This tutorial gives a brief introduction to the usage of MODFLOW6 regarding submodeling. The technique of sub modelling is extensively described in the MODFLOW6 manual (for actual documents click here for the link to the USGS website).
This is what you will do:
• Construct polygons to define the submodel of MODFLOW6;
• Start the iMOD Project Manager and configure it for usage with MODFLOW6;
• Run the MODFLOW6 model and analyse the results;
• Add a well and observe the effect of local network refinements.
For this tutorial you need the following iMOD Data Files/folders in {tutorialfolder} \TUT_MF6:
• MF6.PRJ: describes the model;
• . \DBASE \BND \BND.IDF: describes the model boundaries;
• . \DBASE \RIV \RIVS.IDF: describes the stage of the river;
• . \DBASE \RIV \RIVB.IDF: describes the bottom of the river;
• . \DBASE \RIV \RIVC.IDF: describes the conductance of the river;
• . \DBASE \GEN \THREE_POLYGON_100_50_25.GEN: describes the polygons of the sub models (this files has to be created optionally)
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.
1. Launch iMOD by double clicking the iMOD executable in Windows Explorer.
2. Select the option Create a new iMOD Project.
3. Click the Start button to initiate iMOD with an empty configuration.
Let’s open the model configuration in the iMOD Project Manager.
4. Click the option View from the main window and select the option Project Manager to start the iMOD Project Manager window.
5. Click the Open button (
) and select the file {path of tutorialfolder} \TUT_MF6\MF6.PRJ.
The Project Manager window displays more then 50 Topics. Most of them are not needed in this model set up. From iMOD version 5.0 it is possible to thin-out the list of topics in the Treeview. This gives more insight of the active topics. Let’s select only those topics that are most relevant for MODFLOW6.
6. Select the tab Configuration from the iMOD Project Manager window.
7. Select the option [MODFLOW6] from the Model Configuration dropdown menu.
Now you notice that the number of topics has decreased. That’s nice isn’t it. Now the overview is more comprehensible. Notice that the title of the tab is changed into [Treeview MODFLOW6]. The topics that are currently filled in with data are checked (Active). If we need more topics, we can easily activate the appropriate topic from the list. The Treeview will be updated once we select the tab with the treeview again. Let’s display the location of the rivers.
8. Select the first tab Treeview MODFLOW6.
9. Select the option [(RIV) Rivers] from the Treeview.
10. Click the Draw button (
) to load all three files from the RIV package in the iMOD Manager.
11. Click the Zoom All button (
) from the main window to set the window to fully display the IDF file.
12. Select the option [View] from the main window and than select the option [Show IDF Features] and then the option [IDF Rasterlines].
The following image should be on your graphical canvas.
Figure 11.198: Example of the current window layout.
Let’s define the sub models and their corresponding cell sizes that we want to compute with MODFLOW6. Therefore we need to create a regular GEN file with an additional attribute that represents the cell size. Our first sub model will be the outer limit of our model, we do that by drawing a rectangle, after that we specify two sub model with an irregular boundary. Let’s create a GEN that describes three sub models.
13. Select the option [Edit] from the main window and then the option [Create Features] and finally [Create a GEN] to start the Create GENs window.
14. Select the Draw (
) button to start the Select window.
It starts the Select window in which the shape type can be selected. Our first sub model will be a rectangle, thus we select that shape.
15. Select the item Rectangle.
16. Click the OK button to close the Select window.
17. Click your left mouse button somewhere outside the lower-left raster cel. Our model need to be at least as large as our input data.
18. Drag the mouse to the upper-right corner and click the left mouse button again, somewhere outside the most upper-right raster cell.
So, that’s our first sub model, congrats ! Let’s add the other one.
19. Select the Draw (
) button to start the Select window.
20. Select the item Polygon.
21. Click the OK button to close the Select window.
22. Click your left mouse button somewhere inside our rectangle and draw an irregular polygon by repeatedly clicking your left-mouse button. Make sure there is some space inside, to draw another (our third sub model).
23. Click your right mouse button to finish the polygon.
And finally, we define our last, smallest sub model.
24. Select the Draw (
) button to start the Select window.
25. Select the item Polygon.
26. Click the OK button to close the Select window.
27. Click your left mouse button somewhere inside our polygon and draw an irregular polygon by repeatedly clicking your left-mouse button. In case the Create Gen window blocks your screen, you can pick it up and move during drawing.
28. Click your right mouse button to finish the polygon.
We need to add an attribute to these shapes that represents the cell size inside all of them.
29. Select all entries from the list on the Create GENs window using Ctrl+Left-Mouse-Button or Shift+Left-Mouse-Button.
30. Click the Information (
) button to start the Attribute Values for Current (selected) Polygons/Lines/Points window.
Here, we can add an additional column to represent the cell sizes per shape.
31. Click the Add Attribute button (
) to start a floating Input window.
32. Enter the name [CellSize] at the input field Give an attribute name. iMOD uses this second column to look for the cell size. You are free to choose another attribute name.
33. Click the OK button to close the Input window.
34. Fill in the cell sizes [100,50,25] for the shapes 1 (Rectangle),2(Polygon) and 3(Polygon), respectively.
Your window should look similar to the figure below.
Figure 11.199: Example of the sub model layout.
The only thing left to do is to save this GEN and use it in our MODFLOW6 model.
35. Click the Apply button to accept the values in the window Attribute Values for Current (selected) Polygons/Lines/Points window. It will close automatically.
36. Click the Save As button (
) and save the GEN file, not in the Tutorial folder but in the project databse: in {path of iMOD} \IMOD_USER \DBASE \GEN \THREE_POLYGON_100_50_25.GEN.
37. Click the Save button.
38. Click the Close button on the Create GENs window to close it.
39. Click the Yes button to confirm the closure of the Create GENs window.
To start the MODFLOW6 model we need to include this GEN file. iMOD will prepare all necessary files for the simulation. Most important, iMOD computes the delineation of each sub model such that it connect seamingless. It also constructs the so-called exchange file that describes how each sub model is connected. Okay, enough of that, let’s continue.
40. Click the Simulation Manager button (
) on the iMOD Project Manager window to start the Simulation Manager window.
41. Select the option Standard MODFLOW 6.
42. Enter the name MF6-FIRST-MODEL in Enter or Select Output Folder: field.
43. Select the tab Space dim..
44. Select the option GEN file (Modflow6).
45. Click the Open button (
) and select the file {path of tutorialfolder} \DBASE \GEN
\THREE_POLYGON_100_50_25.GEN.
46. Click the Open button.
You should have the following image on your graphical screen. It shows in bold-lines the extent of each sub model. It also shows the sizes of the individual sub models. Those GEN files (and IDF files) that are created, can be inspected in iMOD. They are in a temporary folder {installfolder} \IMOD_USER \TMP \SUBMODELS_ASCII.GEN and SUBMODEL{i}.IDF
Figure 11.200: Example of the sub modelling discretisation for MODFLOW6.
Let’s save the important flow terms of the model as well.
47. Select the tab Output.
48. Select the option (BND) Boundary Condition in the Results Variable-list.
49. Select the option Layer 1 in the Selected Modellayers list to the right. Use the CTRL-left-mouse to select and deselect items.
50. Repeat the steps above, for the packages KHV, RCH and RIV.
We’re all set to go.
51. Click the Start … button.
52. Click the Yes button to confirm to continue with the simulation.
53. Click the OK button once the simulation is finished.
Your model will be in the folder {installfolder} \IMOD_USER \MODELS \MF6-FIRST-MODEL. As MODFLOW6 simulated three separate sub models, they all have their own output folders. Let’s inspect those.
54. Select the option View from the main window and than select the iMOD Manager to start the iMOD Manager window.
55. Click the Open IDF button (
) from the Maps tabs on the iMOD Manager and open {path of installfolder}\IMOD_USER \MODELS \MF6-FIRST-MODEL \GWF_1 \MODELOUTPUT \HEAD \HEAD \HEAD_STEADY-STATE_L1.IDF
56. Click the Open button.
Let’s open the results for sub models as well.
57. Click the Open IDF button (
) from the Maps tabs on the iMOD Manager and open {path of installfolder}\IMOD_USER \MODELS \MF6-FIRST-MODEL \GWF_2 \MODELOUTPUT \HEAD \HEAD \HEAD_STEADY-STATE_L1.IDF
58. Click the Open button.
59. Click the Open IDF button (
) from the Maps tabs on the iMOD Manager and open {path of installfolder}\IMOD_USER \MODELS \MF6-FIRST-MODEL \GWF_3 \MODELOUTPUT \HEAD \HEAD \HEAD_STEADY-STATE_L1.IDF.
60. Click the Open button.
61. Select all opened HEAD_L1.IDF files from the list on the iMOD Manager window.
62. Select the option View and then the option Show Transparant IDFs.
63. Select the option Map from the main window, then select the option Entire Extent and than the option Linear.
The result of this yields in a complete image of the computed heads.
Figure 11.201: Example of the results of the sub modelling with MODFLOW6.
It is possible to open the flux files of the interchange between sub models as well. Let us open the flux files between model 1 & 2 and the other way around, between model 2 & 1 in order to analyse the water balance.
64. Click the Open IDF button (
) from the Maps tabs on the iMOD Manager and open {path of installfolder}\IMOD_USER \MODELS \MF6-FIRST-MODEL \GWF_1\MODELOUTPUT \BUDGET\BDGGWF_2 \BDGGWF_2_STEADY-STATE_L1.IDF
65. Click the Open button.
66. Click the Open IDF button (
) from the Maps tabs on the iMOD Manager and open {path of installfolder}\IMOD_USER \MODELS \MF6-FIRST-MODEL \GWF_2\MODELOUTPUT \BUDGET\BDGGWF_1 \BDGGWF_1_STEADY-STATE_L1.IDF
67. Click the Open button.
Both files show the amount of groundwater that flows from one sub model towards another. Let check it and see if the water balance is OK.
68. Select both IDF files you just opened in the list on the iMOD Manager window.
69. Select the Map Value Inspector (
) from the iMOD Manager to start the Map Value window.
Note: It should be noted that as your drawn sub-models differ to the one used in this tutorial, the reading you’ll find will be probably different. The important thing here is to know how to check and control whether your simulation went alright.
Figure 11.202: Example of Ground water flow between GWF1 and GWF2.
70. In model GWF1 move your mouse to the coordinate x=550.0; y=950.0 and read that the value for GWF_1=-194.542 m\(^3\)/d.
71. In model GWF2 move your mouse to the coordinate x=525.0; y=875.0 and read the value for GWF_2=119.9561 m\(^3\)/d.
72. In model GWF2 move your mouse to the coordinate x=575.0; y=875.0 and read the value for GWF_2=74.5862 m\(^3\)/d.
73. close the Close button to close the Map Value window.
So, from our first model 194.542 m\(^3\)/d is flowing towards the second sub model, as the sum of 119.956+74.586=194.542 m\(^3\)/d equals that amount. You can inspect more values, as well as the flow in between the second and third model by repeating the last steps.
One of the major advantages of sub modelling is that cell sizes can vary where detail is needed. Suppose we need to compute the drawdown of a well which is positioned in the centre of the model. In fact, our current model network suits the purpose perfectly. We only need to add the well to the PRJ file and run it like we did before. The well is positioned at x=562.5; y=662.5 and has an extraction volume of 500.0 m\(^3\)/d. We’ve added this to a second PRJ already, so we load it in the iMOD Project Manager and run the model.
74. Click the Open button (
) and select the file {path of tutorialfolder} \TUT_MF6\MF6_WEL.PRJ.
75. Click the Simulation Manager button (
) on the iMOD Project Manager window to start the Simulation Manager window.
76. Select the option Standard MODFLOW 6.
77. Enter the name MF6-SECOND-MODEL in Enter or Select Output Folder: field.
78. Select the tab Space dim..
79. Select the option GEN file (Modflow6).
80. Click the Open button (
) and select the file {path of tutorialfolder} \DBASE \GEN
\THREE_POLYGON_100_50_25.GEN.
81. Click the Open button.
82. Click the Start … button.
83. Click the Yes button to confirm to continue with the simulation.
84. Click the OK button once the simulation is finished.
Your model will be in the folder {installfolder} \IMOD_USER \MODELS \MF6-SECOND-MODEL. Let’s inspect those.
85. Select the option View from the main window and than select the iMOD Manager to start the iMOD Manager window.
86. Click the Open IDF button (
) from the Maps tabs on the iMOD Manager and open {path of installfolder}\IMOD_USER \MODELS \MF6-SECOND-MODEL \GWF_1 \MODELOUTPUT \HEAD \HEAD \HEAD_STEADY-STATE_L1.IDF
87. Click the Open button.
88. Click the Open IDF button (
) from the Maps tabs on the iMOD Manager and open {path of installfolder}\IMOD_USER \MODELS \MF6-SECOND-MODEL \GWF_2 \MODELOUTPUT \HEAD \HEAD \HEAD_STEADY-STATE_L1.IDF
89. Click the Open button.
90. Click the Open IDF button (
) from the Maps tabs on the iMOD Manager and open {path of installfolder}\IMOD_USER \MODELS \MF6-SECOND-MODEL \GWF_3 \MODELOUTPUT \HEAD \HEAD \HEAD_STEADY-STATE_L1.IDF
91. Click the Open button.
92. Select 3 the last opened HEAD_L1.IDF files from the list on the iMOD Manager window.
93. Let’s synchronize the legend for the 3 files. Select the option Map from the main window, then select the option Entire Extent and than the option Linear.
It is possible to visualize the total results in 3D, use your experience from previous tutorials to generate this image. Hint: set all types to Cubes to get a continues picture.
Figure 11.203: Example of the 3D results of the sub modelling with MODFLOW6.
Feel free to experiment more. Try to make more refinements (4, 5 sub models). Important to note is that cell sizes need to be an integer multiplications, thus avoid cell size which are e.g. 1.34 larger than the adjacent cell size.
A horizontal barrier (HFB-package) blocks horizontal flow in one direction. A resistance value is given to the barrier to enforce this. MODFLOW6 support the feature as well and it is allows us to let a horizontal barrier pass through different sub models to ensure a correct sealing over the sub model boundaries. With sub models, those barrier need to continue through the sub models. iMOD adds the barrier within the sub model conform a normal model, however, since sub model are active, the connection between sub models needs to be modified as well. Let’s see how that works and moreover, how to check it.
The barrier has been created already and saved in a GEN file, let’s open that one first.
94. Select the option View from the main window and than select the iMOD Manager to start the iMOD Manager window.
95. Select the Overlays on the iMOD Manager window.
96. Click the Open button (
) and open
{path of tutorialfolder} \TUT_MF6\DBASE \HFB \FAULTLINE.GEN.
97. Click the Open button.
As you might see, the fault line crosses the model from south-west to north-east. We’re going to block all flow over this fault line to clearly see its effect. This has been prepared in a PRJ file which we’re going to load into the iMOD Project Manager and run, so:
98. Select the iMOD Project Manager window. It might be hidden on your windows status bar or select the option View from the main window and then select the option Project Manager … to (re)open it.
99. Click the Open button (
) and select the file
{path of tutorialfolder} \TUT_MF6 \MF6_WEL_HFB.PRJ.
In this PRJ file, the HFB package is added, the resistance of the fault is expressed by the combination of the multiplication factor (FCT=1.0) and impulse value (IMP=0.0). The result of this is \(1.0 \times 0.0 = 0.0\) days. A resistance of 0.0 days, act as a impermeable barrier to groundwater flow, we might check the input quickly.
100. Select the option (HFB) Horizontal Flow Barrier from the list of packages and click the (
) sign to open a summary of the properties.
You can see that the configuration is set as defined previously. Okay, all seems to be okay, let’s run the model with the same sub models as we did before, however, we will save the flow budgets in this case as well.
101. Click the Simulation Manager button (
) on the iMOD Project Manager window to start the Simulation Manager window.
102. Select the option Standard MODFLOW 6.
103. Enter the name MF6-THIRD-MODEL in Enter or Select Output Folder: field.
104. Select the tab Space dim..
105. Select the option GEN file (Modflow6).
106. Click the Open button (
) and select the file {path of tutorialfolder} \DBASE \GEN
\THREE_POLYGON_100_50_25.GEN.
107. Click the Open button.
108. Select the tab Output.
109. Select the option KHV in the Results Variable-list.
110. Select the option Layer 1 in the Selected Modellayers list to the right.
In fact, whether you select output for KHV, KVA, BND is irrelevant, all will save the budget for the flow fields as well as the flow that interchanges between sub models. The HFB itself (as well as the PCG) does not generate any output, selected output for this package is redundant.
111. Click the Start … button.
112. Click the Yes button to confirm to continue with the simulation.
113. Click the OK button once the simulation is finished.
Your model will be in the folder {installfolder} \IMOD_USER \MODELS \MF6-THIRD-MODEL. Let’s inspect the shape of the fault line first.
114. Select the option View from the main window and than select the iMOD Manager to start the iMOD Manager window.
115. Select the Overlays on the iMOD Manager window.
116. Click the Open button (
) and open {installfolder} \IMOD_USER \MODELS \MF6-THIRD-MODEL \GWF_1 \MODELINPUT \MF6-THIRD-MODEL_HFB_L1.GEN.
117. Click the Open button.
118. Repeat this for the other two sub models.
119. The line are quite subtle so deselect the IDF’s or increase the line thickness of the GEN files.
Let’s open a GEN file that describes the layout of the sub models.
120. Click the Open button (
) and open {installfolder} \IMOD_USER \MODELS \MF6-THIRD-MODEL \GWF_1 \GEN \BND.GEN.
121. Click the Open button.
To illustrate the setting of the sub models and the the fault line a bit better, colour them differently and make the line a bit thicker, thus:
122. In the iMOD Manger select the file MF6-THIRD-MODEL_HFB_L1.GEN and click the Legend-button (
).
123. Click the option Colour … and select a red colour on the Colour-window.
124. Click the OK-button to close the Colour-window.
125. Increase the Thickness to [3].
126. Click the Apply-button.
127. Repeat this for the other two MF6-THIRD-MODEL_HFB_L1 GEN-files.
128. Select the file BND.GEN and click the Legend-button (
).
129. Click the option Colour … and select a orange colour on the Colour-window.
130. Click the OK-button to close the Colour-window.
131. Increase the Thickness to [3].
132. Select the symbol number [3] from the Symbol No.-dropdown menu.
133. Click the Apply-button.
134. Select all GEN-file in the list on the Overlay tab.
135. Click the Redraw-button (
) to refresh the graphical canvas.
You image should like (more-or-less as you probably have a slightly different sub-division of sub models) this.
Figure 11.204: Example of the Fault line through three sub models with MODFLOW6.
It should be noticed that at the transition of one sub model towards another one, the fault line shows an artefact due to the different grid cell resolution. Let’s see how this influences the fluxes that cross the sub models.
136. Select the option View from the main window and than select the iMOD Manager to start the iMOD Manager window.
137. Select the Maps on the iMOD Manager window.
138. Click the Open IDF button (
) and open {installfolder} \IMOD_USER \MODELS \MF6-THIRD-MODEL \GWF_1 \MODELOUTPUT \BUDGET \BDGGWF_2 \BDGGWF_2_STEADY-STATE_L1.IDF.
139. Click the Open button.
This IDF show the flux for the first sub model toward the second. You can load in the other exchange fluxes for the other sub models as well. For the second sub model those are called BDGGWF_1_STEADY-STATE_L1.IDF and BDGGWF_3_STEADY-STATE_L1.IDF, for the third sub model this is BDGGWF_2_STEADY-STATE_L1.IDF. If you apply a similar legend to all of these IDF-files (I suggest you use the standard-legend that ranges from -2 to +2 from the standard Legend-list (see section 6.6)) and display them in transparency mode, you’ll get the following image.
Figure 11.205: Example of the flow in between sub models that are crossed by a fault line through three sub models with MODFLOW6.
In this example, the grey cells show the zero-exchange. Due to the fact that the resolution changes in between sub models, and an exchange volume is a sum of flow in different directions, it is not that evident to explain why some of the cells are grey and others not. however, if we look at the upper-right grey cell (wich is zero), it demonstrates that no flow is received from sub model 2 towards sub model 1, which is correct as the fault line crosses the sub model at that location. The blue cell above the grey cell, in that particular corner, shows the flux towards the north which is correct as there is a flow connection between sub model 1 en sub model 2. Maybe more clear it is, whenever we look at the heads, you know how to find and load them into iMOD - I assume.
So, this is the result if you plot them all together (with the same legend):
Figure 11.206: Example of the heads in between sub model that are crossed by a fault line through three sub models with MODFLOW6.
Horizontal anisotropy is modelled via the so-called XT3D package in MODFLOW6. This package can handle anisotropy in three directions, X-, Y- and Z. The current iMOD supports the horizontal anisotropy in 2 directions (XY) only. Herewith it is possible to compute similar results as with the conventional ANI-package in iMODFLOW. It should be noted that the implementation of the conventional ANI-package is different, less memory-consuming and probably faster than the XT3D implementation. On the other hand the latter is numerical more exact and combinations can be made with the HFB-package as well as in combination with unconfinedness. In this final part of this tutorial we will examine the capability of XT3D in combination with sub models. Most of the things have been already, so we can start running the XT3D package quickly.
140. Select the iMOD Project Manager window. It might be hidden on your windows status bar or select the option View from the main window and then select the option Project Manager … to (re)open it.
141. Click the Open button (
) and select the file {path of tutorialfolder} \TUT_MF6 \MF6_WEL_ANI.PRJ.
In this PRJ file, the ANI package is added and the RIV package is removed. Furthermore, to meet the requirement of at least a single boundary condition, a constant head is assigned to the lower-left corner with a level of 10.0m+MSL.
142. Click the Simulation Manager button (
) on the iMOD Project Manager window to start the Simulation Manager window.
143. Select the option Standard MODFLOW 6.
144. Enter the name MF6-FOURTH-MODEL in Enter or Select Output Folder: field.
145. Select the tab Space dim..
146. Select the option GEN file (Modflow6).
147. Click the Open button (
) and select the file {path of tutorialfolder} \DBASE \GEN
\THREE_POLYGON_100_50_25.GEN.
148. Click the Open button.
149. Click the Start … button.
150. Click the Yes button to confirm to continue with the simulation.
151. Click the OK button once the simulation is finished.
Your model will be in the folder {installfolder} \IMOD_USER \MODELS \MF6-FOURTH-MODEL. Let’s examine the results.
152. Select the option View from the main window and than select the iMOD Manager to start the iMOD Manager window.
153. Select the Maps on the iMOD Manager window.
154. Click the Open IDF button (
) and open {installfolder} \IMOD_USER \MODELS \MF6-FOURTH-MODEL \GWF_1 \MODELOUTPUT \HEAD \HEAD \HEAD_STEADY-STATE_L1.IDF.
155. Click the Open button.
156. Open the heads for the other two sub models (GWF_2 and GWF_3) as well.
If you apply a similar legend to all of these IDF-files and display them in 3D you’ll get the following image (more-or-less as your sub models might be different).
Figure 11.207: Example of the heads with the usage of XT3D in three sub models with MODFLOW6.
Feel free to experiment more with the XT3D-package (try to specify spatial variable anisotropy-factors and/or angles).