Understanding Pass Through Cells

Starting with version 10.8, the Groundwater Modeling System (GMS) has the ability to handle pass through cells in MODFLOW-USG and MODFLOW-USG Transport projects. What are pass through cells? If you have a 3D UGrid with multiple layers, you can have middle layers with pinchouts or other features that cause that middle layer to not extend through the entire range of the other layers. For example, if you have a three-layer unstructured grid with a pinchout in layer two, then you will have an area where the cells of layer one and layer three are supposed to meet. This area where a middle layer is missing for some of the cells is where pass-through cells are needed.

In actuality, there is a thin cell between the layers. Because of this, in areas where a middle layer is missing a barrier would be formed when running MODFLOW-USG. If you don’t want a barrier in that area, then you will need to add a pass through cell to allow water to flow through the area. This means you need to have the Ibound be greater than zero or the water will not be able to pass through the middle layer and create a “no-flow zone.”

By switching between layers you can see which layers have a thickness of zero and which do not. To inactivate the cells with a thickness do the following:

  1. Open the MODFLOW Global/Basic Package dialog.
  2. Select the Set Pass Through… button.
  3. A message will appear explaining parameters used to determine pass through cells.
  4. In the Pass Through Thickness dialog, set the maximum cell thickness.
Example of setting pass through cells

After assigning the maximum cell thickness, cells that are below that thickness will be designated as pass through cells. The pass through cells will have an inactive IBOUND and will be ignored when making vertical connections in the DISU package.

Note that setting pass through cells requires a stacked grid.

Now that you know about pass through cells, make use of them in your MODFLOW-USG and MODFLOW-USG Transport projects in GMS today!

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Generating a 3D Grid from Raster Data

Have you heard about the 3D UGrid from Rasters tool that’s new to the Groundwater Modeling System (GMS)? Previous versions of GMS required you to build a raster catalog and then use the “Horizons to Solids” command in order to generate a 3D unstructured grid (UGrid) when modeling stratigraphy. The 3D UGrid from Rasters tool, which is in GMS’s toolbox under the “Unstructured Grids” folder, streamlines this process by allowing the two previously separate processes to be set up in the same place and executed simultaneously.

Example of a 3D UGrid generated from rasters

The base components for creating a UGrid with the 3D UGrid from Rasters tool are a 2D UGrid and multiple rasters. The rasters are then added to a table and assigned a horizon number. The term “horizon” refers to the top of each stratigraphic unit that will be represented in a corresponding solid, HUF unit, or 3D mesh layer. Horizons are ordered from the bottom up. For each raster you can choose to fill or clip the layer. Choosing “fill” tells GMS to use the raster to create a UGrid layer. Choosing “clip” tells GMS that any lower surfaces should truncate at that layer. You also have the option of creating sublayers between any rasters that have the “fill” option turned on. You can then set the relative size of each of the sublayers so that they are all proportional, or of differing sizes.

After setting all of the parameters for your UGrid in the rasters table, you then need to set a target location so that GMS knows to calculate elevations at the UGrid cell tops and bottoms or at the points. Lastly, you’ll need to define the minimum thickness that every layer must have, and choose a name for your new UGrid.

If you want more details about how the 3D UGrid from Rasters tool works, you can check out this page of our wiki. You can also look at the newest version of the Horizons with Rasters tutorial.

Head over to GMS, and use this new tool to simplify the stratigraphy modeling process.

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Introducing HydroGeoSphere with GMS

The Ground-water Modeling System (GMS) 10.8 beta includes a model interface that is brand new to the software. HydroGeoSphere (HGS) is a unique three-dimensional control-volume finite element simulator developed by Aquanty that is meant to be able to handle all parts of the terrestrial water cycle. It uses a globally-implicit approach to simultaneously solve the 2D diffusive-wave equation for overland/surface water flow and the 3D form of Richards’ equation for variably saturated groundwater flow. This is different from the many other models that simulate only a portion of the hydrologic cycle. HGS includes components for precipitation, evaporation, overland flow, infiltration, recharge, and more. HGS can simulate both surface and subsurface water flow simultaneously for each time step.

In GMS, the base components for an HGS model include: an unstructured (UGrid), HGS coverages, and an HGS simulation. GMS allows multiple HGS simulations to exist in a single GMS project. A 3D UGrid of the project area is required before building an HGS simulation. There can also be multiple UGrids in one project, although only one UGrid can be assigned to each simulation.

The coverages specific to HGS are boundary conditions, observations, and hydrographs. GMS uses feature objects to define the boundary conditions on an HGS boundary conditions coverage. This includes points, arcs, and polygons. The observations coverage allows you to set observation points that will collect time series information during the simulation run. The hydrograph coverage records hydrograph data during the simulation run.

HGS defines materials with domains and zones. The domain contains information about the type of material. The domain is then assigned a zone number, which is then assigned to a polygon. Multiple domains can be assigned to the same zone.

HGS with GMS

There’s a lot more to HydroGeoSphere than we can cover in one blog post. If you’d like to learn more about HGS, Aquanty has numerous resources on their website. You can look at the HGS Theory Manual or the HGS Reference Manual. They regularly post webinars on their blog and on their LinkedIn. You can also find videos about how to use HydroGeoSphere as well as presentations that have been made by Aquanty’s staff on their YouTube page. We also have our own HGS tutorials that can walk you through the steps of building an HGS model.

We hope you’re excited about the addition of HydroGeoSphere into GMS 10.8, because we certainly are! Download GMS 10.8 to try out HGS today!

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Troubleshooting MODFLOW in GMS

When constructing a MODFLOW model in GMS, there is always the possibility that you will get an error when trying to run your model. While there are a number of things that could be keeping your model from running without an error, here are some tips to help you figure out what may be going wrong.

Example of the MODFLOW Model Checker

Before running MODFLOW, make use of the Model Checker. The Model Checker will analyze all the current input data for any obvious errors or potential problems, which could save you from having to hunt down individual input errors. The Model Checker gives you a few options for sorting and displaying errors. The Model Checker is a useful tool for a basic check of the inputs, however the Model Checker coming up clean doesn’t necessarily guarantee that the solution is correct.

Example of the MODFLOW Model Checker The next thing to look at in your MODFLOW model when you’re trying to figure out what the issue may be is the command line output from the MODFLOW model wrapper dialog. When the model does not converge, an error message should appear in the command line output. This message will help you know where to start resolving the issue.

Another place to look when you’ve encountered an error is the MODFLOW output file (*.out) in the solution files in the Project Explorer. You can use this text file to check for any missing or incorrect values.

Now that we've covered some ways to check your MODFLOW model for errors, here is a common issues that may be what is keeping your MODFLOW model from converging properly:

  • An unbalanced flow budget. This can happen if the inflow is greater than the outflow, which causes extreme flooding, or if the outflow is greater than the inflow, which would cause all cells to go dry.
  • All grid cells in the model are assigned a specified head boundary condition. This leaves nothing for MODFLOW to compute, causing the model to terminate with an error.
  • Improper initial conditions or boundary conditions.
  • You have a highly sensitive model. Highly sensitive areas might keep MODFLOW from converging due to the speed at which flow can be affected.
  • Elevation and layer values have been incorrectly defined or have inaccuracies.

Additional information can be found in the Frequently Asked Questions section of the MODFLOW user manual under the question "My model hasn’t converged. What can I do?"

Use these tips to help your MODFLOW model run smoothly in GMS.

Note this is an update to a previouisly published blog post.

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