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New HYDRUS Modules for
Simulating Preferential Flow,
Colloid-Facilitated Solute Transport,
p , and
Various Biogeochemical Processes in Soils
Jirka Šimůnek1
Miroslav Šejna2, Diederik Jacques3, Günter Langergraber4,
Scott Bradford5, and Rien van Genuchten6
1Department of Environmental Sciences,

University of California, Riverside, CA
2PC-Progress, Ltd., Prague, Czech Republic
3Belgian Nuclear Research Centre (SCK•CEN), Mol, Belgium
4University
y of Natural Resources and Life Sciences,, Vienna ((BOKU University),y), Austria
5US Salinity Laboratory, USDA, ARS, Riverside, CA, USA
6Federal University of Rio de Janeiro, Brazil

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HYDRUS (1D/2D/3D)
Software for Simulating Water Flow and
Solute Transport in One/Two/Three y
Soils
Dimensional Variably-Saturated
Using Numerical Solutions

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HYDRUS and its Modules
 HYDRUS + PHREEQC = HP1/2/3(hydrological + biogeochemical processes)

 HYDRUS + UNSATCHEM(h d l i l + CO2 + major(hydrologicalj iion processes)) HYDRUS + Wetland (CW2D/CWM1)

HP1/2/3 (HYDRUS+PHREEQC)
Simulating water flow, transport and biogeochemical reactions in environmental
soil quality problems

A Coupledp
Numerical Code for
Variably Saturated Water Flow,
Solute Transport and
BioGeoChemistryin Soil Systems(biogeochem processes in constructed wetlands)

 HYDRUS + C-Ride(colloid-facilitated solute transport)

 HYDRUS + DualPerm(preferential water flow and solute transport)(pp )Flow and transport model
HYDRUS-1D 4.0
HYDRUS (2D/3D) 2.x

Biogeochemical model
PHREEQC 2 4
PHREEQC-2.4

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HYDRUS GUI for HP1/2/3

HP1/2/3 (HYDRUS+PHREEQC)
HYDRUS--1D or HYDRUS (2D/3D):HYDRUSyVariably-Saturated
Water Flow
Solute Transport
 Heat Transport
 Gas Transport
 Root Water Uptake


PHREEQC [Parkhurst and Appelo,
Appelo, 1999]:
Available Chemical Reactions:Aqueous Complexation
Redox Reactions
 Ion Exchange (Gains-Thomas)
 Surface Complexation (diffuse double-layer model and nonelectrostatic surface complexation model)
 Precipitation/Dissolution
Precipitation/Dissol tion
 Chemical Kinetics
 Biological Reactions
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Transport and Cation Exchange
Heavyy Metals

HYDRUS GUI for HP1/2/3

Major ions (Ca, Na, Al, Cl) and Heavy Metals (Zn, Pb, Cd)
0 01
0.01

Conceentration (m ol/l)Four text editors
to define thegeochemical model,
model
required output, andsolution compositions

8E 0048E-004Cl

Conce ntration ((m ol/l)

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Jacques, D.,
Jacques
D and JJ. Šimůnek
Šimůnek, Notes on the HP1 software – a coupled code for variably-saturated
variably saturated water
flow, heat transport, solute transport and biogeochemistry in porous media, HP1 Version 2.2,
SCK•CEN-BLG-1068, Waste and Disposal, SCK•CEN, Mol, Belgium, 114 pp., 2010.

0.008
Na

0.006

Ca

0.004
0.002
Al
0
0

3

6

9

Time (days)

12

15

Zn

6E-0044E-004Pb

2E-004Cd
0E 000
0E+000
0

3

6

9

12

15

Time (days)

8-cm column is initially contaminated with heavy metals (in equilibrium with the cationexchanger). The column is then flushed with a solution (CaCl2) without heavy metals.

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U-Transport in Agricultural Field Soils
4.2

80

CEC

60

Steady-state

4

SC

Total

pH

% U(VI) adsorbed

100

HP2 – Reclamation of a Sodic Soil

3.8

40

3.6

20

3.4

Atmospheric

5 cm depth
150

0
2

3

U-species replacedby other cations

4

5

6

pH
Increased deprotonation
Increased U-sorption

151

152

153

154 155 156
Time (year)

157

158

159

160

 Water content variations induce pH variations(dry soil => low pH)
 pH variations => variations in sorption potential(low pH => low sorption – higher mobility)

 Aqueous speciation reactions
C, Ca, Cl, F, H, K, Mg, N(5), Na, O(0), O(-2), P, S(6), U(6) Multi-site cation exchange reactions- Related to amount of organic matter- Increases with increasing pH- UO22+ adsorbs

 Surface complexation reactions- Specific binding to charged surfaces (FeOH)- Related to amount of Fe-oxides

Jacques et al., VZJ, 2008.

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Uranium Transport from Mill Tailing Pile

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HP1 Examples
 Transport of Heavy Metals (Zn2+, Pb2+, and Cd2+) subject to a

multiple pH
pH-dependent
dependent Cation Exchange Transport and mineral dissolution of Amorphous SiO2 andGibbsite Infiltration of a Hyperalkaline Solution in a clay sample(kinetic precipitation-dissolution of kaolinite, illite, quartz, calcite,
dolomite, gypsum, hydrotalcite, and sepiolite)
 Kinetic biodegradation of NTA (biomass, cobalt)
 Long-term Uranium transport following mineral phosphorus
105*25 m
1560 FE
Aqueous Complexation for Uranium Species
Calcite and Gypsum Precipitation/Dissolution
Cation Exchange

ffertilizationtili ti (pH-dependent surface complexation and cation exchange) Transport of Explosives, such as TNT and RDX
 Property Changes (porosity/conductivity) due toprecipitation/ dissolution reactions

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HYDRUS and its Modules
 HYDRUS + PHREEQC
Q = HP1/2/3(hydrological + biogeochemical processes)

 HYDRUS + UNSATCHEM(hydrological + CO2 + geochemical processes)

 HYDRUS + Wetland (CW2D/CWM1)((processes
iin constructedt t d wetlands)
tl d )

 HYDRUS + C-Ride(colloid facilitated solute transport)(colloid-facilitated HYDRUS + DualPerm(preferential water flow and solute transport)

 HYDRUS and HYDRUS (2D/3D)- Variably-Saturated Water Flow
- Solute Transport- HeatH t Transport
Tt- Root Water Uptake
 UNSATCHEM (Šimůnek et al.,al 1996)- Carbon Dioxide Transport- Major Ion Chemistry- Cation Exchange- Precipitation-Dissolutionp((instantaneous and kinetic))- Aqueous Complexation

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UNSATCHEM Module

56

CO2-H2O Species
Silica Species

10 cm

40
30
20
10
0
0

7

-1

EC (dS m )CaCO3, CaSO42H2O, CaMg(CO3)2,
MgCO33H2O, Mg5(CO3)4(OH)24H2O,
Mgg2Si3O7.5)
7 5((OH)3H
2O

3

H4SiO4, H3SiO4-, H2SiO42-

Kinetic reactions: calcite precipitation/dissolution, dolomite dissolution
Activity coefficients: extended Debye-Hückel equations, Pitzer expressions

600

800

1000

1200

1400

15

I

10

R

I

R

I

R

I

400

600

800

1000

1200

1400

800

1000

1200

1400

5
0

XCa, XMg, XNa, XK
PCO2, H2CO3*, CO32-, HCO3-, H+, OH-, H2O

400

10 cm

0

4

200

200

10
0.5

10 cm

50 cm

8
-1 0.5Sorbed Species(exchangeable)

6

2

50

20

3

4

Precipitated Species

10



2

SAR (meq L )3Complexed Species

CaCO3o, CaHCO3+, CaSO4o, MgCO3o,
MgHCO3+, MgSO4o, NaCO3-, NaHCO3o,
NaSO4-, KSO4-

-3

2

7

Ca2+, Mg2+, Na+, K+, SO42-, Cl-, NO3-

To evaluate the effectiveness of HYDRUS to predict: Water content and fluxes
 Concentration of individual cations (e.g., Ca2+, Mg2+)
 OverallO
ll salinity
li it (Electrical(El t i l conductivity
d ti it – EC)( Na )SAR 
 Sodium Adsorption Ratio (SAR)(Ca  Mg )2
 Exchangeable Sodium Percentage (ESP)

Water content (cmm cm )

1

Aqueous
Components

UNSATCHEM - Lysimeter StudyNa Conce
entration [meq/L]

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HYDRUS + UNSATCHEM

0.4
0.3
0.2

6
4
2

0.1
0.0

0
0

200

400

600

800

1000

1200

1400

0

200

400

600

Gonçalves, M. C., J. Šimůnek, T. B. Ramos, J. C. Martins, M. J. Neves, and F. P. Pires, Multicomponent solute transport in soil
lysimeters irrigated with waters of different quality, Water Resources Research, 42, 17 pp., 2006.
Ramos, T. B., J. Šimůnek, M. C. Gonçalves, J. C. Martins, A. Prazeres, N. L. Castanheira, and L. S. Pereira, Field evaluation of amulticomponent solute transport model in soils irrigated with saline waters, J. of Hydrology, 407(1-4), 129-144, 2011.

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HYDRUS and its Modules

UNSATCHEM-2D Module
Major Ion Chemistry Module
Na+

XCa2+

 HYDRUS + PHREEQC = HP1/2/3(hydrological + biogeochemical processes)

 HYDRUS + UNSATCHEM(h d l i l + CO2 + geochemical(hydrologicalh i l processes)) HYDRUS + Wetland (CW2D/CWM1)(processes in constructed wetlands)

 HYDRUS + C-Ride(colloid-facilitated solute transport)

 HYDRUS + DualPerm(preferential water flow and solute transport)(pp )Šimůnek, J., and D. L. Suarez, Two-dimensional transport model for variably saturated porous media withmajor ion chemistry, Water Resources Research, 30(4), 1115-1133, 1994.

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Wetland Module
Constructed Wetlands (CWs) or wetland treatment systems

designed to improve water quality
use the same p
processes that occur in natural wetlands but have the flexibilityyof being constructed effective in treating organic matter, nitrogen, phosphorus, and additionallyfor decreasing the concentrations of heavy metals, organic chemicals, andpathogenspgWetland Modules: Components
CW2D : aerobic and anoxic processes for organic matter, nitrogen and phosphorus
CWM1: aerobic, anoxic and anaerobic processes for organic matter, nitrogen and sulphur

Components:

CW2D : aerobic and anoxic processes for organic matter, nitrogen andphosphorus (Langergraber and Šimůnek, 2005)
CWM1:: aerobic,
CWe ob c, anoxico c andd anaerobice ob c p
processes
ocesses foro oorganicg c matter,e,nitrogen and sulphur (Langergraber et al., 2005)
Subsurface Vertical (CW2D) and Horizontal (CWM1) flow constructedwetlands:
Langergraber, G., and J. Šimůnek, The Multi-component Reactive Transport Module CW2D for Constructed Wetlands for the
HYDRUS Software Package, Manual – Version 1.0, HYDRUS Software Series 2, Department of Environmental Sciences,
University of California Riverside, Riverside, CA, 72 pp., 2006.
Langergraber, G., D. Rousseau, J. Garcia, and J. Mean, CWM1 - A general model to describe biokinetic processes in subsurface
flow constructed wetlands, Water Science Technology, 59(9), 1687-1697, 2009.

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HYDRUS and its Modules

Wetland Modules: Processes
Processes:

 HYDRUS + PHREEQC = HP1/2/3((hydrologicali + biogeochemicalii processes)) HYDRUS + UNSATCHEM(hydrological + CO2 + geochemical processes)

 HYDRUS + Wetland (CW2D/CWM1)(processes in constructed wetlands)

 HYDRUS + C-Ride(colloid-facilitated(colloidfacilitated solute transport)

Heterotrophic Organisms XH

 HYDRUS + DualPerm(preferential water flow and solute transport)

Nitrosomonas XANs

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Colloid-Facilitated Solute Transport Many contaminants should be relatively

immobile in the subsurface since under normal
conditions they are strongly sorbed to soil
 They can also sorb to colloids which often moveat rates similar or faster as non-sorbing tracers
 Experimental evidence exists that many
contaminantst it are transportedtt d nott onlyl in
i a
dissolved state by water, but also sorbed tomovingg colloids.
 Examples: heavy metals, radionuclides,
pesticides, viruses, pharmaceuticals, hormones,andd otherth contaminantst it

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HYDRUS + C-Ride HYDRUS and HYDRUS (2D/3D)- Variably-Saturated Water Flow
- Solute Transport- Heat Transport- Root Water Uptake
 C-Ride (Šimůnek et al.,al 2006)- Particle Transport- colloids, bacteria, viruses, nanoparticlesp- attachment/detachment, straining, blocking- Colloid-Facilitated Solute Transport- transporttt off solutes
l t attached
tt h d tto particles
ti l

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Colloid, Virus, and Bacteria Transport
Air

Colloid-Facilitated Solute Transport
Air

Air-Water Interface Colloids, c

aca

Contaminant sorbed to colloids at air-water interface, Sac

g

kdca

kaca

kdca

kaca
Contaminant sorbed tomobile colloids
colloids, Smc

kaac

kamc

Mobile Colloids, Cc

Water
kstr

sstr
Strained Colloids, Scstr

m

kdac

kac

kdc

Water

Attached Colloids, Scatt

S lid
Solid

kdmc

Dissolved
Di
l dContaminant, C
Kd

s

S lid
Solid

kstr

Instantaneously Sorbed
Contaminant,, Se

kac

kdc

kdic



kaic

i
Kinetically Sorbed
Contaminant,, Sk

Contaminant sorbed to immobile colloids, Sic

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Colloid-Facilitated Solute Transport

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Colloid-Facilitated Solute Transport

Mass Balance of Total Contaminant:Contaminant

 C
S
S
 C SS S
A  S  e   k  w c mc   c ici  aw c ac
t
t
t
t
t
t
 
C  qqC  C  q C S
  D   w Smc Dc c   c c mc  Rx x  x
x 
x 
x
Left-hand side sums the Mass of Contaminant:
- in
i the
th liquidli id phaseh- sorbed instantaneously and kinetically to the solid phase- sorbed to mobile and immobile (attached to solid phase or air–water interface) colloids
Right-hand side considers various Spatial Mass Fluxes- dispersion and advective transport of the dissolved contaminant- dispersion and advective transport of contaminant sorbed tomobile colloids
and Transformation/Reaction (e.g., degradation).

System of coupled equations (solved numerically):a) Five Partial Differential Equations- total mass of contaminant- mass off contaminantt it sorbedb d kikineticallyti ll tot solid
lid phaseh- mass of contaminant sorbed to mobile colloids- mass of contaminant sorbed to attached colloids- mass of contaminant sorbed to strained colloidsb) One Algebraic Equation- mass of contaminant sorbed instantaneously to solid
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HYDRUS and its Modules

Colloid-Facilitated Solute Transport
C-Ride Module

 HYDRUS + PHREEQC = HP1/2/3(hydrological + biogeochemical processes)

 HYDRUS + UNSATCHEM(h d l i l + CO2 + geochemical(hydrologicalh i l processes)) HYDRUS + Wetland (CW2D/CWM1)(processes in constructed wetlands)

 HYDRUS + C-Hitch
Breakthrough curves forf colloidsi (black(line),i ) solute sorbed to colloidsi (blue(line), and solute (red line):
Left: solute and colloids are applied independently
Right: solute is attached initially to colloids(colloid-facilitated solute transport)

 HYDRUS + DualPerm(preferential water flow and solute transport)(pp )The Retardation Factor for colloids is equal to 1 and for solute to 4
Unit input concentrations.

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Preferential Flow and Transport
Fractured RockMacroporous Soil

Physical Nonequilibriump
Models in DualPerm
Solute Transport
a)

b)
Water

SoluteTh DualPerm
The
D lP
M d l
Module

c)
Water

d)
Water
Immob. Mobile

SoluteSoluteMobileImmob. Mobile = im   mo

 = im   mo

Immob.

Water
Slow

Fast

SoluteSlowFast = M  Fa) Uniform Flowb) Mobile-Immobile Waterc) Dual-Porosity (Šimůnek et al.,al 2003)d) Dual-Permeability (Gerke and van Genuchten, 1993)

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Chemical Nonequilibrium
SoluteSo
ute Transport
a spo t Models
ode s in DualPerm
ua e
a)

b)

c)

se

s1 k

d)





sk
c

sk

c

s2 k

c

e
sim
i

Variably-Saturated Water Flow

e)
im

mo

cim

cmo

Solute Transport

Slow Fast

Immob. Mob.



Nonequilibrium Models in
the HYDRUS GUI

smo

e

smok

sm e

sm k

m

f

cm

cf

sf e

sfk

a) One-Site Kinetic Modelb)) Two-Site Model ((kinetic and instantaneous sorption)p)c) Two Kinetic Sites Model(particle transport, e.g., colloids, viruses, bacteria)d) Dual-Porosity
Dual Porosity with One Kinetic Site Modele) Dual-permeability with Two-Site Model

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The DualPerm Module
Water flow and Solute Transport in
Dual-Permeability Variably-Saturated Porous MediaHYDRUS and its Future Modules?
 HYDRUS + Overland Flow(surface runoff and overland flow)

 HYDRUS + Global Optimization(genetic algorithm,
algorithm AMALGAM,AMALGAM …))
 HYDRUS + MODFLOW((hydrologicali processes at a large scale)) HYDRUS + Soil Mechanical Stresses

Pressure head profiles for the matrix (left), isotropic fracture, and fracturewith KxA/KzA=10, and fracture with KxA/KzA=0.1 (right).

(effects of hydrological processes on slope
stability)
 HYDRUS + Freezing, Meteo (atmosphere)…

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Questions and Suggestions?

Thank
Th
k you ffor
your attention