Computer Session

TUTORIALS FOR THE HYDRUS WETLAND MODULE
These tutorials show the use of the HYDRUS Wetland Module (Langergraber and Šimůnek,2006, 2011) for simulating vertical flow (VF) and horizontal flow (HF) wetlands. The following
tutorials are provided in this section.
1) Water Flow in a Vertical Flow Wetland.

2) Reactive Transport in a Vertical Flow Wetland (HYDRUS Wetland Module,
CW2D Biokinetic Model).

3) Water Flow and Reactive Transport in a Horizontal Flow Wetland (HYDRUS
Wetland Module, CWM1 Biokinetic Model).

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References:
Langergraber, G. and J. Šimůnek, Modeling variably-saturated water flow and multicomponent reactive transport in constructed wetlands, Vadose Zone Journal 4, 924-938,2005.
Langergraber, G., and J. Šimůnek, The multi-component reactive transport module CW2D for
constructed wetlands for the HYDRUS Software Package. Hydrus Software Series 2,
Department of Environmental Sciences, University of California Riverside, Riverside,
California, USA, 72p., 2006.
Langergraber, G., D. Rousseau, J. García, and J. Mena, CWM1 - A general model to describe
biokinetic processes in subsurface flow constructed wetlands. Water Sci Technol 59(9),1687-1697, 2009.
Langergraber, G., and J. Šimůnek, HYDRUS Wetland Module, Version 2. Hydrus Software
Series 4, Department of Environmental Sciences, University of California Riverside,
Riverside, California, USA, 56p., 2011.
Langergraber, G., Šimůnek, J. (2012): Reactive Transport Modeling of Subsurface Flow
Constructed Wetlands Using the HYDRUS Wetland Module. Vadoze Zone Journal 11(2)Special Issue "Reactive Transport Modeling", doi:10.2136/vzj2011.0104.

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1

Water Flow in a Vertical Flow Wetland

This example shows the set-up of flow simulations in a VF wetland and the calibration of theflow model using measurements of the volumetric effluent flow rate. The example is based on
the one provided in Langergraber and Šimůnek (2006).
The example consists of the five following steps:
1. Project set up, a 24-h long simulation with 4 loadings of 3-min duration.
2. Simulation is repeated (with the initial conditions obtained in the previous step) toreach pseudo steady-state conditions for water flow.
3. Calibration of soil hydraulic parameters against measured outflow data.
4. Simulation is re-run with the new (calibrated) soil hydraulic parameters.
5. Simulation is repeated (with the initial conditions obtained in the previous step andnew soil hydraulic parameters) to reach pseudo steady-state conditions.

1.1

System Description

The VF wetland has a surface area of 1 m² (1x1 m²), a height of the main layer of the filter bed
is 50 cm. The main layer consists of sand (gravel size 0.06-4 mm). An intermediate layer of
10 cm thickness with a gravel size of 4-8 mm prevents fine particles to be washed out into thedrainage layer (15 cm thick; gravel 16-32 cm) where the effluent is collected by means of tile
drains.
The sandy material used for the main layer has a porosity of 0.30 and the saturated hydraulicconductivity, Ks, of 117 cm/h. Table 1 shows the measured cumulated effluent flow for one
loading interval of 6 hours and a single hydraulic loading of 10 L. The duration of a single
loading is 3 minutes.
Table 1. Measured cumulated volumetric effluent flow
Time
Cum. effluent
Time
Cum. effluent

[min]
[L]
[min]
[L]

20
0.31
270
8.08

40
0.64
300
8.78

60
0.99
330
9.43

80
1.49
360
9.99

100
2.36

120
3.14

140
3.95

160
4.75

180
5.47

Only the 50 cm main layer of the VF bed shall be considered in the simulation.

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200
6.14

240
7.31

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1.2

The HYDRUS Project Setup

Simulation 1 - Set-up:Project Manager (FileProject Manager)
Button ”New”

New Project (or FileNew Project)
Name:
Example 1a
Description: VF wetland - flow simulation
Working Directory: Temporary – is deleted after closing the project
Button ”Next”

Domain Type and Units (EditDomain GeometryDomain Type and Units)
Type of Geometry: 2D - Simple
2D-Domain Options: 2D - Vertical Plane XZ
Units:
cm
Initial Workspace: Xmin=0 cm, Xmax=100 cm, Zmin=0 cm, Zmax=100 cm (toaccommodate the transport domain)
Check "Set View Stretching Factors Automatically"
Button ”Next”



Rectangular Domain Definition (EditDomain GeometrySimple Domain)
Lx = 100 cm, Lz = 50 cm,  = 0°
Button ”Next”

Main Processes (EditFlow and Transport ParametersMain Processes)
Check Box: Water Flow
Button ”Next”

Time Information (EditFlow and Transport ParametersTime Information)
Time Units: hours
Final Time: 24
Initial Time Step:
0.001
Minimum Time Step: 0.0001
Maximum Time Step: 1
Check "Time-Variable Boundary Conditions"
Number of Time-Variable Boundary Records: 8
Number of times to repeat the same set of BC records: 1
Button ”Next”



Output Information (EditFlow and Transport ParametersOutput Information)
Print Options:
Check T-Level Information
Check Screen Output
Check Press Enter at the End
Print Times: Count: 24
UpdateNumber of Subregions: 1
Button ”Next”



Water Flow - Iteration Criteria (EditFlow and Transport ParametersWater
Flow ParametersIteration Criteria )Leave default values
Button ”Next”
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Computer SessionWater Flow – Soil-Hydraulic Model (EditFlow and Transport ParametersWater
Flow ParametersHydraulic Properties Model)
Radio button - van Genuchten-Mualem
Radio button - No hysteresis
Button ”Next”



Water Flow - Soil-Hydraulic Params (EditFlow and TransportParametersWater Flow ParametersSoil Hydraulic Parameters)
Select "Sand" from Soil Catalog
Enter measured values for Qs = 0.30 and Ks = 117 cm/h
Button ”Next”

Time-Variable Boundary Conditions (EditFlow and TransportParametersVariably Boundary Conditions)
Calculations:
duration of a single loading: 3 minutes = 0.05 hours
amount of a single loading: 10 L/m² = 10 mm = 1 cm
actual loading rate: 1 cm / 0.05 h = 20 cm/h
Time-Variable Boundary Conditions:Time
Precip.
[hours] [cm/h]
1 0.0520
2 60
3 6.0520
4 12
0
5 12.0520
6 18
0
7 18.05
20
8 24
0
Button ”Next”

Evap.
[cm/h]
0
0
0
0
0
0
0
0

Transp.
[cm/h]
0
0
0
0
0
0
0
0

hCritA
[cm]
10000
10000
10000
10000
10000
10000
10000
10000

Remaining columns = 0FE-Mesh - FE-Mesh Parameters (EditFE-MeshFE-Mesh Parameters)
horizontal Discretization in X: Count = 11 Button "Update"horizontal Discretization in Z: Count = 21 Button "Update"
Generate Z-Coordinates: RS2 = 4 Button "Generate"
Button ”OK”



Water Flow Initial Conditions:
Click on the Initial Conditions Tab under the View Window.
Or on the Navigator Bar click on Initial Conditions – Pressure Head (or InsertInitial
ConditionsPressure Head)
Select the entire transport domain and click on the Set Pressure Head IC command at
the Edit Bar, check Hydrostatic equilibrium from the lowest located nodal point,check that Bottom Pressure Head Value is set equal to -2 cm.
Button ”OK”

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Computer SessionWater Flow Boundary Conditions:
Click on the Boundary Conditions Tab under the View Window.
Or on the Navigator Bar click on Boundary Conditions – Water Flow (orInsertBoundary ConditionsConstant Head)a) Select Atmospheric Boundary from the Edit Bar, and select the top of the boundary.
b) Select Constant Head from the Edit Bar, select the bottom boundary, and specify-2 cm.

Observation Nodes:
Click on the Domain Properties Tab under the View Window.
Or on the Navigator Bar click on Domain Properties – Observation Nodes (orInsertDomain PropertiesObservation Nodes)
Click the "Insert Observation Node" command on the Edit Bar and insert
5 observation nodes in the middle of the domain and at depths of approximately 5, 10,
20, 30, 40 and 50 cm.



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

Run Calculations
Click the Calculate Current Project command on the Toolbar (or menu command
CalculationCalculate Current Project)Results – Other Information: Observation Nodes (from the Navigator Bar, orResultsObservation Nodes)



Results – Other Information: Boundary Fluxes (from the Navigator Bar, orResultsBoundary InformationBoundary Fluxes)
Select "Constant Boundary Flux"

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Note that we have obtain pseudo-steady-state behaviour for water flux after four
loadings.
Button ”Close”
Save Results
Save the project using the Save command on the Toolbar (or FileSave).

Simulation 2 - Pseudo Steady-State:Project Manager (FileProject Manager)
Select "Example 1a"
Button ”Copy”
Enter New Name: Example 1b
Description: VF wetland - flow simulation - pseudo steady-state
Button ”OK”
Button ”Open” Example 1b

Update of Water Flow Initial Conditions with previous simulation results:
InsertInitial ConditImport
Select file "Example 1a.h3d2"
Button ”Open”
Select "Pressure Head"
Select "The Last (Final) Time Layer"
Button ”OK”
This action requires deleting results. Do you want to continue?
Button ”Yes”

Save New Initial Conditions
Save the project using the Save command on the Toolbar (or FileSave).



Re-Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)View results for "Constant Boundary Flux"

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Steady-state behaviour for water flux is OK
Button ”Close”
Comparison with measured data40

measuredBoundary flux [cm²/h]

35

Simulated (Example 1b)

30
25
20
15
10
5
0
18

19

20

21

22

23

24

Time (hours)

Save Results
Save the project using the Save command on the Toolbar (or FileSave).

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Simulation 3 - Inverse Simulation:Project Manager (FileProject Manager)
Select "Example 1b"
Button ”Copy”
Enter New Name: Example 1c
Description: VF wetland - flow simulation - inverse simulation
Button ”OK”
Button ”Open” Example 1c

Main Processes (EditFlow and Transport ParametersMain Processes)
Check Box: Water Flow
Check Box: Inverse Solution ?
Button ”Next”
Delete resultsInverse Solution (EditFlow and Transport ParametersInverse Solution)
Check Box: Soil Hydraulic Parameters
Other Parameters:
Max Number of Iterations: 10
Number of Data Points in the Objective Function: 15 (i.e. number of measured data,
see Table 1)
Button ”OK”



Output Information (EditFlow and Transport ParametersOutput Information)
Print Options:
Un-Check Screen Output
Button ”OK”



Water Flow – Soil-Hydraulic Params (EditFlow and TransportParametersWater Flow ParametersSoil Hydraulic Parameters)
Check parameters Qr, Alpha, n and l to be fitted
Button ”OK”

Inverse Solution Data (EditFlow and Transport ParametersData for Inverse
Solution)
Assumption:
4th loading will be used for comparing simulation results with measured data
i.e. Inverse Solution Data table (Table 1):
X-column: time + 18 hours,
Y-column: + 300 cm² (1 single loading: 100 cm²)
one single loading = 10 mm = 10 L/m² = 10 * 1000 cm³ / 100 cm = 100 cm²
Inverse Solution Data table:
1
2
3
4
5
6
7

X
18.33
18.67
19.00
19.33
19.67
20.00
20.33

Y
303.1
306.4
309.9
314.9
323.6
331.4
339.5

Type
0
0
0
0
0
0
0

Position
1
1
1
1
1
1
1
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Weight
1
1
1
1
1
1
1

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8
9
10
11
12
13
14
15

20.67
21.00
21.33
22.00
22.50
23.00
23.50
24.00

347.5
354.7
361.4
373.1
380.8
387.8
394.3
399.9

0
0
0
0
0
0
0
0

1
1
1
1
1
1
1
1

1
1
1
1
1
1
1
1

Button ”OK”


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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)View results for "Cumulative Fluxes" - "Constant Boundary Flux"

Button ”Close”
View parameters after inverse simulation at "Inverse Solution Results"
Iteration
SSQ
00.6390D-01
1
0.2036D-01
2
0.2619D-02
3
0.2538D-02

WCR
0.4500E-01
0.4525E-01
0.3168E-01
0.3155E-01

ALPHA
0.1450E+00
0.1639E+00
0.1686E+00
0.1686E+00

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N
0.2680E+01
0.2202E+01
0.2115E+01
0.2115E+01

L0.5000E+00
0.6062E+00
0.6168E+00
0.6174E+00

Computer Session

Simulation 4 - Update Steady-State Water Flow Results 1:
Project Manager (FileProject Manager)
Select "Example 1b"
Button ”Copy”
Enter New Name: Example 1d
Description: VF wetland - flow simulation - update steady-state flow
Button ”OK”
Button ”Open” Example 1d

Water Flow - Soil-Hydraulic Params (EditFlow and TransportParametersWater Flow ParametersSoil Hydraulic Parameters)
Change parameters to estimated values, i.e. Qr = 0.032, Alpha = 0.169, n = 2.11 andl = 0.617
Button ”OK”



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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)Results – Other Information: Boundary Fluxes (from the Navigator Bar, orResultsBoundary InformationBoundary Fluxes)
Select "Constant Boundary Flux" - notice that initially there was not steady state
Button ”Close”

Save Results
Save the project using the Save command on the Toolbar (or FileSave).

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Simulation 5 - Update Steady-State Water Flow Results 2:Project Manager (FileProject Manager)
Select "Example 1d"
Button ”Copy”
Enter New Name: Example 1e
Description: VF wetland - flow simulation - update steady-state flow
Button ”OK”
Button ”Open” Example 1eUpdate of Water Flow Initial Conditions with simulation results:
InsertInitial ConditImport
Select file "Example 1d.h3d2" in working directory
Button ”Open”
Select "Pressure Head"
Select "The Last (Final) Time Layer"
Button ”OK”
This action requires deleting results. Do you want to continue?
Button ”Yes”

Save New Initial Conditions
Save the project using the Save command on the Toolbar (or FileSave).



Re-Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)Compare with measured data:40

measured35

Boundary flux [cm²/h]

Simulated (Example 1b)
30

Simulated (Example 1e)

25
20
15
10
5
0
18

19

20

21

Time (hours)

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22

23

24

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2

Reactive Transport in a Vertical Flow Wetland (CW2D
Biokinetic Model)This example demonstrate the set-up of a project with reactive transport in a vertical flow
wetland (VF wetland) using the CW2D biokinetic model.

2.1

System Description

The VF wetland is the same as in Example 1. The calibrated flow model will be used to set-up
a reactive transport simulation using the CW2D biokinetic model. Table 2 shows the CW2D
influent concentrations.
Table 2. CW2D influent concentrations (as used in "Wetland 1", Langergraber andŠimůnek, 2006)
Component
Concentration

2.2

SO
1

CR
160

CS
120

CI
20

XH
0

XANs
0

XANb
0

NH4N
60

NO2N
0.1

NO3N
0.1

N2
0

PO4P
10

The HYDRUS Project Setup

Simulation 1 - Set-up:Project Manager (FileProject Manager)
Select: Example 1e
Button ”Copy”
Name: Example 2a
Description: VF wetland - reactive transport simulation (CW2D)
Button ”OK”

Open project "Example 2a"
Select: Example 2a
Button ”Open”



Main Processes (EditFlow and Transport ParametersMain Processes)
Check Box: Water Flow
Check Box: Solute Transport
Check the Radio Button: Wetland (the CW2D module should be selected by default)
Button ”Next”
Delete Results: "OK"Time Information (EditFlow and Transport ParametersTime Information)
Final Time: 48 (simulation over 2 days)
Maximum Time Step: 1
Number of times to repeat the same set of BC records: 2
Button ”OK”



Output Information (EditFlow and Transport ParametersOutput Information)
Print Options:
Check T-Level Information
Every n time step: 1
Print Times:
Button ”Default”
Button ”OK”
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Solute Transport – General Info (EditFlow and Transport ParametersSolute
Transport ParametersGeneral Information )Set "Mass units" = µg
Button ”Next”



Solute Transport – Transport Parameters (EditFlow and TransportParametersSolute Transport Parameters Solute Transport Parameters)
Soil specific parameters
Set parameter "Fract." = 0 (mandatory for the Wetland module)
Solute specific parameters (in cm²/h):
Sol
1
2
3
4
5
6
7
8
9
10
11
12
13

Diffus.W.
0.072
0.04560.04560.04560000.08010.08010.08010.08010.08010.

Diffus.G.
769
0
0
0
0
0
0
0
0
0
0
0
0

Button ”OK”
Solute Transport – Reaction Parameters (EditFlow and TransportParametersSolute Transport Parameters Solute Reaction Parameters)
Leave default parameters and browse through all these windows
Button ”Next”



Solute Transport – Constructed Wetland Model (CW2D) Parameters I(EditFlow and Transport ParametersSolute Transport Parameters ConstructedWetland Parameters I)
Explore and leave default parameters
Button ”Next”



Solute Transport – Constructed Wetland Model (CW2D) Parameters II(EditFlow and Transport ParametersSolute Transport Parameters ConstructedWetland Parameters II)
Explore and leave default parameters
Button ”Next”

Time-Variable Boundary Conditions (EditFlow and TransportParametersVariably Boundary Conditions)add influent concentrations:cVal1-1 = 1
cVal1-2 = 160
cVal1-3 = 120
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Computer Session
cVal1-4 = 20
cVal1-8 = 60
cVal1-9 = 0.1
cVal1-10 = 0.1
cVal1-12 = 10
Copy values to all lines

Solute Transport Initial Conditions:Navigator Bar click on Initial Conditions – L1 – Dissolved Oxygen
Select the entire transport domain and click on the Set L1 - IC Dissolved Oxygen
command at the Edit Bar, check Use top value for entire selected region, check thatTop value is set equal 1.
Button ”OK”
Repeat for L2, L3, L4, L8, L9, L10, L12, S5, S6, S7
Note: it is assumed that a clean sand is used and that the filter has not been loaded
previously. Steady-state conditions for reactive transport are reached once the biomass
has reached constant concentrations, which can be expected after longer simulation
time (e.g. ,100 days).



Solute Transport Boundary Conditions:Navigator Bar click on Boundary Conditions – Solute Transport
Select Third-type Boundary from the Edit Bar, and select the top of the boundary.
Pointer to the vector of the boundary Conditions = 1
Button ”OK”

Domain Properties - Observation Nodes:
Insert Observation Nodes

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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)Results – Other Information: Observation Points (from the Navigator Bar)
Select "Observation Points "View results, 1st: check oxygen concentrations
Vertical Variable: select "L1 – Dissolved Oxygen

Note that L1 (Dissolved Oxygen) concentrations at the upper Observation Nodes(Nos.1-4) show numerical oscillations. The reason is that, oxygen consumption is by
far the fastest process among all the reactions considered.
Too avoid these numerical oscillations the maximum time step needs to be reduced.

Advice: L1 (Dissolved Oxygen) concentrations should always be checked prior toother concentrations to avoid numerical instabilities.

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Simulation 2 - Set-up:Project Manager (FileProject Manager)
Select: Example 2a
Button ”Copy”
Name: Example 2b
Description: VF wetland - reactive transport simulation (CW2D) – reduced dt
Button ”OK”

Open project "Example 2b"
Select: Example 2b
Button ”Open”



Time Information (EditFlow and Transport ParametersTime Information)
Maximum Time Step: 0.02
Button ”OK”



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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)Results – Other Information: Observation Points (from the Navigator Bar)
Select " Observation Points "View results, 1st: check oxygen concentrations
Vertical Variable: select "L1 – Dissolved Oxygen

Note that L1 (Dissolved Oxygen) concentrations do not show numerical oscillations
anymore  the maximum time step used is OK.

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Check the other results:
e.g. Growth of heterotrophic bacteria
Vertical Variable: select "S5 – Heterotr. Micro."e.g. Growth of ammonia oxidisers
Vertical Variable: select "S6 – Autotr. Micro - NS"

Button ”Close”
Save Results
Save the project using the Save command on the Toolbar (or FileSave).

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3

Water Flow and Reactive Transport in a Horizontal Flow
Wetland (CWM1 Biokinetic Model)This example demonstrates the set-up of a water flow and reactive transport simulation in ahorizontal flow (HF) wetland using the CWM1 biokinetic model.
The example consists of the following three steps:
1. Project set up, a 24-h long simulation to reach steady-state conditions for water flow.
2. Simulation of a tracer experiment.
a. Set-up of tracer simulationb. Inverse simulation to match measured datac. Updated tracer simulation
3. Simulation of reactive transport (CWM1 biokinetic model).
4. Simulation of reactive transport (CWM1 biokinetic model) and effects of wetland
plants.

3.1

System Description

The HF bed as described by Langergraber and Šimůnek (2012) is used in this example. The HF
bed has a length of 10.3 m, a depth of 0.55 m and a width of 5.3 m. The water level in the bed
is 0.5 m. The gravel of the main layer has d60 of 10 mm and porosity of 41 %.
The first 0.3 m of the bed, the mixing zone, is filled with course gravel (porosity 45 %). The
HYDRUS implementation considers the mixing zone (a red circle in Figure 1, that also showsa typical flow path in a HF bed).

Figure 1: Implementation of the HF bed.
In the HYDRUS implementation, the vertical domain of 10.3 m and 0.6 m was discretized into
33 columns and 23 rows, resulting in a two-dimensional finite element mesh consisting of
805 nodes and 1496 triangular finite elements. An atmospheric boundary condition was appliedat the top of the mixing zone, whereas the effluent boundary was represented using a constanthead boundary condition (0.5 m) at the bottom of the right end of the bed
The HF bed was loaded with wastewater with a hydraulic loading rate of 36 mm.d-1.
To characterize the hydraulic behavior, a tracer experiment with KCl was carried out. The tracer
concentration was measured by measuring the electrical conductivity (EC) in the influent andeffluent of the HF wetland. A KCl solution with EC of 30 mS.cm-1 was added for a duration of
10 minutes and then the tracer breakthrough curve was measured at the effluent of the HF
wetland. During the tracer experiment the background EC was 0.8 mS.cm-1. Table 3 shows
measured effluent EC during a period of 10 days.

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Table 3. Effluent EC measurements (in mS.cm-1) at the HF wetland effluent.
Time
EC effluent
Time
EC effluent[d][mS.cm-1][d][mS.cm-1]

0.5
0.793
5.5
0.847

1
0.800
6
0.865

1.5
0.805
6.5
0.861

2
0.808
7
0.862

2.5
0.801
7.5
0.843

3
0.793
8
0.826

3.5
0.810
8.5
0.815

4
0.812
9
0.807

4.5
0.826
9.5
0.813

5
0.828
10
0.799

The influent concentrations for the CWM1 components are given in Table 4. The CWM1
influent concentrations are the same as those used in CW2D (the tutorial 2 above), when the
CW2D influent concentrations were calculated as follows: CR=SF+SA; CS=XS; and
CI=SI+XI. In the CW2D simulations, phosphate PO4P was considered in the inflow whilesulphur was not.
Table 4. CWM1 influent concentrations (in mg.L-1) in wastewater (taken from "scenario 5" ofLlorens et al., 2011).
CWM1 component
Concentration

SO
0.86

SF
170

SA
27

SI
13

SNH
57

SNO
0

SSO4
33

SH2S
0

XS
33

XI
13

For evaluating the influence of wetland plants on the removal of contaminants in HF beds, thefollowing spatial distribution of root water uptake in the vertical domain was assumed. As
reported by Headley et al. (2005), root biomass was only found in the upper half of the HF bed.
The same assumption that the roots are dense in the upper 20 cm and then decrease rapidly withdepth was made here. The transpiration rate of common reed (Phragmites australis) is assumed
to be 7.4 mm.d-1 and a specific oxygen release of 5 g.m-2.d-1. The selected value of the specificoxygen release is a rather conservative value.
References:
Headley, T., Herity, E., Davison, L. (2005): Treatment at different depths and vertical mixing within a
1-m deep horizontal subsurface-flow wetland. Ecol Eng 25(5), 567-582.
Langergraber, G., Šimůnek, J. (2012): Reactive transport modeling of subsurface flow constructedwetlands. Vadose Zone J 11(2) Special Issue "Reactive Transport Modeling",
doi:10.2136/vzj2011.0104.
Llorens, E., Saaltink, M.W., Poch, M., García, J. (2011): Bacterial transformation and biodegradation
processes simulation in horizontal subsurface flow constructed wetlands using CWM1-RETRASO.
Bioresource Technol 102(2), 928-936.

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Computer Session

3.3

The HYDRUS Project Setup

Simulation 1 - Set-up:Project Manager (FileProject Manager)
Button ”New”

New Project (or FileNew Project)
Name:
Example 3a
Description: HF wetland - flow simulation
Working Directory: Temporary – is deleted after closing the project
Button ”Next”

Domain Type and Units (EditDomain GeometryDomain Type and Units)
Type of Geometry: 2D - Simple
2D-Domain Options: 2D - Vertical Plane XZ
Units:
m
Initial Workspace: Xmin=0 m, Xmax=12 m, Zmin=0 m, Zmax=2 m
Check "Set View Stretching Factors Automatically"
Button ”Next”



Rectangular Domain Definition (EditDomain GeometrySimple Domain)
Lx = 10.3 m, Lz = 0.55 m,  = 0°
Button ”Next”

Main Processes (EditFlow and Transport ParametersMain Processes)
Check Box: Water Flow
Button ”Next”

Time Information (EditFlow and Transport ParametersTime Information)
Time Units: hours
Final Time: 24
Initial Time Step:
0.001
Minimum Time Step: 0.0001
Maximum Time Step: 1
Check "Time-Variable Boundary Conditions"
Number of Time-Variable Boundary Records: 1
Number of times to repeat the same set of BC records: 1
Button ”Next”



Output Information (EditFlow and Transport ParametersOutput Information)
Print Options:
Check T-Level Information
Check Screen Output
Check Press Enter at the End
Print Times: Count: 12
UpdateNumber of Subregions: 1
Button ”Next”



Water Flow - Iteration Criteria (EditFlow and Transport ParametersWater
Flow ParametersIteration Criteria )Leave default values
Button ”Next”
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Computer SessionWater Flow – Soil-Hydraulic Model (EditFlow and Transport ParametersWater
Flow ParametersHydraulic Properties Model)
Radio button - van Genuchten-Mualem
Radio button - No hysteresis
Button ”Next”



Water Flow - Soil-Hydraulic Params (EditFlow and TransportParametersWater Flow ParametersSoil Hydraulic Parameters)
Number of Materials: 2 Button "Update"Material 1 (gravel of main layer):
Select "Sand" from Soil Catalog
Enter values for Qs = 0.41; n = 4 and Ks = 10 m/h
Name: Gravel (Main Layer)
Material 2 (course gravel in mixing zone):
Select "Sand" from Soil Catalogue
Enter values for Qs = 0.45; n = 4 and Ks = 50 m/h
Name: Gravel (Mixing Zone)
Button ”Next”

Time-Variable Boundary Conditions (EditFlow and TransportParametersVariably Boundary Conditions)
Calculations:
hydraulic loading rate = 36 mm.d-1 = 1.5 mm.h-1 = 1.5 L.m-2.h-1
surface area of whole HF bed: 10.3 m x 5.3 m = 54.6 m²
hydraulic loading (whole bed) = 1.5 L.m-2.h-1 x 54.6 m² = 81.9 L.h-1 = 0.0819 m³.h-1
surface area of mixing zone = 0.3 m x 5.3 m = 1.6 m²
hydraulic loading rate (mixing zone) = 0.082 m³.h-1 / 1.6 m² = 0.051 m.h-1
Time-Variable Boundary Conditions:Time
Precip. Evap.
Transp.
[hours] [m/h]
[m/h]
[m/h]
1 24
0.051
0
0
Button ”Next”

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hCritA[m]
100

Remaining columns = 0

Computer Session


FE-Mesh - FE-Mesh Parameters (EditFE-MeshFE-Mesh Parameters)
horizontal Discretization in X: Count = 25 Button "Update"vertical Discretization in Z: Count = 23 Button "Update"
Horizontal Discretization in X:
1
2
3
4
5
6
7
8
9
10
11
12
13

x [m]
0
0.1
0.2
0.3
0.4
0.5
0.7
0.9
1.1
1.4
1.7
2
2.4

dz [m]
0
0
0
0
0
0
0
0
0
0
0
0
0

14
15
16
17
18
19
20
21
22
23
24
25

2.8
3.3
3.8
4.4
5
5.7
6.4
7.1
7.9
8.7
9.5
10.3

0
0
0
0
0
0
0
0
0
0
0
0

Button ”OK”


Set stretching factor (ViewView stretching)
Stretching factor in X-Direction= 1
Stretching factor in Z-Direction= 4
Button ”OK”



Water Flow Initial Conditions:
Click on the Initial Conditions Tab under the View Window.
Or on the Navigator Bar click on Initial Conditions – Pressure Head (or InsertInitial
ConditionsPressure Head)
Select the entire transport domain and click on the Set Pressure Head IC command at
the Edit Bar, check Equilibrium from the lowest located nodal point, check that
Bottom Pressure Head Value is set equal to 0.5 m (water level in the bed = 50 cm).
Button ”OK”



Water Flow Boundary Conditions:
Click on the Boundary Conditions Tab under the View Window.
Or on the Navigator Bar click on Boundary Conditions – Water Flow (orInsertBoundary ConditionsConstant Head)a) Zoom on the upper left part of the transport domain. Select Atmospheric Boundaryfrom the Edit Bar, and select 4 nodes in the upper left corner of the domain (top of themixing zone).

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Computer Sessionb) Zoom on the lower right part of the transport domain. Select Constant Head fromthe Edit Bar, select 1 node at the lower right boundary (outlet of the HF bed)Specify Constant Pressure Head Value: 0.475 m

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Computer SessionMaterial Distribution:
Click on the Domain Properties Tab under the View Window.
Or on the Navigator Bar click on Domain Properties – Material Distribution (orInsertDomain Properties Material Distribution)
Zoom on the left part of the transport domain.
Click the "Gravel (Mixing Zone)" and select the first 3 columns on left side to assign
the mixing zone.

Observation Nodes:
Click on the Domain Properties Tab under the View Window.
Or on the Navigator Bar click on Domain Properties – Observation Nodes (orInsertDomain PropertiesObservation Nodes)
Click the "Insert Observation Node" command on the Edit Bar and insert
6 observation nodes along the flow path.
1 observation node should be located at the effluent node.

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Computer Session

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

Run Calculations
Click the Calculate Current Project command on the Toolbar (or menu command
CalculationCalculate Current Project)Results – Graphical Display: Pressure Head (from the Navigator Bar, orResultsDisplay Quantity Pressure Head)
View results at end of simulation time, i.e. 24 hours

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Computer SessionView also results for velocity vectors.



Save Results
Save the project using the Save command on the Toolbar (or FileSave).

Update of Water Flow Initial Conditions with simulation results from before:
InsertInitial ConditImport
Select file "Example 3a.h3d2" in the project directory
Button ”Open”
Select "Pressure Head"
Select "The Last (Final) Time Layer"
Button ”OK”
Warning: This action requires deleting results. Do you want to continue?
Button ”Yes”



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

Run Calculations
Click the Calculate Current Project command on the Toolbar (or menu command
CalculationCalculate Current Project)Save Results
Save the project using the Save command on the Toolbar (or FileSave).

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Computer Session

Simulation 2a – Set-up Tracer SimulationProject Manager (FileProject Manager)
Select "Example 3a"
Button ”Copy”
Enter New Name: Example 3b1
Description: HF wetland – tracer simulation
Button ”OK”
Button ”Open” Example 3b1

Main Processes (EditFlow and Transport ParametersMain Processes)
Check Box: Water Flow
Check Box: Solute Transport
Check Radio Button "Standard Solute Transport"
Button ”Next”

Time Information (EditFlow and Transport ParametersTime Information)
Time Units: Check Radio Button ”Days”
Final Time: 10
Boundary Conditions: Number of Time-Variably Boundary Conditions: 2
Button ”Next”



Output Information (EditFlow and Transport ParametersOutput Information)
Print Times:
Count: 40 (output every 6 hours = 0.25 days)
Button ”Update”
Button ”Default”
Button ”OK”

Solute Transport – General Info (EditFlow and Transport ParametersSolute
Transport ParametersGeneral Information…)
Set "Mass units" = g
Button ”Next”



Solute Transport – Transport Parameters (EditFlow and TransportParametersSolute Transport Parameters Solute Transport Parameters…)
Leave default values.
Button ”OK”

Time-Variable Boundary Conditions (EditFlow and TransportParametersVariably Boundary Conditions)Time[days]
0.00694
10

Precip.
[m/day]1.224
1.2246

Evap.
[m/day]00…
…
…

cValue 1
g/L^3
30
0.8

cValue 2g/L^300cValue 3g/L^300

KCl solution with EC 30 mS/cm-1 is added for 10 min (= 0.00694 days), afterward
influent concentration is background EC of 0.8 mS/cm-1.
Button ”OK”
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Computer Session
Solute Transport Initial Conditions:Navigator Bar click on Initial Conditions – Concentration
Select the entire transport domain and click on the Set Concentration IC command at
the Edit Bar, check Use top value for entire selected region, check that Top value isset equal 0.8.
Button ”OK”

Solute Transport Boundary Conditions:
Select Third-type Boundary from the Edit Bar, and nodes from mixing zone selected
as Atmospheric BC.
Pointer to the vector of the boundary Conditions = 1 (note that this was already thedefault value).
Button ”OK”



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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)Results – Other Information – Observation points – Concentration

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Computer Session
Comparison with measured data:
0.90

Electrical Conductivity [mS/cm]

Measured data (effluent)Simulated (default)

0.85

0.80

0.75
0

2

4 Time (days) 6

8

10

Simulation 2b – Inverse Tracer SimulationProject Manager (FileProject Manager)
Select "Example 3b1"
Button ”Copy”
Enter New Name: Example 3b2
Description: HF wetland – tracer simulation (inverse)
Button ”OK”
Button ”Open” Example 3b2

Main Processes (EditFlow and Transport ParametersMain Processes)
Check Box: Water Flow
Check Box: Inverse Solution ?
Button ”Next”
Delete resultsInverse Solution (EditFlow and Transport ParametersInverse Solution)
Estimate …:
Check Box: Solute Transport Parameters
Concentration Type:
Check Box: Resident concentration
Other Parameters:
Max Number of Iterations: 10
Number of Data Points in the Objective Function: 20 (i.e. number of measured data,
see Table 3)
Button ”OK”



Output Information (EditFlow and Transport ParametersOutput Information)
Print Options:
Un-Check Screen Output
Button ”OK”

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Computer Session
Solute Transport – Reaction Parameters (Edit  Flow and Transport Parameters Solute Transport Parameters  Solute Transport Parameters)
Check parameters Disp.L. to be fitted for Material 1 (Main layer)
Button ”OK”

Inverse Solution Data (EditFlow and Transport ParametersData for Inverse
Solution)
Inverse Solution Data table:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

X
0.5
1
1.5
2
2.5
3
3.5
4
4.5
5
5.5
6
6.5
7
7.5
8
8.5
9
9.5
10

Y
0.793
0.800
0.805
0.808
0.801
0.793
0.810
0.812
0.826
0.828
0.847
0.865
0.861
0.862
0.843
0.826
0.815
0.807
0.813
0.799

Type
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4
4

Position
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6
6

Weight
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1

Position = Observation node number
Use Observation node number at the outlet of the HF wetland
Button ”OK”


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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)

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Computer Session
Results – Other Information – Observation points – Concentration

Button ”Close”
View parameters after inverse simulation at "Inverse Solution Results"
Iteration
SSQ
00.2382D+00
1
0.8620D-01
2
0.5771D-01
30.5659D-01
4
0.5658D-01

DISPL
0.5000E+00
0.2765E+00
0.1789E+00
0.1912E+00
0.1917E+00

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Computer Session

Simulation 2c – Updated Tracer SimulationProject Manager (FileProject Manager)
Select "Example 3b1"
Button ”Copy”
Enter New Name: Example 3b3
Description: HF wetland – tracer simulation (updated)
Button ”OK”
Button ”Open” Example 3b3

Solute Transport – Transport Parameters (EditFlow and TransportParametersSolute Transport Parameters Solute Transport Parameters…)
Material 1: Disp.L. = 0.192 m
Button ”OK”



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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)Results
Comparison with measured data:
0.90

Electrical Conductivity [mS/cm]

Measured data (effluent)Simulated (default)
Simulated (fitted)

0.85

0.80

0.75
0

2

4 Time (days) 6

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810Computer Session

Simulation 3 – Set-up Reactive Transport Simulations
Project Manager (FileProject Manager)
Select "Example 3a"
Button ”Copy”
Enter New Name: Example 3c
Description: HF wetland – reactive transport simulation (CWM1)
Button ”OK”
Button ”Open” Example 3c

Main Processes (EditFlow and Transport ParametersMain Processes)
Check Box: Water Flow
Check Box: Solute Transport
Check Radio Buttons "Wetland module" and "CWM1"
Button ”Next”

Time Information (EditFlow and Transport ParametersTime Information)
Final Time: 48 (simulation over 2 days)
Maximum Time Step: 0.01 (has to be reduced due to fast oxygen consumption)
Button ” Next”



Output Information (EditFlow and Transport ParametersOutput Information)
Print Options:
Check T-Level information; Every n time step: 10
Print Times:
Count: 24
Button ”Update”
Button ”Default”
Button ”OK”

Solute Transport – General Info (EditFlow and Transport ParametersSolute
Transport ParametersGeneral Information )Set "Mass units" = g
Button ”Next”



Solute Transport – Transport Parameters (EditFlow and TransportParametersSolute Transport Parameters Solute Transport Parameters)
Soil specific parameters
Set parameter "Fract." = 0 for both materials

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Computer Session
Solute specific parameters (in m²/h):
Sol Diffus.W. Diffus.G.
17.21e-6
0.07692
4.56e-603
4.56e-6044.56e-6058.01e-60
68.01e-60
78.01e-6088.01e-6094.56e-6010
4.56e-6
0
11
0
0
12
0
0
13
0
0
14
0
0
15
0
0
16
0
0
17
0
0
Button ”Next”


Solute Transport – Reaction Parameters (EditFlow and TransportParametersSolute Transport Parameters Solute Reaction Parameters)
Leave default parameters and browse through all these windows
Button ”Next”



Solute Transport – Constructed Wetland Model (CWM1) Parameters I(EditFlow and Transport ParametersSolute Transport Parameters ConstructedWetland Parameters I)
Explore and leave default parameters
Button ”Next”



Solute Transport – Constructed Wetland Model (CWM1) Parameters II(EditFlow and Transport ParametersSolute Transport Parameters ConstructedWetland Parameters II)
Explore and leave default parameters
Button ”Next”

Time-Variable Boundary Conditions (EditFlow and TransportParametersVariably Boundary Conditions)
Change Time to 48 hours
add influent concentrations:cVal1-1 = 0.86
cVal1-2 = 170
cVal1-3 = 27
cVal1-4 = 13
cVal1-5 = 57
cVal1-7 = 33
cVal1-9 = 33
cVal1-10 = 13
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Computer Session

Button ”OK”
Solute Transport Initial Conditions:
Note: it is assumed that (1) clean sand is used and (2) the HF bed is filled with
wastewater at the beginning of the simulation. For the initial conditions (1) results inan homogeneous distribution of the bacteria in the filter (a value of 1 mg/kg is
assumed for all bacteria species) and (2) results in initial conditions for solute species
that are the influent concentrations (see above)
Navigator Bar click on FE-Mesh – FE-Mesh Parameters
Button ”Next” for Window Default Domain Properties
Enter initial concentrations for solute compounds L1-L10 and bacteria S11-S16

Button ”OK”
To check initial conditions for compounds: Navigator Bar Initial Conditions
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Computer Session
Solute Transport Boundary Conditions:Navigator Bar click on Boundary Conditions – Solute Transport
Select Third-type Boundary from the Edit Bar, and nodes from mixing zone selected
as Atmospheric BC.
Pointer to the vector of the boundary Conditions = 1 (note that this was already thedefault value).
Button ”OK”



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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)Results – Graphical Display:
View results at the end of simulation time, i.e. 48 hours
e.g. L1 – Dissolved Oxygen

Note that you get this display only after adjusting the scale for contours. Use the menu
command ToolsColor ScaleEdit Scale or simply double click on the Scale panelon the Edit Bar. In the window "Edit Isoband Values and Color Spectra", adjust thescales as follows for L1 - Dissolved Oxygen:

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Computer Session

and for S11 – Heterotrophic Bacteria

The definition of the scale can be saved for future use using the command "Copy..".
The scale can be saved under various names, such as "Dissolved Oxygen" or"Heterotrophic Bacteria".

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Computer Session
Results – Other Information: Observation Points (from the Navigator Bar)
check simulation results at observation points, e.g., select L2 and L3

Button ”Close”
Save Results
Save the project using the Save command on the Toolbar (or FileSave).
Note: Usually simulations need to be run until steady-state is reached, i.e. the patternsof the bacteria concentrations obtained do not change anymore.

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Computer Session

Simulation 4 – Set-up Simulation that Considers Wetland Plants

Project Manager (FileProject Manager)
Select "Example 3c"
Button ”Copy”
Enter New Name: Example 3d
Description: HF wetland – reactive transport simulation (CWM1) + plants
Button ”OK”
Button ”Open” Example 3dUpdate of Water Flow Initial Conditions with simulation results from before:
InsertInitial ConditionImport
Select file "Example 3b.h3d2" in working directory
Button ”Open”
Button "Select All"
Select "The Last (Final) Time Layer"
Button ”OK”
Warning: This action requires deleting results. Do you want to continue?
Button ”Yes”

Save Results
Save the project using the Save command on the Toolbar (or FileSave).



Main Processes (EditFlow and Transport ParametersMain Processes)
Check Box: Water Flow
Check Box: Solute Transport
Check Box: Root Water Uptake
Button ”OK”



Root Water and Solute Uptake: Models (EditFlow and Transport ParametersRoot Water and Solute Uptake Root Water/Solute Uptake Models)
Water Uptake Reduction Model: S-Shaped
Solute Stress Model: No Solute Stress
Button ”Next”



Root Water and Solute Uptake: Root Water Uptake Parameters (EditFlow andTransport Parameters Root Water and Solute Uptake Pressure Head Reduction)
P50 [m] = -1; P3 [-] = 3; PW [m] = -100;
Button ”OK”

Solute Transport – Reaction Parameters (EditFlow and TransportParametersSolute Transport Parameters Solute Reaction Parameters)
L1 (Dissolved Oxygen): cRoot = -675
L5 (Ammonia NH4): cRoot = 50
L6 (Nitrate NO3): cRoot = 50
Button ”OK”

Time-Variable Boundary Conditions (EditFlow and TransportParametersVariably Boundary Conditions)
Calculation:
Transpiration = 7.4 L.m-2.d-1 = 7.4 mm.d-1 = 0.0074 m.d-1 = 0.00031 m.h-1
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Computer Session"Length of soil surface associated with transpiration" = 10 m.
Button ”OK”


Root Distribution:
Click on the Domain Properties Tab under the View Window.
Or on the Navigator Bar click on Domain Properties – Root Water Uptake (orInsertDomain PropertiesRoot Distribution)(1) Click on "Properties in Table" on the Edit bar
Enter the Root distribution as follows:

Note that this table displayes values that are constant for the entire horizontal layer(for all nodes on one horizontal line). It hides values that are different along the line.
Button ”OK”
(2) Zoon on the upper left part of the transport domain. Select the first 4 columns on
the left side of the transport domain (mixing zone)
Click on the "Set Root Water Uptake" on the Edit Bar: Top Value 0  Same value for
all nodes  "OK"Page 41 of 44

Computer Session

Button ”OK”


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

Run Calculations
Click the Calculate Current Project command on the Toolbar (orCalculationCalculate Current Project)Results – Graphical Display: View the same results as without plants
e.g. L1 – Dissolved Oxygene.g. S11 – Heterotrophic Bacteria
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Computer Session

Results – Other Information – Cumulative Fluxes:
Select "Cumulative Actual Root Water Uptake"Calculations:
Cumulative Root Water Uptake (in 2D) = 0.15 m* (in 48 hours)
Transpiration… for the entire wetland surface: 0.15 m² x 5.3 m / 48h = 16.56 L.h-1… for unit surface area: 16.56 L.h-1 x 24 h/d /(5.3*10 m²) = 7.5 L.m-2.d-1
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Computer Session
Results – Other Information – Solute Fluxes:
Select "Concentration number 1 (Dissolved Oxygen)
Select "Cumulative Root Solute Uptake" Note: the minus sign denotes oxygen release

Calculations:
Oxygen Release = -100 g/m (in 48 hours)… for the entire wetland surface: 100 g/m x 5.3 m(width) / 48h = -11.04 g.h-1… for unit surface area: 11.04 g.h-1 x 24 h/d /(5.3*10 m²) = -5 g.m-2.d-1
Same calculations for:L5 (Ammonium N): Root uptake = 7.43 g/m (in 48 hours)  0.37 g.m-2.d-1
L6 (Nitrate N): Root uptake = 0.0105 g/m (in 48 hours)  0.0005 g.m-2.d-1
Save Results
Save the project using the Save command on the Toolbar (or FileSave).

Page 44 of 44