MIKE SHE – Advanced Exercises 1

MIKE SHE
Advanced Exercises
1 WATER QUALITY MODELING ................................................................................... 2
1.1 STEP 1 – OPEN YOUR INTEGRATED MODEL .................................................................. 2
1.2 STEP 2 – TURN ON THE WQ ......................................................................................... 3
1.3 STEP 3 – DEFINE THE BASIC WQ SIMULATION ............................................................. 4
1.4 STEP 4 – DEFINE YOUR SOLUTE SPECIES....................................................................... 7
1.5 STEP 5 – DEFINE THE SATURATED ZONE SOLUTE TRANSPORT PARAMETERS ................ 9
1.6 STEP 6 – DEFINE THE SOLUTE SOURCE ....................................................................... 17
1.7 STEP 7 – DEFINE THE STORING OF RESULTS ............................................................... 19
1.8 STEP 8 – VIEW THE RESULTS ..................................................................................... 20
1.9 STEP 9 – MODIFY SORPTION AND DECAY .................................................................. 21
1.10 STEP 10 – SWITCH THE WQ METHOD TO RANDOM WALK PARTICLE TRACKING ....... 21

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1 Water Quality modeling

Overall Objective
Learn how to setup a MIKE SHE water quality model.
Important learning objectives
After completing this exercise you should be able to
 Setup a water quality model with multiple solutes for the saturated zone
 Run and review the results of a water quality model

1.1 Step 1 – Open your Integrated model

1.1.1 Open your Integrated exercise model.

The Water Quality (WQ) exercise is a simple exercise based on the Integrated exercise.
After you have started MIKE SHE,
 open the model that you completed for the previous Integrated exercise, and
 save it under a new name.

If you haven’t finished the Integrated Exercise, you can open the installed Karup_Example.she file. Some of the steps described here are
already done, but you can still follow along and modify the example file to obtain the desired results.
The water quality model allows you to calculate the movement of dissolved solutes in and between surface water (Overland and Rivers), and
sub-surface water in both the unsaturated and saturated zones. Also available is linear/non-linear solute adsorption/desorption, as well as first-
order decay.

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1.2 Step 2 – Turn on the WQ

The first step is to turn on the WQ options. You may have already noticed these as you have developed the previous exercises.

1.2.1 Include AD water quality

 Click on the “Include Advection-Dispersion…” checkbox at the
bottom of the Simulation Specification dialog.
The water quality model in MIKE SHE is based on the finite
difference advection dispersion equation. To simulate water quality
you must first run the Water Movement (WM), which calculates the
water flow between all of the model cells.
Alternatively, you can calculate the conservative movement of
solutes in the saturated zone using a Random Walk Particle
Tracking (PT) method. We will try this method later in the exercise.
The checkbox that appears (default on) allows you to specify a
different water movement model. This is useful, for example, if you
want to develop a standard water quality simulation and then run it
with several different water movement scenarios – say with 5
different land-use scenarios.

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1.3 Step 3 – Define the basic WQ simulation

In this step, you define the included components, as well as simulation time period, time step control etc.

1.3.1 Include WQ components

 Click on the checkbox across from the “Saturated Flow (SZ)”
 Click on the “Include water quality processes” checkbox
All components of the AD water quality module are available in the
user interface. For now, let’s just use the SZ. We can add other
components later
Note: The water quality simulation in the unsaturated zone is
restricted to the finite difference methods – Gravity Flow and
Richards Equation.

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1.3.2 Define a simulation title

 Add a simulation title and description
It is not mandatory to add a title and description, but these are
written to the output files.

1.3.3 Define a simulation period

 Define the start date the same as the WM start date
 Define the end date of the WQ simulation sometime in the year
2050.
Since the WQ simulation is much longer than the WM simulation,
you must define what the flow field will be for the 70-year WQ
simulation
 Select Constant Water Movement Flow Field and chose the
date 1980 Dec 05
The Start date must be within the WM simulation period, but the End
date can be any time after the Start date.
It is common to have a long WQ simulation based on a much shorter
WM simulation. MIKE SHE gives you two options for filling in the
missing flow results:

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Recycling: If you chose to recycle the flow results, then the flow
results between the Cycle Start and Cycle End dates will be
repeated until the end of the WQ simulation.
Constant Flow Field: This is an extreme version of recycling, where
the WM flow results from a single saved time step will be recycled.
This is the same as using a steady-state flow field for a transient WQ
simulation.
If the WQ simulation period is the same or less than the WM
simulation, then you can also use the first option.
Note: If you are planning to include WQ in MIKE 11, then you must
use the first option. Recycling of the MIKE 11 flow results is not
allowed. If WQ in MIKE 11 is not simulated, then the river is treated
as an infinite solute sink.

1.3.4 WQ time step control

 Use the default values for time step control.
The WQ model time step is automatically controlled to reduce
numerical instabilities.
The Max time step is usually set to a very large number to ensure
that it is not limiting the simulation.
The courant criteria essentially prevent solute from moving across a
cell in a single time step. Thus, if you have small cells or high
velocities, the courant criteria will result in small time steps.
The Max transport limit prevents all of the solute from leaving the cell
in one time step.

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1.4 Step 4 – Define your solute species

1.4.1 Add two species

 Click on the Add item icon and add two species to the table
 Give each species a name and select Dissolved and Sorbed
for the other in the combo box

You can define any number of species in MIKE SHE. However, each
species will be transported independently of each other. There is
currently no interaction between the species.

If you want to simulate solute sorption, then you must define a

sorbed solute as a separate species.

The include checkbox allows you to turn on and off species in the
simulation without having to delete all of the species. This allows you
to define different solute scenarios without having to have separate
simulation setups.
1.4.2 Solute Decay
Under the Water Quality Sorption and Decay, there are two tables – one for
Decay processes and the other for Sorption processes.
 In the Decay table, click on the Add item icon and add two decay
processes to the table
 Give each process a name and different species for each process

Adding a water quality process creates a Decay or Sorption process item in

the data tree under the Overland Flow, Unsaturated Zone, and Saturated
Zone branches, if the water quality is being simulated in these WM

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processes.
Solute decay can depend on the temperature of the surface water, or the soil
temperature in the unsaturated zone or the saturated zone. In the
unsaturated zone, the decay rate can also depend on soil moisture content.

1.4.3 Solute Sorption

 In the Sorption table, click on the Add item icon and add one
sorption processes to the table
 Give the process a name
 Select Equilibrium for the Sorption type,
 Select your dissolved and sorbed species from the combo boxes
(Note: if you haven’t specified one of your species as “Sorbed”, then
the Sorbed combo box will not display any names)
 Leave the rest of the options unchanged

Three different sorption isotherms are available – linear sorption or two non-
linear sorption isotherms
Solute sorption can be instantaneous (equilibrium) or time dependent
(kinetic). The Equilibrium Sorption Fraction allows you to make the sorption
partially or entirely kinetic. The kinetic sorption rate is specified as a
distributed variable in the data tree. If you have specified hysteresis, then
two kinetic rates need to be specified – one for sorption and the other for
desorption.
The Sorption Bias Factor allows you to control the sorption in the secondary
porosity – in the UZ macropores and the SZ rock matrix.

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1.5 Step 5 – Define the saturated zone solute transport parameters

In this step, you define the properties of the saturated zone that control the solute movement, plus the initial solute concentrations.

1.5.1 Define the dispersivity

For now, we will not use the dispersivity, so leave this dialog
unchanged. At the end of the exercise, you can come back here to
re-run the model to evaluate the effect of dispersivity.

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1.5.2 Define the porosity in layers and lenses

 Use a uniform value of 0.3
Remember to define porosity in all layers and lenses.
The porosity is property of the geologic media and is thus, specified
for each geologic layer or lens. The porosity is used to calculate the
advective velocity of the solute and, as such, is the effective porosity
that participates in the flow. In the absence of better data, the
specific yield or the saturated water content are both good
approximations to the effective porosity.

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1.5.3 Define the bulk density in layers and lenses

 Use a uniform value of 1700 kg/m
3

Remember to define the bulk density in all layers and lenses.

The bulk density is property of the geologic media and is thus,
specified for each geologic layer or lens. The bulk density is used to
calculate the solute sorption and does not appear in the data tree
unless you have specified a sorption process.

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1.5.4 Add a Water Quality Layer

 In the Water Quality Layers table, click on the Add item icon
and add one water quality layer to the table

The water quality processes do not necessarily follow the geology.

For example, aerobic/anaerobic zones depend on groundwater
chemistry not geology.
The water quality processes are defined by Water Quality Layers
that are defined in the same way as Geologic Layers. In the current
model, there is only one numerical layer. So, it does not make any
sense to have multiple Water Quality layers because each numerical
layer can only belong to one water quality layer.

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1.5.5 Define lower level

 Specify the lower level as -100m relative to the ground level

Thus, the entire model belongs to the same water quality layer.

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1.5.6 Define species half life

The default value is 1000 years. For now, don’t change this value,
which means that decay will be insignificant for a short simulation.
You can come back later and adjust this value.
There are two half lives – one for the dissolved species and the
other for the sorbed species.

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1.5.7 Define sorption isotherm

The default sorption isotherm from earlier is the linear isotherm.

Thus, here there is only one parameter – the linear Kd which defines
the ratio of dissolved to sorbed concentration. The units of sorbed
3
concentration are g of solute per m of soil, which means that the
3
units of the Kd factor are m /g. A Kd factor of 0 means that there is
no sorption. You can come back later and adjust this factor.
If one of the non-linear sorption isotherms were used here, then
there would be two parameters per sorption process.

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1.5.8 Define the initial solute concentrations

The default initial concentration is 0.0 for both the dissolved and the
sorbed species.
The initial concentration is defined as a property of the
computational layer.

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1.6 Step 6 – Define the solute source

In this step, you define the properties of the sources of solute in the saturated zone.

1.6.1 Define a solute source

 Define a source by clicking on the add item icon

Source 1
Species = Benzene
Location = Subsurface
Type = SZ fixed concentration
Extend type = part domain

Solute sources are very flexible. They can be defined for any
species - on the ground surface or beneath it. Surface sources
include solutes in precipitation or solute mass applied to the ground
surface. For example, agricultural pesticides could be applied as a
precipitation source over the time of application. Nutrients could be
applied as an overland source in units of load, for example, kg/day.
Subsurface sources are typically used for known sources of
concentration or mass in the subsurface, for example, from
underground storage tanks or landfills.
Finally, the extent can be over the entire domain or restricted to a
prescribed area. In both cases, the source strength can be defined
as a station-based value, with different concentrations or loading
rates in different areas – each with its own loading time series.

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1.6.2 Define the source properties

For each solute source, you must define its location and strength

Source 1 (subsurface source)

Extent = extent.dfs2
Top elevation = 0
Bottom elevation = -5
3
Strength = 100 μg/m

Note: for the elevation values, be sure to check the Values relative
to ground checkbox.

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1.7 Step 7 – Define the storing of results

In this step, you define the properties of the saturated zone the control the solute movement, plus the initial solute concentrations.

1.7.1 Define the storing frequency for WQ results

 Set the storing frequency for the water quality results and
mass balance output at 7200 hours (100 days)
The concentration of a species is the only output item for the water
quality simulation. Thus, the gridded concentration of each species
is always stored. Thus, there is no option in the gridded data to
select or unselect the concentration.
Detailed time series of concentrations also cannot be specified. To
plot a breakthrough curve, you need to plot a time series at a point in
the Results Viewer.

1.7.2 Run the Preprocessor and the Simulation

 Click on the icon to start the pre-processor, which will

start the MIKE Zero Launch utility.
 Click OK

 Click on the icon to run the WQ simulation, which will

start the MIKE Zero Launch utility.
 Click OK

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1.8 Step 8 – View the Results

Now view some of the outputs of this exercise using the Result Viewer. Remember, it is always a good idea to run and evaluate your model as you
are setting it up. Otherwise, there is a danger that you when you are finished setting up a big model; you may have many errors that are difficult to
track down.

1.8.1 View the WQ Results

In the Results tab dialog,
 open the gridded results for your species. This is located at the
bottom of the list of available gridded outputs.
 Scroll through some of the time steps. Or, go to the last time
step.
The resulting concentration map includes a color for zero. The plume
is more easily distinguished if the zero value is not plotted. This can
be done by changing the color scale.
 Right click on the map and select Properties…
 In the “Grid” item, select the Color tab
 Click on the New… button
 In the Palette dialog that appears, leave the first page alone by
clicking on Next…
In the second page,
 change the last value to 0.0, and
 change the display color to white
 Click OK, Next, Finish, OK to close out all the dialogs
When you close out the dialogs, the plume will be displayed without
the zero values.
You can go back to the properties to also change the Contour Type

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to “Shaded” to make the color shading smoother.

1.8.2 View the breakthrough curve

 Use the time series icon, , to plot a breakthrough curve

near one of the sources.

If you hold down the Ctrl key while you click on the map, you can
select multiple points for plotting time series plots.

1.9 Step 9 – Modify Sorption and Decay

In Sections 1.4.2 Solute Decay (pg 7) and 1.4.3 Solute Sorption (pg 8), you added decay and sorption processes. If you have time, return to these
dialogs and modify the decay or sorption parameters and re-run the models.
1.10 Step 10 – Switch the WQ method to Random Walk Particle Tracking
The Particle Tracking (PT) module allows you to calculate the source locations and flow paths of particles moving in the saturated groundwater

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zone (SZ). Essentially, the movement of each particle is composed of:

 A deterministic part where the particle is moved based on the local groundwater velocity and
 A stochastic part where the particle is moved randomly based on the local dispersion coefficient.
Particle tracking is only calculated for the saturated zone (SZ) and particles that leave the SZ are not traced any further. Initially, the user assigns a
number of particles in the model grid and additional particles are added during the simulation at, for example, constant concentration boundaries or
in groundwater recharge. Particles are removed with outflow to the SZ boundary conditions, such as wells, rivers, and drains, or exchange with the
unsaturated and overland flow zones.
All particles are assigned a mass, which means that a number of particles within a specific volume correspond to a solute concentration. Therefore
the PT module can be used for solute transport simulations and it is in some cases superior to the conventional numerical solution of the advection-
dispersion equation since numerical dispersion is negligible. However, the module is mostly used for:
 delineation of abstraction well capture zones and upstream zones
 determination of groundwater age
 determination of solute transport times
The PT module uses the concept of “registration” cells, to record the discharge from or passing of particles within the saturated zone. Registration
can be used to delineate capture zones or to observe particles passing through a region of interest, such as a redox zone.

1.10.1 Save your WQ simulation to a new name

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1.10.2 Switch from the AD to the PT solution method

In the Simulation Specification dialog,
 change the radio button
from “finite difference, Advection-Dispersion”
to “random walk particle tracking”

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1.10.3 PT Simulation Specification

 Leave the default values alone

If you are not careful, you can easily have more than 1 million
particles in your simulation. Defining the initial particle density by
number of particles allows you to more easily control the number of
particles in the simulation. If you define the number by initial
concentration, then you have to calculate the initial mass of solute in
the cell, based on the concentration, the mass per particle and the
volume of the cell.
Specifying a uniform distribution or a particular level, can be useful
when trying to reproduce detailed transport processes.
For this exercise, we will only “register” particles at wells.

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1.10.4 Define the simulation period

 Define the start date the same as the WM start date
 Define the end date of the WQ simulation sometime in the year
2050.
Since the WQ simulation is much longer than the WM simulation,
you must define what the flow field will be for the 70-year WQ
simulation
 Select Recycling on flow results and chose the start date and
end date of the WM simulation

The Start date must be within the WM simulation period, but the End
date can be any time after the Start date.
It is common to have a long WQ simulation based on a much shorter
WM simulation. MIKE SHE gives you two options for filling in the
missing flow results:
Recycling: If you chose to recycle the flow results, then the flow
results between the Cycle Start and Cycle End dates will be
repeated until the end of the WQ simulation.
Constant Flow Field: This is an extreme version of recycling, where
the WM flow results from a single saved time step will be recycled.
This is the same as using a steady-state flow field for a transient WQ
simulation.
If the WQ simulation period is the same or less than the WM
simulation, then you can also use the first option.

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1.10.5 Initial number of particles

 Set the initial number of particles per cell to 5
This is the initial number of particles in every SZ cell. If you are not
careful, you can generate very large simulations if you make this
number large.
In this example, we will generate capture zones for all of the wells.
An initial particle distribution is helpful to visualize where the water
comes from for each well.

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1.10.6 Store the PT results

You do not need to do anything in this dialog, but you might often
want to turn off the storing of intermediate particle locations, as this
can generate large files.
However, if you turn off this option, you will not be able to extract
pathlines from the results.

1.10.7 Run the Preprocessor and the Simulation

 Click on the icon to start the pre-processor, which will
start the MIKE Zero Launch utility.
 Click OK

 Click on the icon to run the WQ simulation, which will

start the MIKE Zero Launch utility.
 Click OK

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1.10.8 View the gridded results

There are several gridded files generated by the PT module. These
are always output at the WQ storing time step.
SZ concentration – this is the concentration based on the mass
per particle
Number of particles – this is the current number of particles in
the cell
Accumulated particle count – this is the number of particles
that have entered the cell during the simulation
Number of registered particles – this is the number of particles
that started in the cell that have become registered
Most recent registration zone – this is the registration zone
attached to the last particle to be registered that originated in the
cell
Average age – this is the average age of all the particles in the
cell
Average transport time – this is the average length of time
from when the particle was born in this cell until it was registered
somewhere

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1.10.9 Post process the PT results

The PT model also generates some large output files with particle
locations. This location information cannot be displayed directly in
MIKE ZERO.
The post processing tools for the PT module transform this output
into shape files that can be used in ArcGIS or other GIS software.
In the Results tab,
 Select the PT Registration Extraction item
 Add an Extraction to the table by clicking on the Add Item
icon

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1.10.10 Set up the PT extraction

 Click off the Create shape file for each extraction item
 Click on Extract particles by destination well name
 Leave the rest the way it is.
 Click on the Run button at the very bottom of the dialog

The above steps will extract the starting location of all the particles
that entered a well, sorted by the well that they entered. Each well
capture zone will be added to the same shape file, instead of
creating several shape files for each well.

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1.10.11 Add the PT results to the Result Viewer

MIKE Zero is not a GIS tool, but you can display shape files in
various ways.
Return to the concentration map that you developed in Section 1.8.1
View the WQ Results on page 20. If the map is no longer open, then
open the previous .she file using the Project Explorer and then open
the concentration results.
 In the Projects top-menu, select Add files to the project…
 Use the Add item icon to add a new file to the table and
make sure the new item is set to Shape file
 Use the browse button to select the shape file generated in
the previous step. The file will be in the Results directory for
the current project and the name will start with
“PTReg_Extraction”
The particle starting points will be displayed on top of your
concentration results. However, each particle has a label attached to
it by default. To turn off the labels,
 Right click on the map and select Properties…
 In the dialog, select the PT shape file and turn off the labels
 Click OK to come back to the map.
The capture zones illustrated represent the start locations for all of
the water that entered the wells during the 70 years of simulation
time. However, these start locations are only based on the initial 5
particles per cell that are added at the beginning of the simulation.
Along with the .shp file, there is a corresponding .dbf file. If you open
the .dbf file in Excel, then you can see all of the meta data attached
to each particle, including travel time.

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End of Water Quality modeling exercise

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