Contents

Preface

Copyright

This document refers to MOHID Studio, proprietary computer software which is protected by copyright. All rights are reserved. Copying or other reproduction of this document or related programs is prohibited without prior written consent of Action Modulers, Consultores de Segurança (Action Modulers).

MOHID Water Modelling System is proprietary software of the Instituto Superior Técnico from University of Lisbon.

Warranty

The warranty given by Action Modulers is limited as specified in your Software License Agreement. Please note that numerical modeling software programs are very complex system and may not be free of errors, so you are advised to validate your work. Action Modulers shall not be responsible for any damage arising out of the use of this document, MOHID Studio, MOHID Water Modelling System or any related program or document.

Further Information

For further information about MOHID Studio please contact:

Action Modulers - Consulting & Technology

Estrada Principal, nº29 - Paz

2640-583 Mafra, Portugal

Tel.: +351 261 813 660

Fax: +351 261 813 666

E-mail: geral@actionmodulers.com

Web: http://www.actionmodulers.com

Quick Start Tutorial for MOHID Land

This "Quick Start Tutorial for MOHID Land" is intended to help first-time users creating their first projects, following a sample project, an implementation in Trancão watershed, a tributary to Tagus Estuary, near Lisbon, Portugal.

It is suggested that the user follows the tutorial, which progresses with increasing complexity, trying to redo the provided sample project. After finished exploring all simulations with the sample, it is suggested to revisit the tutorial but then applying the model to its own study site.

The tutorial starts with the sample project for the user to get used to the MOHID Studio environment, project and simulation structure and to start exploring results without any previous knowledge about using MOHID Land.

After the first play-around, the user is invited to create by his own means a simple project on hydrology simulating floods (impermeable watershed), having to generate a Digital Terrain Model (DTM), delineate watershed and define river network, prepare the input files, run the model and explore results as previously.

The tutorial then starts to increment complexity providing a step-by-step to implement a full hydrology simulation (defining soil characteristics, vegetation and evapotranspiration processes), sediment transport, point sources and ending in nutrient transport and transformation (full water quality simulation), resulting in the most complete simulation (all processes connected) that can be run with MOHID Land.

Since keywords and blocks of keywords need to be defined in the input files, for the user convenience, the user is guided to copy data files from the sample project.

This is intended to be a step-by-step tutorial to implement in a straightforward way a MOHID Land project from simpler to complex simulations. Detailed description is not given for processes, keywords, model functioning, etc. For that intent the user should explore MOHID sources:

Action Modulers website – http://www.actionmodulers.com

MOHID website – http://www.mohid.com/

MOHID wiki – http://wiki.mohid.com/wiki

MOHID forum – http://www.mohid.com/forum/

MOHID code repository – http://mohid.codeplex.com/

Exploring a sample project

The tutorial starts providing the user with a sample project so that the user gets used to the MOHID Studio structure and be able to get the simulation running and produce the model results. In this way the tutorial gets straightaway to the ending point where the user may see what is intended to get and then in next chapters the intermediate steps (creating the project and simulations) are explained.

It is assumed that the user already installed MOHID Studio (follow MOHID Studio Install Guide first) and opened already MOHID Studio and is aware and understands the functioning of the different windows, environments and buttons (follow MOHID Studio User Guide first).

This manual applies to MOHID Studio version 1.2.7.

Step 1 – Updating the MOHID Land executable

In MOHID Studio version 1.2.7 the executable provided is outdated so the user needs to update it. Download the executable MOHIDLand_release_doulbe_openmp.zip from Action Modulers web site and extract it to your local hard disk (e.g. D:\MOHIDStudioProjects).

http://www.actionmodulers.pt/Biblioteca/Uploads/Downloads/Walkthroughs/MOHIDLand_release_double_openmp.zip

After downloading and extracting this file, go to the "Administration" tab, press "General" and the "Settings of MOHID Studio" appears, as shown in Figure 1. Highlight the MOHID Land model and browse for the new file.

MOHID Studio - MOHID Land Quick Start Guide v1 02.png
Figure 1 : Updating MOHID Land default executable.

Step 2 – Preparing the sample project

Download the file TrancaoSample.zip (link below) from Action Modulers Web Page to your local disk (e.g. to D:\MOHIDStudioProjects).

http://www.actionmodulers.pt/Biblioteca/Uploads/Downloads/Walkthroughs/TrancaoSample.zip

Create a folder in your hard disk for the project (e.g. D:\MOHIDStudioProjects\TrancaoSample and leave it empty).

Open MOHID Studio where it should appear the "Workspace Manager" window asking to create a new workspace or open a saved one ( Figure 2). Select "Start with an empty Workspace" and name it for instance "Trancao".

MOHID Studio - MOHID Land Quick Start Guide v1 03.png
Figure 2 : MOHID Studio Workspace Manager.

Select "Project" ribbon and in "Solution" group, press "Manage" and the "Solution Management" window appears ( Figure 3) showing the list of solution available. If using MOHID Studio for the first time the list will be empty.

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Figure 3 : MOHID Studio Workspace Manager.

On the same "Solution Management" window press "Import" and the "Import MOHID Solutions" window appears ( Figure 4). Under "Project File Name" browse for the .zip file downloaded earlier (e.g. in D:\MOHIDStudioProjects) and in "Destination Directory" choose the empty directory created previously (e.g. D:\MOHIDStudioProjects\TrancaoSample). The destination directory needs to be empty.

Press "Import" and wait till the end of the process and accept the successful message.

MOHID Studio - MOHID Land Quick Start Guide v1 05.png
Figure 4 : MOHID Studio Workspace Manager.

NOTE: If a solution with the same name of the solution to import already exists, the newly imported solution is automatically renamed (example: Trancao Sample_1).

The solution was imported and now needs to be opened. Select "Project" ribbon and in "Solution" group, press "Open" and the "Solution Management" window appears now with the "Trancao Sample" available. Select it and press "OK".

This will open the "Trancao Sample" solution in "Explorer" tab. Press on the triangle just left to the solution icon to show the domain tree (it will show "Trancao Sample" domain). Press on the triangle just left to the domain icon to show the domain folder structure and simulations available. There are 5 simulations available just the same as the main simulations of this tutorial. In the next steps, the user may copy the necessary files and doesn’t need to create them from scratch.

Step 3 – Recognizing the project structure

With the solution opened and domain tree, domain folders and simulations tree visible, the user should be viewing the same as in Figure 5.

MOHID Studio - MOHID Land Quick Start Guide v1 06.png
Figure 5 : MOHID Studio Explorer Window with MOHID Land Sample.

If having some doubts about the MOHID Studio windows and structure please refer to the MOHID Studio User Guide.

Pressing on each simulation, the "Modules" section on the right pane is filled with "Data Files" (text files with options and info needed to run each simulation) and no files exist in "HDF Files" or "Time Series Files" - see Figure 7. The latter do not exist since the simulation did not run (next step) and these are model results (maps and time series, respectively).

MOHID Studio - MOHID Land Quick Start Guide v1 07.png
Figure 6 : MOHID Studio Explorer - Simulation and associated module data files.

Before running any simulation, check the study area by pressing the folder General Data\Digital Terrain (see Figure 7) and right-clicking the file "FinalDTM_160m_v4.dat" and press "Add to Map…".

MOHID Studio - MOHID Land Quick Start Guide v1 08.png
Figure 7 : MOHID Studio Explorer – Adding the digital terrain to the map.

On the next window, which allows configuring the layer properties, click OK to accept the default values.

MOHID Studio - MOHID Land Quick Start Guide v1 09.png
Figure 8 : Adding the digital terrain to the map – Step 2.

Select the "Map" tab and check the topography of the Trancão watershed that is near the Tagus Estuary and close to Lisbon on the north margin. To have a background map as reference go to "Map" ribbon and on "Background" group press "Web Tiles".

Accept the change in coordinates and select for instance Google Maps or Bing Aerial and press "OK" and it should result similar to Figure 9.

To show the color scale of the topography, right-click the topography layer and press "Properties"; check "Legend", write down the legend text in "Text" box and press "OK". Unhide the legend by pressing "Legend" in the bottom- right corner of "Map" window.

MOHID Studio - MOHID Land Quick Start Guide v1 10.png
Figure 9 : MOHID Studio Map Window with project sample topography.

Step 4 – Running the simulation

To run the model we have to select first the simulation "Sim #1 Impermeable Watershed" in the Project Tree. Then we go to the "Project" ribbon and in "Execute Models" group, we have to press "Run Now".

MOHID Studio - MOHID Land Quick Start Guide v1 11.png
Figure 10 : Running the first simulation.

A window will appear to check if the user wants to run the selected simulation ("Sim #1"), press "OK".

The box window called "Model Controller" below the domains and simulations is filled showing the progress bar of the simulation ( Figure 11). To check more details on the simulation status press "Output" button to be able to see what is the current simulation time, the time step used and average time step so far, the current computer time and the expected computer time when the simulation will end (the content of this log is continuously updated). The "Kill" button on the same box window exists to abort the simulation at any time.

MOHID Studio - MOHID Land Quick Start Guide v1 12.png
Figure 11 : MOHID Studio Model Controller.

When model run finishes (successfully or due to a crash) a window appears, informing that the model has finished. The user has the option like to see the log file (the same as obtained in "Output" in Model Controller but now the final file) - Figure 12.

MOHID Studio - MOHID Land Quick Start Guide v1 13.png
Figure 12 : MOHID Studio Model Finished.

It is always suggested to watch the log to make sure that the simulation ended successfully (browse till the end of the file - Figure 13). If the user does not want to see the log file or closes the log file than is sent back to MOHID Studio and ready to explore results. The log file can be accessed at any time right-clicking each simulation and selecting "View Last Log…".

MOHID Studio - MOHID Land Quick Start Guide v1 14.png
Figure 13 : MOHID Studio Log File reporting that simulation ended with success.

Step 5 – Exploring the Results

After the simulation finished results are ready to be explored. By pressing on the simulation that just finished running ("Sim #1"), the "Modules" section on the right pane is now filled with "HDF Files" and "Time Series Files". HDF files contain time varying information for several properties for the entire domain. Time series are results for defined points showing the properties variation in time, usually with a higher frequency then the HDF files. Later in the manual it will be explained how to configure these outputs (frequency and time series locations).

MOHID Studio - MOHID Land Quick Start Guide v1 15.png
Figure 14 : MOHID Studio Explorer – Module data files and result files.

Double-clicking on an HDF file or a time series file, shows a dialog to select the properties to plot. More information on how to visualize and customize these results is explained in "MOHID Studio User Guide" in chapter 4.6 for HDF and chapter 5 for time series.

To visualize the channel flow in "Bucelas", go to the "Time Series Files" section and double click the file "Node_Bucelas.srn". In the window which appears select the property "channel flow" and press OK.

MOHID Studio - MOHID Land Quick Start Guide v1 16.png
Figure 15 : Selecting a time series to be shown as graph.

A plot like shown in Figure 16 appears. This is the channel flow variation with time in one location.

MOHID Studio - MOHID Land Quick Start Guide v1 17.png
Figure 16 : MOHID Studio time series of channel flow in one location for Sim # 1 in MOHID Land Samples.

NOTE: To see the location of this point and other points that have time series defined, in "Map" ribbon, and "Vector Data" group select "XML" and open NodeTimeSeriesLocation.xml in folder General Data\TimeSeries of the sample project and select as the projection "Geographic" and press "OK". The time series points will be displayed on map. To know the name of each point query on the just opened layer (see MOHID Studio User Guide chapter 4 on how to query layers).

To visualize the channel flow for the entire domain, we have to go back to the "Explorer" and double click on the file "Drainage Network_1.hdf5" in the section "HDF Files". In the window which appears select the feature "channel flow".

MOHID Studio - MOHID Land Quick Start Guide v1 18.png
Figure 17 : Selecting a property to be shown in the map.

Press OK to close the window and load the layers.

In the Map window it’s now possible to see the channel flow for the entire domain. Stepping forward and backward in time can be achieved by using the Time Control window, located in the lower left corner of the Map Window.

You should see now a map with the channel flow for the entire domain, as shown in Figure 18. You can use the time, located in the lower left corner, to step forward in time.

MOHID Studio - MOHID Land Quick Start Guide v1 19.png
Figure 18 : MOHID Studio HDF of channel flow for all the drainage network for Sim #1 in MOHID Land Samples

To know more on how to customize the time series window (axis titles, series names and colors, etc.) and map images (color scale, horizontal scale, etc.) follow MOHID Studio User Guide chapter 4 and 5.

Creating your own project – Simulating Flood Hydrology (Impermeable Watershed)

This section intends to show how to start a new project using in this case a simple example of an impermeable watershed (porous media will not be included). In reality a watershed may behave impermeable during rainy season where soil saturates completely and water is not able to enter soil.

The example used here is for watershed Trancão the same in MOHID Land samples but the explanation can be used to implement the model any study site. One good exercise for a first time user is to try to redo the Trancão project following the instructions.

Step 1 – Creating a new MOHID Land Solution and Domain

Create a new Solution going to "Project" ribbon and in group "Solution" pressing "New". It will be prompted to name the solution in "Name of the Solution". Write down for instance "Trancão Sample Redone" without the quotes.

Create a new domain going to "Project" ribbon and in group "Domain" pressing "New". The following window will appear ( Figure 19).

MOHID Studio - MOHID Land Quick Start Guide v1 20.png
Figure 19 : MOHID Studio create new domain.

The information provided in the "Creating a new domain" window characterizes your domain. The following restrictions must be fulfilled:

  • the domain name must be unique;
  • the root directory must be empty.

In "Domain Name" use your watershed name and for instance "Trancao_200m" in the case of redoing the Trancão sample case since we will create an application with 200mx200m grid (explained after). Since the domain is linked to a horizontal grid (digital terrain model) this naming convention is quite handy when handling different resolution grids for the same watershed.

Browse for an empty "Root Directory". (hint: create in your pc a folder per horizontal resolution used inside the watershed folder implementation).

Leave the path of the digital terrain model ("Digital Terrain Model") empty for now.

Press OK to finish the domain creation.

More information on how to manage solutions and domains can be found in "MOHID Studio User Guide" in chapter 3.

Step 2 - Generate Basic Watershed Info

In this section it is shown how to generate the basic information needed to run the model in a watershed. This includes the Digital Terrain Model (DTM), the drainage network describing the major streams and the watershed delineation. Next all steps to create theses files and create a simulation like "Sim #1" (Impermeable Watershed as seen previously) will be shown.

Step 2.1 - Creating a Digital Terrain Model

To create a DTM it is needed:

  • A horizontal grid. This will be the grid for the model and the grid for all the info inputted to the model in grid format (spatially distributed).
  • Digital terrain elevation data in point format.
  • A polygon with no compute points (e.g. coastal or estuarine waters that do not belong to the watershed and need to be removed from final DTM).

First we need a background layer to center the map to our study area. Going to the "Map" ribbon, "Background" group and press "Web Tiles". Selecting one of the available options (e.g. Bing Aerial) will add a background layer which will help you to identify the study site.

In the case of redoing Trancão sample, zoom in to the study site in Portugal, Lisbon, as shown in Figure 20. Here we will use an additional file to help out: the watershed delineation. Go to "Map" ribbon and in "ASCII" group press "Polygon" and select the file Delineation_v4.xy in project folder "General Data\Digital Terrain" of the Trancão sample; select the "Geographic" coordinates and press "OK". Now your map should look similar to Figure 20.

MOHID Studio - MOHID Land Quick Start Guide v1 21.png
Figure 20 : Lisbon and Trancão watershed area using Bing Aerial as background image.

Horizontal Grid

Now we will create a constant horizontal grid for our study area. Go to "Tools" ribbon and in "Grids" group, press "Constant". The "Construct Constant Space Grid" window appears.

  • In section "2. Preview" check "Auto Update" so that all the changes that are done are immediately visible. Leave unchecked if the process is very slow; in that case you will need to press "Refresh" to visualize your changes.
  • In section "1. Grid Parameters" the user may define:
  • An origin (lower left corner coordinate of the grid) by filling "Origin X" and "Origin Y" with geographic coordinates, or, simply pressing "Pick" it may select in the map the origin point. For the Trancão case select an origin near the lower left part of the watershed delineation.
  • The number of columns and rows or the number of cells in x and y direction. In the Trancão case it was used 106 and 117, respectively.
  • Dx and dy or the cell size (in degrees). In the Trancão case it was used 0.002 in both (around 200mx200m cells).
  • The origin of the grid may be changed at any time. So if your grid is not in the correct position feel free to move it around (press "Pick" and select another origin) and check the result.
  • In section "3. Save Grid" you may save the file if everything is OK, choosing the folder and file name (save it in General Data\Digital Terrain of the project for convenience). If do not want to save the grid just close the tool.

For the Trancão case, the grid should be similar to the one in Figure 21.


MOHID Studio - MOHID Land Quick Start Guide v1 22.png


Figure 21 : MOHID Studio constant grid tool for Trancão watershed.

For the Trancão case, compare the grid generated with the one used in Trancão watershed (Tancao_160m.grd) in folder General Data\Digital Terrain of the sample project.

Digital Elevation Data

MOHID Studio incorporates NASA SRTM elevation (3 arc second resolution, in Trancão area resolution is around 70-90m) making it possible to implement MOHID Land in any small to medium sized watershed in the world with minimum effort[1].

To get the NASA elevation data go to "Map" ribbon and in "Vector Data" group press "HGT". The "HGT Layer" window appears. Check "Load for Selected Grid", select the grid created in the previous step ( Figure 22) and press "OK".

MOHID Studio - MOHID Land Quick Start Guide v1 23.png
Figure 22 : MOHID Studio HGT Window.

The HGT Layer with point elevation data for the grid appears in the map and can be edited just like any other point collection (e.g. change color scale, increase point size) in layer properties (right-clicking the layer and selecting "Properties").

SCREEN SHOTS

No compute Areas

No compute areas are polygons used to flag areas that are water, not containing any valid elevation data, like estuaries, lagoons and coastal areas. If your case do not contain such areas this step may be skipped.

Go to "Tools" ribbon and in "Geometry Layers" group, press "Polygons". The "Construct Named Polygons" window appears and in section "1. Define Polygons on Map" press "Draw" and start picking points that define the water bodies boundary and MOHID Studio generates automatically the polygon formed by the points; double-click at the last point to finish the polygon (see Figure 23). If want to remove the generated polygon use the "Remove" button in section "2. Defined Polygons". In section "3. Save Polygons" press "Save" and select the folder and filename to save the polygon (save it in General Data\Digital Terrain of the project for convenience).

MOHID Studio - MOHID Land Quick Start Guide v1 24.png
Figure 23 : MOHID Studio Polygon Tool to select no compute points in Trancão watershed.

For the Trancão case, you may want to compare the polygon generated with the one used in Trancão watershed (NoComputeArea.xml) in folder General Data\Digital Terrain of the sample project.

Generating the DTM

Finally the generation of the DTM uses all the above steps products: the grid, the elevation points and the no compute points. The elevation information in points will be passed to the grid cells, except in the cells that are no compute points (inside the polygon).

Go to "Tools" ribbon and in "Grid Data Tools" group press "From Points" (create grid data from points) and "Create Grid Data" window appears ( Figure 24). In section "1. Select Grid" select the grid that was generated on the first step. In section "2. Non Compute Areas" check the polygon generated on the third step; remind that several polygons can be selected. In section "3. Base Information" check the "HGT Layer"; remind that several point sources can be selected.

In section "4. Options" select the method to get the elevation for each cell from point collection. If have several point inside each cell (grid is coarser than elevation data) select "Average" and the cell value will be the average of the points inside. If the grid has finer resolution than data (some cells do not have points inside), interpolation need to be done and may select "Triangulation" or "IWD" (inverse weighted distance). If redoing the Trancão sample select "Average".

In section "5. Generate Grid Data" select the folder and filename for the DTM (save it in General Data\Digital Terrain of the project for convenience). Press the "Process" button to generate the DTM.

MOHID Studio - MOHID Land Quick Start Guide v1 25.png
Figure 24 : MOHID Studio Grid Data from points Tool to create a DTM.

For the Trancão case, compare the DTM generated with the one used in Trancão watershed (FinalDTM_160m_v4.dat) in folder General Data\Digital Terrain of the sample project.

Removing Depressions

The generated DTM may have unreal obstacles or depressions and since MOHID Land needs that every cell flows somewhere, accumulation points (depressions) have to be removed. Go to "Tool" ribbon and in "Watershed Tools" press "Remove Depressions".

On section "1. Select DTM" select the DTM created in the previous step. On section "3. "Depression Removal" each singularity found and presented in section 2 may be fixed manually by filling the depression ("sink fill") or by digging through an exit point ("artifact removal") or pressing "Process" to do it automatically. Read the MOHID Studio User Manual about these options. If not sure about which method to use press "Process".

On section "4. Persist Changes" select the folder and filename to save the polygon (save it in General Data\Digital Terrain of the project for convenience) and press "Save".

To be sure that this file is depression free, open the tool again and reanalyze. If it has depression remove them and when saving, save with the same filename as before so that only one file exists.

For the Trancão case, compare the DTM generated with the one used in Trancão watershed (FinalDTM_160m_v4.dat) in folder General Data\Digital Terrain of the sample project.

SCREENSHOT

Step 2.3 - Generating drainage network and defining river cross sections

Generate drainage network

To generate the drainage network go to "Tools" ribbon and in "Watershed Tools" press "Delineate Watershed". The "Delineate Basin" window appears.

In section "1. Select DTM" select the DTM that was generated after depression removal.

In section "2. Delineation Options" define the "Threshold Area". This is the minimum area to generate a river. If the value is low it will generate a very dense river network with rivers up to headwaters; if the value is high it will only generate the main rivers. In the Trancão implementation it was used 1000000 m2 (or 1km2).

In section "3. Output Options" check only on "Network File" and unselect the others. You can always change the paths of the files, by default they are placed in folder General Data\Digital Terrain.

In section "4. Process" press "Process" and the drainage network will appear in the map. Do not close the Watershed Delineation tool!

If the drainage network is not suited, change the threshold area in section 2 and press "Process" in section 4. Repeat this steps until the drainage network density is satisfactory.

Do not close the Watershed Delineation tool!

When the drainage network is OK it is time to delineate the watershed and select only the river stretches inside it. In section "2. Delineation Options" check "Delineate Basin" and press "Pick" to pick the river node that will be the outlet. Use the zoom tool and the drainage network to pick the correct node (and avoid selecting neighbor nodes that are not in the main river) - Figure 25.

MOHID Studio - MOHID Land Quick Start Guide v1 26.png
Figure 25 : MOHID Studio Delineate Watershed Tool to create drainage network and delineation.

In section "3. Output Options" check "Network File", "Delineation" and "Basin Geometry" options. This last file will save the threshold area and outlet cell (I and J) that will be used for the simulation.

In section "4. Process" press "Process" and after is finished may close the tool.

At the end may compare the delineation file (automatically opened in map) with the sample delineation.

Define cross sections

The above steps created the drainage network distribution in space and now it will be defined the cross sections. The cross sections will be distributed accordingly to the Strahler order.

Go to "Tools" ribbon and in "Watershed Tools" group press "Cross Sections". The "Define Cross Sections" window appears ( Figure 26).

On section "1. Network" select the drainage network file just created in the above step.

On section "2. Default Cross Sections" the user needs to create a cross section per Strahler order. To know how many Strahler orders exist in the drainage network do a query on it, selecting nodes near the outlet. One of the output information given is the Strahler order of the node and the nodes near the outlet will have the maximum order.

To create a cross section geometry go to section "Add Cross Section" and define "Top Width", "Bottom W." (bottom width), "Height", Strahler order (1 at the start) and press the plus button, that will add the section to the list. Do this steps until all the Strahler orders existing in the domain have a cross section defined.

It is possible to save your section definition per Strahler order in a file that can be uploaded to this tool (using the save and open icons in section "2. Default Cross Sections"). The sections used in Trancão implementation are stored in file "CrossSectionDefinitions.xml" in folder General Data\Digital Terrain from sample project that can be uploaded using the open icon; in this way the same sections will be used if redoing the sample project.

The cross sections created may be visualized. Select the cross section from the list and the "Cross Section" section in "Properties" and "Graph" will be filled and the section visualized.

Save the work done pressing "Save" in section "4. Save Network". The drainage network file will be saved now with information on section geometry.

MOHID Studio - MOHID Land Quick Start Guide v1 27.png
Figure 26 : MOHID Studio Cross Sections Tool.

Step 3 – Create a new simulation

The latter are the most basic info to define a watershed simulation (DTM and drainage network) and so it is possible to do a simple simulation with impermeable watershed. For more detailed watershed description see next simulation preparation (simulating complete hydrology in chapter 2.3).

On "Explorer" tab, select the Domain name and go to "Project" ribbon and in "Simulation" group press "New". Name your simulation (e.g. Impermeable Watershed), select "Porous Media" and "Geometry" Modules (use Ctrl to select several) and press "Remove" since this simulation will not use them. Press "OK" when finished to have the new simulation ready - Figure 27.

MOHID Studio - MOHID Land Quick Start Guide v1 28.png
Figure 27 : MOHID Studio New Simulation.

Step 4 – Define the simulation

Selecting the just created simulation shows that the simulation has several input files listed in the "Modules" section and in "Data Files".

SCREENSHOT

These files should have all the options needed to run the model including the atmosphere forcing, the location to the drainage network and threshold area used, the main options to run, etc.

All this info is heavy to construct from scratch every time a new project is done so the suggested action is to adapt the setting from an existing project.

Since there are no other simulation to copy from, to do a copy of the settings need to add to your solution another domain to copy. Select your solution and go to "Project" ribbon and in "Domain" group press "Open". Choose from the list the "Trancão Sample" or other project if you have one that you want to copy from. The selected project will appear under the same solution.

To copy the simulation files, select the simulation to copy from (if the domain just added is Trancão sample select the "Sim #1 Impermeable Watershed") and go to "Project" ribbon and in "Simulation" group, press "Copy". The copy window appears and lets you choose which files from the origin simulation to copy and select the destination simulation ( Figure 28).

MOHID Studio - MOHID Land Quick Start Guide v1 29.png
Figure 28 : MOHID Studio copy simulations between domains.

Leave the origin unchanged but select the destination simulation (inside your new domain select the correct simulation). Press "Copy" and after "OK". This will copy all the settings from the origin simulation to the destination. Now some verification needs to occur to ensure that you fill in the data you created (see next steps).

After you are done copying you can remove the added domain from the solution, selecting it and going to "Project" ribbon, "Domain" group and pressing "Remove". This action does not delete the domain from the disk, it just removes the domain from the solution that is virtual. In the case of redoing Trancão sample its files will be needed in the next simulations, so leave it for now.

Step 4.1 – Define DTM for the project

The DTM is a property of the domain and is the same throughout the simulations so is not defined in the simulations data files but in the domain. Edit the domain properties selecting it, right-clicking and selecting "Properties". In The "Digital Terrain Model" browse for the created DTM in the previous steps - Figure 29 (this image is for Trancão sample but is similar to any project).

MOHID Studio - MOHID Land Quick Start Guide v1 30.png
Figure 29 : MOHID Studio Domain Properties where DTM is defined.
Step 4.2 – Define simulation start and end in Model file

The simulation start, end and time step related info is inputted in file Model_X.dat where is X is the simulation number. This file is on "Explorer" tab, under "Modules" and in "Data Files" section.

The start and end dates are identified with keywords "START" and "END" and the format is year, month, day, hour, minute and second integer numbers separated by spaces.

The keyword "GMTREFERENCE" defines the time difference in relation to Greenwich Meridian Time (GMT). If running the model in a place other than in GTM + 0 than need to edit accordingly (positive to east and negative to west).

These values can be edited but if redoing the simulation from Trancão leave it for now.

Step 4.3 – Define Drainage Network in Drainage Network file

All the information related to drainage network (the network definition, the equations used, initial water column, the global manning resistance etc.) is configured in file Drainage Network_X.dat where is X is the simulation number. This file is on "Explorer" tab, under "Modules" and in "Data Files" section.

The only change needed is to define the drainage network file created in the above steps in the keyword NETWORK_FILE. Give to the model the path to the file; complete or relative paths can be used. Relative paths work in every computer so they should be used. Relative paths in MOHID are all relative to exe folder (not seen in MOHID Studio but in "File Explorer"); so if referring to one level up from this folder use "..\". If referring two levels up use "..\..\" and so on.

Step 4.4 – Define atmosphere forcing in Atmosphere file

All the information related to atmosphere properties (precipitation, air temperature, relative humidity, solar radiation and wind forcing) is configured in file Atmosphere_X.dat where is X is the simulation number. This file is on "Explorer" tab, under "Modules" and in "Data Files" section.

In the case of redoing the simulation from Trancão this simulation will only use precipitation (the basic forcing for a watershed model) and a constant value defined by keyword DEFAULTVALUE. This value can be changed but remind that this rain will be constant throughout the simulation and high values can produce high flows and increment simulation time.

Step 4.5 – Define Basin Geometry file

All the information related to watershed delineation as outlet cell and threshold area is configured in file Basin Geometry_X.dat where is X is the simulation number. This file is on "Explorer" tab, under "Modules" and in "Data Files" section.

The threshold area (keyword TRESHOLD_AREA) and outlet location (keywords OUTLET_I and OUTLET_J) can be found in file BasinGeometryInfo.dat that was created when delineating watershed and defining drainage network in section 2.2.2.2). Change these values accordingly to the ones obtained when created the delineation.

Step 4.6 – Other Files

All the information related to runoff options as manning resistance, initial water column or equations used is configured in file Runoff_X.dat and information about which components/domains to connect/disconnect and reference evapotanspiration is configured in Basin_X.dat. These files are on "Explorer" tab, under "Modules" and in "Data Files" section.

Basin file controls which options to compute. It defines for instance if porous media, runoff, drainage network or other model domain are to be used. If some module is disconnected in Basin file it will not be read even if the data file is present in the simulation.

In the case of redoing the simulation from Trancão these files do not need to be changed.

Step 4.7 – Define Output

The last thing to care before running the simulation is where to place time series output and its frequency and what should be the HDF maps frequency. This info in transversal to almost all the data files (all that have output) and to create times series in river and land follow the instructions in MOHID Studio User Guide in chapter 6.6. Hint: Save the time series file in General Data\TimeSeries.

In the case of redoing the simulation from Trancão since the grid is not exactly the original the process needs to be redone using the same stations.

  • Open the location of the stations in "Map" ribbon and in "Vector Data" group press "XML" and open the file "TimeSeriesLocation.xml" and "NodeTimeSeriesLocation.xml" (land and river, respectively) from the folder General Data\TimeSeries in the Trancão sample project and define "Geographic" coordinates.
  • If want to maintain the same time series names (some will be used after) do a query on the station (see MOHID Studio User Guide chapter 4 on how to query layers) and write down the names.
  • Go to "Tools" and in "Time Series" press "Grid Locations" for land points or press "Network Location" for river points. Follow the instruction from MOHID Studio User Guide and pick points at the same locations as the Trancão sample and name them the same. Save the files (choose to save also as .xml so that the location is accessible) in the folder General Data\TimeSeries on the new project (create it). Name them for instance TimeSeriesLocation.dat for land and NodeTimeSeriesLocation.dat for river.

The path to the file just created (e.g. TimeSeriesLocation.dat and NodeTimeSeriesLocation.dat) needs to be defined in each data file that has output with a keyword TIME_SERIE_LOCATION. In Drainage Network_X.dat is the location for the time series file with location in nodes (NodesTimeSeriesLocation.dat) and for the other Modules is the location in the land cells (NodesTimeSeriesLocation.dat). Check that the paths are correct in the data files.

The time series frequency is defined inside the created files with the keyword DT_OUTPUT_TIME (in seconds).

The HDF frequency of output is given in the Modules data files that have output by the keyword OUTPUT_TIME (in seconds).

Always verify if the frequency of output is correct given the simulation period. Usually time series are not very time consuming and do not generate huge result files but in HDF if frequency is too high may make the model run slower and generate huge files that are difficult to manage.

IMPORT NOTE:

In MOHID Studio version 1.2.7 the definition of the drainage network time series is outdated and the correspondent file generated needs to be updated by the user in order to run with the new executable defined at the start. The next versions of MOHID Studio will produce the updated node time series file.

The new definition allows the user to name the time series outputs in the river (e.g. with station names) as possible in the grid time series.

Open the river time series location file (e.g. NodeTimeSeriesLocation.dat) in MOHID Studio going to "Explorer" tab an in General Data\TimSeries folder and it should be similar as shown in Figure 30. The file describes inside the unique block <BeginNodeTimeSerie>/<EndNodeTimeSerie> the nodes that were selected for time series.

MOHID Studio - MOHID Land Quick Start Guide v1 31.png
Figure 30 : Drainage Network time series file in the outdated version produced by MOHID Studio v 1.2.7.

The new executable only allows for the updated version of the file where one block <BeginNodeTimeSerie>/<EndNodeTimeSerie> exists per node where the keyword NODE_ID defines the node and the keyword NAME is where the node name can be customized so that outputs will be saved with that name ( Figure 31).

MOHID Studio - MOHID Land Quick Start Guide v1 32.png
Figure 31 : Drainage Network time series file in the updated version to run with the new executable.

Step 5 – Run the simulation and explore results

Everything now is prepared to run the simulation. Verify one last time that all the paths defined inside the data files exist and that the DTM was defined in the domain. Follow the same instructions as in the previous simulation to run and to explore the results.

The results of this simulation should be very similar to the Trancão sample simulation #1 ( Figure 32) even that the grid is not the same. The user should explore all the results provided by the simulation.

MOHID Studio - MOHID Land Quick Start Guide v1 33.png
Figure 32 : Trancão channel flow in impermeable simulation.

Creating your own project – Simulating Complete Hydrology (Permeable Watershed and Evapotranspiration)

These instructions, in relation to the latter, add the porous media and vegetation modules and defining some properties spatially distributed instead of constant (e.g. manning resistance in runoff).

It will be referred to the MOHID Studio User Guide more often since this simulation is more advanced and is assumed that the user is now comfortable in exploring MOHID Studio.

Step 1 – Generate Advanced Watershed Info

To run a MOHID Land simulation with porous media two variables have to be defined: (i) the soil depth and (ii) the soil types.

In the case you want to use vegetation also a vegetation map needs to be created. In this case vegetation will be described as defined by the user (giving to the model leaf area index and root depth since simulations examples are not for long term) but MOHD Land has also a vegetation growth model[2].

Step 1.1 - Defining soil depth and initial aquifer level

MOHID Land actually calculates the soil depth in an implicit way by subtracting from the surface geometry (the DTM) the soil bottom elevation (border between the porous media and the impermeable bed rock).

MOHID Studio has a tool to roughly estimate soil depth in function of surface slope and from here it calculates the soil bottom elevation. This tool assumes that higher slope areas usually have lower soil depths (due to erosion) and lower slopes usually have higher soil depths (due to deposition). The distribution of soil depths is controlled by the minimum soil depth (where maximum slope occurs) and by maximum soil depth (where minimum slope occurs).

The initial aquifer level is an initial condition to define the saturated area at the beginning of the simulation. This may be defined in the same tool as soil bottom.

Both processes can be done going to "Tools" and in "Watershed Tools" press "Porous Media". The "Construct Soil Depth" window appears ( Figure 33).

In section "1. Select Grid Data" provide the DTM without depressions.

In section "2. Select Parameter" define the minimum depth (for areas where slope is higher than maximum slope – to be defined) and the maximum depth (for areas where the slope is zero). The soil depth will be linearly changing from minimum depth to maximum depth between slopes. In this section is also possible to define the percentage of soil depth where initial aquifer level will be positioned (0% will be at surface and 100% at soil bottom). If redoing the Trancão sample use minimum depth as 0.5m, maximum depth as 3m, maximum slope 0.1 and water depth 5% (corresponding to a relative high initial ground water level – typical "wet scenario").

In section "3. Persist Changes" the soil bottom (and depth) paths are defined and press "Save" to save the defined grids.

For convenience save the soil bottom file ("Bottom") in folder General Data\Digital Terrain and initial aquifer level ("Water Level") in General Data\Initial Conditions.

MOHID Studio - MOHID Land Quick Start Guide v1 34.png
Figure 33 : MOHID Studio construct soil depth and initial aquifer level.

These two files have to be configured in the Porous Media_X.dat file (see below).

Step 1.2 – Create a Soil Map from soil distribution

Distribution of soil types in a watershed may vary in the vertical and in the horizontal extends reason why MOHID Land accepts a wide range of options to configure soil types.

In the simplest case, the user wants to use the same soil type through the entire watershed, a constant soil may be defined (see below).

In the case that we want to simulate the watershed with spatial distribution of soils than the next steps describe how to proceed. It’s assumed that you have information about the soil type in ESRI Shapefiles. MOHID Studio has a feature to pass the information from the ESRI Shapefiles to the horizontal grid so that each cell will have the dominant soil occurring in the area.

Before The user also needs, for preparing of simulation, to have for each soil that appears in the watershed the van Genuchten parameters (saturated conductivity, porosity or saturated content, residual content, parameter alpha and l)[3].

The user should prepare

  • the shapefile with soils ID’s and to improve performance it should not be larger than 100MB (better clip and simplify polygons if much larger) or have a lot of lines (process it to generalize and group polygons with same ID).
  • a grid data. It can be the DTM. It is the file that has the model horizontal grid so that the information in the shape is passed to the same grid.
  • a conversion table between the soil ID’s in the shapefile and the soil ID’s that will be used in the model simulation. In the case that there is no conversion still a table with one to one relation will be useful since MOHID Studio always ask for a conversion table and manually conversion is only feasible if the shapefile has not to many different ID’s.

This process is done in "Tools" ribbon, in "Grid Data Tools" group press "From Shape". The window "Create Grid Data" appears ( Figure 34).

MOHID Studio - MOHID Land Quick Start Guide v1 35.png
Figure 34 : MOHID Studio create grid data from shape in case of soil.

In section "1. Select DTM & Shape file" select the DTM (no depressions), the shapefile and the field of the shapefile that will be used and press "Analyze" that will fill section 2.

In section "2. Value Mapping" all the values in the shapefile appear and the conversion table may be filled or loaded from file.

In section "3. Process" browse where to save the grid and press "Process" to initialize the process. After a while the process is done and the soil grid created. For convenience save this file in folder General Data\Other\PorousMedia of the new project to distinguish it from others.

This product will be referred in the Porous Media_X.dat file (see below). The user has to provide in this file a soil database with van Genuchten parameters for at least the soils that appear in the watershed and this database has to have consecutive IDs starting in 1.

For the Trancão sample find the Eurosoil database[4] shapefile (EUSoil_Trancao_diss.shp) and conversion table (SoilIDConversion.xml) in folder General Data\Other\Soil. The soil database (van Genuchten parameters) for the map is included in the Porous Media_X.dat file.

The soil ID map for each cell should result in something similar to Figure 35.

MOHID Studio - MOHID Land Quick Start Guide v1 36.png
Figure 35 : Trancão soil ID distribution according to Eurosoil database.
Step 1.3 – Creating maps for vegetation, impermeabilization, resistance from land use

Distribution of vegetation, impermeabilization and surface roughness may vary in the in the horizontal extend reason why MOHID Land accepts a wide range of options to configure these parameters.

In the simplest case, the user wants to use a constant value for the entire watershed. In more advanced cases, a procedure similar to the soil types have to be followed.

In the case of generating the maps (Trancão sample example) the requirements are the same as the soil ID’s. In the case of impermeabilization the conversion table will represent the conversion from land use code to a value between 0 and 1 where 1 all the area is impermeable and 0 all the area is permeable. In the case of vegetation the conversion table will represent the conversion from land use code to a vegetation ID that does not need to be consecutive[5]. In the case of runoff manning the conversion table will represent the conversion from land use code to the manning resistance.

This process is done in "Tools" ribbon, in "Grid Data Tools" group press "From Shape". Follow the instructions described in the previous step.

In the vegetation, since in this example, growth model will not be used, also leaf area index and root depth maps can be created the same way using as a convert table the leaf area index and root depth associated to each land use. In this case these properties will be constant throughout the simulation.

For convenience save the impermeabilization file in folder General Data\Other\PorousMedia, the vegetation products in folder General Data\Other\Vegetation and the manning in General Data\Other\Runoff all in the new project.

These products will be referred in the Porous Media_X.dat file, Vegetation_X.dat and Runoff_X.dat (see below).

For the Trancão sample find the CORINE 2006[6] map (Corine2006_trancao.shp) and conversion tables for impermeabilization fraction (clc2006ToImpermeability.xml), SWAT crop code (clc2006ToSWATID.xml), manning resistance (clc2006ToManning.xml), root depth (RootDepthConversion_trancao.xml) and LAI (LAIDepthConversion_trancao.xml) in folder General Data\Other\LandCover. The user should verify/correct the conversion tables before applying them to other watersheds.

The manning map for each cell should result in something similar to Figure 36.

MOHID Studio - MOHID Land Quick Start Guide v1 37.png
Figure 36 : Trancão manning distribution based on Corine 2006 map.
Step 1.4 – Get meteorology data into MOHID Time Series format

This simulation with complete hydrology should have measured meteorological data (precipitation, air temperature, solar radiation, wind velocity and relative humidity) so a constant value as before is not suited. The change from constant to time series file reading is straightforward in MOHID as can be seen in the Trancão sample between Sim #1 and Sim #2 in Atmosphere_X.dat file. But the reading of time series forces the user to prepare time series in the MOHID format.

Follow instructions in MOHID Studio User Guide in chapter 10.1 to understand MOHID format for time series[7].

If redoing the Trancão case copy the atmosphere files (SJT_....srm) from the folder General Data\Boundary Conditions in the sample project to your project in the same location.

After the time series files are done they can be referred in the Atmosphere_X.dat (see below).

Step 2 – Create a new simulation (copy a previous)

As mentioned before new simulations should be copied from others so that the settings are predefined. In this case create a new simulation as before but do not delete any Module (now Porous Media and Geometry are needed) and add Module Vegetation ( Figure 37).

MOHID Studio - MOHID Land Quick Start Guide v1 38.png
Figure 37 : MOHID Studio new simulation with Vegetation added.

Copy the files from the previous simulation to this one so some of the info is already filled.

Step 3 - Define the simulation

The changes from the last simulation is that the atmosphere will be forced in a more realistic way with all the properties and with measured time series and it is added porous media and vegetation.

Step 3.1 – Configure Atmosphere

Copy only the atmosphere data file from the Trancão sample from Sim #2 since it is similar to the needed because it has all the atmosphere properties blocks with read time series.

Modify the time series paths from precipitation, solar radiation, air temperature, relative humidity and wind velocity to the ones that were prepared. In the case of redoing Trancão sample is not needed since the files were copied to the same location.

Step 3.2 – Configure Geometry and Porous Media

Copy only the Porous Media and Geometry data files from the Trancão sample from Sim #2. For the Geometry (vertical geometry) leave the file unchanged if you do not have soil depths higher than 5,5m. If higher depths need to increase number of vertical layers in keyword LAYERS) and/or the thickness of the layers (keyword LAYERTHICKNESS). If the user changes the number of layers than needs to update the Porous Media file in horizon block in keyword KUB – K Upper Boundary).

For the Porous Media file need to update:

  • the bottom of the soil, changing the path to the file in keyword BOTTOM_FILE with the one created above with the tool "Porous Media".
  • the property "SoilID" in horizon definition with the file path of the SoilID created above if using spatially distributed soil with the tool "From Shapefile"; if the user wants to use a constant soil everywhere change keyword INITIALIZATION_METHOD from ASCII_FILE to CONSTANT and the SoilID will be defined by keyword DEFAULTVALUE. Also add keyword REMAIN_CONSTANT : 1.
  • the property "waterlevel" in block beginwaterlevel/endwaterlevel with the file path created above with the tool "Porous Media".
  • the property "impermeablefraction" in block beginimpermeablefraction/endimpermeablefraction definition with the file path of the impermeabilization created above if using spatially distribution with the tool "From Shapefile"; if the user wants to use a constant value everywhere change keyword INITIALIZATION_METHOD from ASCII_FILE to CONSTANT and the impermeable fraction will be defined by keyword DEFAULTVALUE. Also add keyword REMAIN_CONSTANT : 1.
  • The soil database in blocks beginsoiltype/endsoiltype. This info has to exist for all the soil types existing in the watershed (defined in the "SoilID" property) and the database has to have consecutive IDs starting in 1. If doing the Trancão example than there is no need to change nothing since the soil database is consistent with the defined "SoilID" property.
Step 3.3 – Configure Runoff

Copy only the Runoff data file from the Trancão sample from Sim #2.

If using manning spatially distributed and in that case after the copy need to update the file path with the one created above with the tool "From Shapefile" in block BeginOverLandCoefficient/EndOverLandCoefficient. If the user wants to use the same manning resistance everywhere than there is no need to copy the file and it will be used a constant value as in Sim #1.

Step 3.4 – Configure Vegetation

Copy only the Vegetation data file from the Trancão sample from Sim #2.

Copy also in "File Explorer" the content of folder General Data\Other\Vegetation (except VegetationID.dat) from the Trancão sample to the same folder in your project.

Need to update:

  • The vegetation ID in block begin_AgriculturalPractices/ end_AgriculturalPractices with the file path of the vegetation created above if using spatially distribution; if the user wants to use a constant vegetation everywhere change keyword INITIALIZATION_METHOD from ASCII_FILE to CONSTANT and the vegetation will be defined by keyword DEFAULTVALUE. Also add keyword REMAIN_CONSTANT : 1.
  • The path to file PARAMETERS_FILE should be correct since the file was copied to the same folder structure. Verify that all the agricultural practices ID’s existing in the watershed are present in this file[8].
  • The path to file FEDDES_DATABASE should be correct since the file was copied to the same folder structure. Verify that all the agricultural practices existing in the watershed are present in this file[9].
  • The vegetation root depth and leaf area index in property blocks with the file paths created above (tool "From Shapefile") if using spatially distribution; if the user wants to use a constant root depth and leaf area index everywhere change in each of these properties block the keyword INITIALIZATION_METHOD from ASCII_FILE to CONSTANT and the property will be defined by keyword DEFAULTVALUE. Also add keyword REMAIN_CONSTANT : 1.
Step 3.5 – Configure Basin

Copy only the Basin data file from the Trancão sample from Sim #2.

In this file there is no need for changes just notice that it is connected porous media having keyword POROUS_MEDIA : 1, connected evapotranspiration with EVAPOTRANSPIRATION : 1, EVAPOTRANSPIRATION_METHOD : 2 to account transpiration and evaporation and connected vegetation VEGETATION : 1. Also the reference evapotranspiration property is connected (it will be computed from meteorology).

Step 4 – Run the simulation and explore results

Everything now is prepared to run the simulation. Verify one last time that all the paths defined inside the data files exist, that output frequency (time series and HDF) in each file is correct for the simulation period and that the DTM was defined in the domain. Follow the same instructions as in the previous simulation to run and to explore the results. New results are available as Porous Media or Vegetation HDF’s or time series (.srp and .srvg).

If the model runs but the output window shows that cells elevation was changed and at the end the message says that a new bathymetry was created, replace the BOTTOM_FILE in Porous Media_X.dat with the new one (usually appends _v01 to the name of the file). This process is the model changing the bottom so that too thin cells do not occur.

If the model stops with a message that a vegetation ID was not found in vegetation parameters or Feddes database that is because these files need to have all ID’s that are defined in agricultural practices (file paths in Vegetation_X.dat). Add the ID that the model warns about in vegetation parameters file (just need to add one block with the vegetation ID and the same ID in agricultural practice ID) and in Feddes database file (need to choose what will be the Feddes stress heads, see above).

Figure 38 presents the water column map in one instant result of opening the Runoff.hdf5 and selecting property "water column" to plot. The user should explore all the results provided by the simulation.

MOHID Studio - MOHID Land Quick Start Guide v1 39.png
Figure 38 : Trancão water column for full hydrology simulation.

Creating your own project - Simulating sediment transport

To simulate sediment transport the property cohesive sediment needs to exist in the drainage network and in the runoff. In the drainage network there is no separation of water and properties and everything is dealt in the same Module but in runoff a new Module has to be added - the Runoff Properties.

Step 1 – Create a new simulation (copy a previous)

As said before new simulations should be copied from others so that the settings are predefined. In this case create a new simulation as before and add Module Vegetation and add Module Runoff Properties.

Copy the files from the previous simulation to this one so some of the info is already filled.

Step 2 - Define the simulation

The difference from the last simulation is that cohesive sediment property has to be added in Module Drainage Network and that Module Runoff Properties with cohesive sediment has to be added and connected in Module Basin.

Step 2.1 – Add cohesive sediment property and parameters in Drainage Network file

Copy only the Drainage Network data file from the Trancão sample in Sim #3 to this simulation. Verify that the difference was the property block with cohesive sediment that was added. This block defines the initial cohesive sediment concentration everywhere in the river in the water (if any in the beginning) in keyword DEFAULTVALUE, the initial cohesive sediment concentration everywhere in the river in the bottom (kg/m2) in keyword BOTTOM_CONC, the critical shear stress for erosion, over which erosion occurs in keyword CRIT_SS_EROSION, the critical shear stress for deposition, below which deposition occurs in keyword CRIT_SS_DEPOSITION, erodibility in keyword EROSION_COEF and deposition velocity (m/s) in keyword WS_VALUE. All these parameters should be calibrated for the place in question.

Need to verify the path of the drainage network file in keyword NETWORK_FILE since it may be different from the Trancão sample.

Step 2.2 – Define cohesive sediment property and parameters in Runoff Properties

Copy only the Runoff Properties data file from the Trancão sample in Sim #3 to this simulation. Verify that the runoff properties cohesive sediment is very similar to the drainage network but the parameters instead of being inside the property block are outside in independent blocks. This allows that instead of a constant value also an ASCII_FILE may be provided and parameters may be spatially distributed (e.g. dependent on soil). All these parameters should be calibrated for the place in question.

Step 2.3 – Define Basin

Copy only the Basin data file from the Trancão sample in Sim #3 to this simulation. Verify that the runoff properties is connected in basin.

Step 3 – Run the simulation and explore results

Everything now is prepared to run the simulation. Verify one last time that all the paths defined inside the data files exist, that output frequency (time series and HDF) in each file is correct for the simulation period and that the DTM was defined in the domain. Follow the same instructions as in the previous simulation to run and to explore the results. New results are available as Runoff Properties HDF or time series (.srrp).

Figure 39 presents the cohesive sediment map in one instant result of opening the Runoff Properties.hdf5 and selecting property "cohesive sediment" and opening Drainage Network.hdf5 and selecting same property to plot. The user should explore all the results provided by the simulation.

MOHID Studio - MOHID Land Quick Start Guide v1 40.png
Figure 39 : Trancão cohesive sediment for sediment transport simulation.

Creating your own project - Simulating point discharges

To simulate point discharges a new Module is needed – Discharges to define discharge location in the river discharge, flow and properties discharged. And the properties that are discharged need to be present in Module Runoff Properties and Module Drainage Network and dissolved properties discharged need to be present in Module Porous Media Properties (particulated properties do not enter soil) so also this Module needs to be added.

Step 1 – Define the point discharges

Step 1.1 – Define discharges locations

First we need to define where the discharge will be placed, in which node.

To do that open the drainage network file ("Map" ribbon and in "ASCII" group press "Network" and open the file from folder General Data\Digital Terrain and select "Geographic" coordinates).

If redoing the Trancão sample, open also the location of the WWTP ("Map" ribbon and in "Vector Data" press "XML" and open the file "LocalETARS.xml" in folder General Data\Other\WWTP and select "Geographic" coordinates) and query the xml to know the names of the WWTP ( Figure 40). If other project open your location of point sources.

MOHID Studio - MOHID Land Quick Start Guide v1 41.png
Figure 40 : Location of the WWTP discharges in the Tagus sample.

Then query the drainage network and select the nodes where the discharge should be done. Get the "Upstream Node" and write down the node and WWTP name that will be used later.

Step 1.2 – Define flow and property discharged

After the location define the flow discharged and properties discharged (constant or time series) from data or any other assumption. The properties discharged need to exist in MOHID[10]. In case of redoing Trancão constant flow and properties will be used. The values are just for exemplification.

Step 2 – Create a new simulation (copy a previous)

As said before new simulations should be copied from others so that the settings are predefined. In this case create a new simulation as before and add Module Vegetation, add Module Runoff Properties, add Module Discharges and Module Porous Media Properties.

Copy the files from the previous simulation to this one so some of the info is already filled.

Step 3 - Define the simulation

Step 3.1 – Define Discharges file with discharged flow and properties

Copy only the Discharges data file from the Trancão sample in Sim #4 to this simulation. This example has 3 discharges with temperature, salinity, coliform, ammonia, inorganic phosphorus and cohesive sediment. The concentration values are only for exemplification are not real.

Update the number of discharges you want to make and change node discharges locations (keyword NODE_ID) accordingly to the info collected in previous step. Update also discharge names (keyword NAME) to be specific of the studied watershed.

Update discharge flows. If using constant flow define it in keyword DEFAULT_FLOW_VALUE in each discharge and remove or comment keyword DATA_BASE_FILE. If using time series flows use the latter keyword to point to the correct file in MOHID time series format and FLOW_COLUMN to select which column flow is (usually 2).

Adapt the properties blocks and properties discharge concentrations accordingly to user data or other assumptions.

Step 3.2 – Define in Drainage Network file discharged properties

Copy only the Drainage Network data file from the Trancão sample in Sim #4 to this simulation. Verify that keyword DISCHARGES outside property block was set to 1 (so that the discharge file and flow is considered). Verify also that each property has the same keyword DISCHARGES set to 1 so that the property concentration in the river is computed with discharges. If any property had the DISCHARGES set to 0 and the property is discharged than only flow (dilution) will affect the river property concentration and the discharge concentration is the same as being zero for that property.

Need to verify the path of the drainage network file in keyword NETWORK_FILE since it may be different from the Trancão sample.

Step 3.3 – Define in Runoff Properties file discharged properties

Copy only the Runoff Properties data file from the Trancão sample in Sim #4 to this simulation. Verify that the difference to the last simulation is that the discharged properties were added.

Step 3.4 – Define in Porous Media Properties file dissolved discharged properties

Copy only the Porous Media Properties data file from the Trancão sample in Sim #4 to this simulation. This Module is very similar to Runoff Properties and the dissolved discharged properties were added.

Step 3.5 – Activate in in Basin the new Module Porous Media Properties

Copy only the Basin data file from the Trancão sample in Sim #4 to this simulation. Verify that the difference to the last simulation is that the Runoff Properties was connected.

Step 4 – Run the simulation and explore results

Everything now is prepared to run the simulation. Verify one last time that all the paths defined inside the data files exist, that output frequency (time series and HDF) in each file is correct for the simulation period and that the DTM was defined in the domain. Follow the same instructions as in the previous simulation to run and to explore the results. New results are available as Porous Media Properties HDF or time series (.srpp).

Figure 41 presents the coliform bacteria map in one instant result of opening the Drainage Network.hdf5 and Runoff Properties.hdf5 and selecting "fecal coliform" to plot. The user should explore all the results provided by the simulation.

MOHID Studio - MOHID Land Quick Start Guide v1 42.png
Figure 41 : Trancão fecal coliforms for WWTP simulation (arbitrary discharge, just for exemplification).

Creating your own project - Simulating nutrient transport and transformation (nutrient cycles)

This simulation represents the most complete simulation with nutrient cycle using all the Modules in MOHID Land. More complex only with vegetation growing (for long simulations).

The simulation of nutrient transport was already presented in the previous simulation in drainage network, runoff and porous media. The novelty here is the nutrient cycling in the soil through the use of SedimentQuality (bacterial activity including mineralization, nitrification, denitrification, etc.) and in the river using WaterQuality (same processes and algal activity including assimilation, respiration, mortality and grazing, etc.)[11].

Step 1 – Create a new simulation (copy a previous)

As said before new simulations should be copied from others so that the settings are predefined. In this case create a new simulation as before and add Module Vegetation, add Module Runoff Properties, add Module Discharges, Module Porous Media Properties, Module Sediment Quality and Module Water Quality.

Copy the files from the previous simulation to this one so some of the info is already filled.

Step 2 - Define the simulation

Step 2.1 - Add to Porous Media Properties file the properties needed to run the quality models

Copy only the Porous Media Properties data file from the Trancão sample in Sim #5 to this simulation. Verify that a lot of properties were added (the dissolved properties needed to run Sediment Quality and Water Quality) and the most part has the keyword SOIL_QUALITY set to 1 so that the soil quality model may change the concentration due to bacteria activity.

Step 2.2 - Add Sediment Quality file with defined rates

Copy only the SedimentQuality data file from the Trancão sample in Sim #5 to this simulation. In this file are the main options to compute (which species to compute) and the maximum rates (without limitations) for each process. All these parameters should be calibrated for the place in question.

Step 2.3 - Add to Drainage Network file the properties needed to run the quality models

Copy only the Drainage Network data file from the Trancão sample in Sim #5 to this simulation. Verify that a lot of properties were added (the properties needed to run Water Quality and the dissolved ones needed to run Sediment Quality) and the most part has the keyword WATER_QUALITY set to 1 so that the water quality model may change the concentration due to algal and bacteria activity.

Need to verify the path of the drainage network file in keyword NETWORK_FILE since it may be different from the Trancão sample.

Step 2.4 - Add Water Quality file with defined rates

Copy only the WaterQuality data file from the Trancão sample in Sim #5 to this simulation. In this file are the main options to compute (which species to compute) and the maximum rates (without limitations) for each process. All these parameters should be calibrated for the place in question.

Step 2.5 - Add to Runoff Properties file the properties needed to run the quality models

Copy only the Runoff Properties data file from the Trancão sample in Sim #5 to this simulation. Verify that a lot of properties were added (the properties needed to run Water Quality and the dissolved ones needed to run Sediment Quality).

Step 2.6 – Define Other Files

Copy only the Vegetation data file and Discharges data file from the Trancão sample in Sim #5 to this simulation. Verify that the properties existing in the drainage network were added to the discharge. This was not needed but in fact these properties all exist in the WWTP discharge and if were not added, the effect was the same as discharging with zero concentration on these properties.

In the vegetation file it was changed the NITROGEN_STRESS to 1 and PHOSPHORUS_STRESS to 1 so that the nitrogen and phosphorus uptake by plants was considered.

Step 3 – Run the simulation and explore results

Everything now is prepared to run the simulation. Verify one last time that all the paths defined inside the data files exist, that output frequency (time series and HDF) in each file is correct for the simulation period and that the DTM was defined in the domain. Follow the same instructions as in the previous simulation to run and to explore the results. New properties exist in the HDF’s and time series.

Figure 42 presents the phytoplankton map in one instant result of opening the Drainage Network.hdf5 and Runoff Properties.hdf5 and selecting "phytoplankton" to plot. The user should explore all the results provided by the simulation.

MOHID Studio - MOHID Land Quick Start Guide v1 43.png
Figure 42 : Trancão phytoplankton for water quality simulation.

Final Remarks

This quick start-guide to implement MOHID Land intends to help first time users to quickly get used to the model and processes but may also be a starting point for every new implementation. The implementation of MOHID Land in these terms, with increasing complexity and processes added in cumulative way, gives user the sensibility to the major factors affecting hydrology and water quality for each implementation site.

Any difficulties or need for more developed information should be addressed in the MOHID channels given at the start.

We appreciate all the feed-back that you may give on the implementation of MOHID Land projects with MOHID Studio so that this guide can improve with time.


  1. However, if the user wants to use its own data, export it to ASCII grid and use the MOHID tool ConvertToXYZ (Read instruction in http://wiki.mohid.com/wiki/index.php?title=ConvertToXYZ#ASCII_Grid) to have it in format XYZ, points coordinates format for MOHID.
  2. In order to learn how to implement vegetation growth in MOHID Land refer to http://wiki.mohid.com/wiki/index.php?title=Module_Vegetation (advanced option not described here).
  3. This parameters may be obtained from soil texture with pedotransfer functions (e.g. Rosetta software http://www.ars.usda.gov/services/docs.htm?docid=8953).
  4. More info in http://eusoils.jrc.ec.europa.eu/esbn/SGDBE.html
  5. in the case that the user is using vegetation growth (not explained here) this would be SWAT vegetation ID.
  6. More info on http://www.eea.europa.eu/data-and-maps/data/corine-land-cover-2006-raster-2
  7. Hint: if you have the time series data in a spreadsheet to get the time column in days just subtract every date to the reference date.
  8. This file in this case where vegetation growth is not active is only a one to one relation between agricultural practices ID’s and crop ID’s. If the vegetation growth was active this file would have the management practices for each agricultural practices and two agricultural practices could use the same crop ID but with different management.
  9. This file represents for each crop the 4 points that define the Feddes water stress curves in relation to suction head (http://wiki.mohid.com/wiki/index.php?title=File%3APlantFeddes.PNG). The values provided are just for exemplification and the user should verify if the stress heads are suited to each vegetation type.
  10. See a list of recognized properties in MOHID in http://wiki.mohid.com/wiki/index.php?title=Properties_names.
  11. To learn more about these processes follow http://wiki.mohid.com/wiki/index.php?title=Module_SedimentQuality for SedimentQuality and http://wiki.mohid.com/wiki/index.php?title=Module_WaterQuality for WaterQuality.