MIKE SHE Basic Exercises

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1 MIKE SHE - Basic Exercises 1 MIKE SHE Basic Exercises 1 INTRODUCTION HYDROLOGIC PROCESSES SIMULATED BY MIKE SHE APPLICATIONS AROUND THE WORLD THE MIKE SHE USER INTERFACE GETTING STARTED EXERCISE STEP 1 START MIKE SHE STEP 2 THE MIKE ZERO PROJECT SATURATED ZONE (GROUNDWATER) EXERCISE STEP 1 CREATE A NEW MIKE SHE SETUP STEP 2 SETUP THE MAP OVERLAYS STEP 3 SET UP THE SIMULATION STEP 4 SET UP THE MODEL DOMAIN STEP 5 SET UP THE TOPOGRAPHY STEP 6 DEFINE GROUNDWATER RECHARGE STEP 7 GEOLOGICAL MODEL STEP 8 DEFINE ATTRIBUTES OF COMPUTATIONAL LAYERS STEP 9 PRE-PROCESS THE DATA STEP 10 REDEFINE THE HORIZONTAL GRID RESOLUTION STEP 11 SPECIFYING OUTPUTS AND CALIBRATION TARGETS STEP 12 RUN THE SIMULATION STEP 13 VIEW THE RESULTS STEP 14 ADD GEOLOGICAL LENSES STEP 15 ADVANCED USE OF THE RESULTS VIEWER UNSATURATED ZONE (SINGLE COLUMN) EXERCISE STEP 1 CREATE A NEW MIKE SHE SETUP STEP 2 SET UP THE SIMULATION STEP 3 SET UP THE MODEL DOMAIN AND TOPOGRAPHY STEP 4 DEFINE CLIMATE AND VEGETATION STEP 5 BUILD THE UNSATURATED ZONE MODEL STEP 6 PRE-PROCESS THE DATA STEP 7 RUN THE SIMULATION STEP 8 VIEW THE RESULTS STEP 9 EXPLORE THE SIMULATION SENSITIVITY CHANNEL FLOW EXERCISE (MIKE 11) STEP 1 CREATE A NEW MIKE 11 SETUP STEP 2 CREATE A RIVER NETWORK STEP 3 ADD CROSS-SECTIONS STEP 4 ADD BOUNDARY CONDITIONS STEP 5 DEFINE THE HYDRODYNAMIC PARAMETERS STEP 6 RUN THE SIMULATION

2 MIKE SHE - Basic Exercises STEP 7 VIEW THE RESULTS STEP 8 ADD A RAINFALL-RUNOFF COMPONENT INTEGRATED EXERCISE STEP 1 OPEN A MIKE SHE SETUP STEP 2 ADD THE RIVER MODULE STEP 3 REVIEW THE MIKE 11 SETUP STEP 4 ADD THE OVERLAND FLOW MODULE STEP 5 RUN THE MODEL STEP 6 VIEW THE RESULTS STEP 7 INPUT DISTRIBUTED RAINFALL STEP 8 MODIFY THE SUBSURFACE DRAINS STEP 9 ADD LANDUSE STEP 10 ADD REFERENCE EVAPOTRANSPIRATION STEP 11 BUILD THE UNSATURATED ZONE MODEL STEP 12 RUN THE SIMULATION STEP 13 VIEW THE RESULTS 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.

3 MIKE SHE - Basic Exercises 3 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 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 river catchments, such as the 80,000 km 2 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:

4 MIKE SHE - Basic Exercises 4 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 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 Strengthen the calibration and result analysis processes, which is why it includes o o o o 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 o 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.

5 MIKE SHE - Basic Exercises 5 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.

6 MIKE SHE Basic Exercises - Getting Started Exercise 6 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 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.

7 MIKE SHE Basic Exercises - Getting Started Exercise 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.

8 MIKE SHE Basic Exercises - Getting Started Exercise 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.

9 MIKE SHE Basic Exercises - Getting Started Exercise 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.

10 MIKE SHE Basic Exercises - Getting Started Exercise 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 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.

11 MIKE SHE Basic Exercises - Getting Started Exercise 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

12 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 12 3 Saturated Zone (Groundwater) Exercise Overall Objective Build a simple groundwater model Important learning objectives 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.

13 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Open the Examples Project After you have started MIKE SHE Select the button below the project list. Browse to the folder: C:\Program Files\DHI\MIKEZero\Examples\MIKE_SHE Then open the existing project: MIKE SHE Examples.mzp 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 Create a new MIKE SHE document As described in the Getting Started exercise, create a MIKE SHE (.she) document file in the Model directory, and save the document, specifying a name such as SZ1.SHE 3.2 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.

14 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

15 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 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 = Maximum X = Maximum Y = Set the Display style as Blend Colors, which will blend the map colors with any other displayed colors. This will prevent the

16 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 16 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.

17 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

18 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Set simulation title In the Simulation Title dialog Write any title and description you want 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 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.

19 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 19 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. 3.4 Step 4 Set up the Model Domain 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 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-

20 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 20 processor assigns all of the model parameters based on the dfs2- grid 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.

21 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 icon and then on the points. To add points, click on the icon To delete points, click on the 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 Close the.shp editor - without saving your changes Select the File/Close menu. Do not save your changes to the polygon. icon.

22 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Add the.shp polygon to the Overlays In the Foreground dialog: Click on the Add Item icon, 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

23 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

24 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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

25 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 25 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.

26 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 button to open the file browser Scroll through the list and pick the file Precipitation.dfs0 that has the green check mark beside it Click OK 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).

27 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

28 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

29 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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, clicking on one of the Move Item icons,, deleted by, or moved up and down by 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.

30 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

31 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 = [m/s] Vertical Hydraulic Conductivity = 9.3e-5 [m/s] Specific Yield = 0.2 [-] Specific Storage = [1/m] 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.

32 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 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

33 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 33 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 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

34 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

35 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 Important Note, plus the 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)

36 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 36 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) 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

37 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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

38 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 38 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 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.

39 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 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

40 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 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 Run the Preprocessor Click on the icon to start the pre-processor. Verify in the pre-processor tab that all of the input data has been converted to a 500m grid Change the cell size to 400 meter cells In the Model Domain and Grid dialog Change the number of grid cells in the X and Y directions NX = 100 NY = 100 Change the Cell Size to 400 m 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

41 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 41 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. 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 Change the cell size back to 500 meter cells In the Model Domain and Grid dialog Change the number of grid cells in the X and Y directions NX = 65 NY = 70 Change the Cell Size to 500 m 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.

42 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

43 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Define Detailed Time Series Output items Use the Add item icon,, to add 4 items to the list For each item, 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 Obs Obs Obs 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.

44 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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. Gridded output is stored as dfs2 (2D grid time-series files) or dfs3 (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 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.

45 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

46 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Simulation Control In the SZ Computational Control Parameter dialog: Choose Preconditioned Conjugate Gradient, Transient Specify Maximum Head change per iteration = [m] The default values for the simulation convergence parameters are normally suitable and in most cases need not be changed Run the simulation Click on the icon to re-run the pre-processor and then on the icon to run the simulation Step 13 View the Results Upon successful execution of the model you re 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

47 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

48 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 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.

49 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

50 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Add the geological lense In the Geological Lenses dialog Click on the Add Item icon,, to add a lens. Change the name of the lens to Clay

51 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.

52 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Define the top of the lens In the Upper Level dialog Select Grid file (.dfs2) files for Spatial Distribution Use the Browse button to select the file.\model Inputs\Maps\lense3U.dfs2

53 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Define the bottom of the lens In the Lower Level dialog. Select Grid file (.dfs2) files for Spatial Distribution Use the Browse button to select the file.\model Inputs\Maps\lense3L.dfs2

54 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 : (1/m) 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 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.

55 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 z- directions View the Results in the Results Viewer Click on the View Results,, button for the item head elevation in saturated zone.

56 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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.) 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.

57 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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

58 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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

59 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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, Then, Double click on the item len03_grid_meter.shp to turn off the display of the clay lenses. The red check ( be removed. 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. ) will

60 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise 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 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).

61 MIKE SHE Basic Exercises - Saturated Zone (Groundwater) Exercise Animate a selected portion of simulated area. Press the button to zoom into the area of interest. 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 The animation file can be played in Windows Media Player and most other media programs. End of Saturated Zone (Groundwater) Exercise

62 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 62 4 Unsaturated Zone (Single Column) Exercise Overall Objective Build a dynamic, single-column unsaturated zone model Important learning objectives 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 4.1 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.

63 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Select simulation modules In the Simulation Specification dialog Check Saturated Zone Off, Check Unsaturated Zone On, and Choose Richards Equation as the Numeric Engine Check Evapotranspiration On Set simulation title In the Simulation Title dialog Write any title and description you want

64 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Specify simulation period In the Simulation Period dialog: Specify the Start date and End date 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

65 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 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 Map Projection Type = NON-UTM 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.

66 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Define Surface Topography In the Topography Dialog, you can leave the values at their default values uniform and 10 m 4.4 Step 4 Define Climate and Vegetation 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 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

67 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 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 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)

68 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 68 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. 4.5 Step 5 Build the unsaturated zone model In this step, you will specify geometry of the soil profile and hydraulic properties for the layers 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.

69 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 69 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 Define the soil profile distribution In the Soil Profile Definitions dialog. Spatial Distribution : Select Uniform (only one column)

70 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Define the global soil profile In the Global data tree item, under Soil Profile, Click on the Add Item,, to add one soil layer to the profile Change the Depth of the layer to 10 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.

71 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Define the vertical grid discretization In the Global data tree item, under Vertical Discretization 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 saturated can occur in response to precipitation. Typically, the grid becomes increasingly coarse with depth, while following the soil horizon boundaries 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

72 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 72 SHE. 4.6 Step 6 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 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 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.

73 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise View the preprocessed data After successfully running the Preprocessor, Click on the Processed Data Tab located at the bottom of the Navigation Tree.

74 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 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.

75 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Specify the Time step parameters In the Time step control dialog: Specify Initial time step = 2 hrs Specify Max. allowed UZ time step = 2 hrs Leave the rest of the parameters at their default values

76 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Simulation Control The default values for the simulation control parameters are normally suitable and in most cases need not to be changed Storing of Results Click on Storing of Water balance data Set the Storing interval for grid series output (Prec, ET, UZ) to 2 hours. 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. 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.

77 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 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 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 Gridded output is stored as dfs2 (2D grid time-series files) or dfs3 (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.

78 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Run the simulation Click on the icon to re-run the pre-processor and then on the icon to run the simulation. 4.8 Step 8 View the Results Upon successful execution of the model, you re 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 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.

79 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 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 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.

80 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 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.

81 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 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.

82 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 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.

83 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise Step 9 Explore the simulation sensitivity 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? 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

84 MIKE SHE Basic Exercises - Unsaturated Zone (Single Column) Exercise 84 End of Unsaturated Zone (Single Column) Exercise

85 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 85 5 CHANNEL FLOW EXERCISE (MIKE 11) Overall Objective Build a 1D hydraulic model Important learning objectives 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. 5.1 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

86 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 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.

87 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 End date: 27. Jan Under Initial Conditions, specify the hydrodynamic (HD) initial condition. Select the Parameter File option. 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.

88 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 don t use the browse button to specify a results path, then the results will be automatically placed in the current directory 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.

89 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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? 5.2 Step 2 Create a river network Create a MIKE 11 network document As described in Section 2, create a MIKE 11 network (.nwk11) document 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: X min = 0 and Y min = X max = and Y max = Specify the map projection as NON-UTM The map projection for all MIKE SHE files must be NON-UTM 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.

90 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) Network Import Image File Select Layers -> Add/Remove top menu item In the dialog that appears, Use the New Item icon,, to add a line to the table Use the browse button to select the image file.\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 Set the image coordinates Select Layers -> Properties top menu item In the dialog that appears, Set the same coordinates that you used in the SZ exercise Minimum X = 822 Minimum Y = Maximum X = Maximum Y = 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.

91 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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.

92 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) Network Define Branches To define a branch, Downstream end = outflow 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 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

93 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 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. Downstream end = outflow Karup River Haderup River Hauge Creek

94 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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: Karup River: 0 to Haderup River: 0 to Hauge Creek: 0 to 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. 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

95 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 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 Review questions for Step 2 Try to answer the following questions before proceeding with the exercise: 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?

96 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) Step 3 Add cross-sections 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

97 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) Cross-section Open the cross-section file for editing To open the cross-section file Press the Edit button,. Note: Then examine the contents of the cross-section document. 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.

98 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 Review questions for Step 3 Try to answer the following questions before proceeding with the exercise: What is the suffix of the cross-section document? Which two ID s 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? 5.4 Step 4 Add Boundary Conditions 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,

99 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 99.\Model Inputs\MIKE 11\River1.bnd11 The boundary document contains the boundary locations and boundary types for both external and internal boundary conditions 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 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

100 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 100 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 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.

101 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) Review questions for Step 4 Try to answer the following questions before proceeding with the exercise: 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? 5.5 Step 5 Define the hydrodynamic parameters 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.

102 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 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

103 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 Review questions for Step 5 Try to answer the following questions before proceeding with the exercise: What is the suffix of the hydrodynamic document? There is a lot of useful functionality in the HD document. For example 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 5.6 Step 6 Run the simulation

104 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 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 Review questions for Step 6 Try to answer the following questions before proceeding with the exercise: How are you able to see if all the input data has been entered and is valid prior to starting the simulation?

105 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 105 How would you know if the time step affecting the numerical stability of the model? 5.7 Step 7 View the results Results Open MIKE VIEW MIKE 11 results are viewed using MIKE VIEW. All Programs -> DHI Software -> MIKE 11 ->MIKE VIEW 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 Don t 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

106 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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: 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.

107 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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, Stop, and Pause for animating the water level or discharge time series Review questions for Step 7 Try to answer the following questions before proceeding with the exercise: 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? 5.8 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 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) Add the Rainfall-Runoff component Return to the.sim11 document On the Models tab, click on the Rainfall- Runoff option Then create a new.rr11 document using the standard procedure On the Input tab, add the.rr11 file using the browse button 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 In this step, you are creating a catchment. The catchment has an area (440 km 2 ), but not a location. When it rains, 10mm of rain in one day will generate 4.4 million m 3 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

109 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 109 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.

110 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) Add a time series item to the Precipitation File The precipitation time series file must be modified for the NAM model. or In the Project Explorer double click on the Precipitation.dfs0 file located in the Time directory. 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.

111 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 111 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 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 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

112 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 112 or directory. 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 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

113 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 2 Hauge Creek 68 km 2 Haderup River 292 km 2 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 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.

114 MIKE SHE Basic Exercises - CHANNEL FLOW EXERCISE (MIKE 11) 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 Review questions for Step 8 Try to answer the following questions before proceeding with the exercise: 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)

115 MIKE SHE Basic Exercises - Integrated Exercise 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.

116 MIKE SHE Basic Exercises - Integrated Exercise 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 Map Projection Type = NON-UTM Extend the simulation period In the Simulation Period dialog: Specify the Start date and End date 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.

117 MIKE SHE Basic Exercises - Integrated Exercise Step 2 Add the River Module 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 Select simulation modules In the Simulation Specification dialog Check Rivers and Lakes On Your model now has a Rivers and Lakes branch in the Data Tree 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

118 MIKE SHE Basic Exercises - Integrated Exercise 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 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.

119 MIKE SHE Basic Exercises - Integrated Exercise 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.

120 MIKE SHE Basic Exercises - Integrated Exercise 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 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 Saint- Venant 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

121 MIKE SHE Basic Exercises - Integrated Exercise 121 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 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.

122 MIKE SHE Basic Exercises - Integrated Exercise 122 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 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.

123 MIKE SHE Basic Exercises - Integrated Exercise 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.

124 MIKE SHE Basic Exercises - Integrated Exercise 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.

125 MIKE SHE Basic Exercises - Integrated Exercise Step 4 Add the Overland Flow Module Select simulation modules In the Simulation Specification dialog Check Overland Flow (OL) On Your model now has an Overland Flow branch in the data tree 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.

126 MIKE SHE Basic Exercises - Integrated Exercise 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 (5-60 minutes) which would slow down the computation significantly. 6.5 Step 5 Run the Model

127 MIKE SHE Basic Exercises - Integrated Exercise Define Time-Steps In the Time step control dialog: 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.

128 MIKE SHE Basic Exercises - Integrated Exercise 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 Run the Preprocessor Click on the icon to start the pre-processor, which will start the MIKE Zero Launch utility. Click OK

129 MIKE SHE Basic Exercises - Integrated Exercise 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 Run the simulation Click on the icon to run the simulation.

130 MIKE SHE Basic Exercises - Integrated Exercise Step 6 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 View Groundwater Level Results In the Result Viewer dialog: 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? 6.7 Step 7 Input Distributed Rainfall You will now make the simulation a bit more realistic by adding distributed rainfall data.

131 MIKE SHE Basic Exercises - Integrated Exercise 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.

132 MIKE SHE Basic Exercises - Integrated Exercise 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.

133 MIKE SHE Basic Exercises - Integrated Exercise 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

134 MIKE SHE Basic Exercises - Integrated Exercise 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.

135 MIKE SHE Basic Exercises - Integrated Exercise 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.

136 MIKE SHE Basic Exercises - Integrated Exercise 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,, to add 13 lines in the Crop Development table. For each line in the Crop Development table 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 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

137 MIKE SHE Basic Exercises - Integrated Exercise Step 10 Add Reference Evapotranspiration MIKE SHE calculates actual evapotranspiration based on the evapotranspiration rate, the vegetation properties, and the soil moisture Define Evapotranspiration Data In the Reference Evapotranspiration dialog: Use Uniform spatial distribution Use Time-varying (dfs0) data type Use the browse button to select the file.\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 you re using Uniform distribution type, this evapotranspiration rate will be used throughout the model domain 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.

138 MIKE SHE Basic Exercises - Integrated Exercise 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.

139 MIKE SHE Basic Exercises - Integrated Exercise 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 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

140 MIKE SHE Basic Exercises - Integrated Exercise 140 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 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 Step 12 Run the Simulation 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, Use the browse button to select the file.\model Inputs\GIS Data\HeadObservations.dfs0 In the DFS File Selector dialog, you need to select the appropriate Item from the combo box.

141 MIKE SHE Basic Exercises - Integrated Exercise Run the simulation Click on the icon to run the simulation 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 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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