This chapter presents information on editing data in a numerical model workflow for unstructured Voronoi grids (V-Grids) and Quadtree grids (Q-Grids). The numerical models for unstructured grids are generated after you run the Conceptual to Numerical conversion step.
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NoteYou must have a license of Pro or Premium in order to use the Unstructured Grid numerical workflow in Visual MODFLOW Flex. |
The numerical modeling workflow provides the tools for defining, viewing, and editing the numerical model (properties and boundaries assigned to grid cells), creating the model input files, running the MODFLOW-6 or MODFLOW-USG engine, and analyzing the results. The following sections are covered:
| 2.Define Properties 3.Define Boundary Conditions 4.Select Next Step 6.Run |
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For more details on how MODFLOW-USG differs from traditional versions of MODFLOW, please see our website.
For more details on MODFLOW-USG, and the formats for the packages, please see the USGS website.
Define Modeling Objectives (Unstructured Model Grids)
The first step in the workflow for developing and running numerical models in Visual MODFLOW Flex is to define the modeling objectives. This entails selecting the desired simulation options. The selected combination of flow options (e.g. saturated groundwater flow) and transport options (e.g. reaction and sorption models) will narrow the list of available flow and transport engines and generate associated input variables (including units and default values). The purpose of this step is to develop the necessary inputs required to build the model based on your understanding of the relevant physical processes present within the study area.
The numerical workflow for unstructured grids supports the following engines:
| Engines supported in Visual MODFLOW Flex |
| Flow | Transport | Utilities |
|---|---|---|
| •MODFLOW-USG | •not supported | •ZONEBUDGET •MOD-PATH3DU1 |
| •MODFLOW-6 | •MODFLOW-6 | •ZONEBUDGET-6 |
| Notes: 1 - MOD-PATH3DU is a particle-tracking algorithm developed by a collaboration between S.S. Papadopulos & Associates (SSPA) and the University of Waterloo. It is not installed directly with Visual MODFLOW Flex and must be downloaded and installed separately from the mod-PATH3DU website. |
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Understanding Default Values at the Modeling Objectives Step |
| Values set at the Define Modeling Objectives workflow step are used by Visual MODFLOW Flex to populate the applicable arrays for the flow and transport model consistent with the modeling objectives upon reaching the Define Properties Step for the first time. Constant values (discussed below) are the exception to this and are discussed below. Once the applicable arrays have been created in the Model Explorer, changes to the default values at the Define Modeling Objectives will not be reflected in the Flow Model. To reset values for a group of properties (e.g. Conductivity, Storage parameters, or initial heads) delete the relevant node from the Model Explorer Tree, update the default value at the Modeling Objectives step and proceed to the Define Property Zones step to regenerate the deleted arrays with the updated defaults. |
Flow Objectives
Under the left panel of Define Modeling Objectives, you can specify a Start Date for the project. Pumping well data and calibration data (head and concentration observation wells) are entered and save as absolute (calendar) dates. Therefore, it is important to choose a relevant start date at this step that coincides with the start time of your simulation.
Flow and Simulation Type
Currently, only saturated groundwater flow can be simulated using the unstructured grid numerical modeling workflow.
Under Property Settings, you can modify the default flow parameters.
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Start Date |
| The start date will be used to retrieve pumping well and head/concentration observation data for the model run. When you define well data with absolute (calendar) dates, it is important that your start date reflects the actual start time for the model run. The well data must fall on or after that start date. Otherwise, these data will not be included in the simulation. Also the start date cannot be changed once it has been set. If you inadvertently set the wrong start date, you can import your pumping well data and observation data in relative times (eg. starting at 0), and you will see no difference in the numerical model inputs/outputs. |
Start Date
Visual MODFLOW Flex uses a standard Windows date picker; a few tips are shown below on how to use this. For example to set a model start date of January 1, 2000.
•Click on the button shown below, to load the Windows date picker.
•The standard Windows calendar will appear. Click on the month in the header (as shown below):
•All months for the current year will appear as shown below. Click on the year in the header:
•A range of years will then appear as shown below. Click on the range of years in the header:
A list of years for the previous decade will appear. You can then use the < or > buttons to change the year.
•Once you have reached the desired year (2000 for this example), select this on the calendar as shown below:
•A list of months will then appear for that year. Select January for this example, as shown below.
•Finally, select "1" from the calendar as shown below:
The selected date will then appear for the Start Date.
Transport Objectives
The transport objectives are defined on the right panel of the Define Modeling Objectives window. When you select the "Transport Active" check box at the top of the screen, then the options can be defined as explained and shown below.
Retardation Model
Transport engine retardation model options are currently supported in Visual MODFLOW Flex as follows:
| Description | MF-USG | MF-6 |
|---|---|---|
| No Sorption |
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| Linear sorption (equilibrium controlled) |
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| Freundlich (equilibrium-controlled) |
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| Langmuir (equilibrium-controlled) |
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| Dual-domain mass-transfer without sorption |
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| Dual-domain mass-transfer with linear sorption in mobile domain |
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| Dual-Domain with Complex Sorption Options |
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| Triple-Domain with Complex Sorption Options |
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| Quadruple-Domain with Complex Sorption Options |
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| Dual-domain mass-transfer |
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| Dual-domain mass-transfer |
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Reaction
Transport engine reaction model options are currently supported in Visual MODFLOW Flex as follows:
| Description | MF-USG | MF-6 |
|---|---|---|
| No kinetic reactions |
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| First-order irreversible decay |
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| Zeroth-order irreversible decay |
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| Complex Model Reactions1 |
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| Notes: 1 - Complex Reactions available for MODFLOW-6 allow for different reaction models (no kinetic reactions, first-order, and zero order decay) to be independently specified for each species and for each (mobile/immobile domain) in the aqueous and sorbed phases. Complex model reactions are only compatible with the three available complex sorption options (i.e. dual-domain, triple-domain, and quadruple-domain). |
The selections you make for Sorption and Reaction options will determine what parameters you need to define for your model. Default values can be defined in the "Species Parameters" and "Model Parameter" tabs. After the model is created, you can define additional zonation for Transport Properties at the "Define Properties" step. Detailed information regarding these parameters can be found in the MODFOW-USG and MODFLOW-6 User Manuals (please see the references section).
The New Species and Delete Species buttons allow you to add and remove species to your Transport simulation. This option is available only for certain transport engines.
When you Species Parameter tab is selected, use the add button (
) to add a new species, or use the remove button (
) to remove the selected species.
Please Note: the remove button will remove the last species in the list.
The model parameters window is shown below. For more information, see the individual sections describing Species Parameters and Model Parameters.
When you are finished, click
(Next Step) to proceed.
Define Properties (Unstructured Model Grids)
At this step, you can edit the flow (and transport) properties for the model. You can also adjust the view/style setting of properties or export the properties.
You can assign properties while viewing either by Layer, Row, or Column; however you cannot edit properties when the 3D subview is active.
Under the Toolbox, use the combo box to select from the available property groups:
•Flow Parameters
oConductivity: includes horizontal conductivity in the X direction (Kx), in the Y-direction (Ky), and vertical conductivity (Kz)
oStorage: includes Specific Storage (Ss), Specific Yield (Sy), Total Porosity (Tp), and Effective Porosity (Ep)
When transport is included with your model, the following additional property groups may be included:
•Transport Parameters
oInitial Concentration Group - one node for each Species
oSpecies Parameters Group(s) - one or more node for each Species
oModel Parameters Group(s)
Please Note: the number of Species Parameters and Model Parameters (if any) will depend on what Sorption and Reaction options you have defined in the Define Modeling Objectives step. Please also refer to the Theory section.
For each parameter group, you can choose to render by Zones or by a selected attribute (for example the Conductivity group includes attributes for Kx, Ky, and Kz). Based on your selection, the color rendering in the views will change.
Edit
Select the Edit button to edit Property zone values after they have been assigned and the Edit property dialog is launched. Here you can select the zone and then you will have the ability to edit any of the cells that are part of the zone.
The following buttons are available to assist with your edits:
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| Expression Builder |
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| Assign to current cell |
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| Assign to column |
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| Apply to selected cells |
The Expression Builder, which can be accessed by clicking the
button, helps you to construct expressions that can include variables and mathematical functions to update property values.
Also available is the Script tab. If preferred, you can make your edits by using the Script option. On this tab you will find the script for any edits you make on the Edit Cells tab allowing you to learn the script language. You can then use the script to "replay" the same edits again.
Adjusting Style Settings
Most of the display settings for the flow or transport properties of a 3D unstructured grid are the same as what are available a 3D structured (finite difference) grid; these are explained in the settings section, see 3D Gridded Data
The following is a list of the differences for unstructured grids:
•Under Cells, there is no option for "Show Only Borders"
•For Lines, there is no option for "Show Only Grid Frame"
•For Slice, there is an option "Show Cell ID Labels"; this will insert a label of the Cell ID for each cell in the selected slice. This will be useful if you want to adjust the numerical values for single cells (or a group of cells) using the Edit option described below.
•For Slice and ThreeSlices, the slice position for cross-sectional slices is based on a virtual grid; the unstructured grid is divided into 100 equally spaced rows and columns. You can display cross-sections through the USG, as "rows" or "columns", at positions from 1 - 100. Row 1 corresponds to the Y minimum in your model domain, whereas Row 100 corresponds to the Y maximum in your model domain. Column 1 corresponds to the X minimum in your model domain, whereas Column 100 corresponds to the X maximum in your model domain. The layer convention follows the MODFLOW notation, where Layer 1 is at the top.
•For Colormap, the positions are similar as to what you have for Slice described above. The option to display colormap along an arbitrary Cross-section line is currently not supported. For Colormap, there is an additional Slice Type, "Horizontal", which allows for rendering on a flat horizontal plane. In this case, you define the vertical position (shift) of this Horizontal plane, on a location from 1 - 100. Vertical Shift of 1 corresponds to the Z minimum in your model domain, whereas a shift of 100 corresponds to the Z maximum in your model domain. Only active cells in the model domain will be drawn.
•For Isolines (contour lines), the settings for selecting the plane for drawing the isolines are similar to described for Colormap above.
Export Properties
Any of the model properties can be exported to shapefile for further post-processing; see Export for more details.
Define Boundary Conditions (Unstructured Model Grids)
With an unstructured grid, boundary conditions are still defined at the cell-center, as with structured (finite difference) versions of MODFLOW. One of the biggest advantages of unstructured grids is that the cell sizes can be much smaller around these boundary conditions, providing for a higher level of accuracy and better representation. Furthermore, for Voronoi grids, the cell centroids can be made to align exactly with features of interest such as stream channel centerlines and wells (please refer to the Define Unstructured Voronoi Grid section).
The other major differences lie in the way boundary condition cells are identified. With Structured MODFLOW (-2005, etc.), boundary condition cells are identified by row, column, layer, in their respective packages (.RIV, .WEL, .GHB, etc.). With unstructured grids, cells are identified by a CellID; after that, the parameters remain the same as what you see for structured MODFLOW.
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The CellD label for boundary condition cells can be turned on as described below.
Assign
The Assign button allows you to assign new boundary conditions. You have options to assign by Polyline or Polygon, by Using Data Object or by Cells. These options are described further below.
•Polygon or Polyline: Use this option to digitize one or more shapes and assign Boundary Condition attributes to the respective shapes. Use the left mouse button to start drawing and add attributes at the desired locations. Once you have finished digitizing, right click with the mouse to close the shape and select Finish button.
•Entire Layer (Recharge and Evapotranspiration only): Use this option when you want to assign a boundary condition to all cells in the layer.
•Using Data Object: Use this option when you have a polyline or polygon data object already imported into the projects, and you would like to use this shape to define the geometry.
•Cells: Use this option when you want to select individual cells to assign a boundary condition.
The Edit Boundary Condition attributes window will appear as shown below:
Enter the attributes using the various methods; click Finish when you are done. This dialog allows you to copy and paste from Excel to make defining (or editing) the attributes easy.
For more details on the options for defining attributes, see Define Boundary Conditions (Attributes).
If your boundary condition is transient switch the schedule drop down to transient to enter your schedule.
You can copy and paste your time schedule from Excel into this dialog to make defining your boundary condition quicker and easier.
By default the Assign to appropriate layer is selected. This means if you enter values for the attributes of a boundary condition (for example the Starting Head) which would place it into another layer - this will occur automatically once you save your boundary condition.
Edit
When you select the Edit... button you must select a cell containing the boundary condition you wish to edit.
Then the following dialog will appear (similar to defining the boundary condition):
The attributes for each cell containing the boundary condition are displayed and can be edited. The cell you selected will be highlighted in the dialog. If you select other rows in the dialog - the corresponding cell will be highlighted in the viewer.
By default the "Assign to appropriate layer" option is selected. This means if you adjust the attributes of a boundary condition (for example the Stage) which would place it into another layer - this will occur automatically once you save your edits.
Script
If preferred you can make your boundary condition edits by using the Scrip option. On this tab you will find the script for any edits you make on the Edit cells tab allowing you to learn the script language. You can re-use the script to "replay" your edits to your boundary conditions.
Display Settings
The display settings can be launched by right-clicking on the desired object in the model tree, and selecting Settings...
Boundary condition cells can be shown:
The Settings window will load.
Boundary Condition cells can be drawn as Points (vertices) or as Cells
When selecting the Cells option, you will see the option "Show Cell ID labels"; turning this on will draw the Cell ID on top of the selected boundary condition cell type. This is useful if you wish to make edits to specific boundary condition attributes, as explained in the Edit section above.
Delete
To delete a specific boundary condition cell group, right-click on this node in the tree, and select Delete.
Validation
To verify there are no warning or errors associated with a boundary condition, right-click one a specific boundary condition in the Model Explorer tree and select Validate... and if there are any errors or warnings, you will be provided with options to resolve the issue(s), as shown in the dialog below. This is available for Constant Head, River, General Head, and Drain boundary conditions. It will check to see if the attributes of the boundary condition will place it below the bottom of the cell you assigned it to. Then it will give you options to correct this. If you choose to Ignore the errors you may encounter errors when trying to translate and run your model.
Define Observations (Unstructured Model Grids)
At the Define Observations step, you can define and edit observation data that can be used to compare your model to historical/expected values for various model outputs and evaluate your model results. The following types of observations can be added to a numerical model:
•Well Observations: heads or concentrations
•Zone Budget Obs: net volumetric flow exchange of groundwater
oin/out of a specified zone,
obetween a specified zone and another zone, or
obetween a specified zone and specified boundary condition type
Following a successful model run, assigned observations can be compared to simulated values to facilitate model evaluations including history matching/calibration.
Toolbar
Observations can be defined at the Define Observation step by selecting the type of observation to be defined under the toolbox and selecting the assign option:
•Under the Toolbox, use the combo box to select from the various Observation types:
| oZone Budget Obs |
|
•Then use the Assign button to assign the appropriate object type (described below) defining the observation location.
Well Observations
Well observations include groundwater data collected from wells and piezometers and consist of four components:
•Location: x- and y-coordinates of the sampling point
•Elevation: the elevation at which the observation occurred. For monitoring wells, this is typically the midpoint elevation of the screen. For pieozometers, this is typically the elevation of the open-ended bottom of the piezometer.
•Time: the time as an absolute date/time or more commonly as elapsed time relative to the model start date
•Value: the value of the observation:
oHead: the hydraulic head measured in the well or piezometer as top of casing elevation minus depth to water
oConcentration: solute concentration of the specified species (note that an extra field must be present to define the species)
Prerequisites
To define well observations, you must first have a well data object in the Data Explorer with observation data. You can either import the well observation data or create a new well data object and then add/edit the observation data. The "raw" observation well data can be viewed/edited in the Well Data section.
All other boundary conditions can be fully defined at the Define Observations step; however, you may find that using an imported Time Schedule object in the Data Explorer makes the process significantly more efficient.
Assigning the Well Observations
Once you have imported or created a Well observation data object with heads or concentrations, navigate to the Define Observations step in the numerical model workflow. Below the toolbox, select Well Observation and select Assign > using data object. The Create/Add Well Observations dialog will appear:
The Create/Add Well Observations dialog contains two controls:
•The assign button (
): allows you to specify a well data object with observations in the Data Explorer
•The radio button allows you to specify which observation group the well observation object will be added to in the model tree.
The observation wells should then appear a new node on the numerical model tree on the Model Explorer and any observation well points located in the active layer, row, or column will be also be displayed in the appropriate view(s).
Please Note: If you add Observations that are defined in Absolute times and if some or all of the observation times occur before the model start date defined in the modeling objectives, then you will receive a warning message during creation. These head/concentration observations cannot be included in the numerical model and will be filtered out.
Specifying a Well Observation Group
You will be prompted with a choice to append the observations to an existing well group or create a new well group. Well groups can be used to group observation data into logical sets of data based on a meaningful criteria that may facilitate model calibration, analysis, or evaluation. For example you may wish to group observations by watershed, hydrostratigraphic unit/zone, landuse, or property type.
Viewing and Editing Well Observations in CSV Format
Once defined, head or concentration observation data can be viewed/modified in a CSV format:
•Right-click on the Head (or Concentration) Observations node from the Model explorer
•Select "Edit Attributes..." as shown below.
The data contained inside the Observations data object will be displayed in a .CSV file; this should appear in either Notepad or Excel depending on your system configuration; an example is below:
You can use this interface for numerous types of edits/additions:
•Adding a new observation point at a defined XY location
•Change existing data
•Add a new observation time to an existing observation point.
Please Note: the Layer number for the observation point is calculated based on the Obs. Elev; changing the layer number will not change the vertical location of the observation point.
When you are finished with the edits in the .CSV file, you need to save and close this file. Then re-import back the changes into Visual MODFLOW Flex using the steps below:
•Right-click on the Head (or Concentration) Observations node from the Model explorer
•Select "Reload Attributes..."
The modified data will now appear and will be utilized for any charts the next time you translate and run the model.
Defining Zone Observations
Visual MODFLOW Flex allows you to define observations of net volumetric flows using ZoneBudget zones.
Assign ZoneBudget Observations
To define a boundary condition observation data set:
•At the Define Observations step, select the Zone Budget Obs option in the toolbox
•Click Assign > Using data object...
•The Gage Editor window will be displayed allowing you to define the observations
Observation Schedule
The left side of the Gage Editor dialog includes the following controls for all supported types of distributed (non-point) observations (zone budget zones):
•Gage Type: allows you to select the type of observation to be measured and associated project units. Currently, distributed non-point gages/observation types are limited to volumetric observations. Note that well observations are handled separately using well objects (see above).
•Toolbars: the gage toolbars include the following buttons:
o
Add interval: adds an observation time at the end of the table
o
Insert interval after selection: adds an observation time after the selected row
o
Delete selected row(s): deletes selected row(s) from the table
o
Clear sort: clears the sort order (if any) on fields in the observation table
o
Expression builder: opens the Expression builder
o
Assign to column: evaluates the Expression for all cells in the current column
o
Assign to current cell: evaluates the Expression for all selected cells in the current column (press and hold SHIFT or CTRL buttons with left mouse clicks to select multiple cells)
•Table: the table in the left hand side of Gage Editor includes three fields:
oTime: elapsed time relative to the model start date
oValue: the value of the observation. Note that positive flow values for volumetric observations follow the standard MODFLOW convention that positive values indicate flow into the groundwater flow system
oTarget Residual: the target difference between observed values and simulated results (based on project goals, stakeholder input).
•Load Schedule Object: Selecting this option will allow you to load the data from a time schedule object in the Data Explorer and map fields from the schedule object (using the dropdown selectors) to the value and target residual fields.
Zone Budget Observation Spatial Representation
The right side of the Gage Editor includes the spatial definition of the observation:
•Selected Zone (From): The "from" zone selection allows you to specify the zone where groundwater flows are to be observed.
•Selected Zone (To): The "to" zone selection (shown in red) is optional and allows you to specify a different ZoneBudget zone or a boundary condition type present in the model. If not selected, then the net groundwater flows to all adjacent zone budget zones will be observed.
Script
The Script tab allows you to quickly add or modify data based on a script. If you are interested in using the script, try to define a simple gage to observe the structure and add complexity. An example is shown below:
•The header defines the type of observation and (other than the name, which should be wrapped in "quotes") should not be edited.
•The Observation Scope section defines which objects are associated with the observation gage.
•The Location section defines where the observation will be rendered in views when displaying residuals
•The Observation Type defines which observation data are used. You can specify more than one Observation Type block
•The Observation Data includes the set of times, observations, and target residuals for the time above.
Similar to a macro builder, any edits you make on the Edit tab will be reflected at the Script tab. In this way you can experiment with the Gage Editor and learn to build your own scripts.
Define ZoneBudget (Unstructured Model Grids)
ZoneBudget-USG and ZoneBudget-6 are USGS programs for computing subregional water budgets for MODFLOW ground-water flow models using unstructured grids. At the Define Zone Budget Zones step, you can create or assign zone budget zones by digitizing new zones using Assign Polyline, Polygon, or Point (Single Cell), or by using 2D/3D point, polyline, or polygon shape objects from the Data tree using the same methods as in the Finite Difference workflow.
Follow the steps below to create new zone budget zones:
Assign
Polyline
•Use the left mouse button to start digitizing a polyline over the desired cells. Once you have finished digitizing, click on the Finish button from the toolbox, or right click with the mouse and select "Define Attributes". The following window will appear
•Click the New button to assign the selected cells to a New zone; otherwise, you can select to assign cells to an existing zone by selecting the zone from the dropdown list at the top. The selected cells can be assigned to the current layer or multiple layers using the check boxes at the bottom of the window. Once you are finished, click OK.
.
Polygon
•Digitize one or more polygons, and repeat the steps as described above for Polylines.
Single
•Left-click on one or more cells and a point will appear. Once finished, right-click and select "Define Attributes", and follow the steps as described above for Polylines.
Using Data Object....
•The following window will appear.
•Choose the desired point, polyline, or polygon data object from the tree.
•Click on the
button (under Select Data Object)
•A second window will appear:
•Select which zone you want the features to apply to. You have the option to assign the zones to:
oAn existing zone
oA new single zone
oCreate zones for individual features
oCreate zones based on feature attributes
•Select the desired model layers where the zone should be applied
A simple example is shown below for a polygon data object (shown in blue).
After the zones are generated, they will appear in layer view.
When the selected shape contains multiple polyline or polygon features, then a new zone will be created for each feature.
Define Particles (Unstructured Model Grids)
Particles are defined using the same methods as in the Finite Difference workflow. These methods are described in the section describing how to Define Particles in the Finite Difference workflow.
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