iMOD User Manual version 5.2 (html)

11.1Quick Guide on iMOD and MODFLOW6

This guide gives a tour along iMOD main features, the analysis of a MODFLOW6 model and running the model. Alternatively you can run through Tutorials 1 to 5. This Quick Guide will take you probably only 25 minutes. Check the iMOD website ( for a video recording of this Quick Guide.

This guide is dedicated for new users of iMOD. We assume you are at least familiar with GIS software and you have some experience in ground water modelling. Before starting this Quick Guide iMOD must be installed as described in chapter 2.2.

About the set up of this Guide
We guide you step by step through the program. Between the steps we give you some intermezzo’s in text. On several points we refer to Tutorials or Tool description elsewhere in the iMOD manual for further reading/experiencing. All data used in this Quick Guide came together with the installation of iMOD. You find the data in this folder: {installfolder} \tutorials\Quick_Guide_iMOD

This is what you will do step by step


Figure 11.1: MODFLOW6 model area (a picture of RitaE via Pixabay

Intermezzo: iMOD Graphical User Interface (GUI):

Let’s start the tour.

A window appears called start iMOD. Here you are asked to select a new or existing iMOD project, in fact a save of a previous iMOD session. Are curious about how your work will look at the end of this guide? We prepared you a file that brings you right away to a 3D view of your MODFLOW model; including bore logs and model layers. Let’s use that file.

Automatically iMOD loads a dataset of layers, borehole locations (including borelogs) and pathlines to the 3D Tool in a second window called 3D Tool. Your display might look like the figure below (see figure 11.2).


Figure 11.2: 3D display of MODFLOW6 model including flowlines and borelogs.

The model has 19 model layers with a top elevation of the model 200 meter above Mean Sea Level (MSL) and the bottom elevation of  1600 meter below MSL.

Through the 19 layers you see some of the borelogs in the model area and a vague image of the pathlines. We will increase the transparency of the model layers to visualize the boreholes and pathlines more distinctively.

Your display might look like the figure below.


Figure 11.3: Professional 3D display of MODFLOW6 model including flowlines and borelogs. Transparent

There is much more to explore with the 3D Tool but for now we leave with this.

Now we are back on the main iMOD window, the top view.
Let’s try to open and display some model files. Therefore iMOD uses the window iMOD Manager, just containing an overview of all open and loaded files.

Intermezzo: iMOD file Types

Just like in any GIS software, in iMOD you can load different types of files and each file has its own format for performance reasons mainly. These are the main file types:


File type






File containing raster data e.g. digital elevation model or spatially distributed precipitation data.
> In iMOD you can convert Esri grid files (*.ASC) into IDF format.




File containing (poly)lines and/or points describing line- and/or point based data like faults, river stretches or state boundaries.
> In iMOD you can convert Esri shape file (*.SHP) into GEN format.




File containing point information like well locations. If necessary, additional parameter data can be added like abstraction rates for wells, time series data for observation points and borelog description on borelog locations.
> User your Text editor, Excel or a scripting language to create any IPF file.




This file is a steering file for other relates files that describe rivers location including parameters like cross-sections and water levels.




files with pathlines and information about age, velocity and particle numbers. For more information on iMOD file formats see chapter 9.

Let us load 2 file types in iMOD; a grid file containing the land use distribution and a river line.
Standard grid format is the IDF file (see the above intermezzo). For now, the land use grid is an Esri grid file (*.ASC).

As an overlay for a better orientation, we will now load a Line file with the location of the river. The standard line/polygon format in iMOD is the GEN file (see the above intermezzo). For now, we import the river line file as an Esri shape file (*.SHP).

Now we will load input files for a MODFLOW6 model. Before we do so, let us explain in short the data handling in iMOD.

Intermezzo: MODFLOW model file policy

The input of a MODFLOW model contains different parameters like starting conditions, geohydrological parameters and boundary conditions like recharge, abstraction and river elements. In iMOD the input is stored for each parameter in single files, both for Steady State and/or Transient models. Therefore, iMOD has no single large size database file, this is all done for performance reasons. From going through the tutorial data in the previous steps you might found out probably, however, this is how the folder structure might look like for MODFLOW in- and output (see figure 11.4). Feel free to check the folders in more detail in Windows Explorer or your preferred file manager.

pictures/Ch-getting-started/explorer view1.png

Figure 11.4: Folder structure for Modflow model input in folder Database

Instead of importing all MODFLOW6 input files separately to IMOD (as we just did with the land use file), IMOD can store references to all your MODFLOW6 input files in a single file: the Project File (*.PRJ). We will load a prepared PRJ file and display some of the model input files.

As a modeller you recognize in the TreeView a list of available parameters in MODFLOW (as well as parameters for MT3D and SEAWAT).


Figure 11.5: Content iMOD Manager

Now all references to our MODFLOW6 input are loaded as you can see from the (  pictures/Ch-imod-tutorials/plus-sign.png ) icons for the specific topics in the TreeView list. You will recognize MODFLOW topics. You might be interested in the model input for Recharge and the Layer model. Let’s have a look at those input parameters.


Figure 11.6: iMOD display with the TOP level of layer 1 and the river location.

The iMOD Cross-section tool
In the previous step, we loaded the TOP elevation of all layers. Instead of a display in top view only, it is sometimes more helpful to display the layermodel vertically, in a cross section. iMOD supports this option with the Cross-section tool. But first let us also load the borelogs that were used to develop this layer model. We will display the 2 datasets together.


Figure 11.7: Fresh bore profile prepared and ready to be described geologically
(photo: Roelof Stuurman).

pictures/Ch-getting-started/cross section.png

Figure 11.8: View of the Cross Section window with all model layers together with the available borelogs.

In the cross-section window, iMOD has drawn both the TOP elevations of all layers along the line as well as those borelogs that lay within 250m distance of the cross-section.

Intermezzo: iMOD efficient/flexible modelling process

As we saw, MODFLOW input data can be of different types (points, grids, lines). And besides that, grids can also have different cell sizes. For instance, geological information might be available on 250 meter scale while land use data is available on a 25 meter scale. In iMOD you do not need to project data into a fixed model area or size before running a model. You can keep your basic data as it is. iMOD performs the clipping and scaling for you. figure 11.9 explains a bit more about the steps we take in the iMOD approach to run one or more (sub) models.


Figure 11.9: Modelling steps, the iMOD approach.

In the previous steps we loaded the PROJECT FILE with MODELDATA so now we can start the SIMULATION MANAGER to really run the model with MODFLOW6.


Figure 11.10: The Simulation Manager window, define the modeltype and modelname

Intermezzo: MODFLOW6 and submoddeling

MODFLOW6 supports the option to run a model that consist of several nested submodels. It allows the modeller to define different cell sizes for each submodel. Therefore iMOD needs a regular polygon file (*.GEN) describing the polygons of the submodels. This is regular GEN file with an additional attribute that represents the cell size. For this quick guide we’ve prepared for you such a polygon file describing 3 sub models and cell sizes (see figure 11.11).


Figure 11.11: Example of 3 nested submodels. Cell size 500m, 250m and 50m.

For more practice on creating such a file for MODFLOW6 we refer to the MODFLOW6 Tutorial in section 11.17.

13. Return to the Simulation Manager window, tab Space dim., where we selected the option Gen file (MODFLOW6).

  • 14. Click the Open file button (  pictures/h6-h71/image960.png ) next to this option and search for the polygon file named {installfolder} \tutorials\Quick_Guide_iMOD \MODFLOW-submodels.GEN.

  • 15. Click the Open button and the GEN file is loaded to the main window displaying the boundaries of the 3 submodels together with the rasters within each submodel based on the given cell sizes.

  • 16. Click the Start.. button to start the MODFLOW6 model.

  • 17. A window pops up with the name of the model to be created and the question if you are sure to continue. Click the Yes button to continue.
    NOTE: The process of preparation and execution of the model will take 1 or 2 minutes. In the mean time your cursor pointer changes into (  pictures/Ch-getting-started/ID_ICONWAIT.png ), the ’wait’ status.

  • 18. After a successful run a message appears: ’Successful simulation using MODFLOW6’. Click OK to close this message.
    In case the run was not successful, the message is ’an error occurred’. In that case, try to redo the previous steps or report it in the online iMOD forum.

  • 19. Close the Model Simulation window by selecting the Close button.

  • Model results
    Let’s have a look at some model results. figure 11.12 is an example of the folder structure for the (output) folders and files of this MODFLOW6 model. From each of the 3 submodels we will load the calculated head for layer 1.

    pictures/Ch-getting-started/explorer view3.png

    Figure 11.12: MODFLOW6 output for My1stModel over 3 submodels (GWF_{i}).

    Because the 3 IDF files overlap, you only see the first head file on a 500m scale. To see all selected IDF file together we have to apply NODATA Transparency.


    Figure 11.13: Calculated Heads for 3 submodels combined.

    In the pattern of the IDF files you recognize the 3 submodels we defined for this model. The models are calculated in conjunction, so we see a smooth transition between the calculated Heads in the different submodels. In the submodel with the abstraction well we see cellsizes of 25 m.

    Pathline analysis
    In iMOD it is also possible to calculate pathlines, a post processing step based on MODPATH ([Pollock(1994)]). For more info on MODPATH check the TUTORIAL in section 11.5 and section 11.6. From pathline analysis drinking water companies can determine the future water quality of their source. iMOD saves calculated pathlines in an IFF file (ASCII). For this tutorial such an IFF is prepared describing the flowlines for points starting from the surface level towards abstraction wells.


    Figure 11.14: Drinking water quality is influenced by the infiltration area and subsoil characteristics (a picture of Rajesh Balouria via Pixabay).

    NOTE. Our MODFLOW6 model contains 3 submodels. With standard MODPATH7 it is not possible to calculate pathlines crossing boundaries of submodels, this is under development by the USGS still. Therefore this example of the pathlines file was calculated from a MODFLOW6 run without submodels on a 50 meter scale.

    The pathlines have a default grey colour. Let’s colour the pathlines according to age.

    Let us try now to display all files in the 3D viewer, just as we saw in the first steps of this Tutorial.

    Feel free to play around within the 3D tool. Some suggestions:

    Here the Quick Guide for iMOD and MODFLOW6 ends. Hope you enjoyed the ride.