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Model Setup Toolset

Model Setup Toolset

Akuna provides an interface to guide model setup, as well as features to assist in that task. These features include visualizing wells and lithologic contacts, generating surfaces or loading surfaces produced by other geologic modeling software (e.g., Petrel, EarthVision), and specifying material and fluid properties, initial and boundary conditions, and model output. Note that Boundary Conditions and Souces are the only temporal inputs specified in the Model Setup Toolset. Most information related to timing is specified in the simulation toolsets, so that the same conceptual model setup can be used for both historical and future simulations.

This User Guide does not provide simulator specific guidance on Model Setup (e.g., definitions of input parameters). However, Model Setup will guide the user as to how to setup a simulation model, with some limited error checking. Akuna is not designed to check the validity of the translation of the conceptual model into the numerical model inputs.

Akuna was initially designed to be tightly integrated with the ASCEM simulator, Amanzi. However, Akuna is ostensible, and is currently being modified to support other simulators, including STOMP and eSTOMP. For simulator specific guidance, the user is referred to the simulator documentation.

Links to Simulators Documentation:

The information presented below provides guidance on how to create a conceptual model in Akuna, and how to navigate in Akuna's environment. The following information is required for the conceptual model setup:

  • size of the domain and discretization,
  • geology,
  • boundary and initial conditions,
  • fluid and solid properties.

Conceptual Model Creation/Upload

To start a new model, the user must be in the User Workspace perspective and highlight the folder or the home directory, where the model is to be created. Clicking the icon of the Workspace's toolbar will bring up the new Model Name window (Figure 1), where the Model Name can be defined.

    Figure 1. Model Name Window

These are characters not allowed in file or folder name: \ " *  > < ? / : |

Model Setup Window Structure

Once the Model Name is specified, the Model Setup Window appears (Figure 2). This window will give access to dialogue boxes to define the conceptual model.

The Model Setup window consists of a menu and tool bars, and is split into four panes:

  • Model Setup Process Pane: The items in the list provide a workflow to set up a model.
  • Domain Pane: This pane allows the user to add regions for assigning the boundary conditions, initials conditions, material properties, sources and observations. This panel also allows the user to display specific features defined in the model setup process in the Model Setup Viewer
  • Toolset History Pane This pane shows any toolsets that have already been executed with this conceptual model.
  • Model Setup Viewer: The model visualization panel offers a set of tools that allow the user to modify the view of the geologic domain.

Details regarding each of these items are described in the following sections.

Figure 2 Place holder - Model Setup Window

Model Setup Menu Bar and Toolbar

The menu bar offers familiar Windows menus and functions specific to Akuna.

The File Menu (Figure 3) allows the user to open files [not implemented yet] [1], import an existing simulator file [2], save the model [3], and allows the user to create a new simulation (i.e., SR, PE. UQ and SA) [4].

The Edit Menu contains an item allowing the user to undo the last operation performed.

The Setting Menu provides a Conversion chart that contains principal unit conversions.

 

Figure 3. Akuna's Model Setup Menu bar (left) and Tool bar (right)

Akuna also allows the user access to the simulator input file by clicking on the icon [5]. This will bring up the Text Editor Window containg a Tool Bar allowing to edit the Input File with basic editing tools (Figure 4). To leave the text editor window, just Menu Toolbaclick on ..

 

Figure 4. Input File Editor Tool Bar

Model Setup Process

The Model Setup Process allows the user to create a geologic domain, generate a grid, and assign properties to materials, fluids and species (solutes). In addition, initial and boundary conditions are specified in this toolset. Some inputs are required, others are optional, depending on the problem to be solved and the simulator selected.

The model setup is driven by a status code displayed on each of the items listed in the Model Setup Process Pane (Figure 5). The status of the the items will change along the process of selection of options or modification of parameters.

Figure 5. Status Code of Model Setup Workflow

Process Model Specification

The general operational aspects are defined in this section.

The the simulator is selected in this dialog (Figure 6). Information on the governing equations to be solved is also provided here (e.g., variably saturated flow, transport, geochemistry).

Ffigure 6 - Process Model Specification Window.

Model Description

Documentation on the simulation is provided in the Model Description section (Figure 7). The organization name, author’s name and a description of the simulation can be provided here. As indicated in the process tree, Model Description is not required.

Figure 7 : Model Description Window.

Geologic Domain

In the Geologic Domain window (Figure 8), the domain extents are specified.

Figure 8. Geologic Domain Window

This section offers two options to define the modeling domain:

  1. User Defined Domain

    Define the dimensions of the domain by entering the start and the end of the X, Y, and Z-Dimensions. For quickly setting up multiple layer systems, the option to add horizontal layers in one of the dimensions as a list of real numbers is provided in the Define Optional Layers field.

    Change unit values by clicking on the icon. A window will pop-up and allow the user to choose the desired unit.

    Once the domain is defined, the Model Vizualization panel will be updated. The Domain panel will also show any regions that have been defined. These regions can be selectively displayed by highlighting selected regions.

  2. Domain Import from File

    A domain can also be defined by importing an existing file. Amanzi supports the Exodus file format for unstructured grids, which can be imported in this dialog. Surface data import assumes that surfaces have been defined using external software and are in a AVS-compatible file format. If material IDs are to be assigned on a node by node basis, the TF2/TF3 import is needed to import the existing file (Figure 9).

    Figure 9. Drop-down List of File Format Selection

Mesh

This section allows the user to specify the grid (Figure 10). Three mesh types are offered to choose from: Uniform, Non-Uniform, and Semi-Structured. Note that if an Exodus file was imported to define the domain, the mesh cannot be altered in this dialogue.

  • The Uniform mesh option discretizes the modeling domain into uniform blocks in the X-, Y, and Z-dimensions by entering either the number of blocks or the block size in each dimension.
  • The Non-Uniform mesh option discretizes the modeling domain in X-, Y-, and Z-dimensions in segments of various lengths with the grid blocks size distribution according to the specified positioning function. The Positioning Function options are: Uniform, Geometric, Logarithmic Expanding, and Logarithmic Contracting. Mesh segments can also be easily copied to other dimensions by clicking on the corresponding Copy buttons.
Note that no error checking is provided in this Non-Uniform mesh dialogue, and it is the user's responsibility to check that the input data for accuracy.
  • The Semi-Structured mesh option will only be available if the user has imported Surfaces in the Geologic Domain dialogue. As noted above, these are surfaces that are in an AVS format, and have already been created using software external to Akuna. These surfaces will already contain the number of nodes and cells defined on each surface plane. In this dialogue, the user is able to create an Exodus mesh by defining the number of divisions in the vertical using Proportional spacing

The generated Mesh can be visualized in teh Domain Pane by clicking .

Figure 10: Mesh Generation window

If the AMR (Adaptative Mesh Refinement) option has been checked in the Process Model Specification Window, the AMR Controls (Figure 11, [1) and Refinement Indicators (Figure 11, [2]) will be specified in the Mesh Refinement Properties Window.

Figure 11. Mesh Refinement Properties Window.

Solutes

 

This section is only required if Transport is included in the simulation (e.g., Transport option turned On in the Process Model Specification).

Double-clicking Solutes will bring up the Solute Properties window (Figure 11). This section allows the user to define solutes in the simulations involving solute transport. Multiple solutes can be added, and their unique properties. The list of required solutes properties may vary depending on the simulator selected.

  1. Click to add a new solute
  2. Add the solute name in the box appeared under Solute.
  3. Add the value for each parameter required and select the appropriate units .
  4. Return to step 1 to add another solute.

Figure 11. Solute Properties Window

Materials

In this section, soil/rock types and their properties are defined. In the Materials window a new material is added using the icon and entering a unique Material name (figure 12). The right section of the Materials Window is divided in three panes: General, Aqueous and Transport.

In the General pane (Figure 12, [1]), Mechanical and Hydraulic properties can be specified for each material type. The number and type of required properties will vary depending on model specifications previously selected (i.e., simulator, transport processes, etc).

In the Aqueous panel (Figure 12, [2]), both Saturation Function and Relative Permeability Models are defined with a list of options and parameters that will vary depending on the options selected in the model specification.

Additional information on the material currently being defined and the solutes are requested in the Transport panel (Figure 12, [3]) and will vary depending on the simulator (e.g, dispersivity data, tortuosity, sorption isotherms).

This section is only required if Transport processes are involved in the simulation (e.g., Transport option turned On in the Process Model Specification).

 

Figure 12. Materials Window

Fluid

In this section, fluid properties are defined for the Amanzi simulator (Figure 13). Default values for viscosity and density of water (assuming a temperature of 20°C) are entered by default, but may be changed.

 

The fluid definition stage might be deactivated depending on the simulator selected (if the simulator defines fluid properties based on an equation of state.

Figure 13. Fluid Properties Window.

Porous Media

The Porous Media window (Figure 14) allows the user to assign materials (defined in the Material section) to each region (defined in Geological Domain).

Figure 14. Porous Media Window.

Initial Conditions

This section is used to establish state conditions at the start of the simulation for the entire modeling domain (Figure 15). Initial conditions are added using the icon. Note that all of the regions defining initial conditions should have already been created in the Domain panel. Only existing regions can be assigned to an intial condition.

  1. For each Initial Condition, define the name and the region where it applies.
  2. In the Liquid Component section, choose the variable that will be used to define the state of your sytem at the beginning of simulation, and specify the necesarry parameters.
  3. In the Solute Component section, enter the value for the initial solute concentration.
  • Solute Component section is only required if Transport is used in the simulation (e.g., Transport option turned On in the Process Model Specification).
  • The behavior of overlapping conditions differs between simulations. For example, Amanzi does not support overlapping regions, whereas STOMP/eSTOMP supports an overwrite condition for overlapping regions.

 

The available options and required parameters will vary depending on the simulator selected in the Process Model Specification.

 

Figure 15. Initial Conditions Window.

Sources

 

The Sources section is not required.

Time-dependent sources and/or sinks of water and solute (Figure 16) are provided in this section. Sources inject mass or solutes into a region, while sinks withdraw mass or solutes from the region.

Time varied sources are defined by declaring multiple source times. Each Source Time declared in the Time box indicates the start of the new Source condition which is defined in the Liquid Component and Solute Component sections. The Time Function for each Source Time defines the temporal interpolation scheme between the indicated times. If Constant is selected, then no interpolation is performed. The Linear option will linearly interpolate the source between the two time periods. New sources are added using the icon.

  1. Define the name of the source(s) and its region.
  2. By default, the region displayed in the dialog box are regions that have been previously defined (e.g., geologic layers), and the surfaces defining the domain. New regions can be added in the Domain Pane.
  3. Enter the time when the Source starts.
  4. Choose the source release model for water in the Liquid Component section and for solute(s) in the Solute Component section, and enter all the required parameters.
  5. Choose the Time Function for the Liquid and Solute Components of Sources.
Solute Component section is only required if Transport option is turned On in the Process Model Specification

Figure 16. Sources Window.

Boundary Conditions

 

Boundary Conditions is not a required section, though a well-conceived conceptual model will define at least one or more boundary conditions. For most simulators, a default No Flow boundary condition is applied to all boundaries in the modeling domain.

This section allows you to specify time-varying boundary conditions for water and solutes (Figure 17). Each Boundary Condition Time declared in the Time box indicates the start of the new boundary condition which is defined in the Liquid Component and Solute Component sections. The Time Function for each Boundary Condition Time defines the temporal interpolation scheme between the indicated times. If Constant is selected, then no interpolation is performed. The Linear option will linearly interpolate the source between the two time periods. New sources are added using the icon.

  1. Define the name of the Boundary Condition(s) and the region where it applies.
    By default, the region displayed in the dialog box are regions that have been previously defined (e.g., geologic layers), and the surfaces defining the domain. New regions can be added in the Domain Pane.
  2. Enter the time the Boundary Condition starts.
  3. Choose the Boundary Condition type for the Flow part of your simulation in the Liquid Component section and enter all the required parameters.
  4. Enter the Solute(s) Concentration value in the Solute Component section.
  5. Choose the Time Function for the Liquid and Solute Components of the Boundary Condition.
Solute Component section is only required if Transport option is turned On in the Process Model Specification

 

Figure 17: Boundary Conditions Window.

 

End of the Model Setup Process

Once all the parameters are properly assigned, click the Save button at the top left corner of the screen. Once the data for the model is saved, buttons for the tool sets will become active at the top of the window. You may now proceed to various tools sets, including:

Domain

New regions can be added in the Domain Pane, as well as control visualization of selected surfaces/regions in the visualization pane.

  • Clicking on the icon will bring up the Regions Window (Figure 18). In this window, the name of the new region to be added is specified. The Region Type is selected from the drop-down menu (e.g., Line, Point, Swept Polygon). Once the Region Type is selected, information to define the region must be entered (i.e., coordinates).

Figure 18. Region Window

The user is given the option to control the Geologic domain, the Boundary confitions, the Surfaces and other regions (e.g., wells, points) previously definied.

For each category, all features or part of them can be displayed. This can be controlled by activating or not the icons located at the left each feature or features group.

Table 1. Domain Pane Icons and Functions

Icon
Function
/
Activate / desactivate visualization of a group of features (e.g., entire geologic domain)

/

Activate / desactivate visualization of selected features (e.g., entire geologic domain
/
Activate / desactivate visualization of the grid for the entire geologic domain
/
Activate / desactivate visualization of a selcted region of the geologic domain
Allow the user to change the color scale for a group of features

An illustration of the geologic domain with different visualization combinations is provided in Figure 19.

Figure 19. Visualization of the Geologic Domain With Different Visualization Combinations

Toolset History

The Toolset History window gives the user information regarding the sinulation tools that have been run.

Figure 20. Toolset History Pane.

Model Setup Viewer

The toolbar of the model setup viewer is composed of several icons that allows the user to modify the view of the geologic domain (Table 2).

Table 2. Icon and Function of the Model Setup Viewer Toolbar.

Icon
Function
Slice
Scale Rendering
Zoon Forward
Zoom Backward
Translate
Reset Windows
Align X axis
Align Y axis
Align Z axis
Select Background color

The view in the visualization panel may be scaled, rotated, moved, or zoomed in and out.

  • To apply a scale factor, click on the icon , a new window will pop-up (Scaling Factors). Use the cursors to define the desired scale in the three directions. By clicking one the Reset button, the initial scale can be retrieved anytime.
  • To rotate the view: move the mouse cursor on the 3D window while pressing the left mouse button.
  • To zoom the view in and out, use the wheel of the mouse or use the and icons.
  • To move the view: click on the icon and move the mouse cursor on the 3D window while pressing the left mouse button.
  • Click on to align the view on the X axis, double click to reverse the direction
  • Click on to align the view on the Y axis, double click to reverse the direction.
  • Click on to align the view on the Z axis, double click to reverse the direction.
  • The icon allows the user to come back to the initial view.

In order to improve the visualization of the model, the user can also define the background color by clicking on , and can then choose the prefered colorr model (e.g., swatches, HSB, RGB).