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When the full sediment diagenesis sub-model is activated, then EE allows you to visualize the concentrations and resulting nutrient fluxes. If you apply a constant or temporally varying fluxes method, then you can view the sediment flux zones and sediment flux rates.
To display the Water Quality Sediment Diagenesis in the 2DH View, open a new 2DH View from the 2DH View menu or the 2DH View button from the main toolbar of EE main form. Then click the Add New Model Layer from the Layer Control Control (Figure 1). In the 2DH View Option, the primary group is selected as Water Quality Sediment Diagenesis. The drop-down list includes parameters.
- Ammonia Nitrogen (NHX)
- Nitrate Nitrogen (NOX)
- Particulate Biogenic Silica (SiP)
- Dissolved Available Silica (SiA)
- Chemical Oxygen Demand (COD)
- Dissolved Oxygen (DOX)
- Total Active Metal (TAM)
- Fecal Coliform Bacteria (FCB)
- Carbon Dioxide (CO2)
- Particulate Organic Carbon (POC)(Derived)
- Particulate Organic Phosphorus (POP)(Derived)
- Particulate Organic Nitrogen (PON)(Derived)
- Total Nitrogen (TN)(Derived)
- Total Phosphate (TP)(Derived)
- Total Organic Nitrogen (TON)(Derived)
- Total Inorganic Phosphate (TION)(Derived)
- Total Organic Phosphorus (TORP)(Derived)
- Trophic State Index (TSI)(Derived)
- TSS ( Inorganics + Organics)(Derived)
- Total Kjeldahl Nitrogen (TKN)(Derived)
- Total Dissolved Phosphorus (TDP)(Derived)
- Water Quality Zone
- Vegetation Height
- Vegetation layer penetrated
- Biota: Concentration
- Biota: Density
- Biota: Growth Factor
- Biota: Basal Metabolism Temperature Effect
- Biota: Predation Temperature Effect
The method EE uses to calculate the derived parameters can be found in Appendix C of this Knowledge Base.
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Figure 1. Add a WQ layer to the 2DH View.
In terms of biota parameters, the user can select the biota class and the unit display in the biota options, as shown in Figure 2.
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Figure 2. Add Biota Density.
With the new macrohydro options in EFDC+ vegetation can grow between layers. EEMS11.3 now allows vegetation height to be displayed, as well to show when vegetation penetrates layers. Figure 3 shows a map of macrophyte height in the 2DH View and Figure 4 shows a time series of macrophyte height from a selected cell.
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Figure 3. Vegetation Height: Macrophytes.
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Figure 4. Time Series of Macrophytes Height of a selected cell.
The number of vegetation layers penetrated by macrophytes can also be viewed in the 2DH View. The number of water layers that the fixed biota group passes through can be seen in Figure 5.
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Figure 5. Vegetation Layer Penetrated: Macrophytes.
Time Series Extraction
To extract the time series of a WQ parameter from a cell or multiple cells, we can select the cells from the 2DH View and then access the Time Series menu to select New Time Series option or click the icon 
of the main toolbar provides access to the time series graphing utility (Figure 6).
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Figure 6. Access Time Series
Once New Time Series is selected, an Extract Time Series Data form will be displayed, and it is necessary to define the cells and parameters to plot (Figure 7). Define the start and stop day for the time series in Time Series Start/Stop frame (note that the start and stop days should be within the model's start and end date). For the Biota: Growth Factor, there are many options for time series data, including Net Growth Factor, Light Limitation, Temperature Limitation, Limiting Nutrient: P or N, Phosphorus Limitation and Nitrogen Limitation. After clicking the OK button from that form, the time series of the selected WQ parameter will be shown (Figure 8).
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Figure 7. Extract Time Series Data form.
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Figure 8. Time series of WQ parameter from the cells selected.
Use the Average Selected Cells checkbox to plot the time series of the average parameter values from multiple cells selected as shown in Figure 9. Note that after selecting the checkbox, the user needs to click the Update button and then click the OK button. An example of the averaged depth time series from the selected cells is shown in Figure 10.
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Figure 9. Average Selected Cells.
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Figure 10. An averaged light limitation time series plot from selected cells.
The vegetation height at a specific time is illustrated with symbols in 2DV (this feature is added to EEMS11.3) as shown in Figure 11. Vertical Profiles, 2DV View, and Longitudinal Profiles are the same as the description in the Salinity Visualization.
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parameter list of the full sediment diagenesis method is shown in Table 1 and the sediment diagenesis parameters of the constant or temporally varying method are presented in Table 2.
Figure 2 illustrates the sediment diagenesis parameter of particular organic carbon in the 2DH View.
Anchor Figure 1 Figure 1
Figure 1. Add a Sediment Diagenesis layer to the 2DH View.
Anchor Table 1 Table 1
Table 1. List of full sediment diagenesis parameters
| Abbreviation | Parameter Name |
|---|---|
Part.Org.Nitrogen | Particular Organic Nitrogen |
Part.Org.Phosphorus | Particular Organic Phosphorus |
Part.Org.Carbon | Particular Organic Carbon |
PON Sediment Flux | PON Flux between Sediment-Water |
POP Sediment Flux | POP Flux between Sediment-Water |
POC Sediment Flux | POC Flux between Sediment-Water |
NH4-N | Concentration of Ammonium |
NO3-N | Concentration of Nitrogen |
PO4-P | Concentration of Phosphorus |
H2S | Concentration of Hydrogen Sulfide |
Dissolved Silica | Concentration of Dissolved Silica |
Part.Silica | Particular Silica |
Accumulated Benthic Stress | Accumulated Benthic Stress |
Sediment Temperature | Sediment Temperature |
O2 | Concentration of Oxygen |
Ammonium Flux | Ammonium Flux between Sediment-Water |
Nitrate Flux | Nitrate Flux between Sediment-Water |
O2 Sediment Flux | Oxygen Sediment Flux between Sediment-Water |
COD Flux | Chemical Oxygen Demand Flux |
PO4 Flux | Phosphate Flux between Sediment-Water |
Silica Flux | Silica Flux between Sediment-Water |
SD Zone | Sediment Diagenesis Zone |
| Anchor | ||||
|---|---|---|---|---|
|
Table 2. Parameter list of a constant or temporally varying fluxes method
| Abbreviation | Parameter Name |
|---|---|
| SF O2 | Sediment Fluxes Rate Oxygen |
| SF COD | Sediment Fluxes Rate Chemical Oxygen Demand |
| SF SAD | Sediment Fluxes Rate of Dissolved Available Silica |
| SF NO3 | Sediment Fluxes Rate Nitrate |
| SF NH4 | Sediment Fluxes Rate Ammonium |
| SF PO4 | Sediment Fluxes Rate Phosphate |
| SF Zone: Mud | Mud Zone |
| SF Zone: Sand | Sand Zone |
| SF Percent Mud | Percent Mud |
| Anchor | ||||
|---|---|---|---|---|
|
Figure 2. Sediment Diagenesis: Part.Org.Carbon layer in 2DH View.
To view the time series of sediment diagenesis parameters is the same as the one described in the Salinity Visualization.
Figure 3 shows an example of the time series of the PON Sediment Flux from a selected grid cell.
Anchor Figure 3 Figure 3
Figure 3. Time Series of Sediment Diagenesis: PON Sediment Flux.