Setting Sediment Diagenesis - Temporally Varying Flux (Level 2 Step-by-Step Guidance)

1. Introduction

EFDC allows for multiple user defined sets of WQ sediment fluxes.  This allows the user to change the fluxes seasonally, annually, or on whatever temporal basis the model needs.  For each set/time block the user assigns a fixed flux for each constituent.  The flux rates do not change during the time set for the block but can change from one time block to the next.  The default is no time blocks, i.e. there is only one period that is constant.  However, the user can configure as many time blocks as needed. This document shown the user how to specify the fluxes spatially and how to set the temporal changes of the fluxes.

Sometime when using this option the user is met with the warning: "WQBENMAP.INP Warning! Not all of the active cells assigned mud/sand". When specifying spatially varying benthic flux then the user must set a benthic flux map –warning tells you that if you haven't set the mapping for the various rates then you need to set it.

2. Description of Hydrodynamic Model

A hydrodynamic model of West Lake in Hanoi, Vietnam, has been built and is available  for download from the EE website. This model is used as the basis for building a water quality model that is part of this guidance document. Figure 1 provides a representation of the digital terrain model for West Lake. The locations of flow boundary conditions are presented in Figure 2. Flow discharge and temperature used for the model are shown in Figure 3 and a wind rose of the wind data used is shown in Figure 4.



Figure 1. EFDC model bathymetry in West Lake.



Figure 2. Boundary condition map in West Lake.



Figure 3. Flow boundary conditions.



Figure 4. Wind rose of wind data.

3. Description of West Lake Water Quality Model

A simplified water quality model has been set up for this example. Open the water quality model as shown in Figure 5, from Model Control form of EE, RMC on Water Quality sub-item under Modules, and select Settings to open the Water Quality form.


Figure 5. Open Water Quality form. 
 

3.1 Water Quality – Kinetics Tab

The Kinetics tab is shown in Figure 6. Click on the Params button to display the list of parameters simulated in the West Lake model Figure 6.

Figure 6 Kinetics tab - Kinetics Computation Option.


Click the Modify button next to the Use Zones for Kinetics option under Water Column Kinetics frame to edit Kinetic Parameters for current zone as shown in Figure 7.

Figure 7 Kinetics Parameters for zone.


Click the Modify button next to Use Zones for Algal Dynamics option under Water Column Kinetics frame to edit Algal Growth Parameters for current zone as shown in Figure 8.

Figure 8 Algal Growth Parameters for zone.

3.2 Water Quality – Nutrients tab

The Nutrients tab is shown in Figure 9. Within the Nutrient Options and Parameters frame, click (1) Carbon button to edit the carbon parameters (Figure 10); (2) Nitrogen button to edit the nitrogen parameters (Figure 11); (3) Phosphorus button to edit the phosphorus parameters (Figure 12) and (4) COD&DO button to edit the COD&DO parameters (Figure 13).

Figure 9. Water Quality Tab: Nutrients.



Figure 10. Nutrients: (1) Carbon Parameters.



Figure 11. Nutrients: (2) Nitrogen Parameters



Figure 12. Nutrients: (3) Phosphorus Parameters.



Figure 13. Nutrients: (4) COD and DO Parameters.

3.3 Water Quality – Algae

The WQ - Algae tab is shown in Figure 14; within the Solar Radiation for Algae frame click the Modify button to edit the solar radiation parameters shown in Figure 14.Figure 14. Algae tab - Solar Radiation for Algae setting.

3.4 Water Quality – Initial Conditions

The Initial Conditions tab is shown in Figure 15. Within the Initial Conditions frame select Spatially Constant in the drop-down menu and click on Const IC's button to edit each of the water quality parameters IC as shown in Figure 15.

Figure 15. Water Quality: Initial Conditions tab setting.

3.5 Water Quality – Boundary Conditions

The Boundary Conditions tab is shown in Figure 16; click on the Edit button in Time Series Data frame to open Boundary Data Series form to add water quality time series data as shown in Figure 17.


Figure 16. Water Quality: Boundary Conditions tab.


From the Boundary Data Series form, type 1 into the # box or click on Add New button to add a new data series. Use similar steps described in the Building a 2D Lake Water Quality Model example to fill data for all water quality parameters.


Figure 17. Water Quality Boundary Data Series form.

4. Sediment Diagenesis for Temporally Varying Fluxes

1. Proceed to the Benthic tab as shown in Figure 18


Figure 18. Water Quality: Benthic tab.


2. The model domain is divided into three zones by three polygons as shown in Figure 19.


Figure 19. Zones divided in the model domain.


3. From the Benthic tab, select Modify Parameters button to display  the Sediment Diagenesis Option & Parameters as shown in Figure 20.

4. From the Sediment Diagenesis Option & Parameters form, in the top frame, Benthic Nutrient Flux Method, select Specified Spatially/Temporally Varying Fluxes; Set the # of Zones in the Zones box to 3; set # of Times in the Block Times to 3 as shown in Figure 20.


Figure 20. Set Zones and Block Times.


5. Use the arrow buttons in the Zones and Block Times boxes to go to current zones and Block Time 1, set start time of current TIME BLOCK = 0; enter the values of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame Figure 21.


Figure 21. Set parameter for Zones 1 and Block Times 1.


6. Use the arrow buttons in the Zones box to go to Current Zone 2; enter the values of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame as shown in Figure 22.


Figure 22. Set parameter for Zones 2 and Block Times 1.


7. Use the arrow buttons in the Zones box to go to Current Zone 3; enter the values of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame as shown in Figure 23.


Figure 23. Set parameter for Zones 3 and Block Times 1.


8. Use the arrow buttons in the Zones box to go to Current Zone 1 and Current Block Time 2, set start time of current TIME BLOCK = 150; enter the values of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame Figure 24.


Figure 24. Set parameter for Zones 1 and Block Times 2.


9. Use the arrow buttons in the Zones box to go to Current Zone 2 and Current Block Time 2; enter the values of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame as shown in Figure 25.


Figure 25. Set parameter for Zones 2 and Block Times 2.


10. Use the arrow buttons in the Zones box to go to Current Zone 3 and Current Block Time 2; enter the values of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame as shown in Figure 26.


Figure 26. Set parameter for Zones 3 and Block Times 2.


11. Use the arrow buttons in the Zones box to go to Current Zone 1 and current Block Time 3, set start time of Current TIME BLOCK = 1000; enter the values of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame as shown in Figure 27.


Figure 27. Set parameter for Zones 1 and Block Times 3.


12. Use the arrow buttons in the Zones box to go to Current Zone 2 and Current Block Time 3; enter the values of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame as shown in Figure 28.


Figure 28. Set parameter for Zones 2 and Block Times 3.


13. Use the arrow buttons in the Zones box to go to Current Zone 3 and Current Block Time 3; enter the value of parameters in the Spatial/Temporal Varying Benthic Fluxes Rates frame as shown in Figure 29.


Figure 29. Set parameter for Zones 3 and Block Times 3.


14. Click the Ok button to return to the Main Form, then select the Modify Parameters button to open Sediment Diagenesis Options and Parameters form again, then select Mud Zone in the drop-down menu underthe  Zones frame. Click on Set Zones buttons to set zones as shown in Figure 30. When clicking on the Set Zones button, the form shown in Figure 31 is displayed.


Figure 30. Set parameter for Zones.



Figure 31. Sediment Diagenesis: Setting the initial conditions.


15. From Apply Cell Properties via Polygons form, select the Only grid cells inside polygons option under Grid Options frame, then select the Add File button under Polygon Files frame and browse to the "Polygon1.p2d" file in the Boundaries folder; select Constant option under Value to Set frame and set the value = 1. Select Apply Defined Conditions button to assign and message box will be displayed to notify the number of modified cells and modified time, click OK button to apply value to Mud Zone 1 as shown in Figure 32.

16.  From Sediment Diagenesis Options and Parameters form shown in Figure 30, select Sand Zone in drop-down menu under Zones frame then click on Set Zones buttons to set zones. From the Apply Cell Properties via Polygons form, select Only grid cells inside polygons option under Grid Options frame, then select Add File button under Polygon Files frame and browse to the "Polygon1.p2d" file; select Constant option under Value to Set frame and set the value = 1. Select  the Apply Defined Conditions button to assign and a message box will be displayed to notify the number of modified cells and modified time, click OK button to apply value to Mud Zone 1 as shown in Figure 32. 


Figure 32. Set Mud Zone and Sand Zone for polygon 1.


17. From Sediment Diagenesis Options and Parameters form as shown in Figure 30, select Percent Mud in drop-down menu under Zones frame then click on Set Zones buttons to set zones. From Apply Cell Properties via Polygons form, select Only grid cells inside polygons option under the Grid Options frame, then select the Add File button under Polygon Files frame and browse to the "Polygon1.p2d" file in the boundaries folder; select Constant option under Value to Set frame and set the value = 60. Select the Apply Defined Conditions button to assign and message box will be displayed to notify the number of modified cells and modified time, click OK button to apply value to Mud Zone 1 as shown in Figure 33.


Figure 33. Set Percent Mud for Zone 1.


18. From Sediment Diagenesis Options and Parameters form as shown in Figure 30, click on the arrow for Current zone under the Zones frame to select zone 2 and 3, then perform similar steps from 14 to 17 to assign ICs for zone 2 and zone 3 with parameters as below:

  • Zone 2: Polygon file = "Polygon2.p2d"; Mud Zone = 2, Sand Zone = 2, Percent Mud = 45
  • Zone 3: Polygon file = "Polygon3.p2d"; Mud Zone = 3, Sand Zone = 3, Percent Mud = 30

19. After finishing all these settings, from the Sediment Diagenesis Options and Parameters form as shown in Figure 30, click OK to save all setting, close form and return to Model Control form.

20. Click on the icon in the toolbar; the Select Directory: Write Operaton will now be displayed. Select Full Write in the Save Options frame, select EEMS 10 format in Format frame, then click Ok to save the model as shown in Figure 34.


Figure 34. Apply Full write of the model.


5. Viewing Sediment Flux in EFDC_Explorer

When the model has finished saving, click on the icon to open 2DH View window and check the ICs as shown in Figure 35.

Figure 35. 2DH View window (1).


From 2DH View window, RMC on the blank area of Layer Control form and select Add New Layer or click on the  icon to open 2DH View Option form and add new layers as shown in Figure 36.Figure 36. 2DH View window (2).


From the 2DH View Option window (Figure 36), click on Primary Group drop-down menu and select Sediment Fluxes group; click on Parameters drop-down menu and select SF Zone: Mud then click on Add button to view zone Mud in 2DH View window (Figure 37).

Figure 37. View Zone Mud.


From the 2DH View Option form (Figure 36), click on Primary Group drop-down menu and select the Sediment Fluxes group; click on the Parameters drop-down menu and select SF Zone: Sand then click on the Add button to view zone Sand in 2DH View window (Figure 38).


Figure 38. View Zone Sand.


From the 2DH View Option form (Figure 36), click on the Primary Group drop-down menu and select Sediment Fluxes group; click on Parameters drop-down menu and select SF Percent Mud; then click on Add button to view mud percentage of each zone in 2DH View window (Figure 39).


Figure 39 View Percent Mud.


From the 2DH View Option form, click on the Primary Group drop-down menu and select Sediment Fluxes group; click on Parameters drop-down menu and select SF SOD; type 64 in the Time (days) box under the Fluxes Time frame; then click on Add button (Figure 40) to view SOD with block time inside 1 and 2 in 2DH View window as shown in Figure 41.


Figure 40. View Zone SOD with block time inside 1 and 2 (1).


Figure 41. View Zone SOD with block time inside 1 and 2 (2).


From the 2DH View Option form as shown in Figure 40; type 155 in Time (days) box under the Fluxes Time frame; then click the Add button to view SOD with block time inside 2 and 3 in the 2DH View window as shown in Figure 42.

Figure 42. View Zone SOD with block time inside 2 and 3.


Note that if the option use the Spatially & Temporally constant benthic flux is selected then the SOD of zone displayed in 2DH View window is the same as that set by the user.

However, if the option Specified spatially/Temporally varying fluxes has been selected as described in this tutorial, then the SOD value of in 2DH View window will be different. This is due to the impact of percentage of mud specified by the user. This different depends on the equation for SOD:

SOD(time1) = xMud * SOD(zone1,time1) + (1 - xMud) * SOD(zone2,time1)
Where xMud = percent Mud /100