Ms Step Basic

MIKE SHE - Basic Exercises
MIKE SHE
Basic Exercises
1
INTRODUCTION ............................................................................................................. 3
1.1
1.2
1.3
GETTING STARTED EXERCISE .................................................................................. 6

2.1
2.2
STEP 1 CREATE A NEW MIKE SHE SETUP............................................................... 12

STEP 2 SETUP THE MAP OVERLAYS .......................................................................... 13
STEP 3 SET UP THE SIMULATION .............................................................................. 16
STEP 4 SET UP THE MODEL DOMAIN ....................................................................... 19
STEP 5 SET UP THE TOPOGRAPHY ............................................................................ 23
STEP 6 DEFINE GROUNDWATER RECHARGE ............................................................ 25
STEP 7 GEOLOGICAL MODEL .................................................................................. 27
STEP 8 DEFINE ATTRIBUTES OF COMPUTATIONAL LAYERS..................................... 32
STEP 9 PRE-PROCESS THE DATA .............................................................................. 37
STEP 10 REDEFINE THE HORIZONTAL GRID RESOLUTION ......................................... 39
STEP 11 SPECIFYING OUTPUTS AND CALIBRATION TARGETS ................................... 41
STEP 12 RUN THE SIMULATION................................................................................ 44
STEP 13 VIEW THE RESULTS ................................................................................... 46
STEP 14 ADD GEOLOGICAL LENSES ........................................................................ 49
STEP 15 ADVANCED USE OF THE RESULTS VIEWER................................................. 54
UNSATURATED ZONE (SINGLE COLUMN) EXERCISE ...................................... 62

4.1
4.2
4.3
4.4
4.5
4.6
4.7
4.8
4.9
STEP 1 START MIKE SHE......................................................................................... 6

STEP 2 THE MIKE ZERO PROJECT ............................................................................. 6
SATURATED ZONE (GROUNDWATER) EXERCISE ............................................. 12

3.1
3.2
3.3
3.4
3.5
3.6
3.7
3.8
3.9
3.10
3.11
3.12
3.13
3.14
3.15
HYDROLOGIC PROCESSES SIMULATED BY MIKE SHE ................................................. 3

APPLICATIONS AROUND THE WORLD............................................................................ 3
THE MIKE SHE USER INTERFACE............................................................................... 4
STEP 1 CREATE A NEW MIKE SHE SETUP............................................................... 62

STEP 2 SET UP THE SIMULATION .............................................................................. 62
STEP 3 SET UP THE MODEL DOMAIN AND TOPOGRAPHY ......................................... 64
STEP 4 DEFINE CLIMATE AND VEGETATION ............................................................ 66
STEP 5 BUILD THE UNSATURATED ZONE MODEL ..................................................... 68
STEP 6 PRE-PROCESS THE DATA .............................................................................. 72
STEP 7 RUN THE SIMULATION.................................................................................. 74
STEP 8 VIEW THE RESULTS ..................................................................................... 78
STEP 9 EXPLORE THE SIMULATION SENSITIVITY ...................................................... 83
CHANNEL FLOW EXERCISE (MIKE 11) ................................................................. 85

5.1
5.2
5.3
5.4
5.5
5.6
STEP 1 CREATE A NEW MIKE 11 SETUP .................................................................. 85

STEP 2 CREATE A RIVER NETWORK ......................................................................... 89
STEP 3 ADD CROSS-SECTIONS ................................................................................. 96
STEP 4 ADD BOUNDARY CONDITIONS ..................................................................... 98
STEP 5 DEFINE THE HYDRODYNAMIC PARAMETERS .............................................. 101
STEP 6 RUN THE SIMULATION................................................................................ 103
5.7
5.8
6
STEP 7 VIEW THE RESULTS .................................................................................... 105

STEP 8 ADD A RAINFALL-RUNOFF COMPONENT ..................................................... 107
INTEGRATED EXERCISE ......................................................................................... 115

6.1
6.2
6.3
6.4
6.5
6.6
6.7
6.8
6.9
6.10
6.11
6.12
6.13
STEP 1 OPEN A MIKE SHE SETUP......................................................................... 115

STEP 2 ADD THE RIVER MODULE .......................................................................... 117
STEP 3 REVIEW THE MIKE 11 SETUP .................................................................... 118
STEP 4 ADD THE OVERLAND FLOW MODULE ........................................................ 125
STEP 5 RUN THE MODEL ....................................................................................... 126
STEP 6 VIEW THE RESULTS ................................................................................... 130
STEP 7 INPUT DISTRIBUTED RAINFALL ................................................................. 130
STEP 8 MODIFY THE SUBSURFACE DRAINS ........................................................... 132
STEP 9 ADD LANDUSE ........................................................................................... 133
STEP 10 ADD REFERENCE EVAPOTRANSPIRATION ................................................ 137
STEP 11 BUILD THE UNSATURATED ZONE MODEL ................................................ 137
STEP 12 RUN THE SIMULATION ............................................................................. 140
STEP 13 VIEW THE RESULTS ................................................................................. 141
Notes:
The step-by-step exercises in this book are designed to illustrate the basic
functionality available in the user interface and the basic steps required for
integrated groundwater-surface water modeling.
Although the MIKE SHE model used in these exercises is based on a real case
study, it has been significantly simplified to make it run quickly. Thus, the
parameter values may not be representative of real world values. Further, the
simplifications employed are not intended to illustrate best practices in integrated
modeling.
The exercises in Section 1 will run in MIKE SHE's demo mode. Although the rest
of the exercises will not run in the demo mode, the exercises can be easily
modified so that they will run in the demo mode by reducing the number of nodes
or the simulation length. The necessary changes are noted in the exercises.
1 Introduction
In the hydrological cycle, water evaporates from the oceans, lakes and rivers, from the
soil and is transpired by plants. This water vapour is transported in the atmosphere and
falls back to the earth as rain and snow. It infiltrates to the groundwater and discharges
to streams and rivers as base flow. It also runs off directly to streams and rivers that
flow back to the ocean. The hydrologic cycle is a closed loop and our interventions do
not remove water; rather they affect the movement and transfer of water within the
hydrologic cycle.
MIKE SHE is an advanced, flexible framework for hydrologic modelling. It includes a
full suite of pre- and post-processing tools, plus a flexible mix of advanced and simple
solution techniques for each of the hydrologic processes. MIKE SHE covers the major
processes in the hydrologic cycle and includes process models for evapotranspiration,
overland flow, unsaturated flow, groundwater flow, and channel flow and their
interactions. Each of these processes can be represented at different levels of spatial
distribution and complexity, according to the goals of the modelling study, the
availability of field data and the modellers choices. The MIKE SHE user interface
allows the user to intuitively build the model description based on the user's conceptual
model of the watershed. The model data is specified in a variety of formats
independent of the model domain and grid, including native GIS formats. At run time,
the spatial data is mapped onto the numerical grid, which makes it easy to change the
spatial discretisation.
1.1
Hydrologic processes simulated by MIKE SHE
MIKE SHE uses MIKE 11 to simulate channel flow. MIKE 11 includes comprehensive
facilities for modelling complex channel networks, lakes and reservoirs, and river
structures, such as gates, sluices, and weirs. In many highly managed river systems,
accurate representation of the river structures and their operation rules is essential. In
a similar manner, MIKE SHE is also linked to the MOUSE sewer model, which can be
used to simulate the interaction between urban storm water and sanitary sewer networks and groundwater. MIKE SHE is applicable at spatial scales ranging from a single
soil profile, for evaluating crop water requirements, to large regions including several
2
river catchments, such as the 80,000 km Senegal Basin. MIKE SHE has proven
valuable in hundreds of research and consultancy projects covering a wide range of
climatological and hydrological regimes.
The need for fully integrated surface and groundwater models, like MIKE SHE, has
been highlighted by several recent independent studies that can be downloaded from
the MIKE SHE web site. These studies compare and contrast available integrated
groundwater/surface water codes. They also show that few codes exist that have been
designed and developed to fully integrate surface water and groundwater. Further, few
of these have been applied outside of the academic community.
1.2
Applications around the world
MIKE SHE has been used in a broad range of applications. It is being used
operationally in many countries around the world by organizations ranging from
universities and research centres to consulting engineers companies. MIKE SHE has
been used for the analysis, planning and management of a wide range of water
resources and environmental and ecological problems related to surface water and
groundwater, such as:
1.3
River basin management and planning

Water supply design, management and optimization
Irrigation and drainage
Soil and water management
Surface water impact from groundwater withdrawal
Conjunctive use of groundwater and surface water
Wetland management and restoration
Ecological evaluations
Groundwater management
Environmental impact assessments
Aquifer vulnerability mapping
Contamination from waste disposal
Surface water and groundwater quality remediation
Floodplain studies
Impact of land use and climate change
Impact of agriculture (irrigation, drainage, nutrients and pesticides, etc.)
The MIKE SHE User Interface
MIKE SHEs user interface can be characterized by the need to
Develop a GUI that promotes a logical and intuitive workflow, which is why it
includes
o
o
o
o
o
Strengthen the calibration and result analysis processes, which is why it includes
o
o
o
o
A dynamic navigation tree that depends on simple and logical choices

A conceptual model approach that is translated at run-time into the
mathematical model
Object oriented thinking (geo-objects with attached properties)
Full, context-sensitive, on-line help
Customized input/output units to support local needs
Default HTML outputs (calibration hydrographs, goodness of fit, water
balances, etc.)
User-defined HTML outputs
A Result Viewer that integrates 1D, 2D and 3D data for viewing and
animation
Water balance, auto-calibration and parameter estimation tools.
Develop a flexible, unstructured GUI suitable for different modelling approaches,

which is why it includes
o
o
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Flexible data format (gridded data, .shp files, etc.) that is easy to
update for new data formats
Flexible time series module for manipulating time-varying data
Flexible engine structure that can be easily updated with new
numerical engines
The result is a GUI that is flexible enough for the most complex applications
imaginable, yet remains easy-to-use for simple applications.
In addition to the MIKE ZERO Project Explorer, the MIKE SHE document consists of 4
parts:
Along the top - the Tool bar and drop-down Menus
On the left - the dynamic Data tree and tab control
On the right - the context sensitive Dialog area
Along the bottom - the Validation area and Mouse-over data area
Tool bar - contains icon short cuts for many MIKE SHE operations that can be
acccessed via the Menus. Also, it changes depending on the tools that are currently in
use.
Data tree - displays the data items required to run the model as it is currently defined.
If you add or subtract hydrologic processes or change numeric engines, the make up of
the data tree will change.
Dialog Area - is different for each item in the data tree.
Validation area - displays information on missing data or invalid data items. Any items
displayed here are hot linked to the dialog in which the error has occurred.
Mouse-over area - displays dynamic coordinate and value information related to the
mouse position in the map area of any of the spatial dialogs.
MIKE SHE Basic Exercises - Getting Started Exercise
2 Getting Started Exercise

Overall Objective
Learn how to create a MIKE Zero Project and the associated project documents.
Important learning objectives
After completing this exercise you should be able to
Start MIKE SHE or MIKE 11
Create a MIKE Zero project
Create MIKE SHE and MIKE 11 model documents
2.1
Step 1 Start MIKE SHE

2.1.1 Launch MIKE SHE
from the Program Files menu select MIKE Zero:
The MIKE SHE is part of the MIKE Zero suite of modelling tools, which is a global user interface for managing and manipulating data files and
projects for many of the DHI Software products. Thus, when you launch MIKE SHE or one of the other MIKE Zero products you are really
launching MIKE Zero. MIKE Zero then provides the framework from which you can run MIKE SHE or any other product in the MIKE Zero family.
2.2
Step 2 The MIKE Zero project
MIKE Zero is more than a set of modelling tools. MIKE Zero is a project management interface, with a full range of tools for helping you with your
modelling project.

2.2.1 Install the MIKE Zero examples
Click on the Install Examples... button and select to install all

of the MIKE 11, MIKE SHE and MIKE ZERO example files
This copies all of the example files from the Program Files directory
into your My Documents/MIKE Zero Projects directory. The file
versions in the Program Files directory are read-only and provide
you with an uncorrupted version of the example files. If you corrupt
the files, then you can simply re-install the examples.
For the rest of this exercise book, please use the versions found in
the My Documents directory.

2.2.2 Open the MIKE SHE Examples project
Click on the Open Project button
In the file browser, find the MIKE Examples.mzp file in the

Documents/MIKE Zero Projects/MIKE_SHE folder.
Select this file and click Open
A MIKE Zero project includes all of the modelling files; that is all of
model input files, and model output files. It can also include any raw
data files, reports, spreadsheets, plots, etc. In any project, it is a
challenge to maintain an overview of all of these files, not to mention
keeping regular backups and archives of all of these files. The
number of model artefacts can become overwhelming, as you
progress through the calibration and validation phases and then on
to the scenario analysis and report writing phases.
The core of each project is a .mzp file, which contains all of the
references to all of the files. The Location listed is where the
projectname.mzp file is located.
The MIKE Zero Start Page includes two parts:
The Project Overview table lists the projects that you have recently
accessed, along with their creation and last modified dates.
The Project Explorer is a view into the directory with all the files
that are associated with the project.
The MIKE Zero project structure is designed to help you keep control
of your project.
2.2.3 Creating new documents

A MIKE Zero project is a collection of documents. All of the MIKE by
DHI documents can be created from the File\New\File... menu in the
top pull-down menu or by clicking on the New File icon,
toolbar.
, in the
When the New File dialogue appears,
select MIKE SHE on the left hand side,
select Flow Model (.she) on the right hand side,
click OK.
The default MIKE SHE Setup dialog will now appear and the new
.she file will be added to the project under the Model directory.
The .SHE file contains all the user-specified information required to
run MIKE SHE. However, the file does not contain the actual time
series and grid data. MIKE SHE only stores the path names to the
other data files for time-series data and grid data. This greatly
improves the flexibility of the user interface for keeping your model
up-to-date with new data and for running calibration and prediction
scenarios
Alternatively, you can select any of the listed file types on the right
hand side, or even navigate to one of the other items on the left
hand side. For example, you may need to create a water balance
(.wbl) file during calibration, or a new dfs0 time series file, which you
will find under the MIKE Zero list.

2.2.4 Save the document file
The document file that you just created in this case the .she
document is unnamed until you save it.
To save the file
click on the Model directory in the Project Explorer (this

becomes the default location for the file to be saved to)
Use the File\Save menu item, or the Save icon.
In the Save dialogue,
Type in a file name (e.g. SZ1 this file will be used in the next
exercise)
Add a Note, if you want
Click OK
2.2.5 Getting Help

You are welcome to ask your instructor at any time for help.
However, if you are working on your own, there is an extensive online help. The full Help can be accessed from the top Help menu.
From within the dialogs, context sensitive help is available by
pressing the F1 key.
10

2.2.6 Project, File and Tool Explorers
There is a lot of useful functionality in the various Explorers.
Project Explorer an organized overview of all of the files that are
included in your project. The right mouse menu is context sensitive
based on the type of file that you are pointing at. In addition to
adding, removing and archiving files, you can open and view files
with the available MIKE Zero editors.
File Explorer an overview of all the file types that specified in your
project. This gives you a quick way of finding a particular file if you
know the file type.
Tool Explorer an overview of the specialized tools in MIKE Zero.
You can save custom versions of all these tools and run them
whenever you want.
End of Getting Started Exercise
11
MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise
3 Saturated Zone (Groundwater) Exercise

Overall Objective
Build a simple groundwater model
After completing this exercise you should be able to
Use GIS point data and xyz point data to interpolated gridded surfaces in MIKE SHE
Use GIS polygon data to distribute model parameters spatially
Add graphical overlays (bitmaps and shape files) to your model display
Understand the concepts of Geological Model and Computational Layers
Understand the properties and attributes that are attached to a Geological Model
Master the input specifications required for a simple Geological Model
Understand the properties and attributes that are attached to Computational Layers
Master the input specifications required for Computational Layers
Understand the concepts of Setup Data and Processed Data
Run the simulation engine and view results using the Result Viewer
3.1
Step 1 Create a new MIKE SHE setup
The models used in the following exercises are based on the Karup River watershed in western Denmark. The data files are installed in the MIKE
SHE Examples directory.
Note: If you have just finished the Getting Started exercise and you have the SZ1. she file still open, skip to Step 2.
12

3.1.1 Open the Examples Project
After you have started MIKE SHE
Select the
Browse to the folder:

C:\Program Files\DHI\MIKEZero\Examples\MIKE_SHE
Then open the existing project: MIKE SHE Examples.mzp
button below the project list.
If you have opened this project before, the project will be displayed
in the list box. In this case, open by clicking on the project name.
3.1.2 Create a new MIKE SHE document

As described in the Getting Started exercise,
3.2
create a MIKE SHE (.she) document file in the Model directory,

and
save the document, specifying a name such as SZ1.SHE

Step 2 Setup the map overlays
The first thing to do in most projects is to define the maps and overlays that you are going to use in your project.
MIKE SHE allows you to add graphical overlays using bitmaps, ArcView .shp files, etc. These overlays will appear on all maps shown in the
graphical view in the user interface.
13

3.2.1 Set the display area
The basic display area of the model map view is defined in the top
item of the data tree dialog under Display:
Leave the checkbox checked on
The Display item is located at the top of the data tree to make it easy
to add and edit your background maps. In the Display item, you can
add any number of images to your model setup, in a variety of
formats. The images are carried over to the various editors, so you
can keep a consistent display between the set up editor and, for
example, the Grid Editor and the Results Viewer.
The option ' Default map display based on the Model Domain'
means that the map view will be defined by the size of the model
domain that you select in the next section of this exercise.
However, in some cases you may want the displayed map area
should be much larger than the model domain, in which case you
can define the map extents in this dialog.
You can also import the extents from a shape or dfs2 file.
14

3.2.2 Add an image map overlay
In the Foreground dialog under Display:
Click on the Add Item icon,
Notice that a plus sign (+) appears beside the Foreground item in
the data tree. This indicates that sub-items have been added in the
data tree.
The Background and Foreground options refer to the way the
overlays are displayed relative to the input data specified in the other
dialogs.
Also, if you have multiple overlays, the order that they are listed
defines the order in which they are displayed. Thus, you don't
usually want a bitmap at the top of the list, since it would hide all of
the lower overlays.
3.2.3 Define the file and geo-reference the bitmap
Now click on the plus sign beside the Foreground item in the data
tree to expand the data tree. Then click on the sub-item to display
the sub-dialog.
In the subdialog,
click on the browse button,

, and find the file
.\Model Inputs\GIS Data/Karup0.bmp
Define the Area Coordinates of the bitmap

Minimum X = 822
Minimum Y = -1870
Maximum X = 32845
Maximum Y = 33270
Set the Display style as Blend Colors, which will blend the map
colors with any other displayed colors. This will prevent the
15

bitmap from hiding the model data.
Then navigate back to the Display dialog, to ensure that the

map is being displayed correctly.
Since a bitmap image does not contain any geographical information

(it is simply a list of pixel locations and colours), the bitmap must be
oriented in space. To do so, you have provided MIKE SHE with the
coordinates of the lower left and upper right corners of the bitmap.
For this method to work, the bitmap must be oriented in the same
direction and use the same coordinate system as the model grid.
This can cause some problems if the bitmap has been obtained from
scanner, since the map may not be oriented orthogonally on the
scanner and the scanner may slightly distort the image.
In the menu under All Programs/DHI Software/MIKE 11 you will find
a short cut to the ImageRectifer program. This is a little program that
you can use, if necessary, to align an image to the model grid.
3.3
Step 3 Set up the simulation
MIKE SHE includes several simulation modules. The navigation tree in the user interface depends on your choice of simulation modules.
16

3.3.1 Select simulation modules
In the Simulation Specification dialog
Make sure that Saturated Flow is checked On
Make sure that Finite Difference is selected as the saturated

zone Numeric Engine.
The Simulation Specification dialog allows you to select, which flow

components to include in your simulation. For example, if you want
to include only MIKE 11 and the exchange to the saturated zone,
then you only need to select Rivers and Lakes plus Saturated Flow.
This dialog is where you also choose the numeric engine for the
different hydrologic processes.
There are three numeric engine options for the unsaturated

zone and two each for both the Overland flow and Saturated
Flow.
The calculation method for the Evapotranspiration is

automatically selected depending on the Unsaturated Flow
option selected.
The channel flow numerical method is selected in the MIKE 11

Setup.
17

3.3.2 Set simulation title
In the Simulation Title dialog
Write any title and description you want
3.3.3 Specify simulation period

In the Simulation Period dialog:
Specify the Start date and End date

Start Date : 1 June 1980
End Date : 1 July 1980
Demo Note: For the demo version, the maximum length of

simulation is 30 days. If you are not using a demo version, you can
can run the simulation for several years if you like. In this case, use
a Start as early as January 1, 1970 and End as late as 31.
December 1980.
In this dialog, you can either type in the dates or select the dates
from a drop down calendar.
Specification of the simulation period at this early stage in the model
development is not a requirement. However, it is convenient
because the time-varying input data you specify later is validated
against the simulation period. Thus, when you specify a rainfall timeseries file, a check is made to make sure that the time-series covers
the Simulation Period.
18

In most cases, MIKE SHE is run as a transient model. If the model is
run in steady-state, then the steady-state solution also follows this
simulation period, by generating a series of identical steady-state
solutions for each specified time step.
The Hot-start section allows you to start the simulation from the end
of a previous simulation.
Step 4 Set up the Model Domain
3.4
The model domain and the surface topography are required for all MIKE SHE components.
The model domain defines the horizontal extent of the model area, as well as the horizontal discretization used in the model for overland flow,
unsaturated flow and saturated groundwater flow
3.4.1 Define the model domain
In the Model Domain and Grid Dialog
Choose Catchment defined by Shape File
Using the Browse icon, select the file
.\Model Inputs\GIS Data\catchment-meter.shp

Set the grid dimensions to
Number of cells in the X direction, NX = 65
Number of cells in the Y direction, NY = 70
Cell size = 500m
Rotation = 0
Origin (X0, Y0) = 0, 0
Map Projection Type = NON-UTM
The MIKE SHE GUI automatically assigns values of 1 to the internal

cells and values of 2 to the boundary cells.
When you preprocess the data, the preprocessor calculates the
model domain based on the .shp file and defines the model domain
as a dfs2-grid with integer values 1 (internal point), 2 (boundary
point) and zero values for areas outside the model domain. The pre-
19

processor assigns all of the model parameters based on the dfs2grid that is calculated from the polygon that you have specified in
this step.
If you wish to change the model domain, all you have to do is modify
the .shp file or add a new .shp file and preprocess the data again.
However, be aware that previously specified data must still cover the
new polygon. If it does not, then either a warning will be issued
(saying that some values were automatically interpolated) or an error
will be issued (if it can't interpolate the data)
The Map Projection Type allows you to use any valid map projection.
The only restriction is that whichever projection you chose, you must
be consistent with respect to all other map inputs. You cannot mix,
for example, maps from two different UTM zones. The NON-UTM
option implies local coordinates.
20

3.4.2 Edit the Model Domain polygon
In the Model Domain and Grid Dialog
Click on the Edit button,
This will open the .shp editor utility, where you can add, move and
delete nodes on a shp polygon.
In top icon bar, a new set of icons appears,
To select the polygon, click anywhere in the polygon. Click on

the polygon and move the mouse to drag the polygon with the
mouse.
To drag an individual point, click on the

the points.
To add points, click on the
To delete points, click on the
icon and then on
icon
icon
The polygon editor also allows you to create new polygon files. If you
had clicked on the
button, a new shp file would have been
created, where you could add polygons by clicking on the

3.4.3 Close the .shp editor - without saving your changes
Select the File/Close menu.
Do not save your changes to the polygon.
icon.
21

3.4.4 Add the .shp polygon to the Overlays
In the Foreground dialog:
Change the Type to Shape
Now, go to the new Shape:Unknown data tree item, and
Then click on the Browse icon,
In the Open file dialog, find the file

.\Model Inputs\GIS Data\catchment-meter.shp
22
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3.4.5 Adjust the display parameters for the .shp file

In the Shape: catchment_metre.shp dialog
Choose line-color
Increase the line thickness (e.g. 0.5 or 1 mm)
Now in all of your map dialogs, such as the Model Domain and Grid
dialog. The model domain should now appear as a polyline on top of
the map.
3.5
Step 5 Set up the Topography
The surface topography is required for all MIKE SHE components.

The model topography defines the upper bound of the groundwater model as well as the upper surface of the unsaturated zone model. It is also used
as the flow surface for overland flow.

3.5.1 Define Surface Topography
In the Topography Dialog
Choose Point/Line (.shp) for the Spatial Distribution
Select the file

.\Model Inputs\GIS Data\Topo-processed.shp
If the map is covered by black dots, click off the Show shape
raw data checkbox. This will turn off the shape file data points.
Spatially distributed data, such as topography can be specified using

a Uniform value
a Grid file (dfs2),
a Point/Line (.shp) ArcView or ArcGIS map, or
an ASCII file with distributed xyz values (Point XYZ (txt)).
If a .shp file or an xyz-file is used, MIKE SHE will interpolate the data
to the mesh defined in the Model Domain and Grid menu.
Hint: you can always see the Z-value at the cursor position at the
bottom of your Graphical View.
Interpolation method You can choose between Bilinear
interpolation and Triangular Interpolation methods by selecting from
the Interpolation method combo box. Bilinear Interpolation is a good
method for interpolating from gridded data and the Triangular
method is good for interpolating from digitized contour lines. You can
use the Online Help to find out more information on the interpolation
methods, by clicking F1. At the bottom of the Help page, are two
references to Related Items, which will take you to the detailed
descriptions of the interpolation methods.
SURFER If you want to use interpolation methods not available in
MIKE SHE, then you can use a program such as SURFER by
Golden Software. In SURFER, you can save the interpolated
SURFER grid to an XYZ file, and use the bilinear method in MIKE
24

SHE to reproduce the Surfer interpolation.
Try modifying the search radius and see what happens with the
resulting interpolated values. The search radius should be
sufficiently large to ensure that each grid gets a value. For this
exercise 1000 m is sufficient. But, you are welcome to change the
search radius and interpolation method to see what happens.
However, the minimum search radius is two times the cell size.
Search radii below this will have no effect.
In some cases, such as when the grid is very large or the number of
data points is large, then the interpolation can be time consuming.
This can be a problem, since the grid is re-interpolated every time
you enter the dialog, as well as during the pre-processing step. To
make the model more efficient, you can save the interpolation to a
dfs2 file for use directly. To do this, right click on the map view and
select save to a .dfs2 file. After you have saved the dfs2 file, you can
then use it instead of the XYZ file. Note though, that the link to the
original XYZ data is not lost, but simply hidden from view. This
allows you to return to the original data if you want to change the
discretization of the dfs2 file, for example, if you change the size and
shape of the Model Domain and Grid.
3.6
Step 6 Define Groundwater Recharge
For an integrated hydrological model, you normally define the distribution of precipitation and reference evapotranspiration in both time and space.
However, in this exercise, you are building only a groundwater model and thus the precipitation is actually groundwater recharge.
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3.6.1 Define Precipitation Rate and Temporal Distribution
The precipitation is the actual amount of rainfall.
In the Precipitation Rate dialog:
For now, choose Uniform Distribution Type, which means that

the same precipitation rate will be used all over the model
domain.
Change the temporal distribution from constant to time varying.
Click on the
Scroll through the list and pick the file Precipitation.dfs0 that
has the green check mark beside it
Click OK
button to open the file browser
This file browser lists of all of the files in your project that are the
correct file type. The green check beside the file name indicates that
the file contents match the data requirements for example, the
correct time period and units type. If you are in doubt, you can click
on the
button will show you the data requirements.
In this case, you are using spatially uniform recharge data. The
precipitation file contains data from several rain gauges. The
particular rain gauge to use is selected under the Item in the browse
dialog. In this case, you are using only the data from Precipitation
station 1.
Precipitation is specified the same way data is collected from rain
gauges. It can be input as mean-step accumulated values (e.g.
average rainfall per day in units of mm/day) or, as step accumulated
values (e.g. measured rainfall in a tipping bucket rain gauge in units
of mm since the last measurement).
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3.6.2 Define Net Rainfall Fraction
The Net Rainfall Fraction is the fraction of the precipitation that
reaches the groundwater table.
In the Net Rainfall Fraction dialog:
Choose Uniform, which indicates that the same precipitation

rate is used all over the model domain.
Specify Value = 0.2, which indicates that only 20% of the rainfall
reaches the groundwater table.
Normally, the amount of precipitation that reaches the groundwater

table is only a small fraction of the total amount of precipitation
usually between 5 and 25%. The majority either runs off to surface
water, or is returned to the atmosphere as evapotranspiration. Both
of these processes are very dynamic and the actual fraction that
reaches the groundwater table will vary both spatially and
temporally.
When these processes are not simulated, then the Net Rainfall
Fraction is used to reduce the actual precipitation to compensate for
these processes. The Net Rainfall Fraction is a very important
calibration parameter in groundwater modelling.
In the Karup catchment, the soils are very sandy, and well drained.
So, there is little runoff as overland flow. In the Integrated exercise,
we can use the water balance tool to find the calculated average net
rainfall fraction and compare it to this value.
3.7
Step 7 Geological Model
Before defining your computational layers you must input a geological model, which is defined as part of the saturated zone.
A geological model may be defined as a combination of layers and lenses. Once the geological model is defined you may choose computational
layers that are either identical to the geological layers or you may choose different computational layers. If the computational layers differ from the
geological layers MIKE SHE s pre-processor will transfer the hydraulic properties of the geological model to the computational mesh.
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3.7.1 Saturated Zone Model Specification
In the Saturated Zone dialog:
Select Include subsurface drainage, which implies that water

that flows to the drains is removed from the model. Water flows
into the drains, whenever the groundwater table is above the
drain level.
Make sure that the Include pumping wells is not selected, which
says that there are no groundwater pumping wells in the model.
Select Assign parameters via geological layers,
The geology data can be assigned using both Geological layers and
Geological Units. If you chose the geological layers approach then
the hydraulic properties are assigned as spatially distributed within
the layer. If you use gridded data or point data, the hydraulic
properties are smoothly interpolated to the model grid.
If you chose the geological units approach, then you must specify a
distribution of geological units for each geological layer, for example,
by a polygon file. In this case, all of the model cells in each polygon
are assigned a value for each of the hydraulic properties. The
geologic units method is often specified when you use the
AUTOCAL program for parameter estimation and automatic
calibration. In this case, the parameters for each polygon can be
estimated automatically and the model sensitivity for each parameter
calculated.
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3.7.2 Define the number of Geologic Layers
In the Geological Layers dialog:
Rename the existing default layer name to Aquifer.
By default there is already one layer in the model. Additional layers

can be added by clicking on the Add Item icon,
clicking on the Delete Item icon,
, deleted by
, or moved up and down by
clicking on one of the Move Item icons,

Increasing the number of saturated zone model layers allows you to
better represent vertical flow and exchange between geologic layers.
A fine vertical discretization may also be required for solute transport
simulations.
MIKE SHE allows you to have up to 50 layers in the saturated zone.
Most models, however, have less than 10 model layers. The more
model layers you have the higher the computational effort and the
more memory that is needed. If you need more layers, it is always
better to start with a few layers and do the initial calibration. Then
add layers as necessary, while ensuring that the model remains
stable and computational effort remains reasonable.
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3.7.3 Define Layer Bottom (Lower Level)
In the Lower Level dialog for Geolayer 1:
Select Point/Line (.shp) in the Spatial Distribution combo box
Using the file browse button,
, select the file
.\Model Inputs\GIS Data\layer1.shp
Use the Bilinear interpolation method, and
Use a Search Radius of 1000m
Each of the Geological layers includes one item in the data tree for
each of the properties. Additional layers will add additional sets of
items to the data tree.
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3.7.4 Assign Hydrologic Properties
The remaining hydrologic properties are listed under the Lower Level
item. For each item
Select Uniform under the Spatial distribution combo box and

specify the following values:
Horizontal hydraulic conductivity = 0.00052[m/s]
Vertical Hydraulic Conductivity = 9.3e-5 [m/s]
Specific Yield = 0.2 [-]
Specific Storage = 0.0001 [1/m]
3.7.5 Assign drainage option

In the Drainage dialog:
Select Drainage not routed, but removed from model.
In a fully integrated model the drainage water is part of the water

balance and, normally you would want to route the drainage water to
the river. However, in this example, you don't have a river specified
so there is no place to send the water too. Thus, the water that flows
to the drains will be removed from the model, but the amount of
water flowing to the drains can still be evaluated in the water
balance.
Water flows into the drains, whenever the groundwater table is
above the drain level.
The method specified here is the same method as used in
MODFLOW. That is, the drains act as head-dependent-flux
boundaries but only as a water-sink.
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3.7.6 Define Drain Levels
In the Drainage Level dialog:
Select Uniform under Spatial Distribution
Use the value : -0.5 [m] (Note negative sign)
Check on Values relative to ground
The Values relative to ground tells MIKE SHE that you have drains
located 0.5 meter below ground surface in the entire model domain.
If the groundwater table is higher than the drainage level drain flow
will be produced and removed from the model.
3.7.7 Define Drain Time constants

In the Time Constant dialog:
Select Uniform under Spatial Distribution
Use the value = 5.6e-7 [1/s]
The drain time constant can be thought of as an empirical factor that

accounts for the time it takes for the water to drain. For example, in
the case of agricultural drains, the time constant could be affected by
drain spacing, drain diameter, clogging, etc.
In the case of natural drainage, the time constant is affected by the
distribution of drainage ditches and channels.
A value closer to 1 implies that the water drains more quickly and the
drain acts more like a constant head boundary. Whereas, a value
closer to 0 implies that the water drains more slowly.
3.8
Step 8 Define Attributes of Computational Layers
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The computational layers are defined independently of the geological layers. While the Geological Layers have geological attributes, the
Computational Layers include computational attributes such as initial conditions and boundary conditions. The properties of the geological layers are
mapped and interpolated to the computational layers during the model preprocessing.
Although, MIKE SHE allows you to define Computational Layers independent of your Geological Layers, in this exercise computational and
geological layers will be identical.
3.8.1 Define Computational Layers
In the Computational Layers dialog:
Select Defined by geological layers as the Type of Numerical

Vertical Discretization
Use Minimum layer thickness = 0.5 [m]
The Minimum layer thickness is used to keep layers from crossing or

completely pinching out, which would cause numerical difficulties.
If layer does not exist in part you model (e.g. a discontinuous clay
layer), then you need to assign the properties of the layer above or
below in the areas where it does not exist

3.8.2 Initial Conditions
In the Initial Potential Head dialog:
Select Grid file (.dfs2)
Using the file browse button,
, select the file
.\Model Inputs\Maps\init-head-500.dfs2
You are using an initial head from a previous model run, which gives
you a good starting point. In a real model, you might initially start
from a value such as 3m below the topography. However, such a
value will require a run in time, as the model may take several
months to equilibrate.
An alternative is to run the model as a steady-state simulation and
then use the steady-state solution as an initial condition. However,
the steady state solution still might not be a reasonable starting point
depending on how steady the groundwater table is.
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3.8.3 Edit the Lay1L.dfs2 grid
Look at some of the editing options and close the grid editor
without saving.
Demo Note: in Demo mode, you will not be able to save any
changes to the dfs2 file
MIKE SHE includes sophisticated tools for managing gridded data
as well as time series data. The grid editor can also manage a
combination of both time series and gridded data - that is a time
series of grids. This is very useful for time varying distributed
parameters, such as precipitation that is interpolated from rain gage
data, or distributed recharge calculated by third party programs such
as DaisyGIS.
The grid editor is a split window that can be dragged rightwards to
make the map larger. The table of values on the right side reflects
highlighted grid shown on the lefthand map.
Ranges of values can be searched for, selected and changed using
the select and unselect tools,
Tools/Set Value dialog
, plus the
Important Note
The grid editor is a generic grid tool for all DHI Software, and was
originally developed for the Marine programs MIKE 21 and MIKE 3.
However, this often leads to confusion in the node and layer
numbering because MIKE 21 and MIKE 3 use a different numbering
system.
Node numbering: In the Grid Editor (and in MIKE 21 and MIKE 3)
the nodes are numbered starting in the lower left from (0,0), whereas
in MIKE SHE the nodes are numbered starting in the lower left from
(1,1).
Layer numbering: In the Grid Editor (and in MIKE 21 and MIKE 3)
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the layers are numbered starting at the bottom from 0, whereas in
MIKE SHE the layers are numbered starting at the top from 1.
The dfs2 file format includes geographic and cell-size information.
The dfs2 file format is part of the larger dfs file format system
developed by DHI. This includes:
dfs0 files for time series data (e.g. rainfall data at a rain gauge),
dfs1 data, which is not used in MIKE SHE, but used for time
series of lines (e.g. the shape of a coast line)
dfs2 data for time series of 2D grids (e.g. topography or gridded

precipitation),
dfs3 data for time series of 3D grids (e.g. MIKE SHE

groundwater head results)
3.8.4 Outer Boundary Conditions

The Outer boundary is defined by as the row of cells on the outside
of the model domain. The outer boundary is defined by the Model
domain and grid file, as all points with a code value of 2 (boundary
point).
In the Outer Boundary dialog:
Press the Add Item Icon,
Select Zero Flux as the boundary Type
This now gives you a no-flow boundary condition along the entire
outside of the model. If the entire outer boundary is a no flow
boundary, then this step is actually unnecessary because by default
the outer boundary is no flow.
This is realistic in terms of a watershed boundary, but is not really
very realistic in this case, because you are not going to specify a
river boundary now. In this model, you are basically specifying the
river outflow via drainage, in the sense that wherever the water table
approaches the ground surface, water will be removed from the
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37
model.
The outside of the model can be divided into boundary sections, by
clicking on the Add Item icon again.
Then click on the Add Point icon,
, and click on the map to
define the location of the boundary point. The boundaries are
specified clockwise around the model starting at the first point in the
table.
The outer boundary conditions are defined independent of the model
grid. Thus, if you change your model grid the boundaries will be
interpolated automatically to the new grid based on the nearest
boundary cells to the point locations. If you change the shape or
extent of the grid, you should check that your boundaries have not
moved unexpectedly.
Internal boundary conditions Internal boundaries are used to
specify such things as lakes and reservoirs that are not included in
MIKE 11. In this case you could specify a constant head or a general
head boundary for the lake.
Internal boundaries are distinguished from outer boundaries
because on the outside of the model, you can specify flux and
gradient boundaries.
3.9
Step 9 Pre-process the data
Your have now specified all the input required for the model, including
Selecting the model components

Specifying the model domain and grid
Specifying the surface topography
Specifying the net recharge (precipitation and net rainfall factor)
Specifying the geological model (Geological layers), including the hydraulic properties.
Specifying the computational layers, including initial conditions and boundary conditions.
Up to this point, all of the input data has been specified independent of the numeric model. You have specified only the characteristics of the numeric
model that will be run. Before actually running the model you must run the pre-processor. The pre-processor extracts all of the spatial data that you

have included and applies it to the numerical model that you have defined in the Model Domain and Grid and the Computational Layers. The preprocessor writes all input data to a binary Flow-Input-File (fif file) which is then read by the simulation engine when running the simulation.
3.9.1 Run the Preprocessor
Click on the
icon to start the pre-processor.
The preprocessor will start the MIKE Zero Launch utility, which is
allows you to set the process priority for the simulation.
Click OK
If you are starting a very long simulation, then you can also set up
MIKE Zero to alert you when the simulation is finished.
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3.9.2 Viewing the preprocessed data
After successfully running the Preprocessor,
Click on the Processed Data Tab located at the bottom of the

Navigation Tree.
Then, click on the items in the data tree and explore the results.
The pre-processor creates a .fif file that contains the cell values etc.
that will be used in the simulation. The processed data has been
interpolated to the computational mesh, exactly as the simulation
engine will read it. However, the .fif file is a binary format optimized
for use by the numerical engine.
The fif-file embeds all geometric data. Temporal data (time-series
data) are not contained in the fif-file, but are read directly from the
source data files during the simulation.
To view the pre-processed data, an parallel set of dfs2 and dfs3 files
are also created so that the standard MIKE Zero tools can be used
to view the data.
It is the dfs data that is shown in the data tree and listed in the file
name text box. Clicking on the View button opens the Grid Editor
with the current pre-processed data file loaded with all the current
overlays.
If you want to edit values in the Grid Editor and use the edited values
in your simulation, then you need to save the file to a new name
after making the changes. Then specify the modified dfs file in the
Setup data tree.
Spend some time moving around in the Processed Data and make
sure you understand the input data and the relation between Setup
Data and Processed Data.
3.10 Step 10 Redefine the horizontal grid resolution
A very powerful feature of MIKE SHE is that you can change the horizontal grid without redefining your model parameters. Thus, you can perform
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40
sensitivity analysis of your model grid and grid resolution in way that is impossible with other modeling user interfaces.
Demo Note: the demo version is restricted to a maximum of 70x70 cells, so you will not be able to pre-process or run the model with the refined grid.
3.10.1 Change Horizontal Grid Resolution.
In the Model Domain and Grid dialog
Double the number of grid cells in the X and Y directions
NX = 130
NY = 140
Change the Cell Size to 250 m
Click on the
Verify in the pre-processor tab that all of the input data has
been converted to a 500m grid
3.10.3 Change the cell size to 400 meter cells

Change the number of grid cells in the X and Y directions
NX = 100
NY = 100
Run the preprocessor.
When combining dfs2 files and unstructured data files the dfs2 files
put some constraints on the geometry of the computational mesh
you can create.
If the grids are coincident and
the data is real data (e.g. topography) the finer grid will be
interpolated to the coarser grid using the bilinear interpolation to
the center node.
the data is integer data, the integer values will be assigned

based on a global population distribution. For example, if 50%
of your land area is forest, then 50% of your cells will be
assigned the integer code for forest.
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If the grids are not coincident and
the data is real data, then the grids will be interpolated in the
same way as distributed XYZ and .shp data.
The data is integer data, then an error will be generated

because the model cannot interpolate integer data.
3.10.4 Change the cell size back to 500 meter cells

Change the number of grid cells in the X and Y directions
NX = 65
NY = 70
3.10.5 Save your SHE document

3.11 Step 11 Specifying outputs and calibration targets
The Detailed Time Series Output allows time Series plots of simulated data at specific locations to be automatically generated during a simulation. It
also allows simulated output to be compared to observed output and calculates a number of statistics for model error.
Output is generated in HTML format and can be incorporated into web pages to document calibration progress.

3.11.1 Storing of Results
Click on Storing of Water balance data
Set the Storing interval for grid series output to a daily

frequency (24 hours) for Prec(ipitation), SZ-heads and SZfluxes
The Water balance items are used during the post-processing of the
results to calculate water exchanges between the various
components
The Hot start data is used for starting transient simulations from the
end of a previous simulation. This allows you to modify things such
as land use over time, or to do scenario analysis from the same
starting scenario.
Gridded output is stored as dfs2 (2D grid time-series files) or dfs3
(3D grid time-series files). If output data is stored too frequently, you
may get very large and unwieldy result files. Thus, before running
the simulation you should consider how often you need to save the
data.
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3.11.2 Define Detailed Time Series Output items
Use the Add item icon,
For each item,
, to add 4 items to the list
Set the name
Select head elevation in saturated zone under Data Type
Define the X, Y coordinates from the table below:

Name
X-coordinate
Y-coordinate
Obs 5
24103
8419
Obs 35
13800
17607
Obs 37
17508
20887
Obs 65
8866
25549
Define the Depth = 5
Make sure Incl. Obs. Data is not selected
The X and Y location can be selected on the map using the

button.
Observation data will be added in a later exercise.
You are also welcome to add any other points and data items you
like.
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3.11.3 Grid Outputs
In the Grid series output dialog all of the items will be selected if you
have turned on the storing of Water Balance data.
If you did not enable storing of water balance data, then you
should enable storing of
precipitation rate,
depth to phreatic surface,
head-elevation in saturated zone,
groundwater flow in the X-direction, and
groundwater flow in the Y-direction.

(3D grid time-series files). If all output items were saved, you may
get very large result files. Thus, before running the simulation you
should consider which output items you need.
The groundwater flow direction output is required so that you can
plot flow vectors on the plots.
Note: that the SZ-flow time step must be an integer multiple of the
Max SZ time step that is specified in the Time Step Control dialog.
For example, if your Max SZ time step is 24 hours, then the SZ-flow
Storing Time step can be 24, 48, 72 hours , etc. This is true also for
steady state simulations.
3.12 Step 12 Run the simulation
Before running the model, you need to go back to the Setup menu to make a few changes to the simulation specifications, including simulation
period, time-steps and storing of results.
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3.12.1 Specify the Time step parameters
In the Time step control dialog:
Specify Initial time step = 24 hrs
Specify Max allow SZ time step = 24 hrs
Max infiltration amount per time step = 10
Leave the rest of the parameters at their default values

The max infiltration amount and the max precipitation depth per time
step are used to improve the numeric stability of the solution when
there is ponded water on the ground surface.
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3.12.2 Simulation Control
In the SZ Computational Control Parameter dialog:
Choose Preconditioned Conjugate Gradient, Transient
Specify Maximum Head change per iteration = 0.0001 [m]
The default values for the simulation convergence parameters are

normally suitable and in most cases need not be changed.
3.12.3 Run the simulation

Click on the
icon to re-run the pre-processor and then on the
icon to run the simulation.

3.13 Step 13 View the Results
Upon successful execution of the model youre now ready to view the results.
The Results Viewer allows you to view and animate results from all DHI dfs file types. This first exercise will guide you through only the most basic
functionality of the Result Viewer
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3.13.1 Locate the Detailed Time Series Output Results
After successfully running the model,
Click on the Results Tab located at the bottom of the Navigation

Tree.
The Detailed Time Series Output dialog lists the Detailed Time
Series results you have chosen to store during the MIKE SHE
simulation.
If you have specified more than 5 items for detailed time series
output, then you will only see a page of links on the main Detailed
timeseries page. The links will direct you to separate .html files with
5 graphs in each.
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3.13.2 Display the Gridded Results
Now select the Gridded Data Results Viewer
Check on the Add XY flow vectors for the head elevation in the
saturated zone plot
Finally, click on the View Result button to view the simulation

results in the Results viewer tool
The Results Viewer dialog lists the results you have chosen to store
in the MIKE SHE results files.
The XY flow vectors check box adds velocity flow vectors calculated
for each cell.
The Layer no for groundwater items is used to select the numerical
layer number in groundwater models with multiple numerical layers.
3.13.3 View the Results in the Results Viewer
Note that the velocity vectors will not appear in the initial time step, but
rather appear first in the second time step.
3.14 Step 14 Add Geological Lenses

The geological model defined up to now is a 1-layer system of homogenous sand. In this step you will add a clay lens within the sandy aquifer.
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3.14.1 Add the geological lense
In the Geological Lenses dialog
Change the name of the lens to Clay
, to add a lens.
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3.14.2 Define Horizontal Extent of the lens
In the Horizontal Extent dialog
Select Grid file (.dfs2) files for Spatial Distribution
Use the Browse button to select the file

.\Model Inputs\Maps\lense3.dfs2
All the lenses will be assigned the same hydraulic properties. If you
want to assign different hydraulic properties to different lenses, then
you need to add additional lenses (see the step above)
Lenses can also be assigned using polygon shp files.
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3.14.3 Define the top of the lens
In the Upper Level dialog

.\Model Inputs\Maps\lense3U.dfs2
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3.14.4 Define the bottom of the lens
In the Lower Level dialog

.\Model Inputs\Maps\lense3L.dfs2
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3.14.5 Define Hydraulic Properties for the Lense
For each hydraulic property of the lens use a Uniform Spatial

distribution with the following values:
Horizontal Hydraulic Conductivity : 1E-6 m/s
Vertical Hydraulic Conductivity: 1E-7 m/s
Specific Yield : 0.2 (-)
Storage Coefficient : 0.0001 (1/m)
3.14.6 Evaluate the pre-processed data
Run the preprocessor and explore the preprocessed data.

Lenses are treated as separate geologic layers in the cells where
they are located. Thus, the pre-processor reads the lens geometry
(area, top, bottom) and attributes (hydraulic properties) and
interpolates the lens information into the hydraulic properties of the
numerical layer. You will see the affect of the lens by looking at the
hydraulic properties of the layer in the Pre-processed data tab.
3.15 Step 15 Advanced use of the Results Viewer
This step demonstrates some of the advanced features of the Result Viewer that have not been discussed previously.
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3.15.1 Locate the Results
After looking at the Detailed Time Series Output,
click on the Results Viewer item in the Results navigation tree.
The Results Viewer dialog lists the results you have chose to store in
the MIKE SHE results file. In this exercise, you chose to store the
precipitation (groundwater recharge), depth to phreatic surface,
groundwater head, and the groundwater flow in the x-, y- and zdirections.
3.15.2 View the Results in the Results Viewer
Click on the View Results,

, button for the item head
elevation in saturated zone.
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3.15.3 Save view to a the clipboard
In the View top pull-down menu choose Export Graphics -> Copy to
Clipboard
The image can be pasted into most Windows based application
(Word, Excel, etc.)
3.15.4 Time series plot at a point
Press the Time Series button

on the Results Viewer
tool bar
Click once and then while holding down the Ctrl-key, click on
each additional point where you want time series output.
Each selected locations is marked with a yellow x.
Double click on the last point. (if you only want one point
then simple double click without holding down the Ctrl-key)
Check Display and press OK to display the time series.
Export to a dfs0 file

Right-click in the time series plot.
Select Export in the pop-up window.
Check Export and press OK.
Enter an appropriate file name for the dfs0 file
The j,k coordinates listed at the bottom of the Results Viewer go
from 0 to (nx-1) and 0 to (ny-1) in the j and k directions, respectively.
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3.15.5 Extract a profile of water levels
Press the button

on the Results Viewer tool bar to extract a
profile from the simulate output item displayed
Click in the area of interest to select the points along the profile
line. Double click on the last point of the profile to terminate the
profile line. The profile line is indicated with a thick green line.
Check 3D head elevation in saturated zone and press OK
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3.15.6 Display the computational grid on profile.
In the Projects pull-down menu choose
Active View Settings -> Profile
On the Graphical Items tab of the dialog that appears, under
Calculation layers,
check Draw Calculation layer and select Draw as grid to show the
computational grid or Draw as lines to show the upper and lower
surface.
Press OK to view selection
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3.15.7 Modify visible overlays and display the finite difference
mesh in Result Viewer.
First, return to the horizontal view of head elevation in saturated
zone, by either closing the cross-section view or switching via the
Window pull-down menu
In the Projects pull-down menu choose
Active View Settings -> Horizontal
In the dialog that appears,
Double click on the item len03_grid_meter.shp

to turn off the display of the clay lenses. The red check (
be removed.
) will
Then,
Single click on the item SZA_3DSZ.dfs3 to view the available

display options.
Under the Miscellaneous items,

check Element Mesh.
Press OK to execute changes.
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3.15.8 Generate an animation of the head results
In the horizontal view,
Press the
button on the Results Viewer tool bar to
generate an animation of simulated heads.
Enter a File name for the animation (e.g., SZA.avi).
Press OK to save the animation to the file.

Press OK in the next dialog, which specifies the compression
used during the saving.
A higher Frame rate speeds up the animation for long simulations.

The animation file can be played in Windows Media Player and most
other media programs.
Animations can be made of all Result Viewer documents.
Press the button
then the
button to generate a reverse
animation, which starts at the final time and ends at the start of the
simulation.
3.15.9 Change the output time step for the animation.
In the horizontal view,
Press the button
on the Results Viewer tool bar
Change the Animation time step to 2 and units to day.
Press the
button on the Results Viewer toolbar
The animation now displays the head distribution at every other time
step, (every 2 days).
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3.15.10 Animate a selected portion of simulated area.
Press the
Press the
button on the Results Viewer tool bar to
generate an animation of simulated heads for the selected
portion of the simulated area.
Enter a File name for the animation (e.g., SZA_small.avi).
Press OK to generate animation
button to zoom into the area of interest.
The animation file can be played in Windows Media Player and most
other media programs.
End of Saturated Zone (Groundwater) Exercise
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MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise
4 Unsaturated Zone (Single Column) Exercise

Overall Objective
Build a dynamic, single-column unsaturated zone model
4.1
Understand the concepts of Unsaturated Zone (UZ) Modeling

Understand the properties and attributes that are attached to a UZ Model
Master the input specifications required for a simple UZ Model
Understand the properties and attributes that are attached to Soil Types
Master the input specifications required for Soil Profile consisting of different Soil types.
Set up a soil Profile with different vertical spatial resolution.
Understand the concepts of Setup Data and Processed Data
Run the simulation engine and view results using the Result Viewer
Step 1 Create a new MIKE SHE setup
As described in Chapter 2, create a MIKE SHE (.she) document file, and save the document, specifying a name such as UZ1.SHE
4.2
Step 2 Set up the simulation
MIKE SHE includes several simulation modules. The navigation tree in the user interface depends on your choice of simulation modules.
62

Check Saturated Zone Off,
Check Unsaturated Zone On, and
Choose Richards Equation as the Numeric Engine
Check Evapotranspiration On
4.2.2 Set simulation title

In the Simulation Title dialog
Write any title and description you want
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4.2.3 Specify simulation period

Start Date : 1 April 1980
End Date : 1 July 1980
Demo Note: The demo mode only allows 800 time steps. If you are
running this exercise in demo mode, you should only run the
simulation for two months.
Specification of the simulation period at this early stage in the model
development is not a requirement. However, it is convenient
because the time-varying input data you specify later is validated
against the simulation period. Thus, when you specify a rainfall timeseries file, the user interface checks to make sure that the timeseries covers the Simulation Period.
4.3
Step 3 Set up the Model Domain and Topography
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4.3.1 Define Model Domain
In the Model Domain and Grid dialog,
Choose Catchment defined by the dfs2 File
Click on the Create button
In the Create grid data dialog, set
NX, NY = 3
Cell size = 1000 m
Rotation = 0
X0, Y0 = 0
Click Create file
The above steps will create a 3x3 grid file for the unsaturated zone
model. This is the minimum size grid, as it contains only one
calculation point.
The model grid file contains two integer values (1 for the calculation
point and 2 for the boundary points), plus Null values outside the
model area.
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4.3.2 Define Surface Topography
In the Topography Dialog, you can leave the values at their default
values uniform and 10 m
Step 4 Define Climate and Vegetation
4.4
For an integrated hydrological model you normally define the distribution of precipitation and reference evapotranspiration in both time and space,
along with the distribution of vegetation in you catchment.
4.4.1 Define Precipitation
In the Precipitation Rate data item
For the Spatial Distribution, choose Uniform
For Temporal Distribution, choose Time Varying
Use the Browse button to select the precipitation file

.\Model Inputs\Time\precipitation.dfs0
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4.4.2 Specify Evapotranspiration
In the Reference Evapotranspiration data item:
For the Spatial Distribution, choose Uniform
For Temporal Distribution, choose Time Varying
Use the Browse button to select the precipitation file

.\Model Inputs\Time\PotentialEvapo.dfs0
The reference evapotranspiration (ET) is the rate of ET from a

reference surface with an unlimited amount of water. Based on the
FAO guidelines, the reference surface is a hypothetical grass
surface with specific characteristics. The reference ET value is
independent of everything but climate and can be calculated from
weather data. The reference ET is adjusted to the plant type using a
crop coefficient, which are usually available in the literature.
The actual ET is calculated by MIKE SHE during the simulation as a
function of the vegetation demand and water availability.
4.4.3 Specify Vegetation characteristics
In the Vegetation data item.
Select the Uniform option for Spatial Distribution of the

vegetation (only one soil column in the model.
Select the Constant option for the Data Type.
Change the leaf area index (LAI value) = 1
Change the Root depth (RD value) = 500 mm
Typically, for a 2-D model with a network of gird cells a land use map
would be specified.
Note that there were three Data Type options available:
Constant: Constant vegetation characteristics in time, only one

single value of Leaf Area Index (LAI) and Rooting Depth (RD)
67

needs to be specified (see figure);
Time Series File: The time varying vegetation characteristics

are described by a time series file for LAI and RD,
Vegetation Property File (etv): The time series of the

vegetation characteristics are defined by a sequence of
vegetations (e.g. crop rotation scheme) accessed directly from
the Vegetation Database.
Step 5 Build the unsaturated zone model
4.5
In this step, you will specify geometry of the soil profile and hydraulic properties for the layers.
4.5.1 Building your Unsaturated Zone Model
In the Unsaturated Flow data item.
Select the Calculation in all grid points option,
Select Equilibrium profile for Initial Condition, and
Under Macropore flow, select None
Since UZ computations in all grid squares for most large-scale

applications requires excessive computation time, MIKE SHE
enables you to compute the UZ flow in a reduced subset of grid
squares. The subset classification is done automatically by the preprocessing program according to soil types, vegetation types,
climatic zones, and depth to the groundwater table.
Automatic classification The automatic classification requires

a distribution of groundwater elevations. This can be either the
initial depth to the groundwater based on the initial heads, or
you can supply a .dfs2 map of the groundwater elevations.
Specified classification Alternatively a data file specifying

Integer Grid Codes, where UZ computations are carried out can
be specified, and then these calculations are transferred to the
other cells.
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Calculated in all Grid points For smaller scale studies, or

studies where the classification system becomes intractable,
you can specify that computations are to be carried out in all
soil columns.
Partial Automatic Finally a combination of the Automatic

classification and the Specified classification is available.
4.5.2 Define the soil profile distribution

In the Soil Profile Definitions dialog.
Spatial Distribution : Select Uniform (only one column)
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4.5.3 Define the global soil profile
In the Global data tree item, under Soil Profile,
Click on the Add Item,
Change the Depth of the layer to 10 m
Use the browse button to select the soil properties file
, to add one soil layer to the profile
.\Model Inputs\Karup.uzs
Note: Before you click OK, you need to select the Soil type the
file selection dialog. Leave it as Fine Sand.
This dialog is divided into two parts:
The upper part is used to define the soil profile. That is the vertical
distribution of soils that are observed in the field.
The lower part is used to define the numerical grid spacing for
solving the unsaturated zone flow equations.
The Soil type combo box includes a complete list of all of the soil
types that are available the database. You must choose the soil type
here because the soil type is not editable in the main dialog. It has
been done in this way, to avoid slow response times in the Soil
definition dialog when very large databases are being referenced.
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4.5.4 Define the vertical grid discretization
In the Global data tree item, under Vertical Discretization
Click the Add Item icon,

layers
Change the Cell height and No of cells to the following
, to add three different grid spacing
Cell height = 0.1 m
No of cells = 3
Cell height = 0.15 m
No of cells = 6
Cell height = 0.2 m
No of cells = 44
The numerical grid is usually very fine at the top, where rapid
changes in saturated can occur in response to precipitation.
Typically, the grid becomes increasingly coarse with depth, while
following the soil horizon boundaries.
4.5.5 Define Lower Boundary condition

In the Groundwater Table dialog.
Specify the Spatial distribution to be Uniform
Set the Value of the groundwater table = -8m
Check on the Values relative to ground
The combination of negative sign (-8m) and the checkbox for Values
relative to ground means that the groundwater table is 8m below the
ground surface.
The Saturated Zone Component is not included in this model, so no
dialogs for this component are available. However, the Unsaturated
Zone Component requires the groundwater table as the lower
boundary condition, which is the reason that you must specify the
groundwater table here. If the saturated component was included,
the location of the groundwater table would be calculated by MIKE
71
72
SHE.
Step 6 Pre-process the data
4.6
Your have now specified all the input required for the model, including
Selecting the model components

Specifying the model domain and grid
Specifying the surface topography
Specifying the net recharge (precipitation and net rainfall factor)
Specifying the vegetation and evapotranspiration
Specifying the soil profile, including the hydraulic properties.
Specifying the lower boundary condition (groundwater table).
Up to this point, all of the input data has been specified independent of the numeric model. You have specified only the characteristics of the numeric
model that will be run. Before actually running the model you must run the pre-processor. The pre-processor extracts all of the spatial data that you
have included and applies it to the numerical model that you have defined in the Model Domain and Grid and the Computational Layers. The preprocessor writes all input data to a binary Flow-Input-File (fif file) which is then read by the simulation engine when running the simulation.
Click on the
The preprocessor will start the MIKE Zero Launch utility, which is
allows you to set the process priority for the simulation.
Click OK
If you are starting a very long simulation, then you can also set up
MIKE Zero to alert you when the simulation is finished.
4.6.2 View the preprocessed data

After successfully running the Preprocessor,
Click on the Processed Data Tab located at the bottom of the

Navigation Tree.
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4.6.3 Check the pre-processed data
In the Soil Profile Definitions item verify the vertical discretization.
Spend some time moving around in the Processed Data and make
sure you understand the input data and the relation between Setup
Data and Processed Data.
4.7
Step 7 Run the simulation
After running the pre-processor, you can run the actual simulation.
Before running the model, you need to go back to the Setup menu to make a few changes to the simulation specifications, including simulation
period, time-steps and storing of results.
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4.7.1 Specify the Time step parameters
Specify Initial time step = 2 hrs
Specify Max. allowed UZ time step = 2 hrs
Leave the rest of the parameters at their default values
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4.7.2 Simulation Control
The default values for the simulation control parameters are normally
suitable and in most cases need not to be changed.
4.7.3 Storing of Results
Click on Storing of Water balance data
Set the Storing interval for grid series output (Prec, ET, UZ) to 2
hours.

(3D grid time-series files). If output data is stored too frequently, you
may get very large and unwieldy result files. Thus, before running
the simulation you should consider how often you need to save the
data.
In this dialog, you can also chose to store Hot start data. This would
allow you to start a simulation, for example, from the end of a
previous simulation.
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4.7.4 Detailed timeseries output
In the Detailed time series output dialog
Click on the Add Item icon to add a new line to the table
Then select a Data type for detailed time series output, such as
average water content in the root zone
Then click on the target icon,

, which will change the
cursor to a target when you move it onto the grid.
Now click on the center of the grid to set the coordinates of the
point where you want to obtain a detailed time series output.
This dialog can also be used to specify a time series of observations,

if they are available. In this case, the observations will be plotted
along with the related calculated time series for calibration purposes.
4.7.5 Grid Outputs
In the Grid series output dialog some of the output parameters are
enable because the water balance is selected in the Storing of
Results dialog.
Select these additional output items:

Actual evapotranspiration
Water content in the unsaturated zone

(3D grid time-series files). If all output items were saved, you may
get very large result files. Thus, before running the simulation you
should consider which output items you need.
77

Click on the
icon to re-run the pre-processor and then on the

Step 8 View the Results
4.8
Upon successful execution of the model, youre now ready to view the results.
The Results Viewer allows you to view and animate results from all DHI dfs file types. This first exercise will guide you through only the most basic
functionality of the Result Viewer, but you are welcome to explore the rich functionality of this tool.
4.8.1 Locate the Results
After successfully running the model,
Click on the Results Tab located at the bottom of the Navigation

Tree.
The Results Viewer dialog lists the results you have chosen to store
in the MIKE SHE results files.
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4.8.2 View Grid and Point Results
Press the View Results button for Water Content in the UZ
Click on the movie icon,
, in the top toolbar
The Result Viewer opens and displays the results for the first timestep in the top layer of the model. The layer number can be easily
changed by right clicking on the grid and selecting properties.
When you click on the movie icon, the Results Viewer loops through
the time series of water content for the displayed cells. It ends with a
message about an .avi file being saved for the movie.
4.8.3 View the time series profile in cross-section.
When the movie has stopped (or you have stopped it), click on
the UZ-plot viewer toolbar
button
Then double click on the central grid cell.
This opens a 2D view of the time development of the water content

in the profile. The depth is shown along the vertical y-axis and the
simulation time is show along the x-axis.
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4.8.4 Add additional results files to the Results Viewer
Make sure that the REV:1 view is active and then click on the
Projects menu, and Add Files to Project.
Use the Add File icon to add File items
Then click on the Browse button to add the following time series
files
.\Results\UZ1\UZ1_ET_AllCells.dfs2
.\Results\UZ1\UZ1_ET_UzCells.dfs2
Note: the file names will depend on the specified name of
the simulation file.
These files will not be part of your project yet. So, they will not
appear in the list of available files.
Click on the External File button and browse to find the files
Click on Yes to add the files to your current project
The first file above contains the input precipitation rate and the
second file contains the calculated actual ET.
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4.8.5 Overlay the time series on the same graph
Click on the time series icon,
Then double click somewhere in the center of the grid.
This will bring up the Items dialog, where you can select what
items to plot. The top soil cell, and the precipitation, and ET are
clicked on by default
Finally, click on OK
This will display a time series graph with three lines one for each of
the selected items.
The actual evapotranspiration and the precipitation are shown for the
grid cell as they are not dependent on the depth. The water content,
on the other hand, is depth dependent and only displayed for the
selected layers.
These default graph axes are also somewhat poor in this case, since
the precipitation ranges from 0 to 12 mm, yet the water content
ranges only between 0.2 and 0.05.
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4.8.6 Adjust the graph settings
Right click on the graph to get a pop-up menu
Click on Properties to open the Time Series Properties dialog
On the Y-axis tab of the Time Series Properties dialog
Change the Placement for the water content to the Right Axis
Change the right Y-axis To value = 0.5
This moves the scale for the water content to the right hand Y-axis
and changes the scale so that you can better see the relationship
between water content, ET and precipitation.
You are welcome to explore these tabs, and try out a few of the
other features. For example, you could try to change the colours of
the graphs, etc.
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Step 9 Explore the simulation sensitivity
4.9
4.9.1 Change the soil profile

Go back and change the soil profile. For example, you could add
additional soil layers. There is also a coarse sand in the soil
database
The results on the right were obtained by adding a coarse sand layer
below the fine sand at a depth of 1 meter.
Can you explain any differences to your simulation?
4.9.2 Add a time series of root depth

Go back and add a time series for LAI and Root Depth. The easiest
way to do this is to use the soils database.
Go back to the Vegetation item
Change the Data type from Constant to Vegetation property file
Add a line to the table, using the Add item icon
Change the Start date to 1. Jan 1980
Use the browse button to find

.\Model Inputs\MIKE_SHE_vege.etv
Before you click OK, select Grass1
Re-run the model and view the results
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End of Unsaturated Zone (Single Column) Exercise
84
MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11)
5 CHANNEL FLOW EXERCISE (MIKE 11)

Overall Objective
Build a 1D hydraulic model
5.1
Understand the concepts and associated files for building a MIKE 11 hydraulic model
Understand the properties and attributes that are attached to a simulation file
Understand the properties and attributes that are attached to the following files: cross-section, network, boundary and hydrodynamic files.
Step 1 Create a new MIKE 11 setup
As described in Section 2, create a MIKE 11 (.sim11) document file, and save the document, specifying a name such as River.sim11
The sim11 document contains all user-input required to run MIKE 11. The sim11 document links
the different MIKE 11 components together as it contains the references to the other MIKE 11
modules including
Simulation (.sim11) MIKE 11 setup file
River Network (.nwk11) for specifying the river geometry and connections
Cross-section (.xns11) for specifying the river cross-sections and resistance
Boundary Conditions (.bnd11) for specifying the upstream and downstream boundary
conditions
HD Parameters (.hd11) for specifying the hydrodynamic parameters
85

5.1.1 Simulation Parameters Models
Select the Models tab in the sim11 document.
Check the Hydrodynamic checkbox
Select the Unsteady radio-button.
The Models dialog enables you to specify the MIKE 11 models to be used in the hydraulic
model.
The selected options define a hydrodynamic model based on hydrodynamic flow conditions.
5.1.2 Simulation Parameters Input

This dialog contains the references to the necessary MIKE 11 parameter files. In this model,
this includes only the Network, Cross-section, Boundary, and HydroDynamic models.
86

5.1.3 Simulation Parameters Simulation
This dialog contains the basic simulation parameters
Under Time Step, specify

Fixed time step
Time Step = 5 min
Under Simulation Period, specify the Start date and End date for the simulation
Start Date: 1. Jan. 1980
End date: 27. Jan. 1980
Under Initial Conditions, specify the hydrodynamic (HD) initial condition.
Select the Parameter File option.
You dont need to specify the Simulation period now. However, it is convenient because the
time varying input data you specify later on will be validated against this simulation period.
Hence, when you specify a discharge time-series file, the user interface requires that the
time-series cover the Simulation Period.
When selecting the parameter file option the initial conditions are read from the HD
parameter file.
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5.1.4 Simulation Parameters Results
Specify a result filename of your choice with the suffix .res11. For example,
.\Model\Results\River1\River1.res11
Specify the storing frequency as 1, meaning that the results are stored at every
simulation time step.
The MIKE 11 result files always end with the suffix .res11.
If you dont use the browse button to specify a results path, then the results will be
automatically placed in the current directory.
5.1.5 Simulation Parameters Start

If all specified input files exist, the Start button can be pressed and the simulation will
commence.
During the set-up all input files are verified (on the fly). If there are any errors, they will be
shown at the bottom of this dialog.
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5.1.6 Review questions for Step 1
Try to answer the following questions before proceeding with the exercise:
What is the suffix of a MIKE 11 simulation file?
Which input data are specified in the MIKE 11 simulation file?
What is the suffix of a MIKE 11 result file?
Where is the data verification shown?

Step 2 Create a river network
5.2
5.2.1 Create a MIKE 11 network document

As described in Section 2, create a MIKE 11 network (.nwk11) document
5.2.2 Define the min and max area coordinates
The Area Coordinates dialog appears automatically when creating a new river network.
Specify the area coordinates for the hydraulic network:

Xmin = 0
and Ymin = -2000
Xmax = 35000 and Ymax = 35000
Specify the map projection as NON-UTM
The map projection for all MIKE SHE files must be NON-UTM.
5.2.3 Save the file
Before you go on, save your network document. For example,
.\Model Inputs\MIKE 11\River1.nwk11
Note: when you save the file in this way, the file is automatically added to your current
project.
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5.2.4 Network Import Image File
Select Layers -> Add/Remove top menu item

Use the New Item icon,
Use the browse button to select the image file
, to add a line to the table
.\Model Inputs\GIS-Data\Karup0.bmp
Note: The top bar menu depending on the document that is active.
For example if the steps above are only possible if the .nwk11
document is the active document. If you make the .sim11 dialog
active the top menu bar will change.
5.2.5 Set the image coordinates
Select Layers -> Properties top menu item

Set the same coordinates that you used in the SZ exercise

Minimum X = 822
Minimum Y = -1870
Maximum X = 32845
Maximum Y = 33270
If a previously geo-referenced image file is loaded. The georeference information is stored in a file with the same name as the
image file but with the suffix .bmpw.
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5.2.6 Network Delineate River
In the top button bar, click on the Add New Points tool button,
Using your mouse, start at the river mouth (upper left) and follow the river, clicking the
left mouse button to define river points along on the main branch of the Karup River.
When finished with the main branch, repeat this for the two tributaries, with the first point
of the tributary next to the Karup River.
Save your work
The points are only used to geo-position the branches and are not used in the calculation
scheme. Thus, the number of points entered does not effect the simulation time. Nor does it
matter what order the points have been input.
Note: If the point locations are not visible or disappear, you can change any of the display
settings for the various components by opening the Display Settings dialog under Settings ->
Network, in the top menu bar.
This image is a map of the Karup River basin, including two main tributaries. The river
source is in the lower right and exits the map area near the upper left corner.
91

5.2.7 Network Define Branches
To define a branch,
In the top button bar, click on the Define Branch' tool button,
Position your mouse at the upstream end (source) of the river (lower right) and hold
down the left mouse button
With the mouse button held down, follow the river points that you previously added until
you reach the downstream end (river mouth) (upper left) and then let go of the mouse
button. This should connect all of your points along the main branch together with a
black line.
When finished with the main branch, repeat this for the two tributaries, starting at the
upstream end of the tributary and ending at the last point before joining the main
branch.
Save your work
Note: when you define the branch tributaries, you will not be able to connect them to the
main branch. You will do this in a subsequent step.
If you make a mistake while defining the branches, you can delete the branch by clicking on
the Delete Branch tool button,
, and then clicking on the branch that you want to delete.
Remember, though, to click on the Define Branch tool button again.
Note: If the branches are not visible or disappear, you can change any of the display
settings for the various components by opening the Display Settings dialog under Settings ->
Network, in the top menu bar
5.2.8 Network - Define the Branch properties
To open the branch properties dialog
Right click on the branch and choose Edit from the pop up menu
Then select the branch in the dialog box,
Click on OK
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Downstream end = outflow
93
This will open the Network Tabular View at the branch properties dialog.
The Network Tabular View can also be opened by using the Ctrl-t keyboard shortcut.
In the Network Tabular View, for each Branch
Specify the Branch name as shown

Haderup River
Karup River
Hauge Creek
Change the Topo ID to model cross (The spelling here is important, see Note below)
Close the Tabular View and return to the Network Editor.
Note: the current branch in the Tabular View is highlighted on the map
Downstream end = outflow
Note: The Topo ID is referenced to the Cross-section database. That is, if the Topo ID does
not match the Topo ID in the Cross-section database, then the referencing will fail.
Karup
River
Haderup
River
Hauge
Creek
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5.2.9 Network - Define river node chainages

You must define the chainage of the ends of each river branch
Right click on the upstream or downstream river node and select Point Properties from
the pop-up menu
Change the Chainage Type to User Defined
Then change the Chainage value to the following values, where 0 is the chainage at the
uppermost upstream point:
52000
Karup River: 0 to 52000

Haderup River: 0 to 14200
14200
Hauge Creek: 0 to 12100

Chainage is the linear distance along the river. Since the cross-section locations are based
on chainage locations, you must define the chainage of the upstream and downstream ends
of the river branch.
12100
0
The internal notation of MIKE 11 is such that the flow direction is positive with increasing
chainage. This requires that the starting point of the river branch (Chainage = 0) is at the
upstream end of the branch. And the end point of the branch is at the mouth of the river
(maximum chainage value).
However, in many river surveys the downstream end of the river network (ie. the mouth of
the river) is the starting point. In this case, the Flow Direction in the Tabular View must be set
to Negative.

5.2.10 Network Connect Branch
To connect two branches to one another,
Click on the Connect Branch tool button,
Then select the downstream end of the connecting branch, hold the mouse button while
dragging the pointer towards the connecting point at the main branch. MIKE 11 displays
a line indicating that the branches are connected.
Repeat to connect the other tributary to the main branch.
Save your document.
5.2.11 Network Add Network to Simulation file

When the network file is defined it must be added to the simulation document.
Switch to the Simulation document (.sim11) by using the Window pull down menu in the top
menu bar
In the Input tab
select your Network file by using the Browse button,
on the Network line
When you use the browse button, only the valid file types that are part of your current project
will be displayed. If you want to use a file that is not yet part of your project, then you can
click on the [External File] button to access a regular Windows explorer dialog. Then you
will be asked if you want to add the file to your project. If you answer Yes, then a short cut to
the file will be added to your project.
What is the suffix of the network file? What is the main purpose with the network file?
How is a branch delineated and defined?
What is chainage and how is it defined?
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Step 3 Add cross-sections
5.3
5.3.1 Cross-section Load an existing cross-section file

For this exercise, a pre-defined cross-section file is available.
To add the cross-section file to the simulation document (.sim11):
Use the Browse button to locate the file

.\Model Inputs\MIKE11\Karup.xns11
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5.3.2 Cross-section Open the cross-section file
for editing
To open the cross-section file
Press the Edit button,
Then examine the contents of the cross-section

document.
Note:
Cross-sections are identified by a Branch ID and a

TOPO ID
Cross-section data are relative to the specified

Datum value.
Cross-section data are editable through both the

table and the graphical View.
The marker values in the table are defining the

extent of the cross-section to be used in the
simulation.
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5.3.3 Cross-section Display cross-section locations in the network
After you have added the cross-section file to the simulation document, the data can be
displayed on the network.
To view the cross-section locations,
Open the network document (.nwk11) by selecting it from the drop-down menu under
Window in the top menu bar.
The cross-section locations should be visible as rectangles on the network.

If the cross-section locations are not visible
Did you add the cross-section document to the simulation document?
Check to make sure that the Branch ID and TOPO ID in the network and the crosssection document are consistent (spelled the same).
Check to make sure that the cross-sections are turned on under Settings -> Network,
where you can change any of the display settings for the various components.

5.4
What is the suffix of the cross-section document?
Which two IDs connects the network and the cross-section data?How are the cross-section data geo-referenced on the network?
What is the purpose of chainage values and how are they defined?
What is the purpose of marker values and how are they used?
When is the cross-section locations displayed in the network editor?

Step 4 Add Boundary Conditions
5.4.1 Create a MIKE 11 boundary condition document

As described in Section 2, create and save a MIKE 11 boundary (.bnd11) document. Then
before you go on, save your boundary document. For example,
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.\Model Inputs\MIKE 11\River1.bnd11
The boundary document contains the boundary locations and boundary types for both
external and internal boundary conditions.
5.4.2 Boundary Add to Simulation file
To add the boundary file to the simulation document (.sim11):
Use the Browse button,
, on the Boundary data line to find your .bnd11 file
5.4.3 Boundary Add Boundary Items to the river network

MIKE 11 requires a boundary condition at every upstream and downstream open boundary,
that is, at every node where there is no defined connection. This is normally the mouth of the
river network and the upstream end of each branch.
To add the boundary data to the river network,
Open the Network editor, by clicking on the Network Editor dialog, or by selecting your
network document from the Window pull down menu in the top menu bar.
Right click on the node at the downstream end (mouth) of the Karup River
In the pop-up menu select

Insert -> Boundary -> Hydro Dynamic
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Repeat this for the upstream end of the Karup River and each of the tributaries
When the boundary conditions are added to the MIKE 11 network and there is a boundary
condition file defined in the simulation file (.sim11 file), then the boundary locations are
automatically added in the Boundary editor.
5.4.4 Boundary - Assign the boundary data to each Boundary Item
Open the Boundary Editor by selecting the boundary (.bnd11) document from the
Window pull down menu in the top menu bar.
Change each of the four boundary item as follows:
For the upstream boundaries (Chainage = 0), the boundary type should be Inflow
For the downstream boundary at the mouth of the Karup River, the boundary type
should be Water Level.
To add the time series information to the boundary condition
Click on one of the boundary items in the in the upper table
Then, in the lower table click on the browse button
and locate the time series file
.\Model Inputs\MIKE 11\Karup.dfs0
In the file browser, the valid item types in the dfs0 file will be available in the Item
column. In this file, there is only one valid item for each boundary type.
Save the file and close it
The upstream boundaries are Inflow, but there is no inflow at the source of the river. If you
were simulating only part of a river network, then you would use the measured inflow rate.
At the mouth of the river, you have defined a Water level boundary. You must define at least
one water level boundary, or else the system is indeterminate there might be several valid
water levels if all the boundaries are flow boundaries.
The time series data must be in the MIKE ZERO time series format (*.dfs0 files). You can
use the time series editor to view the dfs0 file by clicking on the [Edit] button. This file is
rather boring, though, because for this exercise, you have defined a constant downstream
water level.
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5.5
What is the suffix of the boundary document?
Which types of boundary conditions are normally applied for a hydrodynamic model?
How is the MIKE 11 boundary data stored?
When are the boundary locations displayed in the Network editor?

Step 5 Define the hydrodynamic parameters
5.5.1 Create a MIKE 11 hydrodynamic document

As described in Section 2, create and save a MIKE 11 boundary (.hd11) document. Then
before you go on, save your boundary document. For example,
.\Model Inputs\MIKE 11\River1.hd11
The Hydrodynamic document contains all the simulation parameters connected to the
hydrodynamic model.
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5.5.2 Hydrodynamic Add to Simulation file
To add the hydrodynamic file to the simulation document (.sim11):
Use the Browse button,
, on the HD Parameters line to find your file
5.5.3 Hydrodynamic Set wave approximation

On the Wave Approx. tab,
change the Wave approximation to High Order Fully Dynamic.
The High Order Fully Dynamic wave approximation contains:
Acceleration term
Hydrostatic gradient term
Bed friction term
Gravity term
This allows larger time steps and is especially applicable for:
Fast transients
Tidal flows
Steep channels
Rapidly changing backwater effects
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5.5.4 Hydrodynamic Set initial condition
On the Initial tab, under Global Values,
Change the radio button to Water Depth, and
Change the default value for Water Depth to 1.0
Note: In MIKE 11, you need to make sure your changes are registered before you save.
MIKE 11 was the first MIKE Zero product and not all of the dialog controls register your
changes when you make them. The changes are first registered when you leave the
control. Thus, when you change the default value to 1.0, the change will be lost if you leave
the dialog even if you click Save unless you click in a different control (e.g. click in the
Discharge text box). A quick way to check if your changes have been registered is to always
check that the dialog title bar contains the words Modified . However, this
only reflects the previous change and your last change will still not be registered unless you
have clicked outside of the control in which you made the last change.

What is the suffix of the hydrodynamic document?
There is a lot of useful functionality in the HD document. For example
5.6
the Add. Output tab lists the additional results that can be saved,
the Time Series Output tab allows you to automatically generate dfs0 time series results files
the Groundwater Leakage tab allows you to simulate baseflow loses from the stream based on a unit gradient, and
the Maps tab allows you to generate flood maps

Step 6 Run the simulation
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5.6.1 MIKE 11 Run the simulation
In the simulation document (.sim11), select the Start tab.

If the Run Parameters and HD Parameters bulbs are green, all the needed input data has
been entered and validated.
Press START to begin the simulation, and display a progress bar.
Your simulation should run, but you will get a number of warning messages.
Warning 65: there is a difference in the bed level
This warning is telling you that, at the point were they join, the bed level in the main branch is
different that the bed level in the tributary. This is normal, but you should look carefully at
such warnings to make sure you dont have a data error.
Warning 47: ... the water level has fallen below the bottom of the slot ___ times.
This warning is simply telling you that your solution is not numerically stable. This is also
normal for this case, because you dont really have any water in the river because it is not
connected to MIKE SHE or a rainfall runoff model. The slot that is referred to is a numerical
trick to keep the river from completely drying out.
Tips: If you encounter problems getting a MIKE 11 simulation to run, the following are some
tips that might make a difference:
Smaller time steps increase the stability of the simulation. However, this will increase
the length of time that the simulation takes to run.
Correct initial conditions can make the simulation more stable.
If the time steps are increasing very slowly, you can start subsequent simulations from a
results file using the Hot Start option for the initial conditions.

How are you able to see if all the input data has been entered and is valid prior to starting the simulation?
104
How would you know if the time step affecting the numerical stability of the model?
Step 7 View the results
5.7
5.7.1 Results Open MIKE VIEW

MIKE 11 results are viewed using MIKE VIEW.
All Programs -> DHI Software -> MIKE 11 ->MIKE VIEW
5.7.2 Results Open MIKE 11 Results File

(.res11)
When you launch MIKE View, you will
automatically be directed to a browse dialog to find
your results file. Your results file should be located
in the located that you specified at the end of Step
1 in this exercise.
click OK in the Data Load Selection dialog.
Note, the Dont ask me again checkbox at the

bottom of this dialog
Later, when you come back to MIKE View you can

open a results file from the top menu bar
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5.7.3 Results MIKE View Overview
When the results are loaded to MIKE VIEW a plan view of the network is displayed.
In the top toolbar, you can use the following tools to explore the results
Time series plot:
Profile plot:
Cross-section plot:
5.7.4 Results Time series plots
Select the time series view tool
Select Data type (Water level or discharge).
Select OK
Now, click on a point in the river network where you wish to see the results (Note, the
cursor will change when you hover over a valid calculation point),
Alternatively, you can click on the List button in the Data Type Selection dialog, which will
give you a list of available calculation points.
The time series plot with the selected data is then shown.
Right mouse click -> Add TS to add additional time series to the plot.
Right mouse click -> External TS to add external dfs0 files to the plot.
106
107
5.7.5 Results Profile plots
Select the profile plot tool
Click on a branch or branches. Double-click or Ctrl + mouse click to

finish selecting branches.
In the Close profile? pop-up dialog, select Yes.
In the Data Type Selection dialog, choose Water level or Discharge,

and click OK.
Shown on the profile plot are the Bed level, the Bank level, and the
Maximum and minimum water level or discharge (depending on the
chosen data type).
Standard animation tool buttons are available for Play
Pause
, Stop
, and
for animating the water level or discharge time series.

5.8
What is the suffix of a MIKE 11 result file?
Where are MIKE 11 results viewed?
How can MIKE 11 results be viewed?
Is it possible to make animations of water level or discharge?

Step 8 Add a rainfall-runoff component
The results to this point are rather boring because there is not really any water being added to the river. Normally, the hydraulic model is coupled to
an inflow boundary or a rainfall runoff model. If the MIKE 11 model is coupled to MIKE SHE, the MIKE SHE is essentially a distributed rainfall-runoff
model.
In this step, you will create a simple rainfall-runoff catchment based on the Karup catchment.
Demo note: The following step cannot be done in Demo mode.
108
5.8.1 Add the Rainfall-Runoff component
Return to the .sim11 document
On the Models tab, click on the RainfallRunoff option
Then create a new .rr11 document using the

standard procedure
On the Input tab, add the .rr11 file using the

browse button
5.8.2 Add a RR catchment
Click on the [Edit] button to edit the .rr11 file
In the Catchments tab, add a catchment by clicking on the [Insert catchment] button
Add a Name, such as Karup
Set the Model type to NAM
Set the area to 440 km
2
2
In this step, you are creating a catchment. The catchment has an area (440 km ), but not a
3
location. When it rains, 10mm of rain in one day will generate 4.4 million m of potential
runoff. The NAM model apportions this potential runoff into the various components of the
hydrologic cycle and calculates an actual runoff including the timing the runoff hydrograph.
The NAM model does this by means of various of the factors and time constants that you
must specify. In this exercise, you will leave all of these factors at their default values, but in
a real case, you would calibrate all of these factors against the measured stream flow
hydrographs.
The problem is that many of these factors are not physically based. They represent some
physical process, but are lumped together for the entire catchment. Hence, rainfall runoff

models are commonly called lumped parameter models. Although, the parameters
represent physical processes, their values are not easily correlated to physical
measurements. For example, the Time constant for routing interflow represents the average
length of time it takes for near surface groundwater to flow reach a stream. However, you
cannot measure this time; you can only calibrate the parameter against the measured
hydrograph soon after a rainfall event.
The fact that the model parameters cannot be correlated against measured values makes
lumped parameter models difficult to use for scenario analysis. For example, if you want to
change the land-use distribution in your catchment you cannot easily predict how a time
constant should be changed.
MIKE SHE largely resolves this problem by using physically based parameters. Parameters
must still be averaged on a cell basis, but this is a much smaller scale than a catchment. The
average surface roughness for runoff in a cell, for example, may not actually be
measurable, but the manner in which it changes in response to a change in land-use is
more predictable. So, a physically based, distributed model such as MIKE SHE is more
suitable for scenario analysis.
Never the less, lumped parameter models have a long history in surface water modelling.
They are very useful for generating stream flow hydrographs in response to rainfall events.
They are widely used for hydraulic and flood analysis. For this reason, lumped parameter
approaches have also been added to MIKE SHE directly the Linear Reservoir
Groundwater, the 2-Layer Unsaturated Zone, and the Semi-Distributed Overland methods
are all lumped parameter options.
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5.8.3 Add a time series item to the Precipitation File
The precipitation time series file must be modified for the NAM
model.
In the Project Explorer double click on the Precipitation.dfs0 file

located in the Time directory.
or
Use the Open icon and browse to the file

.\Model Inputs\Time\Precipitation.dfs0
This will open the dfs0 Time series Editor.
Select the Properties option in the top Edit menu
In the File Properties dialog that appears, click on the [Append]

button
This will add a new time series item at the end of the list. In the new
time series item, change
The Name from Untitled to something else (e.g. Rainfall)
The Type from Undefined to Rainfall
The Unit to millimeter (should be the default)
The TS Type from Instantaneous to Step Accumulated
Click OK to close the dialog
The NAM model requires that the precipitation be specified as

rainfall in a period (e.g. mm over the previous 24-hour period). This
is the way rainfall is often measured and is called Step-Accumulated.
Mean step accumulated refers to the rate over the previous period
(e.g. mm/hour over the previous 24-hour period).
Instantaneous measurements are typically things like temperature,
where the measurement occurs at a particular time.
110

Less commonly used are Accumulated and Reverse mean step
accumulated time series types. For example, the pumped volume
from a groundwater well could be added together every week to
make sure that the yearly licensed volume is not exceeded. The
Reverse means step accumulated refers to the rate in the coming
time period rather than the past time period.
5.8.4 Use the calculator to edit the precipitation values
Now you need to fill the new time series item with data
Select the Calculator option in the top Tools menu
In the Expression field type

i10=i9 * 24
Click OK to perform the calculation and close the dialog
Check your new data to make sure it was calculated correctly.
Save and close the file
You have now filled item 10 with the amount of rainfall in each 24 hour time step that was
measured at Station 9.
In a real model, you would do the above calculation for each rainfall station and distribute the
rainfall across the catchment based on Theissen polygons.
For this exercise, you will limit ourselves to assigning the rainfall from one station to the
entire catchment.
5.8.5 Add a time series item to the Evapotranspiration File

The evapotranspiration time series file must also be modified for the NAM model.
In the Project Explorer double click on the PotentialEvap.dfs0 file located in the Time
111

directory.
or
Use the Open icon and browse to the file

.\Model Inputs\Time\PotentialEvap.dfs0
Then repeat the above two steps for this file.

Note: In the calculation step, the time step is 24 hours, the existing values are in mm/day,
and the values must be converted to mm.
5.8.6 Add the time series to the .rr11 file
In the .rr11 editor, you have to add the rainfall and evaporation time series.
Click on the Timeseries tab,
Use the Browse button to locate the two files that you modified above.
Save and close the .rr11 document
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5.8.7 Link the rainfall runoff model to the river network
In the tabular view for Network editor, you have to add the
catchment/branch connections
In the Rainfall-runoff links dialog,
Add three items, by selecting the line in the table and clicking
the Insert key on your keyboard
Divide the catchment area among the three tributaries and

distribute the rainfall-runoff along the entire branch length
Haderup River 80 km
Hauge Creek 68 km
Haderup River 292 km
The areas above were proportioned based on the branch lengths. In

a real model, the actual contributing areas for each branch would be
calculated based on the area of each subcatchment.
5.8.8 Run the model
If you have done everything correctly, they you should not have any Validation messages
and you should be able to simply press the Start button.
There will be some minor water balance correction messages after the simulation has run.
113

5.8.9
View the results
Return to MIKE View and look at your

results.
There will be three .res11 files. One for the

river hydraulics and two for the NAM
model.
The rr.res11 file will give you the discharge
time series for the catchment. The
river1.res11 file will give you water level or
discharge in the river at all calculation
points.

Why do you need a rainfall-runoff model?
How is a lumped parameter model different than MIKE SHE?
What is the difference between a step-accumulated and mean step-accumulated time series?
End of CHANNEL FLOW EXERCISE (MIKE 11)
114
MIKE SHE Basic Exercises - Integrated Exercise
6 Integrated Exercise
Overall Objective
Extend the SZ1 model to make it into a fully integrated groundwater-surface water model
Understand how the River Module interacts with the Saturated Zone Module
Understand the specification of River Channel coupling branches
Understand how distributed and time-varying rainfall data are input
Understand how boundary conditions can be modified
Understand how subsurface drains link to the river
Understand how detailed time-series outputs can be extracted and combined with field data for calibration purposes.
Understand the input data required for an unsaturated zone model
Understand how the unsaturated and saturated zone models interact
Understand the input data required for the evapotranspiration model

6.1
Step 1 Open a MIKE SHE setup
As described in Section 2, open the MIKE SHE (.she) document file that you created in Exercise SZ1, and use the Save As command to save the
document to a different name, such as Integ1.SHE.
115

6.1.1 Verify the Model Domain
The SZ1 exercise should already have a 500x500m discretization
and use a shape-file for domain delineation. However, before you go
to the next step, check that the Model Domain settings are:
NX = 65
NY = 70
Cell Size = 500
Rotation = 0
X0 = 0
Y0 = 0
6.1.2 Extend the simulation period


Start Date : 1 January 1970
End Date : 31 December 1980
Demo Note: If you are using the demo version of MIKE SHE do not
extend the simulation period.
116

Step 2 Add the River Module
6.2
You will now add a river to the groundwater model that you created in the SZ1 exercise. In this exercise, you will use an existing MIKE 11 river
setup that is slightly more detailed than the one you created in the River1 exercise.
Check Rivers and Lakes On
Your model now has a Rivers and Lakes branch in the Data Tree.
6.2.2 Add the River Module

In the Rivers and Lakes Dialog
Use the browse button to select the existing sim11 file

.\Model Inputs\MIKE 11\karup.sim11
Press the
button to enter the MIKE 11 simulation editor
117

6.3
118
Step 3 Review the MIKE 11 setup
If you did not do the River exercise, then you should carefully work through this step. If you did the River exercise, then can skip this step or simply
note the differences between this setup and one you created.
6.3.1 Explore the MIKE 11 simulation document
The sim11 file contains a complete river model setup. You are not
going to build a river model as part of this exercise.
The Simulation editor includes five tabs.
The Models tab allows you to select the model components.
The Input tab allows you define the links to the model input files. A
typical MIKE 11 model for MIKE SHE requires the following
documents:
river network (nwk11),
cross-sections (xns11),
boundary conditions (bnd11), and
hydraulic parameters (HD11).
The Simulation tab allows you to set the time step and simulation
length. However, the simulation length is overridden by MIKE SHE.
The Results tab allows you to set the output file name and storing
frequency for the output. In dynamic simulations the time step for
MIKE 11 can be quite small, so it is often necessary to reduce the
storing frequency.
The Start tab allows you to see if there are any data input errors in
your setup and start the simulation when you are ready.
6.3.2 Change the Results directory

The current results directory should be changed to the Results
directory.
.\Results\Karup\Karup.res11
Use the browse button on the Results tab to change the

directory
Save your changes.
119

6.3.3 Explore the Branch Network
On the Input tab of the Simulation editor
Press the
button on the Network line.
All information in MIKE11 can be accessed and modified from the

network editor. You are now in the Network Editor, which is the core
editor of MIKE 11. From here, you can build and modify you river
model.
This network is a little more detailed than the one you did for the
previous exercise
6.3.4 Routing Branches

Switch to the Network Tabular View, by either
Selecting View from the top menu and then Tabular View or
Using the Crtl-t keyboard shortcut from the graphical view
In the Branches Dialogue, note that the Branch Type for all
branches are set to Kinematic Routing
A regular branch will calculate the water level based on the SaintVenant equation (Kinematic, Diffusion or Dynamic Wave
formulations). For detailed simulations, you would generally use
regular branches.
However, often it is convenient to use simpler routing formulations,
where the water in the river is moved down the river without
120

actually calculating the water levels. Water levels are calculated
afterwards knowing the flow rate in the cross-section and backcalculating a water level.
The main advantage of the routing methods is their speed. They
require less data, they are numerically stable and you can use very
long time steps if you want.
The downside is that the calculated water levels are less precise and
hydrodynamic effects are ignored. Water levels are simply calculated
based on the amount of water in the river in the current time step.
You may also combine different approaches, for instance by using
simple routing techniques on the upstream, steep branches and the
dynamic wave approaches on the downstream low-gradient
branches.
6.3.5 Routing Settings
In the Kinematic Routing Method dialogue you do not need to
specify anything. If no specifications are made, the model will:
Calculate water levels using the Manning Equation assuming

that the energy slope equals the bed slope derived from crosssections (Manning numbers are specified in the HD11 file
default is M=30, n=1/M).
Use the No-Discharge Transformation option, which implies that

inflows are summed along the branch and transferred to the
downstream end of the branch in the same time-step. This is
the same as a full pipe with a unit of water entering one end and
pushing a unit out the far end.
The Muskingum methods dampen the peak flows as they travel

downstream, which is necessary when the travel time in the
river is much longer than the time step. For example, in large
river networks, it may take save days or longer for a flood wave
to travel from the source to the river mouth.
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You may include additional routing points at different locations along
a branch, but this will not be covered in this course.
In this exercise, you are using the simplest option, where no routing
is used. Thus, whatever water flows into the branch network at the
boundaries or as lateral inflow, will be transferred downstream in the
same time-step.
MIKE SHE keeps track of and conserves mass and does not allow
water to infiltrate from the river to the groundwater if the river is
empty.
6.3.6 MIKE SHE MIKE 11 Coupling
In this dialogue, you specify which MIKE 11 branches will be coupled
to MIKE SHE. You may choose to include some of the MIKE 11
branches or all of them, or even just part of a branch.
The coupling specification includes the definition of the river-aquifer
exchange, including the river bed leakage coefficient. The river
leakage can also depend on the hydraulic conductivity of the aquifer
material when the MIKE SHE cell size is much bigger than the river
width.
By default, exchange between MIKE SHE and MIKE 11 is only oneway. Overland surface water will flow into MIKE 11, but water will not
flow into back onto the ground surface if the river floods. There are
two options for flooding.
Cells can be defined by flood codes, where they will be flooded

if the elevation of the cell is below the water level in the nearest
H-point.
Alternatively, you can allow overbank spilling. In this case, the

river will discharge the water onto the ground surface based on
a weir formula.
122

6.3.7 View Cross-Sections
In the Network Editor (Graphical View) at each of the red markers on
the river, a cross-section has been defined.
Move the cursor to a red marker and right click
Choose Edit from the pop-up menu
Choose Cross Section at: , and
click OK.
This will take you to the Cross-section Editor. Look at a couple of

cross-sections.
Alternatively, you can open the cross-section document directly from
the Simulation Editor (.sim11).
Note:
Cross-sections are identified by a Branch ID and a TOPO ID
Cross-section data are relative to the specified Datum value.
Cross-section data are editable in the table and graphical by

dragging the points in the plot.
The marker values in the table define the extent of the crosssection to be used in the simulation.
Close the Cross-Section Editor and return to the Network editor,

without saving any changes.
123

6.3.8 View the Boundary Conditions
The boundary nodes are marked on the network with blue markers
at 90 degrees to the cross-section markers.
Right click on the boundary marker
Chose Edit in the pop-up menu, and select the Boundary item
This will open the boundary editor with the current boundary point
highlighted.
Now take a quick look at the boundary specifications in MIKE 11.
All the upstream ends are defined as Inflow boundaries with zero
inflow. The downstream mouth of the river is defined as a water level
boundary.
Close the Boundary Editor and return to the Network Editor,

without saving any changes.
Close the Network Editor, without saving any changes.
Close the Simulation Editor.
124

Step 4 Add the Overland Flow Module
6.4

Check Overland Flow (OL) On
Your model now has an Overland Flow branch in the data tree.
6.4.2 Define Infiltration Fraction

Normally, the amount of infiltration is determined by the infiltration
rate of the top layer of the soil. When you add the overland flow
module without specifying the unsaturated zone module, then a new
parameter is added under Precipitation.
The Infiltration Fraction is used to specify the fraction of the rainfall
that is infiltrated versus the fraction that is available for ponding.
The default value is 1.0, which means that all of the rainfall is
infiltrated and there will be no ponding.
This will not be the case when you add the unsaturated zone later in
this exercise.
125

6.4.3 Specify the Overland flow parameters
In the Overland Flow dialog (in the MIKE SHE GUI), specify
Mannings M equal to zero.
Detention storage equal to zero, and
Initial water depth equal to zero.
The Karup catchment is quite sandy, and in this simulation there are
no serious storm events. Thus, in reality, overland flow is
insignificant for this simulation.
However, the overland flow module is required whenever the
channel flow component is included. You can run overland flow
without the channel flow component but not the opposite. If you do
not want to include overland flow you can essentially disable
overland flow by specifying a Mannings M = 0.
If you left in the overland flow component, the overland flow
simulation would require that the model run with small time-steps (560 minutes) which would slow down the computation significantly.
6.5
Step 5 Run the Model
126

6.5.1 Define Time-Steps
Define time-step control parameters a shown in the dialog to the

right.
MIKE SHE uses different time-steps for the different hydrologic

processes. Normally, the Overland flow time-step is the smallest and
the Groundwater time-step the largest. The MIKE 11 time step is
controlled in MIKE11.
The overland flow time-step is large in this simulation because you
have disabled the overland flow simulation by setting the Mannings
M to zero. To simulate overland flow you would typically need a
time-step on the order of 5-60 minutes, and possibly less than this if
you are using the explicit solver and overbank spilling to simulate
fooding.
The Max. precipitation depth per time-step is used to reduce the
time-step during heavy rainfall events.
The Max. infiltration amount per timestep is used to reduce the time
step when water is ponded on the surface, for example, during a
flood.
These two parameters are only important if the unsaturated zone
model is included. You should set these to high values, so that the
simulation time step is not reduced.
127

6.5.2 Overland flow parameters
Make sure that you are using
the SOR solver, and
the Manning equation
for calculating overland flow.

If you want to calculate flooding, then the explicit solver is
recommended. However, the time step constraints on the explicit
solver are much more restrictive.
Click on the
icon to start the pre-processor, which will start
the MIKE Zero Launch utility.
Click OK
128
6.5.4 View the River Link setup

In the Processed Data Tab the most recent pre-processed file is
automatically loaded
Click on the Load button read in the Processed Data
Go to the River Links Item in the data tree to view the pre-processed
river links:
View the location of the river links in the computational mesh.
The MIKE 11 network is interpolated to the cell boundaries of the

model grid. The interpolated river locations are called river links.

Click on the
129

Step 6 View the Results
6.6
You will now view some of the outputs of this exercise using the Result Viewer. 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 will have a lot errors that are difficult to track
down.
6.6.1 View Groundwater Level Results
In the Result Viewer dialog:
6.7
Look at whatever outputs you may find interesting, such as the SZ Exchange with river and the SZ drainage flow from point?
Is the model predicting any significant drain flow? Why or why not? What is happening to the drain water in this exercise?
Can you view river results?
Do the results make sense so far?

Step 7 Input Distributed Rainfall
You will now make the simulation a bit more realistic by adding distributed rainfall data.
130

6.7.1 Define rainfall stations
The rainfall will be spatially distributed using a dfs2-grid file with
integer codes that are linked to a specified rainfall time-series.
In the Precipitation Rate dialog:
Choose Spatial Distribution = Station based
Choose Data Type = Grid Codes (.dfs2)
Press
and pick the file:
.\Model Inputs\Maps\Precipitation.dfs2
You are now using a dfs2-grid code file to distribute rainfall timeseries data. Each code (area) now needs to be associated with a
rainfall time-series. The grid file contains 9 different codes (1-9). The
value of the code is not important and may be anything. Each area
(defined by a code) just needs to be associated with a rainfall timeseries.
Station areas may also be assigned using .shp file polygons.
131

6.7.2 Associate the station areas with Time-series data
The navigation tree now allocates space for 9 rainfall stations.
Initially the station name is derived from the Grid code value. You
may change the station name if you want.
You now need to link a rainfall time-series to each station (code).
Set the Temporal Distribution to Time varying (.dfs0).
Click the browse button and select the precipitation file

Precipitation.dfs0
At the bottom of the file selection dialog, under Items, select the
appropriate precipitation station from the combo box list.
Press Ok.
Repeat this for each grid code (station).
6.8
Step 8 Modify the Subsurface Drains
In the SZ1 exercise, subsurface drains were included 0.5 meter below ground surface throughout the model domain. Thus, whenever the water
table goes above the drainage level, water will drain from the saturated zone. In the SZ1 exercise, this drainage was exported from the model
domain. You will now change the drainage setup so that drainage water is routed to the river instead.
132

6.8.1 Modify the Subsurface Drain Reference System
Choose Drainage routed downhill based on adjacent drain

levels
Leave the Level and Time Constant the same as in the SZ1
exercise.
Drainage routing can be a very complex process. Simply removing

the water from the model is the simplest drainage option. However,
in most situations, drainage actually discharges to the river system.
The simplest routing method for the drainage is to route it downhill
based on the drain levels. The drainage will enter the river whenever
it intersects a river link. However, this can lead to ponding in local
depressions in flat terrains.
More complicated is the second option, where the drainage is routed
downhill but only from certain cells.
The Distributed drainage options allow you to route drainage to
specific MIKE 11 nodes or MOUSE manholes.
6.9
Step 9 Add Landuse
133

6.9.1 Add the Evapotranspiration and Unsaturated flow
modules
Check Unsaturated Flow (UZ) on (Richards Equation)
Check Evapotranspiration (ET) on
The Land Use, Evapotranspiration, and Unsaturated Flow sections

are added to the data tree.
134

6.9.2 Define Vegetation Map (Field map)
In the Vegetation dialog:
Use Station based Spatial distribution
Specify Grid Codes (dfs2) as the Data Type
Use the browse button to select the file

.\Model Inputs\MAPS\Landuse.dfs2
The map now displays your vegetation distribution. The map (dfs2
file) contains 4 different integer codes that define 4 different areas.
You now need to define the vegetation types and growth function is
are associated with the 4 different areas.
135

6.9.3 Define Vegetation Types for each Vegetation Area
Each of the 4 different vegetation areas in the vegetation map
appears as a sub-item in the data tree.
Select the Grid code = 1 item
Change the ID to Grass Crops
Set the Temporal Distribution to Vegetation property file
Use the new items icon,

Development table.
For each line in the Crop Development table
, to add 13 lines in the Crop
Use the browse button to select the vegetation property file

(database file):
MIKE_SHE_vege.ETV
From the pull-down Veg type combo box pick Grass1
Set the Start date to 1. Jan. 1969
Repeat the above steps for each line in the Crop Development
table, with a start date of 1970, 1971, etc.
For the remaining three vegetation types, set the Temporal

distribution to Constant
Use the following values for the remaining items:
Grid code = 2: Forest, LAI = 6, Root Depth = 800
Grid code = 3, Shrubs, LAI = 2, Root Depth = 440
Grid code = 4, Wetlands, LAI = 4, Root Depth = 500
136

6.10 Step 10 Add Reference Evapotranspiration
MIKE SHE calculates actual evapotranspiration based on the evapotranspiration rate, the vegetation properties, and the soil moisture.
6.10.1 Define Evapotranspiration Data
In the Reference Evapotranspiration dialog:
Use Uniform spatial distribution
Use Time-varying (dfs0) data type

.\Model Inputs\TIME\PotentialEvap.dfs0
Reference evapotranspiration can be specified in the same manner

as precipitation as constant or time-varying values and as uniform or
spatially distributed values.
As youre using Uniform distribution type, this evapotranspiration
rate will be used throughout the model domain.
6.11 Step 11 Build the Unsaturated Zone Model

The unsaturated zone model calculates recharge to the groundwater model and is closely linked to the actual evapotranspiration, as the roots
remove water from the unsaturated zone. Soil physical properties are stored in a soil-database. The link between soil-type distribution maps and
soils in the soil-database are established similarly to the link between vegetation-distribution maps and vegetation types.
137

6.11.1 Calculation Column Classification
In the Unsaturated Flow dialog:
Choose Calculated in all grid points for the column classification

type
MIKE SHE allows you to lump calculation profiles together rather

than calculating unsaturated zone flows in each single profile. This is
done to speed up the computational time. However, the lumped
(Automatic) classification is not always suitable. For instance it is not
suitable if overland flow is an important feature or if there are very
dynamic and spatially varying flooding patterns within the model
domain.
Demo Note: the demo version is restricted to a maximum of 155 UZ
computational cells. So, if you are running this exercise without a
valid license, then you should select the Automatic classification
type.
138

6.11.2 Define the Soil Profile Distribution Map
In the Soil Profile Definitions dialog:
Use Distributed for the Spatial Distribution
Use Grid codes (dfs2) distribution data type
Use the browse button to select the dfs2 grid file

.\Model Inputs\MAPS\soil.dfs2
The soil map contains three different code values, which now need
to be associated with three soil profiles.
6.11.3 Define Soil Profiles (horizons)

Each of the 3 different soil areas in the soils map appears as a subitem in the data tree.
Select the Grid code = 1 item
Change the ID to Fine Sand
Define one soil horizon for the profile by specifying Depth = 37
Use the browse button to select the UZ soil-database file

.\Model Inputs\Karup.uzs
Define Vertical Discertization as shown in the dialog to the right.
Repeat the above for the other two soil types using
139
For Grid Code = 2 use Coarse Sand
For Grid Code = 3 use Coarse Sand in the for the upper 2
meters and use Fine Sand in the remaining 35 meters
6.11.4 DEMO MODE only: Define Groundwater Table for UZ

Classification
Demo Note: If you are using the Demo mode, then you must use the
Automatic classification method, which requires you to specify a
water table
The depth to the groundwater table is one of the criteria that are
used when the automatic (lumped) unsaturated zone classification is
used.
In the Groundwater depths dialog:
Use initial water table for classification
Define 6 depth classes 1,2,3,4,5 and 10 meters.
6.12 Step 12 Run the Simulation

6.12.1 Add Field Data to the observations
In the SZ1 exercise, you added 4 observation points, but did not
include the observation data.
To add the observation data, you need to
Choose Data type head elevation in saturated zone
Check on the Incl. Obs. Data checkbox
For each observation point,

.\Model Inputs\GIS Data\HeadObservations.dfs0
In the DFS File Selector dialog, you need to select the

appropriate Item from the combo box.
140

Click on the
6.13 Step 13 View the Results

You will now view some of the outputs of this exercise using the Result Viewer. 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 will have a lot errors that are difficult to track
down.
6.13.1 View Groundwater Level Results
In the Result Viewer dialog:
Look at whatever outputs you may find interesting?
View the river results?
Do the results make sense ?
End of Exercise Integrated 1
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MIKE SHE - Basic Exercises

GETTING STARTED EXERCISE .................................................................................. 6

STEP 1 CREATE A NEW MIKE SHE SETUP............................................................... 12

UNSATURATED ZONE (SINGLE COLUMN) EXERCISE ...................................... 62

STEP 1 START MIKE SHE......................................................................................... 6

SATURATED ZONE (GROUNDWATER) EXERCISE ............................................. 12

HYDROLOGIC PROCESSES SIMULATED BY MIKE SHE ................................................. 3

STEP 1 CREATE A NEW MIKE SHE SETUP............................................................... 62

CHANNEL FLOW EXERCISE (MIKE 11) ................................................................. 85

STEP 1 CREATE A NEW MIKE 11 SETUP .................................................................. 85

MIKE SHE - Basic Exercises

STEP 7 VIEW THE RESULTS .................................................................................... 105

INTEGRATED EXERCISE ......................................................................................... 115

STEP 1 OPEN A MIKE SHE SETUP......................................................................... 115

MIKE SHE - Basic Exercises

Hydrologic processes simulated by MIKE SHE

Applications around the world

MIKE SHE - Basic Exercises

River basin management and planning

MIKE SHEs user interface can be characterized by the need to

A dynamic navigation tree that depends on simple and logical choices

Develop a flexible, unstructured GUI suitable for different modelling approaches,

MIKE SHE - Basic Exercises

Along the top - the Tool bar and drop-down Menus

On the left - the dynamic Data tree and tab control

On the right - the context sensitive Dialog area

MIKE SHE Basic Exercises - Getting Started Exercise

2 Getting Started Exercise

Start MIKE SHE or MIKE 11

Create a MIKE Zero project

Create MIKE SHE and MIKE 11 model documents

Step 1 Start MIKE SHE

from the Program Files menu select MIKE Zero:

Step 2 The MIKE Zero project

MIKE SHE Basic Exercises - Getting Started Exercise

Click on the Install Examples... button and select to install all

MIKE SHE Basic Exercises - Getting Started Exercise

Click on the Open Project button

In the file browser, find the MIKE Examples.mzp file in the

Select this file and click Open

MIKE SHE Basic Exercises - Getting Started Exercise

2.2.3 Creating new documents

When the New File dialogue appears,

select MIKE SHE on the left hand side,

select Flow Model (.she) on the right hand side,

MIKE SHE Basic Exercises - Getting Started Exercise

click on the Model directory in the Project Explorer (this

Use the File\Save menu item, or the Save icon.

In the Save dialogue,

Add a Note, if you want

2.2.5 Getting Help

MIKE SHE Basic Exercises - Getting Started Exercise

End of Getting Started Exercise

MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise

3 Saturated Zone (Groundwater) Exercise

Use GIS polygon data to distribute model parameters spatially

Understand the concepts of Geological Model and Computational Layers

Master the input specifications required for a simple Geological Model

Master the input specifications required for Computational Layers

Understand the concepts of Setup Data and Processed Data

Step 1 Create a new MIKE SHE setup

MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise

Browse to the folder:

Then open the existing project: MIKE SHE Examples.mzp