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MIKE SHE Basic Exercises
MIKE SHE Basic Exercises
MIKE SHE
Basic Exercises
1 INTRODUCTION ..................................................................................................... 3
1.1 HYDROLOGIC PROCESSES SIMULATED BY MIKE SHE .......................................... 3
1.2 APPLICATIONS AROUND THE WORLD ................................................................... 3
1.3 THE MIKE SHE USER INTERFACE ..................................................................... 4
2 GETTING STARTED EXERCISE ........................................................................... 6
2.1 STEP 1 – START MIKE SHE .............................................................................. 6
2.2 STEP 2 – THE MIKE ZERO PROJECT .................................................................. 8
3 SATURATED ZONE (GROUNDWATER) EXERCISE ......................................... 14
3.1 STEP 1 – CREATE A NEW MIKE SHE SETUP ..................................................... 15
3.2 STEP 2 – SETUP THE MAP OVERLAYS ................................................................ 18
3.3 STEP 3 – SET UP THE SIMULATION .................................................................... 21
3.4 STEP 4 – SET UP THE MODEL DOMAIN .............................................................. 24
3.5 STEP 5 – SET UP THE TOPOGRAPHY ................................................................. 29
3.6 STEP 6 – DEFINE GROUNDWATER RECHARGE .................................................. 32
3.7 STEP 7 – GEOLOGICAL MODEL ......................................................................... 34
3.8 STEP 8 – DEFINE ATTRIBUTES OF COMPUTATIONAL LAYERS .............................. 39
3.9 STEP 9 – PRE-PROCESS THE DATA ................................................................... 45
3.10 STEP 10 – REDEFINE THE HORIZONTAL GRID RESOLUTION ................................. 47
3.11 STEP 11 – SPECIFYING OUTPUTS AND CALIBRATION TARGETS ............................ 49
3.12 STEP 12 – RUN THE SIMULATION ...................................................................... 52
3.13 STEP 13 – VIEW THE RESULTS ......................................................................... 53
3.14 STEP 14 – ADD GEOLOGICAL LENSES .............................................................. 56
3.15 STEP 15 – ADVANCED USE OF THE RESULTS VIEWER ........................................ 61
3.16 STEP 16 CREATE A WATER BALANCE ................................................................ 69
4 UNSATURATED ZONE (SINGLE COLUMN) EXERCISE ................................... 76
4.1 STEP 1 – CREATE A NEW MIKE SHE SETUP ..................................................... 76
4.2 STEP 2 – SET UP THE SIMULATION .................................................................... 76
4.3 STEP 3 – SET UP THE MODEL DOMAIN AND TOPOGRAPHY ................................. 79
4.4 STEP 4 – DEFINE CLIMATE AND VEGETATION .................................................... 81
4.5 STEP 5 – BUILD THE UNSATURATED ZONE MODEL .............................................. 83
4.6 STEP 6 – PRE-PROCESS THE DATA ................................................................... 87
4.7 STEP 7 – RUN THE SIMULATION ........................................................................ 89
4.8 STEP 8 – VIEW THE RESULTS ........................................................................... 93
4.9 STEP 9 – EXPLORE THE SIMULATION SENSITIVITY .............................................. 97
5 CHANNEL FLOW EXERCISE (MIKE 11) ............................................................ 99
5.1 STEP 1 – CREATE A NEW MIKE 11 SETUP ........................................................ 99
5.2 STEP 2 – CREATE A RIVER NETWORK .............................................................. 104
5.3 STEP 3 – ADD CROSS-SECTIONS .................................................................... 112
5.4 STEP 4 – ADD BOUNDARY CONDITIONS .......................................................... 115
5.5 STEP 5 – DEFINE THE HYDRODYNAMIC PARAMETERS ....................................... 118
5.6 STEP 6 – RUN THE SIMULATION ...................................................................... 121
5.7 STEP 7 – VIEW THE RESULTS ......................................................................... 122
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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. The exercises are not intended to
illustrate best practices in integrated 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.
Although the entire 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.
As the exercises are performed it is recommended that the reader initially spends
some time familiarizing themselves and understanding the figures on each page
before reading the text on that page as this greatly aids in the understanding of the
exercise instructions.
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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 modeller’s 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 net-
works 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
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resources and environmental and ecological problems related to surface water and
groundwater, such as:
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.)
1.3 The MIKE SHE User Interface
MIKE SHE’s 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 A dynamic navigation tree that depends on simple and logical choices
o A conceptual model approach that is translated at run-time into the
mathematical model
o Object oriented “thinking” (geo-objects with attached properties)
o Full, context-sensitive, on-line help
o Customized input/output units to support local needs
Strengthen the calibration and result analysis processes, which is why it includes
o Default HTML outputs (calibration hydrographs, goodness of fit, water
balances, etc.)
o User-defined HTML outputs
o A Result Viewer that integrates 1D, 2D and 3D data for viewing and
animation
o Water balance, auto-calibration and parameter estimation tools.
Develop a flexible, unstructured GUI suitable for different modelling approaches,
which is why it includes
o Flexible data format (gridded data, .shp files, etc.) that is easy to
update for new data formats
o Flexible time series module for manipulating time-varying data
o 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.
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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.
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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.
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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.
Note: The project opens with all the directories expanded out. So,
you might like to close up some of the directories in the Project
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Note:
The project explorer is very useful for organizing files and managing
your modeling projects. But, it does have its limitations.
Some MIKE SHE projects can become very large with thousands of
files and directories, making the Project explorer difficult to use.
The MIKE Zero interface does not force you to use the Project
Explorer. However, switching back and forth between using and not
using the Project Explorer is difficult because the default Results
directories are different.
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If you are starting these exercises from the present step please install the MIKE SHE examples to Documents/MIKE Zero Projects/MIKE_SHE to
ensure consistency and write access. If you have just finished the Getting Started exercise they are located in the Documents/MIKE Zero
Projects/MIKE_SHE folder you created in Step 2.2.3 above. Use this location for these exercises.
If you have just finished the Getting Started exercise skip this step
3.1.1 Open the Examples Project
After you have started MIKE SHE
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.
Note: The project opens with all the directories expanded out. So,
you might like to close up some of the directories in the Project
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original .shp 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.
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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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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.
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Note that the velocity vectors will not appear in the initial time step, but
3.13.3 View the Results in the Results Viewer
rather appear first in the second time step.
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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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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.)
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Note that the time series time steps are equal to the storing time
steps. The Detailed time series output option allows you to save the
output at every time step.
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Extraction icon,
Check to make sure that the Extraction ran successfully, by
looking for “Normal termination” in the message window
MIKE SHE saves the results in many different files. The results are
grouped by process (e.g. OL, UZ, SZ) and by output type (i.e. 2D or
3D). The extraction process reads all of the various output files and
builds a set of water balance files. These files can be efficiently read
by the water balance utility.
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The water balances are defined in a water balance .config file, which
is located in the installation directory.
If you want to create customized water balances, then you can edit
the configuration file. This process is described in the User Guide.
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icon,
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In the graphic to the right, we can see that there was 31 mm of net
precipitation during the simulation. That is the Total precipitation
times the Net rainfall fraction.
Note that the water balance items are all normalized to units of mm,
which allows for easy comparison between the different
components. If you want to convert depths of mm to volumes, you
need to multiply the depth by the internal model area. That is, the
total model area minus the area of the outer boundary cells. If you
load the pre-processed data into the Grid Editor, select the Model
and Domain item. Then, you can use the statistics function in the
Grid Editor to find out the number of internal versus external cells.
Note that the sum of the water balance terms in the graphic do not
add to zero. This is because the signs have been removed. In the
water balance calculation, Inflows are negative and Outflows and
Storage increases are positive. Thus, in the graphic to the right, the
water balance is:
Storage change [+14] + Drain flow [+17] – Infiltration [-31] = 0
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icon,
If you chose the Table format for the Output file, then the output will
be in a tab-delimited ASCII file that you can open in Excel.
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The water balance time series file includes all of the available water
balance items. In the current water balance almost all of the items
are zero.
The cumulative water balance sums the items over all of the stored
time steps. Thus, the total precipitation to the right is 31.104 mm,
which is the same as the 31mm in the graphic total water balance
above.
Note, though, that the sign of the precipitation is negative in the time
series file. Generally, all the items in one time period will sum to
zero. There are exceptions, though, that are described in detail in
the Water Balance documentation.
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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.
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Click on the Add Item, , to add one soil layer to the profile
Change the Depth of the layer to 20 m
Use the browse button to select the soil properties file
.\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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Click the Add Item icon, , to add three different grid spacing
layers
Change the Cell height and No of cells to the following
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 saturation can occur in response to precipitation.
Typically, the grid becomes increasingly coarse with depth, while
following the soil horizon boundaries.
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You don’t 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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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 affect 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.
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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
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Note: The Tabular View can also be opened from the map view by using the [Crtl-t]
Haderu Haug
keyboard shortcut p e
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Chainage is the linear distance along the river. Since the cross-section locations are based 0 12100
on chainage locations, you must define the chainage of the upstream and downstream ends
of the river branch. 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 0
the river) is the starting point. In this case, the Flow Direction in the Tabular View must be set
to Negative.
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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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Use the Browse button, , on the Boundary data line to find your .bnd11 file
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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.
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
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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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Use the Browse button, , on the HD Parameters line to find your file
Select the Edit button to edit the HD input parameters
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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.
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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 don’t 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 don’t 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.
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Cross-section plot:
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Standard animation tool buttons are available for Play , Stop , and
Pause for animating the water level or discharge time series.
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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 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 flow to 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.
Nevertheless, 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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Then follow the same steps from the Precipitation to add a new item to the time series.
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. ET)
The Type from Undefined to Evaporation
The Unit to millimeter (should be the default)
The TS Type from Instantaneous to Step Accumulated
Click OK to close the dialog
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
i2=i1
Click OK to perform the calculation and close the dialog
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 (in a 24 hour period).
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6 Integrated Exercise
Overall Objective
Extend the SZ1 model to make it into a fully integrated groundwater-surface water model
Important learning objectives
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.
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Demo Note: If you are using the demo version of MIKE SHE do not
extend the simulation period.
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TOPO ID
Chainage Values
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Note This will not be the case when you add the unsaturated zone
later in this exercise.
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