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ASCEM : Model Setup

  1. ASCEM
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ASCEM : Model Setup

Introduction

Objective

This tutorial demonstrates how to create a conceptual model in Akuna. In ASCEM parlance, this is referred to as a conceptual model, since there is a division in the model setup process as to where information is required. Although the following data is not strictly conceptual, the following information is required for the conceptual model setup: size of the domain and its discretization, the geology, boundary and initial conditions, and fluid and solid properties. This information is usually static across all types of simulations that might be executed with a particular model setup. For example, the discretization of the grid is not expected to change between model calibration (PE) and an uncertainty analysis (UQ). However, the time periods over which the simulations are executed may change. For this reason, numerical information such as time stepping and numerical algorithms is not entered in the conceptual model setup, but within the different toolsets (e.g., SR, SA, PE and UQ).

Toolsets/modules exercised

The following Akuna modules are being exercised:

  1. Create a hydrogeological model domain and mesh
  2. Specify material and fluid properties
  3. Specify initial and boundary conditions

Pre-requisite

This tutorial provides step-by-step instructions on how to set up a model from scratch. The user is expected to have Akuna properly installed, and to know how to navigate the Akuna main window (see Akuna Navigation Tutorial).

Problem Description

The tutorial problem is a one-dimensional, three-layer, unsaturated flow and transport problem, where

  1. steady-state unsaturated flow is calculated with a constant infiltration rate, providing the initial conditions for year 1950;
  2. discharge of water and 99Tc occurs at the top of the model domain, which represents the ground surface, between 1950.1-1950.26 years; and
  3. continuing infiltration of water drives the 99Tc plume downward to the bottom boundary of the model domain, which represents the water table.

Starting Model Setup

Start the model setup by creating a new model in the Akuna Main window.

  1. In the User Workspace panel, highlight the folder or the home directory, where the model is to be created.
  2. Click the image0 icon in the menu (Note: the image1 icon is only active when highlighting a folder).
  3. Type the model name (in this case, type Richards-1D-transport) in the pop-up window (Figure 1).
image2
Figure 1. Name a new model.

This will bring up the Model Setup window (Figure 2). The Model Setup window has four panels:

  • Model Setup Process (left top): The items in this list provide a general guide to setting up a model. All blue color labels within the panel link to different steps of the model setup process. Double clicking a blue colored link will bring up a dialog for filling in related information. Items in the tree will be disabled if prerequisites have not been met.
  • Domain (left middle): The user can add the regions that can be used for assigning the boundary conditions, initial conditions, material properties and observations.
  • Toolset History (left bottom): This panel shows the toolsets using this conceptual model.
  • Model Visualization (right): This panel provides a visual display of the domain used in this conceptual model.
image3
Figure 2. Akuna Model Setup window.

Import Model Setup

Section 4 describes how to create a hydrological model from scratch.

Alternatively, the user can import an existing Amanzi input file (*.xml). | To import a file,

  1. Click the image4 icon
  2. Select the path to the existing Amanzi input file

This opens the Amanzi File Parser window. The parser checks for

formatting errors in the existing input file and alerts the user if errors are found. After checking through the input file in this window, click Load. In the Model Setup window, one will see the domain in the Model Visualization panel. Also, one will see parameters are already filled in each component of the Model Setup Process panel (Figure 2). One may change the parameters following the processes described in Section 4.

Model Setup Process

Add model description

Double click Model Description in the Model Setup Process panel (Figure 2). This will bring up the Model Description window. In this window, the user can add descriptive text for the model. The description can be left empty, but it is common to include authors names.

  1. Add text to the text box  Figure 3).
  2. Click Apply and Close.

image5

Figure 3. Model Description window.

Create a domain

Double click Geologic Domain in the Model Setup Process panel (Figure 2). This will bring the Geologic Domain window. The user needs to specify the dimensions of the model domain, and also different regions (e.g., different geological formations) if they exist. Currently, only a rectangular three-dimensional domain is supported.

  1. Have User Defined selected.
  2. Click all the X-, Y- and Z-Dimensions
  3. Insert 0 for Start X, Start Y and Start Z.
  4. Insert 4.0 for End X.
  5. Insert 1.0 for End Y
  6. Insert 107.52 for End Z.
  7. Insert 0, 39.9, 80.22, 107.52 in Define Optional Layers in Z. This specifies that there are three regions in the z direction, having their interfaces at z = 39.9 and z = 80.22.

Verify the input against Figure 4, and click Apply and Close. In the Model Setup window (Figure 2), the Model Visualization panel will be updated to display the model domain. For a better view of this tutorial problem, click the image6 icon on the top. A domain with three layers in the XZ coordinates (Figure 5) will be displayed.  If the layers do not appear, click the image7 icon that appears next to the Geologic domain regions in the Domain center panel to the left of the visualization window. This will turn the layer visibility on. To toggle off, click the image8 icon immediately to the right of the icon.

image9

Figure 4. Geologic Domain window.

image10
Figure 5. Model Visualization panel updated.

Select Model Specifications

Double click Process Model Specification in the Model Setup Process panel (Figure 2). This will bring up the Process Model Setup window.  Because Akuna can be used with any simulator, it is necessary to select the Amanzi  simulator.  Here, transport processes are also specified.

  1. Select Amanzi in the Simulator panel
  2. Select Variably saturated (Richards) in Flow
  3. Select Explicit first-order in Transport in the *Specifications panel.*

Verify input against Figure 6 and click Apply and Close.

image11

Figure 6. Process Model Setup window.

Define Solutes

Double click Solutes in the Model Setup Process panel (Figure 2). This will bring up the Solute Properties window. Multiple solutes can be added, and their unique diffusion coefficients.

  1. Click image12 to add a new solute.
  2. Add the solute name Tc-99 in the box appeared under Solute
  3. Add 1e-9 m2/s in Diffusion coefficient.

Verify the input against Figure 7 and click Apply and Close.

image13

Figure 7. Solute Properties window.

Define Materials

Double click Materials in the Model Setup Process panel (Figure 2). This opens the Materials window (Figure 8). In this window, you can specify the material properties for each layer. Note that a hard return (enter on the keyboard) may be required so that the entries are properly read by Akuna.

  1. Click image14 to add a new material
  2. Add the name of material Facies1 in the box

In the Mechanical Properties panel

  1. Add 2720.0 in Particle density
  2. Add 0.4082 in Porosity

In the Hydraulic Properties panel,

  1. Select Permeability in Type
  2. Add 1.9976E-12 in x and y, and 1.9976E-13 in z

In the Saturation Function panel,

  1. Choose van Genuchten in Capillary Pressure Model.
  2. Add 1.9467E-04, 0.0 and 0.2294 in alpha, Sr and m.

In the Relative Permeability panel

  1. Choose Mualem in Type
  2. Click Apply
  3. Repeat the same steps for Facies2 and Facies3 according to Table 1.

Verify the materials summary against Figure 8, and click Apply and Close.

Table 1. Material properties used in this tutorial


image15
Figure 8. Materials window.

Define Fluid Properties

Double click Fluid in the Model Setup Process panel (Figure 2). This will bring up the Fluid Properties panel (Figure 9). The fluid here is water, and assuming a temperature of 20 oC:

  1. Add 1.002e-3 Pa-s for Fluid Viscosity
  2. Insert 998.2 kg/m3 for Fluid Density

Verify the input against Figure 9 and click Apply and Close.

image16
Figure 9. Fluid Properties window.

Assign Porous Media

Double click Porous Media in the Model Setup Process panel (Figure 2). This opens the Porous Media window (Figure 10). In this window, the user can specify which material is assigned to each region defined in Geological Domain (Section 4.2).

  1. Select Region between surface 0 and surface 1, and choose Facies2 for Assignment
  2. Select Region between surface 1 and surface 2, and choose Facies1 for Assignment
  3. Select Region between surface 2 and surface 3, and choose Facies3 for Assignment

Verify the material assignment against Figure 10, and click Apply and Close.

image17

Figure 10. Porous Media window.

Assign Initial Conditions

Double click Initial Conditions in the Model Setup Process panel (Figure 2). This opens the Initial Conditions window (Figure 11). The user can specify initial conditions for different regions.

  1. To add a new condition, click image18 .
  2. Add name IC
  3. Select All from the Regions list

In the Liquid Component panel,

  1. Choose Linear Pressure for Liquid Component
  2. Add 101325 for Value
  3. Add 0 for Reference X, Reference Y, Reference Z, Gradient X and Gradient Y
  4. Insert -9793.5192 for Gradient Z

In the Solute Component panel,

  1. Select Tc-99
  2. Add 0.0 for Concentration

Verify the input against Figure 8, and click Apply and Close.

image19

Figure 11. Initial Conditions window.

Assign Boundary Conditions

Double click Boundary Conditions in the Model Setup Process panel (Figure 2). This opens the Boundary Conditions window (Figure 12). In this window, the user can specify different boundary conditions for different boundaries and also different time periods.

  1. To add new conditions for one region, click image20 in the Name panel
  2. Add the name of the region B17 in the box
  3. Select +Z Boundary in the Regions panel (top right)
  4. To add a new time period, click image21 in the Time panel
  5. Add 0 y for the name in the box

In the Liquid Component panel,

  1. Select Inward mass flux for Water Component
  2. Insert 1.1071e-07 (kg/m^2/s) in the box
  3. Select Constant for Time Function

In the Solute Component panel,

  1. Select Tc-99
  2. Add 0.0 for Concentration
  3. Select Constant for Time Function
  4. Repeat the same steps for other time periods (1950.1y, 1950.2y and 2500y) according to Table 2

Repeat the above procedure for the Bottom boundary according to Table 2.

Table 2. Boundary conditions used in this tutorial

Name

Regions

Time

Liquid Component

Solute Component

B17

+Z

0 y

Inward mass

flux | 1.1071e-07 kg/m^2/s | Time Function: Constant

Tc-99
0.0, 1/l
Time

Function: Constant

1950.1 y

Inward mass

flux | 0.000330423 kg/m^2/s | Time Function: Constant

Tc-99
2.26688E-06,

/l | Time Function: Constant

1950.2 y

Inward mass

flux | 1.48666e-6 kg/m^2/s | Time Function: Constant

Tc-99
0.0, 1/l
Time

Function: Constant

2500 y

Inward mass

flux | 1.48666e-06 kg/m^2/s | Time Function: Constant

Tc-99
0.0, 1/l
Time

Function: Constant


Verify the input against the Table 2, and click Apply and Close.

image22

Figure 12. Boundary Conditions window.

Create Mesh

Double click Mesh in the Model Setup Process panel (Figure 2). This opens the Mesh Generation window (Figure 13). In this window, the user can specify the number of discretization in the model domain.

  1. Have Uniform selected
  2. Select Define by Number of Blocks
  3. Insert 1 for nX
  4. Insert 1 for nY
  5. Insert 100 for nZ

Verify the input against Figure 13, and click Apply and Close.

image23

Figure 13. Mesh Generations window.

The generated mesh can be visualized in Model Visualization panel as shown in Figure 14 (by clicking image24 in the Domain panel).


image25

Figure 14. Generated mesh.

Ready?

Once all the parameters are properly assigned, the Model Setup panel (Figure 1) indicates that by Ready in the bottom left corner. Save the data by clicking the Save button image26 at the top left corner of the screen. If the data has not yet been saved, upon exiting, the user will be asked to save as well. Once the data for the model is saved, buttons for the tool sets will become active. One may proceed to various tools sets, including single-run (SR), parameter estimation (PE), uncertainty quantification (UQ) and sensitivity analysis (SA). For the next step, please see the tutorial associated with each toolset.