iMOD User Manual version 5.2 (html)

11.6Tutorial 5: Solid Tool

This tutorial gives a short introduction in enhancing the groundwater flow model from section 11.5 with an aquitard that has been characterized by several boreholes. See for a more detailed description of the Solid Tool section 7.4.


This is what you will do:

Required Data

For this tutorial you need the following iMOD Data Folders:

All these files are located in/below the folder:{installfolder} \tutorials \TUT_ SOLID_BUILDING.

Note: {installfolder} refers to the full path of the directory you installed iMOD in (e.g. D:\iMOD).
Note: If you are a left-handed person and you converted your mouse button settings, ’left mouse button’ should be ’right mouse button’ and vice versa in these tutorials.

Beside this data you will need the iMODFLOW executable to make the model computations, see step 1. in section 11.5.

Getting Started

Let’s start as we did in section 11.5 by loading the outline of the island (*.PNG file) and the contour lines (*.GEN file). First we add a sketch of the outline of the island.

Now we add the contour lines.

We continue by loading the IDF of the uppermost interface of our model (the actual surface-level).

Now we have an IDF of the uppermost interface we need to have an IDF for our lowermost interface as well (to start with; this can be modified later). So, we will copy the SURFACE_LEVEL.IDF and assign a default value of 20m-MSL and call it BEDROCK.IDF. We have done that for you, so please open this file in iMOD.

These two files describe the vertical and horizontal limits of our model. In-between there exists an aquitard that has been identified by several boreholes, when they we’re installing the well.


Figure 11.80: Sketch of a flow pattern that might occur in our island model.

Boreholes When they drilled the well in the early 80’s, the borehole company found some clays with low permeable material (less than 0.0001 m/day). Probably these are some ancient deposits, but they can interfere with the flowpath to the well screen and therefore might decrease the level of sustainability of the well. To this end, they decided to collect more information about the extent of this clay layer by drilling additional boreholes. A total of 5 boreholes were drilled, let’s start by loading these in iMOD.

The syntax of the file BOREHOLES.IPF is as described in more detail in section 9.7. For now, each location of the boreholes has an x- and y- coordinate and a reference to an attached textfile that describes the actual borelog. Let’s see how the subsoil should look like whenever we include the boreholes.


Figure 11.81: Example of a 3D-image of boreholes of the hypothetical island.

From the figure given above, it seems that our estimation of the bedrock depth is not accurate as the boreholes show an increasing bedrock depth from the west to the east. Moreover, we can clearly observe a clay layer (green) in-between the aquifer (yellow). This clay layer has its greatest thickness in the centre of the island (off course) and thins out to the side of the island. Probably eroded by some ancient seas. We are going to use the Solid Tool to construct the interfaces that describe the top- and bottom elevation of the aquitard, as well as adapting the bedrock level of the limestone.

Create a Solid

A solid is a representation of the subsoil divided into separate interfaces, such as clay and other lower- or higher permeabilities. It contains a set of continuous interfaces that exist throughout the model domain and can be used in a groundwater flow model.


Figure 11.82: The ’Create New Solid’ window.

iMOD will use the selected IDF-files (SURFACE_LEVEL.IDF and BEDROCK.IDF) as the uppermost and lowermost interfaces of our model. It is important that the files are selected in the right sequence (from the top to the bottom). iMOD can add extra interfaces whenever you specify that, so based on the two selected IDF-files iMOD can create extra interfaces in-between. In our modeling project, we need at least two model layers, one to describe the groundwater head above the aquitard, and one to describe the situation underneath.

As you can see, the names for the top and bottom interfaces are changed into INT_L1.IDF and INT_L4.IDF. These are copied from the SURFACE_LEVEL.IDF and BEDROCK.IDF, respectively. The other interfaces INT_L2.IDF and INT_L3.IDF are interfaces that iMOD created and are by default the mids in-between the surface (L1) and the bedrock level (L4). All these files are located in the folder . \IMOD_USER \SOLIDS \ISLAND.


Figure 11.83: Example of the initial Solid.

You can see how the current solid looks like, it contains a single aquifer on top of the (blue to pink) aquitard, and another aquifer beneath it. It is not very accurate though, compared to the boreholes. We are going to manipulate the aquitard such that is resembles the boreholes more realistic.

Here, you can enter a name for the cross-section. We suggest that you enter the name [CROSSB7B1B5B3], so it will be clear, in future, what cross-section this is.

Furthermore, this window offers the possibility to start your initial guess for the cross-section using the current values for those interfaces.


Figure 11.85: The ’Fit Interfaces’ window.

iMOD will fit the interface along the cross-section on the values read from the appropriate IDF, so in this case iMOD will create a line for the [Top Layer 2] (third row in the table) on the content of the ISLAND \INT_L3.IDF. The accuracy of this fit is determined by the Tolerance, which is set to [1.0] meter, which is rather high for this case; however, it is fine for now. Feel free to change the tolerance values to see the impact.

iMOD will fit each line to the corresponding IDF-files, the result is presented below.


Figure 11.86: Result of the initial guess for the cross-section based on the values entered in the previous ’Fit Interfaces’ window.

Now we can do two things:

Note: iMOD will connect the interfaces through all boreholes in the cross-section. Bear in mind that boreholes, even some distance away from your cross section, might be projected on the cross-section. This can blur your view. To avoid distant boreholes to be projected, decrease the Fade, view depth on the Misc. tab on Cross-Section Properties window. Go there by clickin the properties button (  pictures/h6-h71/image965.png ) on the Location tab.


Figure 11.87: Result of adjusting the nodes on each line such that the line crosses each borehole at the right position using the ’Fit’ button.

For now we will accept this cross-section.

Okay, let us define the other cross-sections. Therefor go to the tab locations in the window Draw Cross-Section and follow the steps 27. upto 31. for the different cross-sections. Simply press the New Cross-Section button (  pictures/h72-end/image1104.png ) again to start another cross-section. We suggest you draw the following cross-sections (you’re free to draw other combinations as well):

[CROSSB7B1B5B3]: B7-B1-B5-B3 (you just did this one!)
[CROSSB6B1B2]: B6-B1-B2
[CROSSB4B7B2B3]: B4-B7-B2-B3
[CROSSB4B6B3]: B4-B6-B3

iMOD will save the current cross-sections into separate files, e.g. called CROSSB7B1B5B3.SPF in the . \IMOD_USER \SOLIDS \ISLAND folder. Also the ISLAND.SOL will be adjusted such that it includes a reference to this CROSSB7B1B5B3.SPF. Please have a look in the ISLAND.SOL by pressing the Information button (  pictures/h72-end/image1105.png ).

Your result might look like the following example.


Figure 11.88: Example of the outline of the cross-sections.

Bear in mind that the area outside the cross-sections will be extrapolated from all cross-sections. You’re allowed to define other cross-sections in those areas too, to direct the interpolation more.


Figure 11.89: Example of a 3D image of the outline of the cross-sections.

Because a solid with cross-sections is active now, the Fence Diagrams tab is active now. On that tab you’ll find a list of all the cross-sections, you can select them all or select them individually.


Figure 11.90: 3D image of the individual cross-section [CROSSB7B1B5B3].

Our next step is to create a fully 3D interpretation of the interfaces by numerical interpolation. The interpolation is based on the cross-sections.

In this window you’ll be allowed to determine what elevations/interfaces need to be computed. Since the top elevation for our first model layer is the SURFACE_LEVEL.IDF (see step 6.) we will not recompute that interface, so we turn it off.

We will overwrite our initial elevations/interfaces since that will increase the performance of our next interpolations. Moreover, we will be able to see any update of our interfaces more easily.


Figure 11.91: Example of the ’Compute Interfaces’ window.

iMOD uses as default Kriging interpolation. This is far-out the best suitable interpolation method for these interfaces.


Figure 11.92: Example of the used Kriging Settings.


Figure 11.93: Example of the cross-section CROSSB7B1B5B3 after interpolation.

Pretty cool, but also a bit unrealistic. We can modify each cross-section easily to become more smooth.


Figure 11.94: Editing the interfaces of cross-section CROSSB7B1B3B5.


Figure 11.95: Editing the interfaces of cross-section CROSSB6B1B2.

Be aware of the fact that whenever you move a node into the neighbourhood of another node from another line, iMOD will try to snap it. Whenever the line turns green, lines will be overlapping each other perfectly, which means that there will be no thickness left for an aquitard. In this way, you can create a hole in the aquitard.


Figure 11.96: The cross-section CROSSB6B1B2 after manual modification.


Figure 11.97: 3D image of the computed elevations of cross-section CROSSB6B1B2 and one of the intersecting cross-sections.


Figure 11.98: Same cross-sections as previous figure, but now seen from below using transparency view settings.

The Kriging algorithm generates the uncertainty of the estimate as a standard deviation (m). These files can be visualised per interface, they are saved in the same folder as the computed interfaces and included the name _STDEV in the IDF file names, e.g. \IMOD_USER\SOLIDS\ISLAND\INT_L2_STDEV.IDF.


Figure 11.99: Example of the estimated standard deviation of the estimated interface.

Okay, for now this looks quite nice, we’re done with our solid.

We will examine what the consequences are for the flow paths towards the well. In section 11.5 we’ve constructed a model from scratch and we will anticipate on your knowledge to do that again. We start with the requirements for this particular three-layered model.

We have used this Project Manager in section 11.5 in detail. Please refer to that section for more information. Here, we will create the necessary model configuration as outlined in table 11.4. In blue you find the changed parameters.

Table 11.4: Model requirements for a confined, steady-state three layered model.

Parameter model layer IDF/Constant Value
2,3 1
(SHD) Starting Heads 1,2,3 0.0 m+MSL
2 ’SURFACE_LEVEL.IDF’ with Addition Value -1.0 m
(BOT) Bottom Elevation 1 . \DBASE \SURFACE_LEVEL.IDF
(BOT) Bottom Elevation 1 ’SURFACE_LEVEL.IDF’ with Addition Value -1.0 m
(KHV) Horizontal Permeability 1,2,3 25.0 m/day
(KVA) Vertical Anisotropy 1,2,3 1.0
(KVV) Vertical Permeability 1 25.0 m/day
2 0.001 m/day (1000 days/m)
(WEL) Wells 3 . \DBASE \WELL.IPF
(RCH) Net Recharge 1 0.5 [standard unit is mm/day]

So, the only difference with our previous/first model in table 11.2 is that we use different values for our Top- and Bottom elevations. We could open the Project file you saved in section 11.5 but for reasons of error reduction, we now load the prepared Project file.


Figure 11.100: Example of the computed heads using the adjusted subsurface geometry.

You can see what the effects are from the hole in the aquitard (denoted by the white arrow). So, let’s compute the flowlines towards the well. Instead of computing a forward tracing, we will compute a backward trace from the well back to its infiltration areas.


Figure 11.101: Windows a: ’Start Point Definition’ and b: ’Pathline Simulation.

We’ve have used this functionality before (see section 11.5, steps 18. onwards), so we will be brief this time.

If your model ran correctly you find 3 checks in the section on the right Existing Budget terms and the other tabs of the window will be available (see figure 11.101-b). If this is not the case, you probably ran the model without including output for budgets and no pathlines can be calculated yet. Go back to step 57. to run the model again including flux output.

If you did not save any IPS file, follow the steps 18. onwards mentioned in section 11.5, to fill in this window. Though we need to do a slight modification too. Since we’ve changed the interfaces of our model we should change the Pathline settings accordingly. So, …


Figure 11.102: The ’Input Properties’ window that appears when choosing ’Start Pathline Simulation...’ from the main menu, followed by selecting the ’Input’ tab, and clicking the ’Properties’ button at the right of ’Top- and Bottom files’ field of the ’Pathline Simulation’ window.

iMOD will display the results directly on screen.

Finally, we complete this Tutorial with the results of our well capture zone in a 3D environment.


Figure 11.103: The final pathlines representing the capture zone of the well; capture zone is here defined as that part of the groundwater flow system that contributes water to the pumped well.