
1000.00 days

Distance (cm)

-20

-40

-60

-80

-100
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1
Total concentration of Pola (mol/kg water)

Figure 6 – Profiles of Pola concentrations for the example STDECAY.

6

Verification problem 4 in Jacques and Šimůnek (2005).
Note that in the manual of HP1 version 1.0 (Jacques and Simunek, 2005), the decay coefficient was wrongly
printed as 0.2 d-1 instead of 0.02 d-1.

7

22

3.6
SEASONCHAIN: First-OrderContaminants During Unsteady Flow8

Decay

Chain

of

Nonlinearly

AdsorbingIn this example we consider the transport of three (non)linearly adsorbing contaminants, Conta,
Contb, and Contc that are involved in a sequential first-order decay chain defined as:Conta↓( Kd ,nF )µ'w,k ,conta
⎯⎯⎯⎯
⎯
→
conta

SoraContaContb↓ ( K d , nF )µ'w, k ,contb
⎯⎯⎯⎯
⎯
→

Contc
↓ ( K d , nF )contb

SoraContbµ

w, k ,contc
⎯⎯⎯⎯
⎯
→

(1)

contc

SoraContc

where µw',k are the first-order rate constants connecting two contaminants, µw,k is the first-order
rate constant for Contc, Kd and nF are the Freundlich isotherm parameters for the threecontaminants, and SoraConta, SorbContb, and SorcContc are the three surface species related toConta, Contb, and Contc on three surfaces Sora, Sorb, and Sorc, respectively. Reaction
parameters for the three contaminants are given in Table 1. Model simulations were carried out
for a 1-m deep homogeneous soil profile during 1000 d, assuming transient flow. Upper
boundary conditions were taken as daily precipitation rates representative for the Campine
Region in Belgium. Evaporation was neglected during the simulations. The lower boundary
condition was defined as free drainage. A uniform initial pressure head of –60 cm was assumed
for the entire soil profile. For solute transport, the following initial and boundary conditions wereconsidered: (1) initial concentrations equal to zero for all three contaminants, (2) third-type
solute fluxes as the top boundary conditions with 1, 0.1, and 0 mol l-1 for Conta, Contb, andContc, respectively, and (3) zero-gradient bottom boundary condition. Profile concentrations atselected times are shown in Figure 7.
Table 1 Hydrological, transport, and reaction parameters for the example SEASONCHAIN.
Parameter
Hydraulic parametersθr (cm cm )θs (cm3cm-3)
α (cm-1)
3

-3

n (-)
Ks (cm d-1)
Transport parameters

DL (cm)ρ (g cm )-3

Reaction parameters

Kd (cm3 g-1)
nF (-)µw' ,k (d-1)µw,k (d-1)

Value
0.078
0.43
0.036
1.56
24.96

Conta

Contb

ContC

0.5
1
0.005
-

2.5
0.9
0.06
-

5
0.8
0.02

1
1.5

Kd is the Freundlich distribution coefficient, nF is the Freundlich exponent. µw,k and µ'w,k are
the first-order decay coefficients (see Eq. (1) ).

8

Verification problem 5 in Jacques and Šimůnek (2005).

23

Distance (cm)

-20

-40

-60

-20

-60

-80

-100

-100

0

-20

0 days
250.00 days
500.00 days
1000.00 days
1095.00 days

-40

-80

0
0.02 0.04
0.06
0.08
0.1
Total concentration of Contb (mol/kg water)

0
0.2
0.4
0.6
0.8
1
Total concentration of Conta (mol/kg water)

Distance (cm)00 days
250.00 days
500.00 days
1000.00 days
1095.00 days

Distance (cm)00 days
250.00 days
500.00 days
1000.00 days
1095.00 days

-40

-60

-80

-100
0
0.02 0.04
0.06
0.08
0.1
Total concentration of Contc (mol/kg water)

Figure 7 – Profile plots of Conta, Contb and Contc concentrations at selected times for the example
SEASONCHAIN.

3.7

CATEXCH: Transport of Heavy Metals Subject to Multiple Cation Exchange9

In this problem, the transport of ten components (Al, Br, Ca, Cd, Cl, K, Mg, Na, Pb, and Zn)
through a soil column is modeled. Initial and inflow concentrations of the ions are given in Table
2. The cation exchange capacity is equal to 0.011 mol/1000 cm³. The soil core has a length of 8
cm and is discretized into 40 cells of 0.2 cm. The flow velocity is 2 cm d-1 and the dispersivity is
2 cm. Simulations were performed for 15 days. The maximum time step used in HP1 was 0.015
d. Selected results are present in Figure 8 through Figure 11.

9

Verification problem 6 in Jacques and Šimůnek (2005).

24

Table 2 Initial and inflow concentrations for the example CATEXCH.
mmol l-1

Initial pore water Initial concentrations of Inflow concentrations
composition
exchangeable cations*
Al
0.5
0.92
0.1
Ca
1 10-42.88 10-4
5
Cd
0.09
0.17
0
K
2
1.06
0
Mg
0.75
1.36
1
Na
6
0.62
0
Pb
0.1
0.34
0
Zn
0.25
0.76
0
Br
11+
3.7
Cl
1 10-4
10
pH
5.5
2.9
*
Calculated in equilibrium with the initial pore water composition.
+
Br is used to impose a charge balance at pH of 5.5.

Total concentration of Ca (mol/kg water)

5.5
5

pH

4.5
4
3.5
3
2.5
0

3

6
9
Time (days)

15

0.00010
69Time (days)-2.0 cm
-4.0 cm

0.002

0.001

0
0

Total concentration of Zn (mol/kg water)

0.0002

3

0.003

3

6
9
Time (days)

12-6.0 cm-8.0 cm

15

12

15

-6.0 cm-8.0 cm

-2.0 cm
-4.0 cm

0.00030

0.004-6.0 cm-8.0 cm

-2.0 cm
-4.0 cm

Total concentration of Cd (mol/kg water)

12

0.005

0.00070.00060.00050.00040.00030.00020.000100369Time (days)-2.0 cm
-4.0 cm

12-6.0 cm-8.0 cm

Figure 8 – Time series of pH (top left), total concentrations of Ca (top right), Cd (bottom left), andZn (bottom right) at four depths for the example CATEXCH.

15

0.0025

0.01

0.002

0.008
CaX2 (mol/kg water)

KX (mol/kg water)

25

0.00150.001

0.0005

0.004

0.002

0

0
0

3

6
9
Time (days)

12

15

0

3

-6.0 cm-8.0 cm

-2.0 cm
-4.0 cm6
9Time (days)

12

15-6.0 cm-8.0 cm

-2.0 cm
-4.0 cm

0.00050.00180.0015
ZnX2 (mol/kg water)

0.0004
CdX2 (mol/kg water)

0.006

0.00030.00020.00010.00120.00090.00060.0003

0

0
0

3

6
9
Time (days)-2.0 cm
-4.0 cm

12-6.0 cm-8.0 cm

15

0

3

6
9
Time (days)-2.0 cm
-4.0 cm

12-6.0 cm-8.0 cm

Figure 9 – Time series of molalities of sorbed K (top left), Ca (top right), Cd (bottom left), and Zn(bottom right) at four depths for the example CATEXCH.

15

26

0
-1
-2
-3
-4
-5

-2
-3
-4
-5

-6

-6

-7

-7

-8

-8
2.5

3

3.5

4
pH

4.5

5

5.5

0

0

-2

-4
-5

-2
-3
-4
-5

-6

-6

-7

-7

-8

0 days0.50 days
1.00 days
3.00 days
9.00 days
15.00 days

-1

Distance (cm)-30.001 0.002 0.003 0.004 0.005
Total concentration of Ca (mol/kg water)0

0 days0.50 days
1.00 days
3.00 days
9.00 days
15.00 days

-1

Distance (cm)

0 days0.50 days
1.00 days
3.00 days
9.00 days
15.00 days

-1

Distance (cm)Distance (cm)00 days0.50 days
1.00 days
3.00 days
9.00 days
15.00 days

-8
00.00010.00020.0003
Total concentration of Cd (mol/kg water)

00.00010.00020.00030.00040.00050.0006
Total concentration of Zn (mol/kg water)

Figure 10 – Profiles of pH (top left), Ca (top right), Cd (bottom left), and Zn (bottom right) atselected times for the example CATEXCH.

27

0
-1
-2
-3
-4
-5

-2
-3
-4
-5

-6

-6

-7

-7

-8

-8
0

0.0005 0.001 0.0015 0.002 0.0025
KX (mol/kg water)

0

0

-2

-4
-5

0 days0.50 days
1.00 days
3.00 days
9.00 days
15.00 days

-2
-3
-4
-5

-6

-6

-7

-7

-8

0.01

-1

Distance (cm)-30.002 0.004 0.006 0.008
CaX2 (mol/kg water)0

0 days0.50 days
1.00 days
3.00 days
9.00 days
15.00 days

-1

Distance (cm)

0 days0.50 days
1.00 days
3.00 days
9.00 days
15.00 days

-1

Distance (cm)Distance (cm)00 days0.50 days
1.00 days
3.00 days
9.00 days
15.00 days

-8
00.0001 0.0002 0.0003 0.0004 0.0005
CdX2 (mol/kg water)

00.00030.00060.00090.00120.00150.0018
ZnX2 (mol/kg water)

Figure 11 – Profiles of molalities of sorbed K (top left), Ca (top right), Cd (bottom left), and Zn(bottom right) at selected times for the example CATEXCH.

3.8

MINDIS: Transport with Mineral Dissolution10

A 100-cm long soil column, consisting of amorphous SiO2 and gibbsite (Al(OH)3), is leachedwith a solution containing 5.10-7 mol l-1 Si, 1.10-6 mol l-1 Al, and 1.10-3 mol l-1 Na (to obtain an
inflow pH of 11.15). Initial concentrations are 1.76 10-3 mol l-1 Si, 8.87 10-9 mol l-1 Al, and 1 1012
mol l-1 Na, corresponding to a pH of 6.33. In each 1-cm thick cell, 0.015 mol amorphous SiO2
and 0.005 mol gibbsite is present. The flow velocity is 2 cm/day and the dispersivity is 1 cm.
Results are given in Figure 12.

10

Verification problem 7 in Jacques and Šimůnek (2005).

28

0Distance (cm)

-20
-40
-60
-80
-100
6

6.5

7

8

8.5
pH

9

8.00 days
15.00 days
25.00 days

9.5

10

10.5

11

50.00 days
100.00 days
150.00 days

0

0

-20

-20
Distance (cm)Distance (cm)

0 days2.00 days
4.00 days

7.5

-40
-60
-80

-60
-80

-100

-100
0

0.00050.001
0.00150.002
0.0025
Total concentration of Si (mol/kg water)
0 days2.00 days
4.00 days

8.00 days
15.00 days
25.00 days

0.003

0

50.00 days
100.00 days
150.00 days

0

0

-20

-20

-40
-60
-80

5e-0050.00010.000150.0002
Total concentration of Al (mol/kg water)
0 days2.00 days
4.00 days

Distance (cm)Distance (cm)-40

8.00 days
15.00 days
25.00 days

0.000250.00 days
100.00 days
150.00 days

-40
-60
-80

-100

-100
0

0.003

0 days2.00 days
4.00 days

0.006
0.009
0.012
SiO2(a) (mol/1000 cm³ of soil)
8.00 days
15.00 days
25.00 days

0.015

50.00 days
100.00 days
150.00 days

0

0.003
0.006
0.009
gibbsite (mol/1000 cm³ of soil)
0 days2.00 days
4.00 days

8.00 days
15.00 days
25.00 days

0.012

50.00 days
100.00 days
150.00 days

Figure 12 – Profiles of pH (top), total Si (middle left) and Al (middle right) concentrations, andamounts of amorf SiO2 (bottom left) and gibbsite (bottom right) at selected times for the example
MINDIS.

3.9
MCATEXCH: Transport of Heavy Metals in a Porous Medium with a pHDependent Cation Exchange Complex
This example considers the transport of several major cations (Na, K, Ca, and Mg) and three
heavy metals (Cd, Zn, and Pb) through a 50-cm deep multi-layered soil profile during
unsaturated steady-state flow. Each soil layer has different soil hydraulic properties and cationexchange capacities (CEC) (Table 4). The top 28 cm of the soil is assumed to be contaminatedwith three heavy metals (initial pH = 8.5), while an acid metal-free solution (pH = 3) infiltrates
into the soil (Table 3). Assuming that the cation exchange complex is associated solely with theorganic matter, CEC increases significantly with increasing pH due to the acid-base properties of

29

its functional groups. The higher the pH, the more functional groups of the organic matter are
deprotonated and thus the higher the cation exchange capacity. This behavior is represented by amulti-site cation exchange complex consisting of six sites, each having a different selectivity
coefficient for the exchange of protons (see Appelo et al., 1998). Finally, chloride is present in
the soil solutions, resulting in the formation of aqueous complexes with the heavy metals.
Table 4 Soil hydraulic properties and cation exchange capacities of five soil layers (Seuntjens, 2000).
Horizon
A
E
Bh1
Bh2
Bh/C

Layer
thickness
(cm)
13
10
5
5
17

θr

θs

α

n

Ks
(cm day-1)

l

0.065
0.035
0.042
0.044
0.039

0.476
0.416
0.472
0.455
0.464

0.016
0.015
0.016
0.028
0.023

1.94
3.21
1.52
2.01
2.99

93
311
39
860
1198

0.5
0.5
0.5
0.5
0.5

(cm-1)

Cation exchange
capacity(eq/1000 cm³ soil)
0.01830.01140.06640.05420.0116

Table 3 pH and solution concentrations used in the simulation (µmol l-1).
Solution
pH
Na*
K
Ca
Mg
0-28 cm depth
8.5
401.9
120
98
5
28-50 cm depth
8.5
454.0
120
98
5
Applied water
3.5
127.5
120
98
5
*
Concentration of Na is adjusted to obtain the desired pH.

Br
780
780
780

Cl
0
0
0

Cd
0.8
0.0
0.0

Pb
2.5
0
0

Zn
50
0
0

Table 5 Overview of aqueous equilibrium reactions and corresponding equilibrium constants (data fromphreeqc.dat database, Parkhurst and Appelo, 1999).
Nr
(1)
(2)
(3)
(4)
(5)

Aqueous speciation reaction
H2O = OH- + H+
Na+ + H2O = NaOH + H+
K+ + H2O = KOH + H+
Ca2+ + H2O = CaOH+ + H+
Mg2+ + H2O = MgOH+ + H+

(6)
(7)
(8)
(9)
(10)
(11)
(12)
(13)

X2+ + H2O = XOH+ + H+
X2+ + 2 H2O = X(OH)2 + 2 H+
X2+ + 3 H2O = X(OH)3- + 3 H+
X2+ + 4 H2O = X(OH)42- + 4 H+
X2+ + Cl- = XCl+
X2+ + 2 Cl- = XCl2
X2+ + 3 Cl- = XCl3X2+ + 4 Cl- = XCl42-

Cd-10.08-20.35-33.30-47.35
1.98
2.60
2.40
-

Log_K
-14
-14.18-14.46-12.78-11.44Pb-7.71-17.12-28.06-39.70
1.60
1.80
1.70
1.38

Zn
-8.96
-16.90-28.40-41.20
0.43
0.45
0.5
0.2

The soil profile is assumed to contain five distinct layers with different soil hydraulic properties
and cation exchange capacities. Table 4 gives thicknesses of the different horizons, parameters
for the van Genuchten’s equations for the water retention and hydraulic conductivity functions(van Genuchten, 1980), and the total cation exchange capacities. The higher exchange capacitiesof the Bh1 and Bh2 horizons reflect their enrichment with the immobilized organic matter. Flowis assumed to be steady at a constant flux of 0.05 m day-1 (18.25 m year-1), which causes the soil
profile to be unsaturated (water contents vary between 0.37 and 0.15 as a function of depth). The

30

bottom boundary condition for water flow is free drainage. HYDRUS-1D was used to calculate
the steady-state water content profile corresponding to these boundary conditions. The
dispersivity and diffusion coefficient were taken to be 0.05 m and 9.2 10-10 m2 s-1, respectively.
An overview of the considered aqueous equilibrium reactions is given in Table 5. The role ofchloride as a complexing agent is described by reactions (10) through (13). Other geochemical
reactions that are considered are the heterogeneous multi-site ion-exchange reactions. The
exchange coefficients for major cations and heavy metals were assumed to be the same for all
exchange sites. Table 6 gives parameters for this multi-site exchange complex.
Selected results are shown in Figure 13 and Figure 14.
Table 6 Log K parameters for multi-site exchange complex.
Yexchanger(1)
HY(2)

NaY
KY
MgY2
CaY2
CdY2
PbY2
ZnY2
-1.0
-0.3
-0.4
-0.2
-0.2
0.05
-0.2
HYa
HYb
HYc
HYd
HYe
HYf
1.65
3.3
4.95
6.85
9.6
12.35
(1)
The value for NaY is taken from Appelo et al. (1998). Values for the other complexes are taken from thephreeqc.dat database (Parkhurst and Appelo, 1999) and adapted relative to the K for NaY.
(2)
Values taken from Appelo et al. (1998).

1.2

8

1
Cd (µmol kg water -1)

9

pH

7
6
5
4

0.8
0.6
0.4
0.2

3

0
0

0.25

0.5
Time (years)-0.5 m

0.75

1

0

0.25

0.5
Time (years)

0.75-0.5 mFigure 13 – Outflow curves of pH (left) and Cd (right) for the example MCATEXCH.

1

0

0

-0.1

-0.1
Distance (m)Distance (m)

31

-0.2
-0.3
-0.4

-0.3
-0.4

-0.5

-0.5
3

4

5

0 years0.30 years
0.50 years

6
pH

7

8

9

0

0.70 years
1.00 years

0.2

0.4
0.6
0.8
Cd (µmol kg water -1)

0

0

-0.1

-0.1

-0.2
-0.3

1

1.2

0.70 yearss
1.00 yearss

0 yearss
0.30 yearss
0.50 yearss

Distance (m)Distance (m)

-0.2

-0.2

-0.3

-0.4
-0.4
-0.5
0

0.1

0.2
0.3
0.4
1 - (Hsite over total CEC) (-)
0 years0.30 years
0.50 years

0.70 years
1.00 years

0.5

0.6

-0.5
0

0.001

0 years0.30 years

0.002
0.003
Cd-site over total CEC (-)
0.50 years
0.70 years

0.004

1.00 years

Figure 14 – Profiles of pH (top left), Cd (top right), the fraction of deprotonated cation exchangesites (bottom left), and the fraction of cation exchange sites with Cd (bottom right) at selected times
for the example MCATEXCH.

32

4 Step-By-Step Instructions for Selected Examples

4.1

Dissolution of Gypsum and Calcite

4.1.1 Problem Definition
Sulfate-free water is infiltrated in a 50-cm long uniform soil column under steady-state saturated
flow conditions. The reactive minerals present in the soil column are calcite (CaCO3) andgypsum (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 soil solution is in equilibrium with the reactive
minerals and with the atmospheric partial pressure of oxygen. As a result of these equilibria, theinitial soil solution contains only Ca and the oxidized components of S and C.
Calculate the movement of the dissolution fronts of calcite and gypsum over a period of 2.5
days.
4.1.2 Input
Project Manager
Button: "New"Name: "HP1-1"
Description: "Dissolution of calcite and gypsum in the soil profile"
Button: "OK"Main Processes
Heading: Dissolution of calcite and gypsum in soil profile
Uncheck: "Water Flow" (Note: this is a steady-state water flow problem)
Check: "Solute Transport"
Select: "HP1 (PHREEQC)"
Button: “Next”
Geometry Information
Depth of the Soil Profile: 50 (cm)
Button: “Next”
Time Information
Final Time: 2.5 (days)
Maximum Time Step: 0.05 (days)
Button: “Next”

33

Print Information
Unselect: T-Level information
Select: Print at Regular Time IntervalTime Interval: 0.025 (days)
Print Times: Number of Print times: 5
Button: “Next”
Print Times
Button: "Default"
Button: "OK"HP1 – 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 in later in the editor Additional output of the Solute Transport – HP1
Definitions dialog window.
Button: “Next”
Water Flow – Iteration Criteria
Button: “Next”
Water Flow – Soil Hydraulic Model
Button: “Next”
Water Flow – Soil Hydraulic Parameters
Qs: 0.35
Ks: 10 (cm/d)
Button: “Next”
Water Flow – Boundary Conditions
Upper Boundary Condition: Constant Pressure Head
Lower Boundary Condition: Constant Pressure Head
Solute Transport – General Information
Stability Criteria: 0.25 (to limit the time step)
Number of Solutes: 6
Button: “Next”
Solute Transport – HP1 Components and Database Pathway
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 can not 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. Since 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.

34

Check: "Create PHREEQC.IN file using HYDRUS GUI"
Button: “Next”
Solute Transport – HP1 Definitions
Definitions of Solution Compositions
Define the initial condition, i.e., the solution composition of water in the soilcolumn, with the solution number 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 solution number 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
-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/1000 cm³ soil (i.e., 2.176 x 10-5 mol/kg soil * 1.8
kg/1000 cm³ soil).
Equilibrium_phases 1-101
gypsum 0 3.9E-5
calcite 0 3.9E-5
O2(g) -0.68

Button: "OK"35

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
Bulk D : 1.8 (g/cm³)
Disp: 1 (cm)
Button: “Next”
Solute Transport – Boundary conditions
Upper Boundary Condition
Bound. Cond. 3001
Soil Profile – Graphical Editor
Menu: Conditions -> Initial Conditions -> Pressure Head
Button: "Edit Condition"
Select All
Top Value: 0
Menu: Conditions -> Observation Points
Button: "Insert"
Insert 5 observation nodes, one for every 10 cm
Menu: File -> Save Data
Menu: File –> Exit
Soil Profile – Summary
Button: “Next”
Run Application

4.1.3 Output
The standard HYDRUS-output can be viewed using commands in the right Post-processing partof the project window. Only the total concentrations of the components, which were defined in
the Solute Transport – HP1 Components dialog window can be viewed using the GUI H1D.
HP1 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 Manager
Directory: gives the path to the project group folder
Input and output files of a given project are in the folder: directory\project_name36where directory is the project group folder
project_name is the project name
Following HP1 output files are created for the HP1-1 project:
Createdfiles.out
Phreeqc.out
HP1-1.hse

An ASCII text file containing a list of all files created by HP1 (inaddition to the output files created by the HYDRUS module of
HP1);
An ASCII text file, which is the standard output file created by the
PHREEQC module in HP1;
An ASCII text file, tab-delimited, that includes a selected output of
all geochemical calculations in HP1 carried out before actual
transport calculations. Inspection of this file can be done with any
ASCII editor or spreadsheet, such as MS Excel;

obs_nod_chem21.out
obs_nod_chem41.out
obs_nod_chem61.out
obs_nod_chem81.out
obs_nod_chem101.out A series of ASCII files, tab-delimited, with the selected output forthe defined observation nodes (21, 41, 61, 81, and 101) at specifictimes (every 0.025 days). Numerical values can be seen by opening
this file in any ASCII editor or a spreadsheet, such as MS Excel. A
single plot of time series at five observation nodes can be generated
for each geochemical variable with the ts_*.plt files using the
GNUPLOT graphical program (see below);
nod_inf_chem.out
An ASCII file, tab-delimited, with the selected output for acomplete soil profile at the defined observation times. Numericalvalues can be seen by opening this file in any ASCII editor or a
spreadsheet, such as MS Excel. A single plot of the profile data at
different observation times can be generated for each geochemicalvariable with the pd_*.plt files using GNUPLOT (see below);
ts_pH.plt
pd_pH.plt
ts_pe.plt
pd_pe.plt
A series of ASCII files containing command line instructions togenerate time series (ts_) or profile (pd_) plots of pH or pe using
GNUPLOT;
ts_tot_Ca.plt
pd_tot_Ca.plt
ts_tot_Cl.plt
pd_tot_Cl.plt
ts_tot_S.plt
pd_tot_S.plt
ts_tot_C.plt
pd_tot_C.plt
A series of ASCII files containing command line instructions togenerate time series (ts_) or profile (pd_) plots with total
concentrations of Ca, Cl, S, and C using GNUPLOT; note that thisinformation can also be viewed through the H1D GUI;
ts_eq_gypsum.plt
pd_eq_gypsum.plt
ts_eq_calcite.plt

37

pd_eq_calcite.plt
ts_d_eq_gypsum.plt
pd_d_eq_gypsum.plt
ts_d_eq_calcite.plt
pd_d_eq_calcite.plt

A series of ASCII files containing command line instructions togenerate time series (ts_) or profile (pd_) plots with the amount of
the minerals gypsum and calcite using GNUPLOT;A series of ASCII files containing command line instructions togenerate time series (ts_) or profile (pd_) plots with the change in
the amount of the minerals gypsum and calcite using GNUPLOT;

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 need any additional special installation.
After opening the Window version of GNUPLOT by clicking on wgnuplot.exe, a plot can bedirectly generated by carrying out these commands:
File -> OpenBrowse to project folder
Open the template file of interest (*.plt)
The figure can be adapted using line commands (see tutorials for GNUPLOT on the internet).
After adaptations, the command lines can be saved to be used later on.
The default terminal for the plots is Windows. 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 folder.

38

0

0

-10

-10
Distance (cm)Distance (cm)4.1.4 Overview of Selected Results: Profile Data

-20

-30

-50

-50
5.5

6

6.5

0 days0.50 days

7

7.5
pH
1.00 days
1.50 days

8

8.5

9

5.5

9.5

6

6.5

0 days0.50 days

2.00 days
2.50 days

0

0

-10

-10
Distance (cm)Distance (cm)

-30

-40

-40

-20

-30

-40

7

7.5
pH
1.00 days
1.50 days

8

8.5

9

9.5

2.00 days
2.50 days

-20

-30

-40

-50

-50
0

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

1.00 days
1.50 days

0.016

0

0

0

-10

-10

-20

-30

-40

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

2.00 days
2.50 days

Distance (cm)Distance (cm)-20

1.00 days
1.50 days

0.016

2.00 days
2.50 days

-20

-30

-40

-50

-50
0

1e-0052e-0053e-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

2e-0053e-0054e-005
calcite (mol/1000 cm³ of soil)
1.00 days
1.50 days

5e-0052.00 days
2.50 days

Figure 15 – Profiles of pH (top left), total aqueous C concentration (top right), total aqueous Caconcentration (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.

39

Total concentration of C (mol/kg water)

4.1.5 Overview of Selected Results: Time Series

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

2.5

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

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
1.5Time (days)

2-40.0 cm
-50.0 cm

2.5

0

0.5

-10.0 cm
-20.0 cm
-30.0 cm1
1.5Time (days)2

2.5-40.0 cm
-50.0 cm

Figure 16 – Time series of pH (top left), total aqueous C concentration (top right), total aqueous Caconcentration (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.

40

4.2

Dissolution of Gypsum and Calcite and Transport of Cd

4.2.1 Problem Definition
Transport of a heavy metal through the soil column is investigated. Under high pH conditions,
Cd precipitates as otavite (CdCO3). However, due to changing geochemical conditions in the soilcolumn, solubility of Cd is changing. This example studies Cd mobility through the soil column.
The physical and geochemical set up, as in paragraph 4.1.1, is used as the basis. The infiltratingwater is contaminated with a small amount of Cd (1 x 10-6 M Cd). Otavite is added to thegeochemical model with a small initial amount (1 x 10-10 mol/1000 cm³ of soil).
Calculate the percentage of Cd in the aqueous phase. The basic statement SYS("Cd") gives thetotal moles of Cd in the system, whereas the statement TOT("Cd") gives the total concentrationof Cd in the aqueous phase. The total amount of water (in kg) is obtained using the BASIC
statement TOT("water").
4.2.2 Input
Project Manager
Select project: "HP1-1"
Button: "Copy"
New Name: "HP1-2"
Description: "Mineral dissolution/precipitation: Cd transport"
Button: "OK"Main Processes
Heading: Mineral dissolution/precipitation: Cd transport
Button: "OK"
Solute Transport – General Information
Number of Solutes: 7
Button: “Next”
Solute Transport – HP1 Components and Database Pathway
Add CdButton: “Next”
Solute Transport – HP1 Definitions
Definitions of Solution Compositions
Add the concentration of Cd into the boundary solution (solution 3001)
solution 3001
pH 7 charge
Cl 2
Ca 1
O(0) 1 O2(g) -0.68

41

C(4) 1 CO2(g) -3.5
Cd 1E-3

Button: "OK"Geochemical Model
Add the mineral otavite to the EQUILIBRIUM_PHASES assemblage and define its
initial amountequilibrium_phases 1-101
gypsum 0 3.9E-5
calcite 0 3.9E-5
Otavite 0 1E-10
O2(g) -0.68

Button: "OK"
Additional Output
Add Cd to the list of –totals
Add otavite to the list of –equilibrium_phases
Add a USER_PUNCH to calculate the percentage of Cd in solution:
selected_output-totals Ca Cl S C Cd
-equilibrium_phases gypsum calcite otavite
user_punch-headings Percentage_Cd_in_solution@-start
10 if (Sys("Cd") > 0) then perCd = 100 * tot("Cd")* tot("water") / sys("Cd") else perCd = 0
20 punch perCd-end

Note on headings: A specific format of the headings can be used to have anappropriate labeling of the axes in the GNUPLOT templates. The underscore _is interpreted as a white space; the symbol @ separates the name of a variablefrom its unit. Thus, for the headings defined above, the corresponding axis text
in the GNUPLOT template is "Percentage Cd in solution (-)".
Button: "OK"
Button: "OK"Run Application

42

4.2.3 Output
Profiles of Cd, otavite and percentage of Cd in the solution are shown in Figure 17. The plot of
the percentage of Cd in the solution is generated by opening the file 'pd_user_Percentage Cd insolution.plt' using GNUPLOT (USER_PUNCH variables are indicated by *_user_*.plt).
0 days0.50 days
1.00 days
1.50 days
2.00 days
2.50 days

Distance (cm)

-10

-20

-30

0 days0.50 days
1.00 days
1.50 days
2.00 days
2.50 days

-10

-20

-30

-40

-40

-50

-50

0

0 1.5e-0063e-0064.5e-0066e-0067.5e-006
Total concentration of Cd (mol/kg water)

0

1.5e-006 3e-006 4.5e-006 6e-006
otavite (mol/1000 cm³ of soil)

0 days0.50 days
1.00 days
1.50 days
2.00 days
2.50 days-10

Distance (cm)0Distance (cm)

0

-20

-30

-40

-50
0

10

20

30
40
50
60
70
Percentage Cd in solution (-)

80

90

100

Figure 17 – Profiles of total aqueous Cd (top left), the amount of otavite (top right), and thepercentage of Cd in solution (bottom) at selected print times during dissolution of calcite andgypsum and Cd transport.

43

4.3
Dissolution of gypsum and calcite and transport of Cd – the effect of higher Cl
concentrations on the Cd mobility
4.3.1 Problem Definition
Aqueous components, which form strong complexes with Cd, will enhance the mobility of Cd.
The same physical and geochemical set up as in the previous example (paragraph 4.2) is used
here, but the composition of the inflowing water is changed after 1 day to a solution with ahigher CaCl2 concentration (1 x10-2 M).
4.3.2 Input
Project Manager
Select project: "HP1-2"
Button: "Copy"
New Name: "HP1-3"
Description: "Mineral dissolution/precipitation: Cd transport and effect of Cl"
Button: "OK"Main Processes
Heading: Mineral dissolution/precipitation: Cd transport and effect of Cl
Button: "OK"Time Information
Check: "Time-Variable Boundary Conditions"
Number of Time-Variable Boundary Conditions: 2
Button: "OK"
Solute Transport – HP1 Definitions
Definitions of Solution Compositions
Add solution 3002: The boundary solution with the higher CaCl2 concentration
Add solution 4001: The bottom boundary solution – pure water
solution 3002
pH 7 charge
Cl 20
Ca 10
O(0) 1 O2(g) -0.68
C(4) 1 CO2(g) -3.5
Cd 1E-3solution 4001

Button: "OK"
Button: "OK"Time Variable Boundary Conditions

44

Time: 1, 2.5 (in column)
cTop: 3001, 3002
cBot: 4001, 4001
Button: "OK"Run Application
4.3.3 Output
Figure 18 compares the time series of Cd concentrations and the profile of the amount of otavite
between the project described in paragraph 4.2 and the current project.
At the first observation depth, breakthrough curves of Cd are quite similar. The calcite andotavite dissolution fronts already reached this depths after 1 day (see Figure 17), and the high Cl
concentration entering the system after 1 day has only a small effect on these dissolution fronts.

Total concentration of Cd (mol/kg water)

However, deeper in the soil, an increase in Cd concentration occurs already after 1.5 days at 20
cm depth in the case when high Cl concentrations enter the system after 1 day. Note that in thecase of a constant low Cl concentration, the Cd peak does not pass the depth of 20 cm until after
2.5 days. In the case when a high Cl concentration enters the system after 1 day, the otavite
dissolution front does not follow the calcite dissolution front, as was observed in the case when aconstant low Cl concentration enters the system. Otavite dissolution follows the Cl concentration
Total concentration of Cd (mol/kg water)

4.5e-006
4e-006
3.5e-006
3e-0062.5e-006
2e-006
1.5e-006
1e-0065e-007
0
0

0.5

1
1.5
Time (days)

3e-0062.5e-006
2e-006
1.5e-006
1e-0065e-007
0
0

2.5

0.5

1
1.5
Time (days)

0

0

-10

-10

-20

-30

-40

2

2.5

-40.0 cm
-50.0 cm

-10.0 cm
-20.0 cm
-30.0 cm

-40.0 cm
-50.0 cmDistance (cm)Distance (cm)-10.0 cm
-20.0 cm
-30.0 cm2

3.5e-006

-20

-30

-40

-50

-50
0

1e-0062e-0063e-0064e-006
otavite (mol/1000 cm³ of soil)

5e-0060 days0.50 days

1.00 days
1.50 days

2.00 days
2.50 days

6e-0060

5e-0070 days0.50 days

1e-006
1.5e-006
otavite (mol/1000 cm³ of soil)
1.00 days
1.50 days

2e-0062.5e-00

2.00 days
2.50 days

Figure 18 – Comparison between a simulation when a solution with a low Cl concentration enters thesystem (described in paragraph 4.2, left figures) and a simulation when a solution with a high Cl
concentration enters the system after 1 day (described in paragraph 4.3, right figures) for time seriesof Cd concentrations at different depths (top figures) and profiles of the amount of otavite (bottom
figures).

45

0.02

-10.0 cm
-20.0 cm
-30.0 cm
-40.0 cm
-50.0 cm

Total concentration of Cl (mol/kg water)

0.018
0.016
0.014
0.012
0.01
0.008
0.006
0.004
0.002
0
0

0.5

1
1.5
Time (days)2

2.5

Figure 19 – Time series of Cl at selected depths (observation nodes) for the example described in
section 4.3.

infiltration front (see Figure 18). Due to the high Cl concentrations, solubility of Cd is increased
and otavite is not formed anymore after 1.5 days.

46

4.4

Transport and Cation Exchange (Single Pulse)

4.4.1 Problem Definition
This example is adapted from Example 11 of the PHREEQC manual (Parkhurst and Appelo,1999). We will simulate the chemical composition of the effluent from an 8-cm column
containing a cation exchanger. The column initially contains a Na-K-NO3 solution in equilibriumwith the cation exchanger. The column is flushed with three pore volumes of a CaCl2 solution.
Ca, K, and Na are at all times in equilibrium with the exchanger. The simulation is run for oneday; the fluid flux density is equal to 24 cm/d (0.00027777 cm/s).
The column is discretized into 40 finite elements (i.e., 41 nodes). The example assumes that thesame solution is initially associated with each node. Also, we use the same exchanger
composition for all nodes.
The initial Na-K-NO3 solution is made by using 1 x 10-3 M NaNO3 and 2 x 10-4 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 atmospheric partial pressure of oxygen). The
amount of exchange sites (X) is 1.1 meq / 1000 cm³ 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.
In this example, only the outflow concentrations of Cl, Ca, Na, and K are of interest.
4.4.2 Input
Project Manager
Button "New"Name: CEC-1
Description: Transport and Cation Exchange, single pulse
Button "OK"Main Processes
Heading: Transport and Cation Exchange, single pulse
Uncheck "Water Flow" (steady-state water flow)
Check "Solute Transport"
Select “HP1 (PHREEQC)”
Button “Next”
Geometry Information
Depth of the soil profile: 8 (cm)
Button “Next”
Time Information
Time Units:

Seconds (Note that you can also just put it in days, this would also
be OK)
Final Time:
86400 (s)Initial Time Step:
180 (s)Minimum Time Step: 180 (s)Maximum Time Step: 180 (s) (Note: constant time step to have the same conditions asin the original comparable PHREEQC calculations)

47

Button “Next”
Print Information
Number of Print Times: 12
Button "Select Print Times"
Button “Next”
Print Times
Button: “Default”
Button: “OK”
HP1 – Print and Punch Controls
Button: "Next
Water Flow - Iteration Criteria
Lower Time Step Multiplication Factor: 1
Button “Next”
Water Flow - Soil Hydraulic Model
Button “Next”
Water Flow - 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”
Water Flow - Boundary Conditions
Upper Boundary Condition: Constant Pressure Head
Lower Boundary Condition: Constant Pressure Head
Button “Next”
Solute Transport - General Information
Number of Solutes: 7
Button “Next”
Solute Transport – HP1 Components and Database Pathway
Add seven components: Total_O, Total_H, Na, K, Ca, Cl, N(5)Check: "Create PHREEQC.IN file using HYDRUS GUI"
Button: “Next”
Solute Transport – HP1 Definitions
Definitions of Solution Compositions
Define the initial condition 1001:• K-Na-N(5) solution• Use pH to obtain the charge balance of the solution• Adapt the concentration of O(0) to be in equilibrium with the atmosphericpartial pressure of oxygen

48

Define the boundary condition 3001:• Ca-Cl solution• Use pH to obtain the charge balance of the solution• Adapt the concentration of O(0) to be in equilibrium with the atmosphericpartial pressure of oxygen
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
pH 7 charge
Ca 0.6
Cl 1.2O(0) 1 O2(g) -0.68

Geochemical Model
Define for each node (41 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).
EXCHANGE 1-41 @Layer 1@
X 0.0011-equilibrate with solution 1001

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.
Button: “Next”
Solute Transport - Transport Parameters
Bulk Density: 1.5 (g/cm³)
Disp.:
0.2 (cm)
Button “Next”
Solute Transport - Boundary Conditions
Upper Boundary Condition: Concentration Flux
Add the solution composition number (i.e., 3001) for the upper boundary condition
Lower Boundary Condition: Zero Gradient

49

Button “Next”
Soil Profile - Graphical Editor
Menu: Conditions->Profile Discretizationor Toolbar: Ladder
Number (from sidebar):41
Menu: Conditions->Initial Conditions->Pressure Heador Toolbar: red arrow
Button "Edit condition", select with Mouse the entire profile and specify 0 cm pressure
head.
Menu: Conditions->Observation Points
Button "Insert", Insert a node at the bottom
Menu: File->Save Data
Menu: File->Exit
Soil Profile - Summary
Button “Next”
Close Project
Run projectNote: This exercise will produce the following warnings: "Master species N(3) is present insolution n but is not transported.". The same warning occurs for N(0). N(3) and N(0) are twosecondary master species from the primary master species N. Only the secondary master species
N(5) was defined as a component to be transported (the Solute Transport – HP1 Components
dialog window). HP1, however, checks if all components, which are present during thegeochemical calculations, are defined in the transport model. If not, a warning message is
generated. In our example, the concentrations of 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) ascomponents to be transported or define an alternative primary master species representing nitrate(such as Nit-) using SOLUTION_MASTER_SPECIES and SOLUTION_SPECIES.
4.4.3 Output
Display results for “Observation Points” or “Profile Information”. Alternatively, Figure 20 canbe created using information in the output file obs_nod.out.

50

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

The results for this example are shown in Figure 20. The concentrations for 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.

51

4.5

Transport and Cation Exchange (Multiple Pulses)

4.5.1 Problem Definition
This example is the same as the one described in paragraph 4.5, 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

4.5.2 Input
Project Manager
Click on CEC-1
Button "Copy"
New Name: CEC-2
Description: Transport and Cation Exchange, multiple pulses
Button "OK", "Open"
Main Processes
Heading: Transport and Cation Exchange, multiple pulses
Button: “Next”
Geometry Information
Button: “Next”
Time Information
Time Units:
hours
Final Time:60 (hr)Initial Time Step:
0.1 (hr)
Minimum Time Step: 0.05 (hr)Maximum Time Step: 0.1 (hr)Number of Time-Variable Boundary Records:
Button “Next”
Print Information
Number of Print Times: 12
Button "Select Print Times"
Default
Button “Next”

452

Solute Transport - General Information
Button “Next”
Solute Transport – HP1 Components and Database Pathway
Button: “Next”
Solute Transport – HP1 Definitions
Definitions of Solution Compositions
Add additional boundary solution compositions with numbers 3002 and 3003.
Define a bottom boundary solution: Solution 4001 – pure water
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
solution 4001 bottom boundary solution#pure water

Button: "OK"
Button: “Next”
Solute Transport - Boundary Conditions
Upper Boundary Condition: Concentration Flux
Lower Boundary Condition: Zero Gradient
Button “Next”
Time-Variable Boundary Conditions
Fill in the time, and the solution composition number for the top boundary
Time
8
18
38

cTop
3001
3002
3001

cBot
4001
4001
4001

53

60

3003

4001

Soil Profile - Graphical Editor
Menu: Conditions->Observation Points
Button "Insert", Insert nodes at 2, 4, 6, and 8 cm
Menu: File->Save Data
Menu: File->Exit
Soil Profile - Summary
Button “Next”
Run Project

4.5.3 Output

Total concentration of K (mol/kg water)

Figure 21 gives the K concentration at different depths in the profile. Figure 22 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.

0.00120.001
0.00080.00060.00040.000200

1020-2.0 cm
-4.0 cm

30
Time (hours)

40

50

60

-6.0 cm-8.0 cm

Figure 21 – Time series of K concentrations at four depths for the multiplepulse cation exchange example.

54

Concentrations (mol/kg water)

0.00120.001
0.00080.00060.00040.0002
0
0

10

20

Cl

30
Time (hours)
Na

40

K

50

60

Ca

Figure 22 – Outflow concentrations for the multiple-pulse cation exchange
example.

4.6

Transport of Cations and Heavy Metals in a Multi-Layered Soil

4.6.1 Background
Cation adsorption onto negatively charged solid surfaces can greatly affect the rate of the heavy
metal transport in soils. The degree of adsorption of a particular cation depends on its
concentration, the concentration of other cations in the soil solution, and the adsorbed
concentration of the major cations and heavy metals. The competition between major cations andheavy metals for adsorption sites can be described using a multicomponent equilibrium ion
exchange approach (e.g., Selim and Amacher, 1997, and references therein). In addition to major
cations and heavy metals, protons also adsorb to the solid surfaces. Due to the acid-baseproperties of the functional groups on the surfaces of minerals and organic matter, the percentage
of H+ adsorption decreases significantly with increasing pH. This leads to an increased capacityof the surfaces to adsorb major cations and heavy metals at higher pH values. This behavior canalso be described by means of a multi-site cation exchange complex consisting of several sites,
each having a different selectivity coefficient for the exchange of protons (see also paragraph3.9). Appelo et al. (1998), for example, used six sites to describe cation exchange in the presenceof organic matter and Fe-oxyhydroxides.
4.6.2 Problem Definition
This example simulates the migration of major cations and heavy metals in a multi-layered 1-m
deep soil profile using the multi-site cation exchange model.
Soil hydraulic and physical parameters () of the dry Spodosol located at the “Kattenbos” site near Lommel, Belgium, were taken from
Seuntjens (2000, Tables 3.1 and 7.1). The cation exchange complex was assumed to be
associated solely with organic matter. The cation exchange capacity hence is directly related tothe amount of exchangeable protons on the organic matter, taken to be 6 meq/g of the organic

55

matter (proton dissociating groups on fulvic acids are 6 – 10 meq/g and 4 – 6 meq/g on humic
acids, Tipping, 2002).
Table 7 Soil hydraulic and other properties of six soil horizons (from Seuntjens, 2000).
Horizon

Depth
(cm)

ρ
(g cm³)

Organic
Carbon%θrθsα(cm-1)

nKs(cm
day-1)

A
E
Bh1
Bh2
BC
C1
C2

0–7
7 – 1919 – 24
24 – 28
28 – 50
50 – 75
75 – 100

1.31
1.59
1.3
1.38
1.41
1.52
1.56

2.75
0.75
4.92
3.77
0.89
0.12
0.08

0.065
0.035
0.042
0.044
0.039
0.030
0.021

0.48
0.42
0.47
0.46
0.46
0.42
0.39

0.016
0.015
0.016
0.028
0.023
0.021
0.021

1.94
3.21
1.52
2.01
2.99
2.99
2.99

95.04
311.0438.88
864
1209.6
1209.6
1209.6

Steady-state water flow of 1 cm day-1 is assumed in this example. The composition of the
inflowing water changes as a function of time:•••0 – 27.9 days: Ca: 0.005 mol l-1, Cl: 0.01 mol l-1
27.9 – 28.9 days: Ca: 0.05 mol l-1, Cl: 0.1 mol l-1
28.9 – 80 days: Ca: 0.005 mol l-1, Cl: 0.01 mol l-1

These upper boundary conditions correspond with experimental conditions in a lysimeter
experiment described in Seuntjens (2000). At the bottom of the lysimeter, capillary wicks with alength of 38 cm were installed. Taking into account the hydraulic properties of the wick and thesteady-state water flow of 1 cm/d, the lower boundary pressure head is –28.3 cm. For the initial
distribution of the pressure heads, it is assumed that the pressure head throughout the soil profile
is initially in gravitational equilibrium with the lower boundary condition, (i.e. -28.3 at thebottom and -128.3 cm at the top, and linearly increasing with depth between).
Table 8 Initial pH and concentration for 9 components.

Concentration(µmol/l)
A
E
Bh1
Bh2
BC
C1
C2

pH

Cl

Na

K

Ca

Mg

Cd

Zn

Pb

3.4
3.5
3.6
3.8
4.4
4.4
4.5

69
69
69
69
69
69
69

64
64
64
64
64
64
64

4
4
4
4
4
4
4

97
65
39
33
55
76
27

8
8
8
8
8
8
8

0.80
0.38
0.43
0.41
0.63
0.33
0.20

50
24
23
21
33
21
14

2.5
1.2
1.1
1.0
1.6
1.0
0.7

The transport of 10 components is considered: Na, K, Ca, Mg, Cd, Zn, Pb, Cl, Br and C(4). In
addition, Total_O and Total_H are included. Initial concentrations for the first nine components
are given in Table 8. Br- is used as a charge balance ion to have the desired initial pH, also
defined in Table 8. O(0) and C(4) are considered in equilibrium with the atmospheric partialpressure of oxygen and carbon dioxide. Initial concentrations of Ca2+, Cd2+, and Zn2+ were56
obtained from Seuntjens (2000; Table 7.1). Pb2+ concentrations were arbitrarily set to be 20
times smaller than the Zn2+ concentrations (no data available).
4.6.3 Cation Exchange Capacities
Assuming an average exchange capacity of 6 meq/g of organic matter, the exchange capacity is
obtained as: ρb(gram soil/cm³) x OC (% or gram organic matter/100 g soil) × 6 meq/gram oforganic matter. For example, for the A horizon, this results in 0.216 meq/cm3 of soil. This value
must then be transformed to units of moles/1000 of cm³ soil (i.e., 0.216 moles/1000 cm3 of soil).
4.6.4 Input
Project Manager
Button: "New"Name: "CatExch"
Description: "Cation exchange in a multilayered soil"
Button: "OK"Main Processes
Heading: Cation exchange in a multilayered soil
Check: "Water Flow"
Check: "Solute Transport"
Select: "HP1 (PHREEQC)"
Button: “Next”
Geometry Information
Lenghts Units: cm
Number of Soil Materials: 7
Depth of the Soil Profile: 100 (cm)
Button: “Next”
Time Information
Final Time: 80 (days)
Initial Time Step: 0.001 (days)
Minimum Time Step: 1E-5 (days)
Maximum Time Step: 0.5 (days)
Check: "Time Variable Boundary Conditions"
Number of Time-Variable Boundary Records: 3
Button: “Next”
Print Information
Unselect: T-Level information
Select: Print at Regular Time IntervalTime Interval: 0.5 (days)
Print Times: Number of Print times: 4
Button: “Next”
Print Times
Button: "Default"

57

Button: "OK"HP1 – Print and Punch Controls
Check: "Make GNUplot Templates"
Button: “Next”
Water Flow – Iteration Criteria
Button: “Next”
Water Flow – Soil Hydraulic Model
Button: “Next”
Water Flow – Soil Hydraulic Parameters
Insert the hydraulic properties from Table 7.

Button: “Next”
Water Flow – Boundary Conditions
Upper Boundary Condition: Constant Flux
Lower Boundary Condition: Constant Pressure Head
Water Flow – Constant Boundary Fluxes
Upper Boundary Flux: -1 (cm/day) (downward flux)
Solute Transport – General Information
Stability Criteria: 0.25
Number of Solutes: 12
Button: “Next”
Solute Transport – HP1 Components and Database Pathway
Twelve Components: Total_O, Total_H, Na, K, Ca, Mg, Cd, Zn, Pb, Cl, Br, C(4)Check: "Create PHREEQC.IN file using HYDRUS GUI"
Button: “Next”
Solute Transport – HP1 Definitions
Definitions of Solution Compositions
Define the initial solutions for each of the seven layers (Table 8), and use solution
numbers 1001-1007 and the keyword SOLUTION_SPREAD:

58
•
•

Use pH to obtain 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.

Note: columns of SOLUTION_SPREAD, as well as the headings and thesubheadings must be tab-delimited (see PHREEQC-2 manual, Parkhurst andAppelo, 1999). A convenient way to prepare the input for the
SOLUTION_SPREAD keyword is to use MS Excel to make different input rows
and columns and to copy it to the H1D GUI:

Define the boundary condition 3001:• Ca-Cl solution: low concentration• Use pH to obtain the charge balance of the solution• Adapt the concentration of O(0) to be in equilibrium with the atmosphericpartial pressure of oxygen
Define the boundary condition 3002:• Ca-Cl solution: high concentration• Use pH to obtain the charge balance of the solution• Adapt the concentration of O(0) to be in equilibrium with the atmosphericpartial pressure of oxygen
Define the boundary condition 4001:• Pure water

1001
1002
1003
1004
1005
1006
1007

horizona A
horizon E
horizon Bh1
horizon Bh2
horizon BC
horizon C1
horizon C2

SOLUTION_SPREAD
NumberDescription

3.4
3.5
3.6
3.8
4.4
4.4
4.5

pH

69E-3
69E-3
69E-3
69E-3
69E-3
69E-3
69E-3

Cl

64E-3
64E-3
64E-3
64E-3
64E-3
64E-3
64E-3

Na
4E-3
4E-3
4E-3
4E-3
4E-3
4E-3
4E-3

K
9.7E-02
6.5E-02
3.9E-02
3.3E-02
5.5E-02
7.6E-02
2.7E-02Ca
8.0E-038.0E-038.0E-038.0E-038.0E-038.0E-038.0E-03Mg
8.0E-04
3.8E-04
4.3E-04
4.1E-04
6.3E-04
3.3E-04
2.0E-04Cd
5.0E-02
2.4E-02
2.3E-02
2.1E-02
3.3E-02
2.1E-02
1.4E-02Zn
2.5E-03
2.4E-02
2.3E-02
2.1E-02
3.3E-02
2.1E-02
1.4E-02Pb

Br
charge
1E-3
1E-3
1E-3
1E-3
1E-3
1E-3
1E-3

O(0)
O2(g) -0.68
1E-3
1E-3
1E-3
1E-3
1E-3
1E-3
1E-3

C(4)
CO2(g) -3.5
1E-3
1E-3
1E-3
1E-3
1E-3
1E-3
1E-3

59

60

solution 3001
pH 7 charge
units mol/kgw
Ca 0.005
Cl 0.01O(0) 1 O2(g) -0.68
solution 3002
pH 7 charge
units mol/kgw
Ca 0.05
Cl 0.1O(0) 1 O2(g) -0.68
solution 4001 #pure water

Button: "OK"Geochemical Model
The geochemical model will be defined after different layers of the soil profile havebeen defined using Soil Profile – Graphical Editor. Information about the
distribution of different layers can then be used in the definition of the geochemical
model (see below).
Additional Output
Define the additional output to be written to selected output files.
selected_output-totals Cd Ca Cl
user_punch-headings Adsorbed_Cd@mol/kg_soil-start10 bd = bulkdensity(cell_no)
40 PUNCH mol("CdX2")*tot("water")/bd-end

Button: "OK"
Button: “Next”
Solute Transport – Solute Transport Parameters
Add the bulk density for the seven layers (): 1.31, 1.59, 1.3, 1.38, 1.41, 1.52, 1.56 (g/cm³)
Disp: 1 (cm)
Button: “Next”
Solute Transport – Boundary conditions
Upper Boundary Condition: Concentration Flux BC
Lower Boundary Condition: Zero Concentration Gradient61

Time Variable Boundary Conditions
Time (days)
27.9
28.9
80

cTop
3001
3002
3001

cBot
4001
4001
4001

Soil Profile – Graphical Editor
Button: "Edit Condition"
Select: with the mousenodes 8 to 19: specify Material 2
nodes 20 to 24: specify Material 3
nodes 25 to 28: specify Material 4
nodes 29 to 50: specify Material 5
nodes 51 to 75: specify Material 6
nodes 76 to 100: specify Material 7
Menu: Conditions -> Initial Conditions -> Pressure Head
Button: "Edit Condition"
Select All
Top Value: -128.3
Bottom Value: -28.3
Deselect: Use top value for both
Menu: Conditions -> Observation Points
Button: "Insert"
Insert 4 observation nodes, one every 25 cm
Menu: File -> Save Data
Menu: File –> Exit
Soil Profile – Summary
Button: "OK"
Solute Transport – HP1 definitions
Geochemical Model
Button: "Exchange"
Add for each layer the cation exchange complex X with its size in mol/1000cm³ ofsoil.
Equilibrate each cation exchange complex with the corresponding initial solution for
a particular soil layer (i.e., 1001 to 1007)
EXCHANGE 1-7 @Layer 1@
X 0.216-equilibrate with solution 1001
EXCHANGE 8-19 @Layer 2@
X 0.072-equilibrate with solution 1002
EXCHANGE 20-24 @Layer 3@
X 0.384

62-equilibrate with solution 1003
EXCHANGE 25-28 @Layer 4@
X 0.312-equilibrate with solution 1004
EXCHANGE 29-50 @Layer 5@
X 0.075-equilibrate with solution 1005
EXCHANGE 51-76 @Layer 6@
X 0.011-equilibrate with solution 1006
EXCHANGE 77-101 @Layer 7@
X 0.007-equilibrate with solution 1007

Button: "OK"
Button: "OK"Run Application

4.6.5 Output
Time series of Cl, Ca, and Cd at selected depths are shown in Figure 23. Cd concentration
increases when Cl concentration increases due to aqueous complexation between Cd2+ and Cl-.

Total concentration of Ca (mol/kg water)

Total concentration of Cl (mol/kg water)

63

0.035
0.03
0.025
0.02
0.015
0.01
0.005
0
0

10

20

30

40
50
Time (days)

70

80

0.004
0.00350.003
0.00250.002
0.00150.001
0.0005
0
0

10

20

30

-25.0 cm
-50.0 cm

-75.0 cm-100.0 cm-25.0 cm
-50.0 cm

Total concentration of Cd (mol/kg water)

60

0.005
0.004540
50Time (days)

60

70

80

-75.0 cm-100.0 cm

0.000250.00020.000150.00015e-005

0
0

10

20

30

-25.0 cm
-50.0 cm

40
50
Time (days)

60

70

80

-75.0 cm-100.0 cm

Figure 23 – Time series of Cl (top left), Ca (top right), and Cd (bottom) concentrations at selected depths(observation nodes) for the example described in section 0.

64

4.7

Horizontal Infiltration of Multiple Cations and Cation Exchange

4.7.1 Problem Definition
This exercise simulates horizontal infiltration of multiple cations (Ca, Na, and K) into theinitially dry soil column. It is vaguely based on experimental data presented by Smiles and Smith[2004]. The cation exchange between particular cations is described using the Gapon exchange
equation [White and Zelazny, 1986]. For an exchange reaction on an exchange site X involving
two cations N and M with charge n and m:
N1/nX + 1/m M = M1/mX + 1/n N(2)

the Gapon selectivity coefficient KGMN is:[M1 / m X ] ⎡⎢⎣N n + ⎤⎥⎦ 1 / n
K GMN =
[N 1 / n X ] ⎡⎢⎣ M m + ⎤⎥⎦ 1 / m(3)

where [] denotes activity. The activity of the exchange species is equal to its equivalent fraction.
The Gapon selectivity coefficients for Ca/Na, Ca/K, and Ca/Mg exchange are KGCaNa = 2.9,
KGCaK = 0.2, and KGCaMg = 1.2. It is assumed that the cation exchange capacity cT (molckg-1 soil)
is constant and independent of pH.
Consider a soil column 20-cm long with an initial water content of 0.075. Infiltration occurs on
the left side of the column under a constant water content equal to the saturated water content.
Consider a free drainage right boundary condition.
Some physical parameters of the column are: bulk density = 1.75 g/cm³; dispersivity = 10 cm;
the soil water retention characteristic and unsaturated hydraulic conductivity curve are describedwith the van Genuchten – Mualem model with the following parameters: θs = 0.307, θr = 0, α =0.259 cm-1, n = 1.486, Ks = 246 cm/day, and l = 0.5. The CEC is 55 meq/kg soil.
As initial concentrations take: [Cl] = 1 mmol/kg water, [Ca] = 20 mmol/kg water, [K] = 2
mmol/kg water, [Na] = 5 mmol/kg water, [Mg] = 7.5 mmol/kg water, and [C(4)] = 1 mmol/kg
water. The pH is 5.2, and the solution contains an unknown concentration of SO24 as a majoranion. The inflowing solution has the following composition: [Ca] = 0.002345 mol/kg water,[Na] = 0.01 mol/kg water, [K] = 0.0201 mol/kg water, [Mg] = 0, and [Cl] = 0.035 mol/kgw. The
pH is 3.2, and the solution contains an unknown concentration of SO42- as major anion.
Look at profile data of the water content, pH, concentrations of the cations and anions, and theamount of sorbed cations. Express sorbed concentration in meq/kg soil.
4.7.2 Definition of the Geochemical Model and its Parameters
1. The CEC should be expressed in mol/1000 cm3 of soil in HP1. Recalculate the amount of
CEC.

65

[Answer: 0.09625 mol/1000 cm³ soil]
2. Define the thermodynamic data for describing the exchange process with the Gapon
convention and the Gapon selectivity coefficients.
A new master exchange species have to be defined, say G.
The exchange reactions (Eq. 2) have to be written in terms of half reactions:
(4)
(5)
(6)
(7)

G- + K+ = KG
G- + Na+ = NaG
G- + 0.5 Ca+2 = Ca0.5G
G- + 0.5 Mg+2 = Mg0.5G

with appropriate values of the exchange coefficients. Thus, log KGK, log KGNa, log KGCa,
and log KGMg are needed for equations 4, 5, 6, and 7, respectively. It is assumed that theKG value for the half reaction with Na is 1, i.e. log KGNa = 0.0. The thermodynamic
constants for the other half reactions are then calculated from the defined Gapon
selectivity coefficients relative to KGNa.
Calculate log KGK, log KGCa, and log KGMg.
Solution:
Exchange reactions are written in terms of half reactions. The reaction:
Na-G + 0.5 Ca2+ = Na+ + Ca0.5-G

KGCaNais written as the sum of the half reactions:(1) G- + Na+ = Na-G
(2) G- + 0.5 Ca2+ = Ca0.5-G

KGNa
KGca

Consequently:
log(KCaNa) = log(KGCa) - log(KGNa)
We express the exchange coefficients relative to Na+. Thus, taking log(KGNa) equal to0, log(KGCa) = log(KGCaNa). Similarly, for the reaction:
K-G + 0.5 Ca2+ = K+ + Ca0.5-G

KGCaK

the following two half reactions can be written as:(1) G- + K+ = K-G(2) G- + 0.5 Ca2+ = Ca0.5-G

KGK
KGca

Then, log(KGCaK) = log(KGCa) - log(KGK). And similarly, log(KGK) = log(KGCa) log(KGCaK). The same reasoning is applied also to derive KGMg.

66[Answer: log KGK = 1.16
log KGCa = 0.462
log KGMg = 0.383]
4.7.3 Input
Project Manager
Button "New"Name: CEC-4
Description: Horizontal infiltration with Cation Exchange
Button "OK"Main Processes
Heading: Horizontal infiltration with Cation Exchange
Check "Water Flow"
Check "Solute Transport"
Select “HP1 (PHREEQC)”
Button “Next”
Geometry Information
Depth of the soil profile: 20 (cm)Decline from vertical axes: 0 (horizontal flow)
Button “Next”
Time Information
Time Units:
Minutes
Final Time:144 (min)Initial Time Step:
0.01 (min)Minimum Time Step: 0.01 (min)Maximum Time Step: 2
Button “Next”
Print Information
Number of Print Times: 6
Button "Select Print Times"
Button "Default(log)"
Button “Next”
HP1 – Print and Punch Controls
Select: Make GNUPLOT templates
Button: "Next
Water Flow - Iteration Criteria
Lower Time Step Multiplication Factor: 1.3
Button “Next”
Water Flow - Soil Hydraulic Model
Button “Next”
Water Flow - Soil Hydraulic Parameters

67

Catalog of Soil Hydraulic Properties: Loam
Qr: 0
Qs: 0.307
Alpha: 0.259 (cm-1)
n: 1.486
Ks: 0.170833 (cm/min)
Button “Next”
Water Flow - Boundary Conditions
Initial Condition: in Water Contents
Upper Boundary Condition: Constant Water Content
Lower Boundary Condition: Free Drainage
Button “Next”
Solute Transport - General Information
Number of Solutes: 9
Button “Next”
Solute Transport – HP1 Components and Database Pathway
Add the nine components: Total_O, Total_H, Ca, Na, K, Mg, Cl, C(4), S(6)Check: "Create PHREEQC.IN file using HYDRUS GUI"
Button: “Next”
Solute Transport – HP1 Definitions
Additions to Thermodynamic Database••

Define the master exchange species G
Define the master species. An identical reaction for the master exchange
species has to be included.
EXCHANGE_MASTER_SPECIESG GEXCHANGE_SPECIES
G- = G-; log_k 0
G- + K+ = KG; log_k 1.16
G- + Na+ = NaG; log_k 0
G- + 0.5 Ca+2 = Ca0.5G; log_k 0.462
G- + 0.5 Mg+2 = Mg0.5G; log_k 0.383

Button: "OK"Definitions of Solution Compositions•••

Define the initial solution as solution 1001
Define the boundary solution as solution 3001
Assume that the solutions are in equilibrium with the atmospheric partialpressure of oxygen and carbon dioxide
solution 1001 initial solution
pH 5.2

68

Cl 1
Ca 20
K 2
Na 5
Mg 7.5
C(4) 1 CO2(g) -3.5
O(0) 1 O2(g) -0.68
S(6) 1 charge
solution 3001 boundary solution
pH 3.2Ca 2.345
Na 10
K 20
Cl 35
C(4) 1 CO2(g) -3.5
O(0) 1 O2(g) -0.68
S(6) 1 charge

Button: "OK"Geochemical Model••

Define an exchange assemblage for 101 nodes
Equilibrate the exchange sites with the initial solution
Exchange 1-101
G 0.09625-equilibrate with solution 1001

Button: "OK"
Additional Output•••

Add SELECTED_OUTPUT to ask for output of total concentrations of thecomponents
Add USER_PUNCH to save the absorbed concentrations as meq/kg soil. The
default output in HP1 for an exchange species is mol/kg water. This can be
asked by –molalities NaG in SELECTED_OUTPUT or as a BASIC
statement (10 punch mol("NaG")) in USER_PUNCH. BASIC statements toconvert 'mol/kg water' to 'meq/kg soil' can be added to USER_PUNCH. The
following two variables are needed:o The bulk density: use the HP1-specific BASIC statement
bulkdensity(number), where number is the cell number of a givennode, to obtain the bulk density for a given node. The number of thecell is obtained by the BASIC statement cell_no.
o The water content: obtained as tot("water").
Add meaningful headings for the punch output.
SELECTED_OUTPUT-totals Cl Ca K Na Mg S

69

USER_PUNCH-headings
Sorbed_Ca@meq/kg_soil
Sorbed_Mg@meq/kg_soil
Sorbed_Na@meq/kg_soil Sorbed_K@meq/kg_soil-start10 bd = bulkdensity(cell_no) #kg/1000cm³ soil
40 PUNCH mol("Ca0.5G")*tot("water")/bd*1000 #in meq/kg
50 PUNCH mol("Mg0.5G")*tot("water")/bd*1000 #in meq/kg
60 PUNCH mol("NaG")*tot("water")/bd*1000 #in meq/kg
70 PUNCH mol("KG")*tot("water")/bd*1000 #in meq/kg-end

Button: "OK"
Button: “Next”
Solute Transport – Solute Transport Parameters
Bulk Density: 1.75 (g/cm³)
Disp: 10 (cm)
Button “Next”
Solute Transport - Boundary Conditions
Upper Boundary Condition: Concentration Flux
Bound. Cond.: 3001
Lower Boundary Condition: Zero Gradient
Button “Next”

Soil Profile - Graphical Editor
Menu: Conditions -> Initial Conditions -> Water content
Button: "Edit Condition"
Select All
Top Value: 0.075
Button: "Edit Condition"
Select first node
Value: 0.307
Menu: Conditions -> Observation Points
Button: "Insert"
Insert 4 observation nodes at 3, 6, 9, and 12 cm
Menu: File -> Save Data
Menu: File –> Exit
Soil Profile - Summary
Button “Next”
Run Application

4.7.4 Output
Explore the HYDRUS output and the GNUPLOT templates.

0

0

-5

-5
Distance (cm)Distance (cm)

70

-10

-15

-15

-20
0.05

-20
0.1

0.15
0.2
0.25
0.3
Mass of water (kg/1000 cm³ of soil)
12.00 min27.47 min62.90 min

0

0.35

0

0

-5

-5

-10

-15

0.01
0.015
0.02
0.025
0.03
Total concentration of Cl (mol/kg water)
12.00 min27.47 min62.90 min0.035

144.00 min

-10

-15

-20
0.00450.006
0.0075
Total concentration of Na (mol/kg water)
0 min
2.29 min5.24 min12.00 min27.47 min62.90 min

-20
0.001

0.009

0.002

0.003
0.004
0.005
0.006
0.007
Total concentration of K (mol/kg water)

0 min
2.29 min5.24 min144.00 min

0

-5

-5
Distance (cm)

0

-10

-15

-20
0.008

0.005

0 min
2.29 min5.24 min144.00 min

Distance (cm)Distance (cm)0 min
2.29 min5.24 minDistance (cm)-1012.00 min27.47 min62.90 min0.008

144.00 min

-10

-15

0.01

0.012
0.014
0.016
0.018
0.02
Total concentration of Ca (mol/kg water)

0 min
2.29 min5.24 min12.00 min27.47 min62.90 min144.00 min

0.022

-20
0.003

0.004
0.005
0.006
0.007
Total concentration of Mg (mol/kg water)
0 min
2.29 min5.24 min12.00 min27.47 min62.90 min0.008

144.00 min

Figure 24 – Profiles of water content (top left), and total aqueous concentrations of Cl, Na, K, Ca and
Mg at selected print times during horizontal infiltration of multiple cations (the example is describedin section 4.7).

0

0

-5

-5
Distance (cm)Distance (cm)

71

-10

-15

-15

-20

-20
0.6

0.7

0.8
0.9
Sorbed Na (meq/kg soil)

0 min
2.29 min5.24 min12.00 min27.47 min62.90 min

1

1.1

3

6

0 min
2.29 min5.24 min144.00 min

0

0

-5

-5
Distance (cm)Distance (cm)

-10

-10

-15

9
Sorbed K (meq/kg soil)
12.00 min27.47 min62.90 min1215

144.00 min

-10

-15

-20

-20
27

28

0 min
2.29 min5.24 min

29

30
31
32
Sorbed Ca (meq/kg soil)

33

12.00 min27.47 min62.90 min144.00 min

34

13

14

0 min
2.29 min5.24 min15
Sorbed Mg (meq/kg soil)
12.00 min27.47 min62.90 min16

17

144.00 min

Figure 25 – Profiles of sorbed concentrations of Na, K, Ca, and Mg at selected print times duringhorizontal infiltration of multiple cations (the example is described in section 4.7).

72

4.8

U Transport and Surface Complexation

4.8.1 Problem definition
This exercise simulates the leaching of U under saturated, steady-state flow conditions. U
adsorbs on Fe-oxides in the soil profile.
Consider a 50-cm deep loamy soil with a saturated hydraulic conductivity of 1 cm/day. Take aporosity of 0.43, a bulk density of 1.31 g/cm³, and a dispersivity of 1 cm. The Fe2O3 content of
the soil is 0.02 weight percentage. The capacity of the surface is calculated assuming that Fe2O3
has 0.875 reactive sites per mole of Fe (Waite et al., 1994).
Following elements are considered: Ca, Cl, K, Mg, Na, U(6), and C(4). In this geochemicaltransport problem that is pH-sensitive, also Total_O and Total_H need to be transported. U
adsorption is described by a non-electrostatic surface complexation model. As a consequence of
this, a charge on the solid surface is not balanced by counter-ions in a double layer near thesurface. Therefore, the aqueous phase will have a charge imbalance that will be of the same size,
but having an opposite sign, as the charge on the surface. The entire system (i.e., solid surface +aqueous phase) will then be charged balanced. Therefore, also the 'Charge' of the aqueous
solution has to be transported. Note that when an electrostatic surface complexation model,
which takes into account the composition of the double layer, is used, the aqueous phase will becharged balanced, and so will be the solid surface and the double layer.
A solution composition of rain water is assumed for both initial and boundary conditions: [Cl] =69 µmol/kg water, [Ca] = 6 µmol/kg water, [K] = 4 µmol/kg water, [Na] = 64 µmol/kg water,[Mg] = 8 µmol/kg water. The concentration of O2 and CO2 are assumed to be in equilibrium withthe atmospheric partial pressure of O2(g) and CO2(g). The U concentration in the initial solution
composition is considered to be very low ([U] = 10-24 M), and much larger (10-7 M) in theboundary solution.
This problem is carried out using the PHREEQCU.DAT database. This is the PHREEQC.DAT
database with the definition of additional U-species (from Langmuir, 1997 – a database fromwww.geo.tu-freiberg.de/~merkel/Wat4f_U.dat). Sorption is described using solid complexation
reactions on the surface site called Hfo_w (line 3448 in the database). Solution complexation
species are defined further in the database. Note that only one U-species adsorbs (uranyl):
Hfo_wOH + UO2+2 = Hfo_wOUO2+ + H+
log_k 2.8
4.8.2 Calculation of the Size of the Surface Sorption Site
The capacity of the surface should be expressed in mol/1000 cm³ of soil. The capacity is
calculated as:(0.0002) [g Fe2O3/g soil] * 1.31 [g soil/cm3] * (1/160) [mol Fe2O3/g Fe2O3] * 2 [mol Fe/mol
Fe2O3] * 0.875 [moles sites/mol Fe ] * 1000 [cm³/1000cm³] = 0.00286 mol/1000 cm³

73

4.8.3 Input
Project Manager
Button: "New"Name: "UTransport"
Description: "U transport and complexation"
Button: "OK"Main Processes
Heading: U transport and complexation
Uncheck: "Water Flow" (steady state saturated water flow)
Check: "Solute Transport"
Select: "HP1 (PHREEQC)"
Button: “Next”
Geometry Information
Depth of the Soil Profile: 50 (cm)
Button: “Next”
Time Information
Final Time: 200 (days)
Button: “Next”
Print Information
Unselect: T-Level information
Select: Print at Regular Time IntervalTime Interval: 0.025 (days)
Print Times: Number of Print times: 5
Button: “Next”
Print Times
Button: "Default"
Button: "OK"HP1 – Print and Punch Controls
Check: "Make GNUplot Templates"
Button: “Next”
Water Flow – Iteration Criteria
Button: “Next”
Water Flow – Soil Hydraulic Model
Button: “Next”
Water Flow – Soil Hydraulic Parameters
Qs: 0.43
Ks: 1 (cm/day)
Button: “Next”
Water Flow – Boundary Conditions
Upper Boundary Condition: Constant Pressure Head

74

Lower Boundary Condition: Constant Pressure Head
Solute Transport – General Information
Stability Criteria: 0.25
Number of Solutes: 11
Button: “Next”
Solute Transport – HP1 Components and Database Pathway
Database Pathway:
Browse: phreeqcU.dat
Eleven Components: Total_O, Total_H, Charge, Ca, Cl, Mg, Na, K, C(4), U(6), and U(5)Check: "Create PHREEQC.IN file using the HYDRUS GUI"
Button: “Next”
Solute Transport – HP1 Definitions
Definitions of Solution Compositions
Define the initial condition 1001:•
Rain water without U•
Use the pH to obtain charge balance of the solution•
Put C and O in equilibrium with the atmospheric partial pressure ofoxygen and carbon dioxide, respectively
Define the boundary condition 3001:•
Rain water with U•
Use the pH to obtain charge balance of the solution•
Put C and O in equilibrium with the atmospheric partial pressure ofoxygen and carbon dioxide, respectively
solution 1001
-ph 7 charge-pe 15.2939-units mol/kgw
C 1 CO2(g) -3.5
Ca 6E-6
Cl 69E-6
K 4E-6
Mg 8E-6
Na 64E-6
O(0) 1 O2(g) -0.68
solution 3001 rain water-ph 7 charge-pe 15.2939-units mol/kgw
C 1 CO2(g) -3.5
Ca 6E-6
Cl 69E-6
K 4E-6
Mg 8E-6
Na 64E-6
O(0) 1 O2(g) -0.68

75

U(6) 1E-7

Button: "OK"Geochemical Model•••

Define the surface complexation assemblage for 101 nodes
Add identifier –no_edl
Equilibrate the exchange sites with the initial solution
Surface 1-101
Hfo_w 0.00287-no_edl-equilibrate with solution 1001

Button: "OK"
Additional Output
Define the additional output to be written to selected output files.
selected_output-totals U
user_punch-headings Adsorbed_U@mol/kg Percentage_adsorbed_U@log(Kd)-start10
Usorbed=mol("Hfo_wOUO2+")*tot("water")/bulkdensity(cell_no)
20 PUNCH Usorbed
30
if(SYS("U(6)")>0)
thenpercentage=
mol("Hfo_wOUO2+")*tot("water") / SYS("U(6)") * 100
else percentage = 0
40 if (SYS("U(6)")>0) then Kd = log10(Usorbed /tot("U(6)")) else Kd = -9999
50 PUNCH percentage Kd-end

Button: "OK"
Button: “Next”
Solute Transport – Solute Transport Parameters
Bulk density: 1.31 (g/cm³)
Disp: 1 cm (cm)
Button: “Next”
Solute Transport – Boundary conditions
Upper Boundary Condition
Bound. Cond. 3001
Soil Profile – Graphical Editor
Menu: Conditions -> Initial Conditions -> Pressure Head
Button: "Edit Condition"

76

Select All
Top Value : 0
Menu: Conditions -> Observation Points
Button: "Insert"
Insert 5 observation nodes: add observation nodes at 0.5, 2, 5, 15, 25 and 50 cm
Menu: File -> Save Data
Menu: File –> Exit
Soil Profile – Summary
Button: “Next”
Run Application
4.8.4 Output
U-profiles at selected print times are shown in Figure 26.
00 days40.00 days
80.00 days
120.00 days
160.00 days
200.00 days

Distance (cm)

-10

-20

-30

-40

-50
0
1e-0092e-0093e-009Total concentration of U (mol/kg water)

Figure 26 – Profiles of aqueous concentration of U for the example described in section 4.8.

77

4.9

First-Order Kinetic PCE Degradation Network

4.9.1 Background
Perchloroethylene (PCE, also called tetrachloroethylene) degrades slowly under reducing
conditions, mainly due to microbiological transformations. One of the most important pathways
for anaerobic biodegradation of PCE is by reductive dechlorination in a sequential way. Figure
27 (after Schaerlaekens et al., 1999) shows this pathway for six components: PCE,
trichloroethylene (TCE), cis-1,2-dichloroethylene (cis-DCE), trans-1,2-dichloroethylene (transDCE), 1,1-dichloroethylene (1,1-DCE), and vinyl chloride (VC). VC then eventually degrades toethylene (ETH), which is environmentally acceptable and does not cause direct health effects.
Although the reaction kinetics of the biodegradation depend on a variety of environmental
conditions (such as redox potential, biomass, and compounds affecting solubility), the kinetics
here is described independently of environmental conditions.
When the DCE (dichloroethylene) species are lumped, the transport problem can be formulated
as a transport of a single sequential degradation chain, which can then be solved directly using
HYDRUS-1D (e.g., Schaerlaekens et al., 1999; Casey and Šimůnek, 2001; see also one of the
HYDRUS-1D tutorials). However, the HP1 code can handle the full reaction network as definedin Figure 28 (i.e., with three separate DCE species), while considering different distribution
factors α and yield coefficients γ.

Figure 27 – Perchloroethylene (PCE) degradation pathway. (Figure from Schaerlaekens et al.,1999).

78

α1

PCE

k1 , y1TCE

k 2 , y2α2α3cis-DCEtrans-DCE
1,1-DCE

k3
k4

y3

VC

k6 , y4

ETH

k7

k5

Figure 28 – Degradation pathway of PCE using first-order rate constants.
Table 9 Definition of parameters and their values for the PCE biodegradation problem(from Case 1 and 2 in Sun et al., 2004). Rate parameters are for a reference temperature of
20°C.

Parameter

Symbol Values

Velocity
Dispersion coefficientFirst-order degradation rate 1
First-order degradation rate 2First-order degradation rate 3
First-order degradation rate 4First-order degradation rate 5First-order degradation rate 6First-order degradation rate 7
Distribution factor, TCE to cis-DCE
Distribution factor, TCE to trans-DCE
Distribution factor, TCE to 1,1-DCE
Yield coefficient, PCE to TCE
Yield coefficient, TCE to DCE
Yield coefficient, DCE to VC
Yield coefficient, VC to ETH

v
D
k1
k2
k3
k4
k5
k6
k7
α1
α2
α3
y1
y2
y3
y4

Verification
0.4
0.4
0.075
0.070
0.020
0.035
0.055
0.030
0.000001
0.72
0.15
0.13
0.79
0.74
0.64
0.45

Unit
m d-1
m² d-1
d-1
d-1
d-1
d-1
d-1
d-1
d-1
-

4.9.2 Problem Definition
In this example, we will simulate the transport and degradation of PCE and its daughter products
in a soil column. Degradation not only occurs as sequential reactions, but also partly as parallel
degradation reactions (see Figure 28). Degradation coefficients, yield factors and distribution
factors are given in Table 9.
Saturated flow conditions in a 2.0 m long soil column are maintained for 150 days. The
inflowing solution contains only 10 mmol of PCE/kg of water.
Physical properties of the soil are a porosity of 0.5, the saturated hydraulic conductivity of 1
cm/day, and a dispersivity of 10 cm. Other soil hydraulic parameters are irrelevant for saturated
conditions.
4.9.3 Input

79

Project Manager
Button: "New"Name: "TCE-1"
Description: "TCE first-order degradation network"
Button: "OK"Main Processes
Heading: TCE first-order degradation network
Uncheck: "Water Flow" (steady-state saturated water flow)
Check: "Solute Transport"
Select: "HP1 (PHREEQC)"
Button: “Next”
Geometry Information
Depth of the Soil Profile: 200 (cm)
Button: “Next”
Time Information
Final Time: 150 (days)
Initial Time Step: 1E-5 (days)
Minimum Time Step: 1E-5 (days)
Maximum Time Step: 0.25 (days)
Button: “Next”
Print Information
Unselect: T-Level information
Select: Print at Regular Time IntervalTime Interval: 1 (day)Print Times: Number of Print times: 5
Button: “Next”
Print Times
Button: "Default"
Button: "OK"HP1 – Print and Punch Controls
Check: "Make GNUplot Templates"
Button: “Next”
Water Flow – Iteration Criteria
Button: “Next”
Water Flow – Soil Hydraulic Model
Button: “Next”
Water Flow – Soil Hydraulic Parameters
Qs: 0.5
Ks: 1 (cm/days)
Button: “Next”
Water Flow – Boundary Conditions

80

Upper Boundary Condition: Constant Pressure Head
Lower Boundary Condition: Free drainage
Solute Transport – General Information
Stability Criteria: 0.25
Number of Solutes: 9
Button: “Next”
Solute Transport – HP1 Components and Database Pathway
Six Components: Total_O, Total_H, Pce, Tce, Dcecis, Dcetrans, Dceee, Vc, and Eth
Check: "Create PHREEQC.IN file using HYDRUS GUI"
Button: “Next”
Solute Transport – HP1 Definitions
Additions to Thermodynamic Database
Define new solution master species
Define new solution species
Define Rate equations
SOLUTION_MASTER_SPECIES
Pce
Pce
Tce
Tce
DcecisDcecisDcetrans
Dcetrans
Dceee
Dceee
Vc
Vc
Eth
Eth

0
0
0
0
0
0
0

Pce
Tce
DcecisDcetrans
Dceee
Vc
Eth

SOLUTION_SPECIESPce = Pce ; log_k 0.0
Tce = Tce ; log_k 0.0
Dcecis = Dcecis ; log_k 0.0
Dcetrans = Dcetrans ; log_k 0.0
Dceee = Dceee ; log_k 0.0
Vc = Vc ; log_k 0.0
Eth = Eth ; log_k 0.0
RATES
PCEdegrad-start10 REM par1 = k
20 rate = parm(1)*TOT("water")*MOL("Pce")
30 moles = - rate * TIME
40 SAVE moles-end
TCEdegrad-start10 REM par1 = k
20 rate = parm(1)*TOT("water")*MOL("Tce")
30 moles = - rate * TIME

1
1
1
1
1
1
1

81

40 SAVE moles-end
DCEcisdegrad-start10 REM par1 = k
20 rate = parm(1)*TOT("water")*MOL("Dcecis")
30 moles = - rate * TIME
40 SAVE moles-end
DCEtransdegrad-start10 REM par1 = k
20 rate = parm(1)*TOT("water")*MOL("Dcetrans")
30 moles = - rate * TIME
40 SAVE moles-end
DCEeedegrad-start10 REM par1 = k
20 rate = parm(1)*TOT("water")*MOL("Dceee")
30 moles = - rate * TIME
40 SAVE moles-end
VCdegrad-start10 REM par1 = k
20 rate = parm(1)*TOT("water")*MOL("Vc")
30 moles = - rate * TIME
40 SAVE moles-end
ETHdegrad-start10 REM par1 = k
20 rate = parm(1)*TOT("water")*MOL("Eth")
30 moles = - rate * TIME
40 SAVE moles-endDefinitions of Solution Compositions
Define the initial condition 1001:• Pure water
Define the boundary condition 3001:• Pce concentration
solution 1001 initial solution
solution 3001 boundary solution
Pce 1082

Button: "OK"Geochemical Model
Define for each node the geochemical model, i.e., KINETIC keywords:
KINETICS 1-101 @Layer 1@
PCEdegrad-formula Pce 1.0 Tce -0.79-parms 0.075
TCEdegrad-formula Tce 1.0 Dcecis -0.5328 Dcetrans -0.111 Dceee 0.0962-parms 0.070
DCEcisdegrad-formula Dcecis 1.0 Vc -0.64-parms 0.020
DCEtransdegrad-formula Dcetrans 1.0 Vc -0.64-parms 0.035
DCEeedegrad-formula Dceee 1.0 Vc -0.64-parms 0.055
VCdegrad-formula Vc 1.00 Eth -0.45-parms 0.030
ETHdegrad-formula Eth 1.00
-parms 0.000001

Button: "OK"
Additional Output
Define the additional output to be written to selected output files.
selected_output-totals Pce Tce Dcecis Dcetrans Dceee Vc Eth

Button: "OK"
Button: “Next”
Solute Transport – Solute Transport Parameters
Bulk density: 1.5 (g/cm³)
Disp: 10 (cm)
Button: “Next”
Solute Transport – Boundary conditions
Upper Boundary Condition
Bound. Cond. 3001

83

Soil Profile – Graphical Editor
Menu: Conditions -> Initial Conditions -> Pressure Head
Button: "Edit Condition"
Select All
Top Value: 0
Menu: Conditions -> Observation Points
Button: "Insert"
Insert 5 observation nodes, one every 50 cm
Menu: File -> Save Data
Menu: File –> Exit
Soil Profile – Summary
Button: “Next”
Run Application
4.9.4 Output

0.002
0.00180.00160.00140.00120.001
0.00080.00060.00040.0002
0
0

20

40

60

0.0 cm-50.0 cm-100.0 cm

80
100
Time (days)

120-150.0 cm-200.0 cm

140

160

Total concentration of Vc (mol/kg water)

Total concentration of Dcecis (mol/kg water

Time series, profiles, and outflow curves are shown in Figure 29, Figure 30, and Figure 31,
respectively.
0.001
0.00090.00080.00070.00060.00050.00040.00030.00020.0001
0
0

20

40

60

0.0 cm-50.0 cm-100.0 cm

80
100
Time (days)

120

140

160

-150.0 cm-200.0 cm

Figure 29 – Time series of Dcecis (left) and Vc (righ ) at selected depths (observation nodes) for theexample described in section 4.9.

0

0

-50

-50
Distance (cm)Distance (cm)

84

-100

-100

-150

-150

-200

-200
0

0.00050.001
0.0015
0.002
Total concentration of Tce (mol/kg water)
0 days30.00 days

60.00 days
90.00 days

0.0025120.00 days
150.00 days

00.00020.00040.0006
Total concentration of Eth (mol/kg water)
60.00 days
90.00 days

0 days30.00 days

0.0008120.00 days
150.00 days

Figure 30 – Profiles of Tce (left) and Eth (righ ) at selected print times for the example described inparagraph 4.9.

Concentration (mol/kg water)

0.00120.001
0.00080.00060.00040.0002
0
0

20

40

TCE
PCE
cis-DCE6080100Time (day)120trans-DCE
1,1-DCE
VC

Figure 31 – Outflow curves for the example described in section 4.9.

Eth

140

160

85

4.10

First-Order Kinetic PCE Degradation Network: Leaching of Initial PCE Source

4.10.1 Background and Problem Definition
In this example, the boundary condition problem described in paragraph 4.9 is changed to an
initial condition problem. It is assumed that the top 50 cm of the soil profile is contaminated with
PCE. We assume that the amount of non-aqueous (immobile) PCE is 0.01 mol/1000 cm³ of soil.
Knauss et al. (2000) reported the following partial molal thermodynamic quantities for the PCE
liquid aqueous dissolution reaction:∆rHº = -1790 J/mol(8)∆rSº = -59 J/mol K(9)∆rCpº = -354.6 J/mol(10)where R is the gas constant (8.31441 J/mol), and ∆rHº, ∆rSº, and ∆rCpº are the change of entropy,
enthalpy, and heat capacity of reaction at standard conditions (T0 = 298 K). The following
equation is used in PHREEQC to define the temperature dependence of solubility constants(Parkhurst and Appelo, 1999):
AA
log( K ) = A1 + A2T + 3 + A4 log( T ) + 52
(11)T
T
Temperature dependence of the solubility coefficient can be described with a three-term
extrapolation expression with coefficients A1, A3, and A4 using the following relations(Puigdomènech et al., 1997):
A1 =[

A3 = −A4 =]1∆ r S° − ∆ rC °p (ln T 0 + 1)
2.303R(1∆ r H ° − ∆ rC °pT 02.303R1∆ rC °p ln (10 )2.303R

)

(12)
(13)
(14)

Calculate coefficients A1, A3, and A4:[Answer: A1 = -127.10
A2 = 5612
A4 = 42.64]

4.10.2 Input
Project Manager
Select project: "TCE-1"

86

Button: "Copy"
New Name: "TCE-2"
Description: " TCE first-order degradation network: initial value problem"
Button: "OK"Main Processes
Heading: TCE first-order degradation network: initial value problem
Button: "OK"
Solute Transport – HP1 Definitions

Addition to Thermodynamic Database
Add the definition of the solid phase TCE
PHASES
PCE_lqPce = Pce
-analytical_expression -127.10 0 5612 42.64 0

Definitions of Solution Compositions
Define an initial solution 1002 in equilibrium with the PCE_lq phase
Define a pure water boundary solution
solution 1002 initial solution top layerPce 1 Pce_lq 0
solution 3001 boundary solution

Button: "OK"Geochemical Model
Add initial pollution in the top 50 cm
Equilibrium_phases 1-26
PCE_lq 0 0.01

Button: "OK"

Additional Output
Add PCE_lq to –equilibrium_phases
selected_output-totals Pce Tce Dcecis Dcetrans Dceee Vc Eth-equilibrium_phases PCE_lq

Button: "OK"
Button: "OK"

87

Soil Profile – Graphical Editor
Menu: Conditions -> Initial Conditions -> Concentrations
Concentration number: 1
Button: "Edit Condition"
Select nodes 1-26
Solution composition: 1002
Menu: File -> Save Data
Menu: File –> Exit
Run Application

4.10.3 Output

0

0

-50

-50
Distance (cm)Distance (cm)Selected output is shown in Figure 32 and Figure 33.

-100

-100

-150

-150

-200

-200
0

0.002

0 days30.00 days

0.004
0.006
0.008
PCE_lq (mol/1000 cm³ of soil)
60.00 days
90.00 days

0.01

120.00 days
150.00 days

00.00030.00060.00090.00120.0015
Total concentration of Pce (mol/kg water)
0 days30.00 days

60.00 days
90.00 days

0.0018120.00 days
150.00 days

Figure 32 – Profiles of the solid phase PCE_lq (left) and the aqueous concentrations of Pce (right) atselected print times for the example described in section 4.10.

88

Concentration (mol/kg water)

0.00070.00060.00050.00040.00030.00020.0001
0
0

20

40

TCE
PCE
cis-DCE6080100Time (day)trans-DCE
1,1-DCE
VC

120

140

Eth

Figure 33 – Outflow concentrations for the example described in section 4.10.

160

89

4.11 First-Order Kinetic PCE Degradation Network: Initial Source Trapped in
Immobile Water Phase

4.11.1 Problem Definition
It is assumed that the solid PCE phase is trapped in immobile zones in the soil profile, instead ofin the mobile aqueous phase as assumed in the example in section 4.10. Degradation reactions
occur only in the mobile aqueous phase. Assume the following properties (in addition to those
assigned in paragraph 4.10): the immobile water content: 0.1, the first-order exchange
coefficient: 0.01 day-1.

4.11.2 Input
Project Manager
Select project: "TCE-2"
Button: "Copy"
New Name: "TCE-3"
Description: " TCE first-order degradation network: initial value problem MIM"
Button: "OK"Main Processes
Heading: TCE first-order degradation network: initial value problem MIM
Button: "OK"
Solute Transport – General Information
Check: Dual-Porosity (Mobile-Immobile Water) Model (Physical nonequilibrium)
Solute Transport – HP1 Definitions

Definitions of Solution Compositions
Delete solution 1002
Add the initial solution for the immobile water phase in equilibrium with the PCE
solid:
solution 1001 initial solution mobile phasesolution 2001 initial solution immobile phase
Pce 1 Pce_lq 0
solution 3001 boundary solution

Button: "OK"Geochemical Model90

Add the PCE contamination in the top 50 cm in the immobile zone. Numbers for theimmobile zone starts at numbers of node +1 and end at two times the number ofnodes. For this project, numbers for the immobile zone are thus from 102 to 202.
Equilibrium_phases 102-128
PCE_lq 0 0.01

Button: "OK"
Button: "OK"
Solute Transport – Transport Parameters
Mass Tr.: 0.01 (day-1)
ThImob: 0.1
Button: "OK"Soil Profile – Graphical Editor
Menu: Conditions -> Initial Conditions -> Concentrations
Concentration number: 1
Button: "Edit Condition"
Select all
Solution composition: 1001
Menu: Conditions -> Initial Conditions -> Sorbed Concentrations
Concentration number: 1
Button: "Edit Condition"
Select nodes 1-26
Solution composition: 2001
Button: "Edit Condition"
Select nodes 27-101
Solution composition: 1001
Menu: File -> Save Data
Menu: File –> Exit
Run Application

4.11.3 Output
Selected output is shown in Figure 34 and Figure 35:910Distance (cm)

-50

-100

-150

-200
0

0.002

0.004
0.006
0.008
PCE_lq (mol/1000 cm³ of soil)
60.00 days
90.00 days

120.00 days
150.00 days

0

0

-50

-50
Distance (cm)Distance (cm)

0 days30.00 days

0.01

-100

-150

-100

-150

-200

-200
0

5e-005 0.0001 0.00015 0.0002 0.00025 0.0003 0.0003
Total concentration of Pce (mol/kg water)
60.00 days
90.00 days

0 days30.00 days

120.00 days
150.00 days

00.00050.001
0.0015
Total concentration of Pce (mol/kg water)
60.00 days
90.00 days

0 days30.00 days

0.002

120.00 days
150.00 days

Figure 34 – Profiles of the solid phase PCE_lq (top), aqueous concentrations of Pce in the mobile (right)
and immobile (right) water phases at selected print times for the example described in section 4.11.

Concentration (mol/kg water)

0.000140.000120.00018e-0056e-0054e-0052e-005
0
0

20

40

TCE
PCE
cis-DCE6080100Time (day)trans-DCE
1,1-DCE
VC

120

140

Eth

Figure 35 – Outflow concentrations for the example described in section 4.11.

160

92

4.12

Coupled Nta Degradation and Biomass Growth

4.12.1 BackgroundThe exercise is based on example 15 from the PHREEQC-2 manual (Parkhurst and Appel, 1999)
and on the paper of Tebes-Stevens et al. (1998). The main topic is the biodegradation ofnitrylotriacetate (Nta).
The degradation of Nta, in presence of oxygen and biomass, is written as:
HNta 2 - + 1.62 O 2 + 1.272 H 2 O + 2.424 H + =0.576C 5 H 7 O 2 N + 3.12H 2 CO 3 + 0.424NH +4(15)

where HNta2- is C6H7O6N.
A multiplicative Monod rate expression is used to describe the Nta degradation:⎛ c HNTA − 2 ⎞⎛ cO 2
⎞
⎟⎟⎜⎜
⎟⎟
RHNTA2- = -qm Xm ⎜⎜
+
+
K
C
K
C
HNTA − 2 ⎠⎝ a
O2 ⎠
⎝ s

(16)

where RHNTA2- is the rate of degradation [mol/l/hr], qm is the maximum specific rate (1.418E-3
mol/g cells/hr), Xm is the biomass (initially 1.36E-4 g cells per liter of water), Ks is the half
saturation constant for substrate (7.64E-7 mol/l) and Ka is the half saturation constant for
acceptor (6.25e-6mol/l).
The biomass production is described as:
Rcells = -YRHNTa-2 - bXm(17)

where Rcells is the rate of cell growth [g cells/L/hr], Y is the microbial yield coefficient (65.14 gcells/mol Nta), and b is the first-order biomass decay coefficient (0.00208 hr-1).
The two equations (16) and (17) are coupled: Eq. (16) needs the current amount of biomass,
whereas Eq. (17) needs the biodegradation rate of Nta. PHREEQC Basic statements to be used in
the rate equation allows for this coupling.

4.12.2 Problem Definition
Consider a column of 5 m. The porosity is 0.4. A constant water flux of 0.2 m/hr is applied undersaturated steady-state flow conditions. The dispersivity is 5 cm and the bulk density is 1.5 g/cm³.
The Nta concentration in the infiltrating water is 5.23 µmol/kgw. Both the initial and infiltratingwater contain 0.49 µmol/kgw C, 31.25 µmol/kgw O2, 1000 µmol/kgw Na, and 1000 µmol/kgw
Cl. Initially, there is 50 µg biomass per 1000 cm³ of soil. All other parameters are as defined
above.
Investigate time series and profile data of Nta and Biomass for an infiltration experiment of 24
hr.

93

4.12.3 Input
Project Manager
Button: "New"Name: "Nta"
Description: "Nta degradation and biomass growth"
Button: "OK"Main Processes
Heading: Nta degradation and biomass growth
Check: "Water Flow"
Check: "Solute Transport"
Select: "HP1 (PHREEQC)"
Button: “Next”
Geometry Information
Length Units: m
Depth of the Soil Profile: 5 (m)Button: “Next”
Time Information
Time Units: Hours
Final Time: 24 (hours)
Button: “Next”
Print Information
Unselect: T-Level information
Select: Print at Regular Time IntervalTime Interval: 0.025
Print Times: Number of Print times: 6
Button: “Next”
Print Times
Button: "Default"
Button: "OK"HP1 – Print and Punch Controls
Check: "Make GNUplot Templates"
Button: “Next”
Water Flow – Iteration Criteria
Button: “Next”
Water Flow – Soil Hydraulic Model
Button: “Next”
Water Flow – Soil Hydraulic Parameters
Qs: 0.4
Ks: 0.2 (m/hr)
Button: “Next”

94

Water Flow – Boundary Conditions
Upper Boundary Condition: Constant Pressure Head
Lower Boundary Condition: Constant Pressure Head
Solute Transport – General Information
Stability Criteria: 0.25
Number of Solutes: 7
Button: “Next”
Solute Transport – HP1 Components and Database Pathway
Database Pathway:
Browse: ex15.dat
Six Components: Total_O, Total_H, C, Nta, Na, Cl, N
Check: "Create PHREEQC.IN file using HYDRUS GUI"
Button: “Next”
Solute Transport – HP1 Definitions

Additions to Thermodynamic Database
Define rate equations
RATES
degradNTA-start10 qm = parm(1)20 Ks = parm(2)30 Ka = parm(3)40 Xm = kin("Biomass")
50 D = mol("HNta-2") / (Ks +mol("HNta-2"))
60 A = mol("O2") / (Ka +mol("O2"))70 rate = -qm*Xm*D*A
80 moles = rate * time
90 put(rate,1)
100 SAVE moles-end
Biomass-start10 Y = parm(1)20 b= parm (2)30 degradNta = get(1)40 rate = -Y*degradNta - b*M
50 moles = -rate*Time
60 if (M+moles) < 0 then moles = - M
70 SAVE moles-endDefinitions of Solution Compositions
Define the initial condition 1001:
Define the boundary condition 3001:
solution 1001

95

pH 7 charge-units mol/kgw
O(0) 6.25E-005
C 4.9E-7
Na 0.001
Cl 0.001
solution 3001
pH 7 charge-units mol/kgw
O(0) 6.25E-005
C 4.9E-7
Na 0.001
Cl 0.001
Nta 5.23E-6

Button: "OK"Geochemical Model
Define for each node the geochemical model, i.e., KINETICS keywords:
kinetics 1-101
degradNTA-formula Nta 1. C -3.12 H -1.968 O -4.848 N -0.424-parms 1.407E-3 7.64E-7 6.25e-6
biomass-formula H 0.0-parms 65.14 0.00208-m0 50E-6

Button: "OK"

Additional Output
Define the additional output to be written to selected output files.
SELECTED_OUTPUT-totals Nta-kinetics biomass

Button: "OK"
Button: “Next”
Solute Transport – Solute Transport Parameters
Disp: 0.05 (m)Button: “Next”
Solute Transport – Boundary conditions
Upper Boundary Condition
Bound. Cond. 3001
Soil Profile – Graphical Editor

96

Menu: Conditions -> Initial Conditions -> Pressure Head
Button: "Edit Condition"
Select All
Top Value: 0
Menu: Conditions -> Observation Points
Button: "Insert"
Insert 5 observation nodes at a depth interval of 1 m
Menu: File -> Save Data
Menu: File –> Exit
Soil Profile – Summary
Button: “Next”
Run Application

4.12.4 Output

0.00025

5e-006biomass (mol/1000 cm³ of soil)

Total concentration of Nta (mol/kg water)

Time series and profiles of selected variables are shown in Figure 36 and Figure 37.

4e-0063e-0062e-0061e-0060.00020.000150.00015e-005
0

0
0

5

10
15
Time (hours)-1.0 m-2.0 m
-3.0 m20-4.0 m
-5.0 m

25

0

5

10
15
Time (hours)-1.0 m-2.0 m
-3.0 m20

25-4.0 m
-5.0 mFigure 36 – Time series of Nta concentrations and biomass at selected depths (observation nodes) for theexample described in section 4.12.

0

0

-1

-1
Distance (m)Distance (m)

97

-2
-3

-2
-3
-4

-4

-5

-5
0

1e-0062e-0063e-0064e-0065e-006
Total concentration of Nta (mol/kg water)
0 hours
4.00 hours
8.00 hours
12.00 hours

16.00 hours
20.00 hours
24.00 hours

6e-0060

5e-0050.00010.000150.0002
biomass (mol/1000 cm³ of soil)

0 hours
4.00 hours
8.00 hours
12.00 hours

0.000216.00 hours
20.00 hours
24.00 hours

Figure 37 – Profiles of Nta concentrations and biomass at selected print times for the example describedin section 4.12.

98

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