Section 3 Process Descriptions

Previous chapters have presented an overview of the architecture and capabilities of the WQ Module, together with a summary of its interactions with TUFLOW FV. This chapter presents the details of each simulation class (see Table 2.1) in terms of its available model classes, the constituent models within those model classes, and the associated computed variables.

Process descriptions are listed in this section primarily by name in tables and networks, without inclusion of detail. This is for clarity, with the detailed process descriptions and equations being provided in the Appendices. To facilitate this linkage with supporting material, each process tabulated in this section has been hyperlinked directly to the relevant Appendix, and these hyperlinks colour coded as sources or sinks relative to each computed variable presented.

Again for clarity, potential interactions of a computed variable with higher order computed variables (for example oxygen with phytoplankton) are included in this section only in descriptions of those higher order variables and processes. Further:

Where a computed variable’s process is modified by a lower order computed variable (e.g. silicate sediment flux modified by oxygen), then the lower order computed variable name is shown diagrammatically in a contrasting style overlying relevant process arrows in network diagrams
Where a computed variable or process directly modifies a lower order computed variable (e.g. phytoplankton respiration consumes dissolved oxygen) then the lower order computed variable is explicitly included in tables and networks
Computed variables listed in the tables are hyperlinked to supporting information in Appendix P
Optional model classes (such as pathogens) are not included in the simulation class conceptual images (such as Figure 3.1) for clarity, but are first described in the simplest simulation class for which they can be deployed. Optional model classes are included in simulation class network diagrams only if they directly influence other water quality computed variables (e.g. pathogens do not, so are excluded from broader network diagrams).

The manual’s introduction should be reviewed for guidance on the use of interactive components deployed in this section.

3.1 Simulation Class: DO

3.1.1 Overview

The intent of this simulation class is that it provide a relatively simple entry point to commence water quality modelling. There are many applications for this class. For example it might be used to examine basic oxygen dynamics across seasons in a water supply reservoir or a relatively newly constructed urban lake, or the potential impacts of dense desalination plant return waters on local coastal sediment oxygenation processes.

This simulation class includes only the oxygen model class as mandatory, but given oxygen’s central role in environmental processes, it provides both a solid foundation for fundamental environmental investigations, and a platform from which to expand to more advanced simulation classes. The pathogens model class can be optionally included.

Figure 3.1: Simulation Class: DO (as an estuarine example)

3.1.2 Model Class: Oxygen

The following constituent models are available to select from within the oxygen model class.

3.1.2.1 Constituent Model: O2

The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.2 and Table 3.1. $\newcommand{\blockindent}{\hspace{0.5cm}}$

Figure 3.2: Constituent model: O2

Table 3.1: **Constituent model properties: O2**
Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m$^3$	Atmospheric aeration	$\cdot\blockindent$Wind speed $\cdot\blockindent$Dissolved oxygen
		Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties

In this relatively simple model, the only process requiring parameterisation is the sediment flux of oxygen.

3.1.3 Model Class: Pathogens (optional)

The following constituent models are available to select from within the pathogen model class.

3.1.3.1 Constituent Model: Free

The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.3 and Table 3.2.

Figure 3.3: Constituent model: Free

Table 3.2: **Constituent model properties: Free**
Computed Variables	Units	Processes	Interacting Quantities
Alive pathogen	CFU/100mL	Settling	$\cdot\blockindent$Settling model
		Mortality	$\cdot\blockindent$Salinity $\cdot\blockindent$Temperature $\cdot\blockindent$Mortality parameters
		Light inactivation	$\cdot\blockindent$Light and band splitting $\cdot\blockindent$DO $\cdot\blockindent$Inactivation parameters
		Attachment	$\cdot\blockindent$Attachment parameters
		Detachment	$\cdot\blockindent$Attachment parameters
Dead pathogen	CFU/100mL	Settling	$\cdot\blockindent$Settling model
		Mortality	$\cdot\blockindent$Salinity $\cdot\blockindent$Temperature $\cdot\blockindent$Mortality parameters
		Light inactivation	$\cdot\blockindent$Light and band splitting $\cdot\blockindent$DO $\cdot\blockindent$Inactivation parameters

3.1.3.2 Constituent Model: Attached

The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.4 and Table 3.3. This constituent model is the same as the Free constituent model, but allows for pathogens to attach to sediments.

Figure 3.4: Constituent model: Attached

Table 3.3: **Constituent model properties: Attached**
Computed Variables	Units	Processes	Interacting Quantities
Alive pathogen	CFU/100mL	Settling	$\cdot\blockindent$Settling model
		Mortality	$\cdot\blockindent$Salinity $\cdot\blockindent$Temperature $\cdot\blockindent$Mortality parameters
		Light inactivation	$\cdot\blockindent$Light and band splitting $\cdot\blockindent$DO $\cdot\blockindent$Inactivation parameters
		Attachment	$\cdot\blockindent$Attachment parameters
		Detachment	$\cdot\blockindent$Attachment parameters
Dead pathogen	CFU/100mL	Settling	$\cdot\blockindent$Settling model
		Mortality	$\cdot\blockindent$Salinity $\cdot\blockindent$Temperature $\cdot\blockindent$Mortality parameters
		Light inactivation	$\cdot\blockindent$Light and band splitting $\cdot\blockindent$DO $\cdot\blockindent$Inactivation parameters
Attached pathogen	CFU/100mL	Attachment	$\cdot\blockindent$Attachment parameters
		Detachment	$\cdot\blockindent$Attachment parameters

Neither of the pathogen constituent models have complementary lower order computed variables, and their operation does not influence the concentrations of any other computed variables.

3.1.4 Computed variables

The only mandatory computed variable is this simulation class is dissolved oxygen, and as such the overarching simulation class network diagram is the same as that presented in Figure 3.2. If pathogens are simulated, then the corresponding simulation class network diagram is the (unconnected) aggregation of Figure 3.2 and either Figure 3.3 or Figure 3.4.

3.2 Simulation Class: Inorganics

3.2.1 Overview

The intent of this simulation class is that it provide a framework for simulating typical water quality conditions where organic matter does not play a significant role in ecosystem processes. For example it might be used to examine basic inorganic nutrient processing in nearshore coastal environments that include relatively unimpacted sandy bed conditions, or mine voids that receive little catchment inflow. This simulation class could equally be applied to smaller, well flushed estuaries that receive relatively little catchment derived organic matter, or to basic studies of lakes and water supply reservoirs. The latter cases (amongst others) might also use this simulation class as a stepping stone towards subsequent and more detailed simulations that include organic matter cycling. This would simply require upgrade from this simulation class to the organics simulation class.

This simulation class includes the oxygen, silicate, inorganic nitrogen, inorganic phosphorus, phytoplankton and (optionally) pathogen model classes.

Figure 3.5: Simulation Class: Inorganics (as an estuarine example)

3.2.2 Model Class: Oxygen

This model class is the same as that described in Section 3.1.2.

3.2.3 Model Class: Silicate

The following constituent models are available to select from within the silicate model class.

3.2.3.1 Constituent Model: Si

The constituent model code and associated variables, processes and potentially interacting simulated quantities are provided in Figure 3.6 and Table 3.4.

Figure 3.6: Constituent model: Si

Table 3.4: **Constituent model properties: Si**
Computed Variables	Units	Processes	Interacting Quantities
Silicate	mg/L or mmol/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties

This is a relatively simple model, with the only process requiring parameterisation being the sediment flux of silicate. By default, this process depends on overlying dissolved oxygen concentrations, but this can optionally be turned off if required.

3.2.4 Model Class: Inorganic nitrogen

The following constituent models are available to select from within the inorganic nitrogen model class.

3.2.4.1 Constituent Model: AmmoniumNitrate

The constituent model code and associated variables, processes and potentially interacting simulated quantities are provided in Figure 3.7 and Table 3.5.

Figure 3.7: Constituent model: AmmoniumNitrate

Table 3.5: **Constituent model properties: AmmoniumNitrate**
Computed Variables	Units	Processes	Interacting Quantities
Ammonium	mg/L or mmol/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Nitrification	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrification parameters $\cdot\blockindent$Ammonium
		Wet atmospheric deposition	$\cdot\blockindent$Rainfall
		Dry atmospheric deposition	$\cdot\blockindent$Atmospheric parameters
		Anaerobic oxidation of ammonium	$\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Anammox parameters $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate
		Dissimilatory reduction of nitrate to ammonium	$\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$DNRA parameters
Nitrate	mg/L or mmol/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Nitrification	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrification parameters $\cdot\blockindent$Ammonium
		Denitrification	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Denitrification parameters $\cdot\blockindent$Nitrate
		Wet atmospheric deposition	$\cdot\blockindent$Rainfall
		Dry atmospheric deposition	$\cdot\blockindent$Atmospheric parameters
		Anaerobic oxidation of ammonium	$\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Anammox parameters $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate
		Dissimilatory reduction of nitrate to ammonium	$\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$DNRA parameters

This is a slightly more complex model than those described previously, and this reflects the complexity of inorganic nitrogenous environmental chemistry. In addition to specification of two computed variables and their respective sediment flux properties, rates and related parameters for nitrification and denitrification are also specifiable. By design, the library defaults for these processes are set to zero so that all processes are initially inactive. Users may activate these processes by specifying non-zero rate parameters.

Whilst dissolved oxygen potentially modifies some processes described to this point (e.g. computed sediment flux rates), nitrification is the first of these processes that also potentially consumes dissolved oxygen. Specifically, if nitrification is simulated (i.e. non-zero rate parameters are specified) and allowed to include the effect of dissolved oxygen (the default), then dissolved oxygen concentrations are drawn down as the process operates.

Table 3.6: **Complementary lower order computed variables: AmmoniumNitrate**
Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m$^3$	Nitrification	$\cdot\blockindent$Water temperature $\cdot\blockindent$Nitrification parameters $\cdot\blockindent$Ammonium

3.2.5 Model Class: Inorganic phosphorus

The following constituent models are available to select from within the phosphorus model class.

3.2.5.1 Constituent Model: FRPhs

The constituent model code and associated variables, processes and potentially interacting simulated quantities are provided in Figure 3.8 and Table 3.7.

Figure 3.8: Constituent model: FRPhs

Table 3.7: **Constituent model properties: FRPhs**
Computed Variables	Units	Processes	Interacting Quantities
FRP	mg/L or mmol/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Wet atmospheric deposition	$\cdot\blockindent$Rainfall

This is a relatively simple constituent model, but one that is critical to the simulation of higher order computed variables such as phytoplankton.

3.2.5.2 Constituent Model: FRPhsAds

The constituent model code and associated variables, processes and potentially interacting simulated quantities are provided in Figure 3.9 and Table 3.8.

Figure 3.9: Constituent Model: FRPhsAds

Table 3.8: **Constituent model properties: FRPhsAds**
Computed Variables	Units	Processes	Interacting Quantities
FRP	mg/L or mmol/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Wet atmospheric deposition	$\cdot\blockindent$Rainfall
		Adsorption and desorption	$\cdot\blockindent$Suspended solids $\cdot\blockindent$FRP $\cdot\blockindent$Adorption parameters
FRP adsorbed	mg/L or mmol/m$^3$	Adsorption and desorption	$\cdot\blockindent$Suspended solids $\cdot\blockindent$FRP $\cdot\blockindent$Adorption parameters
		Settling	$\cdot\blockindent$Suspended solids $\cdot\blockindent$Suspended solids settling parameters
		Dry atmospheric deposition	$\cdot\blockindent$Atmospheric parameters

In order for this constituent model to be used, the TUFLOW FV Sediment Transport (ST) Module must be activated to simulate at least one fraction of suspended sediment (several fractions may be so set). A WQ Module simulation will not start if the TUFLOW ST Module is not activated. In order to use this FRPhsAds constituent model therefore, the following must be in place:

The TUFLOW FV ST Module must be activated and implemented
At least one sediment fraction must be set up and executed within TUFLOW FV via the inclusion of a sediment control file, and specification of either of the following TUFLOW FV commands:

include sediment == 1,0 ! Do not include sediment in density calculations

include sediment == 1,1 ! Include sediment in density calculations

If multiple sediment fractions are specified to be simulated by the ST Module, then TUFLOW FV sends all these fraction concentrations as a sum through the API to the WQ Module, and this sum is used as the sediment concentration against which adsorption is computed. The WQ Module uses this information to compute FRP adsorption and loss of adsorbed FRP through settling. It is recognised that there are limitations of this approach. Future releases of TUFLOW FV and the WQ Module will address some of these limitations and allow for:

User control of which ST Module sediment fractions are used in adsorption calculations, and
Use of the TUFLOW FV ST Module settling and resuspension routines to dynamically link settling and resuspension of adsorbed FRP

3.2.6 Model Class: Phytoplankton

The following constituent models are available to select from within the phytoplankton model class. The differentiator between constituent models is the treatment of internal (to a phytoplankton cell) nutrient simulation.

3.2.6.1 Constituent Model: Basic

This basic phytoplankton constituent model assumes that the ratios of both internal nitrogen and phosphorus concentrations to internal chlorophyll a (or carbon) concentration are fixed. These internal nutrients are not simulated explicitly, but increase and decrease proportionately with increasing and decreasing carbonaceous biomass, according to the specified (or default) nitrogen-chlorophyll a and phosphorus-chlorophyll a (or their carbon equivalents) ratios. Carbonaceous biomass is simulated dynamically and is the measure of phytoplankton concentration. Internal nutrient concentrations are not required to be specified as initial or boundary conditions, and are not treated as computed variables.

The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.10 and Table 3.9. Silicate interactions only apply if phytoplankton is set to uptake silicate via specification of silicate limitation function parameters (section 4.7.3.5.1). The configuration for phytoplankton simulation presented below applies only to the inorganics simulation class. A different, and expanded, configuration applies when phytoplankton is simulated using this basic constituent model in the organics simulation class. This expanded configuration is described in section 3.3.7.1.

Figure 3.10: Constituent model: Basic

Table 3.9: **Constituent model properties: Basic**
Computed Variables	Units	Processes	Interacting Quantities
Phytoplankton	$\mu$g Chl a/L or mmol C/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen
		Excretion	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
		Settling	$\cdot\blockindent$Settling model $\cdot\blockindent$Cell density

The three processes that govern phytoplankton behaviour are:

Primary productivity (the photosynthetic conversion of light and carbon to stored energy and oxygen, also referred to as growth)
Respiration (the expenditure of stored energy and oxygen), and
Settling

A range of light, temperature, salinity, nitrogen, phosphorus and silicate limitation functions can be parameterised and applied in various combinations to the first two processes above, and a range of settling models are available to tailor the third. By design, the associated library default rates are set to zero so as to render all processes initially inactive. Specification of non-zero rates activates these processes.

The distinguishing property of this phytoplankton constituent model is that internal (phytoplankton cell) nutrient concentrations are considered to be fixed proportions of cell chlorophyll a (or carbon) concentrations. They are therefore not treated as computed variables, but rather as multiples of phytoplankton chlorophyll a (or carbon) (which is treated as a computed variable). The key implication of this is the method of calculation of the nitrogen and phosphorus uptake and limitation functions applied to primary productivity. These calculations depend only on ambient (i.e. external to a phytoplankton cell) water column nitrogen and phosphorus concentrations.

Simulation of phytoplankton dynamics in the inorganics simulation class directly modifies the concentrations of a range of other computed variables. These are listed in Table 3.10. Silicate interactions only apply if phytoplankton is set to uptake silicate.

Table 3.10: **Complementary lower order computed variables: Basic**
Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light
Ammonium	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
		Excretion	$\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
Nitrate	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
FRP	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Ammonium $\cdot\blockindent$Silicate (if activated)
		Excretion	$\cdot\blockindent$Ammonium $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$Ammonium $\cdot\blockindent$Silicate (if activated)
Silicate (if activated)	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Ammonium $\cdot\blockindent$FRP
		Excretion	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP
		Mortality	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP

3.2.6.2 Constituent Model: Advanced

This phytoplankton constituent model directly simulates internal (phytoplankton cell) nitrogen and phosphorus concentrations. These are allowed to vary between upper and lower limits, expressed as ratios to chlorophyll a (or carbon) concentrations. Internal nutrient concentrations (not as ratios) are required to be specified as initial and boundary conditions, and are treated as computed variables.

The constituent model code and associated variables, processes and potentially interacting simulated quantities are provided in Figure 3.11 and Table 3.11. Silicate interactions only apply if phytoplankton is set to uptake silicate. The configuration for phytoplankton simulation presented below applies only to the inorganics simulation class. A different, and expanded, configuration applies when phytoplankton is simulated using this advanced constituent model in the organics simulation class. This expanded configuration is described in section 3.3.7.2.

Figure 3.11: Constituent model: Advanced

Table 3.11: **Constituent model properties: Advanced**
Computed Variables	Units	Processes	Interacting Quantities
Phytoplankton	$\mu$g Chl a/L or mmol C/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
		Excretion	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Settling	$\cdot\blockindent$Settling model $\cdot\blockindent$Cell density $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
Internal nitrogen	mg N/L or mmol N/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Uptake	$\cdot\blockindent$Water temperature $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Internal phosphorus
		Excretion	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Settling	$\cdot\blockindent$Settling model $\cdot\blockindent$Cell density $\cdot\blockindent$Internal phosphorus
Internal phosphorus	mg P/L or mmol P/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Silicate (if activated)
		Uptake	$\cdot\blockindent$Water temperature $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Internal nitrogen
		Excretion	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Silicate (if activated)
		Settling	$\cdot\blockindent$Settling model $\cdot\blockindent$Cell density $\cdot\blockindent$Internal nitrogen

The three processes that govern phytoplankton behaviour are:

Primary productivity (the photosynthetic conversion of light and carbon to stored energy and oxygen, also referred to as growth)
Respiration (the expenditure of stored energy and oxygen), and
Settling

The distinguishing property of this phytoplankton constituent model is that internal (phytoplankton cell) nutrient concentrations are simulated directly. They are therefore treated as computed variables. The key implication of this is the method of calculation of the nitrogen and phosphorus uptake and limitation functions applied to primary productivity. These calculations depend on both internal nutrient stores and ambient (i.e. external to a phytoplankton cell) water column nitrogen and phosphorus concentrations.

Simulation of phytoplankton dynamics in the inorganics simulation class directly modifies the concentrations of a range of other computed variables. These are listed in Table 3.12. Silicate interactions only apply if phytoplankton is set to uptake silicate.

Table 3.12: **Complementary lower order computed variables: Advanced**
Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if simulated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light
Ammonium	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if simulated)
		Excretion	$\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if simulated)
		Mortality	$\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if simulated)
Nitrate	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Ammonium $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if simulated)
FRP	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Ammonium $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if simulated)
		Excretion	$\cdot\blockindent$Ammonium $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if simulated)
		Mortality	$\cdot\blockindent$Ammonium $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if simulated)
Silicate (if simulated)	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
		Excretion	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
		Mortality	$\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus

3.2.7 Model Class: Pathogens (optional)

This model class is the same as that described in Section 3.1.3.

3.2.8 Computed variables

The relationships between all available computed variables and processes is this inorganics simulation class are presented in Figure 3.12. Depending on the constituent model classes deployed, not all of the computed variables and processes shown in the figure will necessarily be active. All network link labels have been removed (other than denoting the relevant phytoplankton model), and optional non-interacting model classes (e.g. pathogens) omitted, for clarity.

Figure 3.12: Simulation class: Inorganics

3.3 Simulation Class: Organics

3.3.1 Overview

The intent of this simulation class is that it provide a relatively advanced water quality modelling tool. There are many applications for this class. For example it might be used to examine detailed reservoir phytoplankton dynamics or the response of an estuary to both inorganic and organic pollutant loading.

This simulation class includes the oxygen, silicate, inorganic nitrogen, inorganic phosphorus, organic matter, phytoplankton and (optionally) pathogen model classes.

Figure 3.13: Simulation Class: Organics (as an estuarine example)

3.3.2 Model Class: Oxygen

This constituent model class is the same as that described in Section 3.1.2

3.3.3 Model Class: Silicate

This constituent model class is the same as that described in Section 3.2.3

3.3.4 Model Class: Inorganic nitrogen

This constituent model class is the same as that described in Section 3.2.4

3.3.5 Model Class: Inorganic phosphorus

This constituent model class is the same as that described in Section 3.2.5

3.3.6 Model Class: Organic matter

The following constituent models are available to select from within the organic matter model class. The differentiator between constituent models is the exclusion or inclusion of refractory organic matter.

3.3.6.1 Constituent Model: Labile

This organic matter constituent model considers only labile particulate and dissolved organic matter. The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.14 and Table 3.13. Both the Figure and Table (and Table 3.14) make reference to dissolved inorganic carbon (DIC). This is for completeness only because the WQ Module does not currently support simulation of DIC. Doing so is not required in order to deploy either the labile or refractory organic matter constituent model within the WQ Module.

Figure 3.14: Constituent model: Labile

Table 3.13: **Constituent model properties: Labile**
Computed Variables	Units	Processes	Interacting Quantities
Labile particulate organic carbon	mg C/L or mmol C/m$^3$	Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Settling	$\cdot\blockindent$Settling model
Labile particulate organic nitrogen	mg N/L or mmol N/m$^3$	Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Settling	$\cdot\blockindent$Settling model
Labile particulate organic phosphorus	mg P/L or mmol P/m$^3$	Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Settling	$\cdot\blockindent$Settling model
Labile dissolved organic carbon	mg C/L or mmol C/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$POC
		Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
Labile dissolved organic nitrogen	mg N/L or mmol N/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$PON
		Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
Labile dissolved organic phosphorus	mg P/L or mmol P/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$POP
		Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate

The four processes that govern (labile) organic matter behaviour in this constituent model are:

Sediment flux
Hydrolysis (the conversion of particulate organics to dissolved organics)
Mineralisation (the conversion of dissolved organics to inorganics), and
Settling, of only particulate organics

A range of rate constants can be specified to control these processes, or the defaults used. By design, the library default rates are set to zero so as to render all processes initially inactive. Specification of non-zero rates activates these processes.

Simulation of labile organic dynamics in the organics simulation class directly modifies the concentrations of other computed variables. These are listed in Table 3.14.

Table 3.14: **Complementary lower order computed variables: Labile**
Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$DOP
Nitrate	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate $\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$DOP
Ammonium	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate $\cdot\blockindent$DON
FRP	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate $\cdot\blockindent$DOP
DIC	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate $\cdot\blockindent$DOC

3.3.6.2 Constituent Model: Refractory

This organic matter constituent model considers both labile and refractory particulate and dissolved organic matter. The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.15 and Table 3.15. Both the Figure and Table (and Table 3.16) make reference to dissolved inorganic carbon (DIC). This is for completeness only because the WQ Module does not currently support simulation of DIC. Doing so is not required in order to deploy either the labile or refractory organic matter constituent model within the WQ Module.

$**Constituent model: Refractory**$

Figure 3.15: Constituent model: Refractory

Table 3.15: **Constituent model properties: Refractory**
Computed Variables	Units	Processes	Interacting Quantities
Labile particulate organic carbon	mg C/L or mmol C/m$^3$	Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Settling	$\cdot\blockindent$Settling model
		Breakdown	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$RPOM
Labile particulate organic nitrogen	mg N/L or mmol N/m$^3$	Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Settling	$\cdot\blockindent$Settling model
		Breakdown	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$RPOM
Labile particulate organic phosphorus	mg P/L or mmol P/m$^3$	Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Settling	$\cdot\blockindent$Settling model
		Breakdown	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$RPOM
Labile dissolved organic carbon	mg C/L or mmol C/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$POC
		Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
		Activation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$RDOC
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$RDOC
Labile dissolved organic nitrogen	mg N/L or mmol N/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$PON
		Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
		Activation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$RDON
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$RDON
Labile dissolved organic phosphorus	mg P/L or mmol P/m$^3$	Sediment flux	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Sediment properties
		Hydrolysis	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$POP
		Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
		Activation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$RDOP
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$RDOP
Refractory particulate organic carbon	mg C/L or mmol C/m$^3$	Settling	$\cdot\blockindent$Settling model
		Breakdown	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
Refractory dissolved organic carbon	mg C/L or mmol C/m$^3$	Activation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$RDOC
Refractory dissolved organic nitrogen	mg N/L or mmol N/m$^3$	Activation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$RDOC $\cdot\blockindent$RDON
Refractory dissolved organic phosphorus	mg N/L or mmol N/m$^3$	Activation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$DOC $\cdot\blockindent$RDOC $\cdot\blockindent$RDOP

The processes that govern (labile and refractory) organic matter behaviour in this constituent model are:

Sediment flux
Hydrolysis (the conversion of particulate organics to dissolved organics)
Mineralisation (the conversion of dissolved organics to inorganics)
Breakdown (the conversion of refractory particulate organic matter to labile particulate organic matter)
Photolysis (the conversion of refractory dissolved organic matter to labile dissolved organic matter and corresponding inorganics)
Activation (the conversion of refractory dissolved to labile dissolved organic matter)
Settling, of only particulate organics

Simulation of labile and refractory organic dynamics in the organics simulation class directly modifies the concentrations of other computed variables. These are listed in Table 3.16.

Table 3.16: **Complementary lower order computed variables: Refractory**
Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen
Nitrate	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
Ammonium	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$RDON
FRP	mg/L or mmol/m$^3$	Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$RDOP
DIC		Mineralisation	$\cdot\blockindent$Water temperature $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Nitrate
		Photolysis	$\cdot\blockindent$Radiation $\cdot\blockindent$RDOC

3.3.7 Model Class: Phytoplankton

This constituent model class is the same as that described in Section 3.2.6, except that in the current constituent model class, phytoplanktonic losses are to labile organic computed variables rather than inorganic nutrients. These processes and interactions are described below.

3.3.7.1 Constituent Model: Basic

As per Section 3.2.6.1, this phytoplankton constituent model assumes that the ratios of both internal nitrogen and phosphorus concentrations to internal chlorophyll a (or carbon) concentration are fixed. These internal nutrients are not simulated explicitly, but increase and decrease proportionately with increasing and decreasing carbonaceous biomass, according to the specified (or default) nitrogen-chlorophyll a and phosphorus-chlorophyll a (or their carbon equivalents) ratios. Carbonaceous biomass is simulated dynamically and is the measure of phytoplankton concentration. Internal nutrient concentrations are not required to be specified as initial or boundary conditions, and are not treated as computed variables.

The constituent model code and associated computed variables, processes and potentially interacting simulated quantities are provided in Figure 3.16 and Table 3.17. Silicate interactions only apply if phytoplankton is set to uptake silicate via specification of silicate limitation function parameters (section 4.7.3.5.1). The configuration for phytoplankton simulation presented below applies only to the organics simulation class. A different, and simpler, configuration applies when phytoplankton is simulated using this basic constituent model in the inorganics simulation class. That simplified configuration is described in section 3.2.6.1.

Figure 3.16: Constituent model: Basic

Table 3.17: **Constituent model properties: Basic**
Computed Variables	Units	Processes	Interacting Quantities
Phytoplankton	$\mu$g Chl a/L or mmol C/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen
		Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$DOP $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$POC $\cdot\blockindent$PON $\cdot\blockindent$POP $\cdot\blockindent$Silicate (if activated)
		Settling	$\cdot\blockindent$Settling model $\cdot\blockindent$Cell density

The three processes that govern phytoplankton behaviour are:

Primary productivity (the photosynthetic conversion of light and carbon to stored energy and oxygen, also referred to as growth)
Respiration (the expenditure of stored energy and oxygen), and
Settling

Simulation of phytoplankton dynamics in the organics simulation class directly modifies the concentrations of a range of other computed variables. These are listed in Table 3.18. Silicate interactions only apply if phytoplankton is set to uptake silicate.

Table 3.18: **Complementary lower order computed variables: Basic**
Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light
Ammonium	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
Nitrate	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
FRP	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Ammonium $\cdot\blockindent$Silicate (if activated)
Silicate (if activated)	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Ammonium $\cdot\blockindent$FRP
		Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$DOP
		Mortality	$\cdot\blockindent$POC $\cdot\blockindent$PON $\cdot\blockindent$POP
Labile particulate organic carbon	mg/L or mmol/m$^3$	Mortality	$\cdot\blockindent$PON $\cdot\blockindent$POP $\cdot\blockindent$Silicate (if activated)
Labile particulate organic nitrogen	mg/L or mmol/m$^3$	Mortality	$\cdot\blockindent$POC $\cdot\blockindent$POP $\cdot\blockindent$Silicate (if activated)
Labile particulate organic phosphorus	mg/L or mmol/m$^3$	Mortality	$\cdot\blockindent$POC $\cdot\blockindent$PON $\cdot\blockindent$Silicate (if activated)
Labile dissolved organic carbon	mg/L or mmol/m$^3$	Excretion	$\cdot\blockindent$DON $\cdot\blockindent$DOP $\cdot\blockindent$Silicate (if activated)
Labile dissolved organic nitrogen	mg/L or mmol/m$^3$	Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DOP $\cdot\blockindent$Silicate (if activated)
Labile dissolved organic phosphorus	mg/L or mmol/m$^3$	Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$Silicate (if activated)

3.3.7.2 Constituent Model: Advanced

As per Section 3.2.6.2, this phytoplankton constituent model directly simulates internal (phytoplankton cell) nitrogen and phosphorus concentrations. These are allowed to vary between upper and lower limits, expressed as ratios to chlorophyll a (or carbon) concentrations. Internal nutrient concentrations (not as ratios) are required to be specified as initial and boundary conditions, and are treated as computed variables.

The constituent model code and associated variables, processes and potentially interacting simulated quantities are provided in Figure 3.17 and Table 3.19. Silicate interactions only apply if phytoplankton is set to uptake silicate. The configuration for phytoplankton simulation presented below applies only to the organics simulation class. A different, and simplified, configuration applies when phytoplankton is simulated using this advanced constituent model in the inorganics simulation class. That configuration is described in section 3.2.6.2.

Figure 3.17: Constituent model: Advanced

Table 3.19: **Constituent model properties: Advanced**
Computed Variables	Units	Processes	Interacting Quantities
Phytoplankton	$\mu$g Chl a/L or mmol C/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
		Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$DOP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$POC $\cdot\blockindent$PON $\cdot\blockindent$POP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Settling	$\cdot\blockindent$Settling model $\cdot\blockindent$Cell density $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
Internal nitrogen	mg N/L or mmol N/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Uptake	$\cdot\blockindent$Water temperature $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Internal phosphorus
		Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$DOP $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$POC $\cdot\blockindent$PON $\cdot\blockindent$POP $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Settling	$\cdot\blockindent$Settling model $\cdot\blockindent$Cell density $\cdot\blockindent$Internal phosphorus
Internal phosphorus	mg P/L or mmol P/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Silicate (if activated)
		Uptake	$\cdot\blockindent$Water temperature $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Dissolved oxygen $\cdot\blockindent$Internal nitrogen
		Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$DOP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Silicate (if activated)
		Mortality	$\cdot\blockindent$POC $\cdot\blockindent$PON $\cdot\blockindent$POP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Silicate (if activated)
		Settling	$\cdot\blockindent$Settling model $\cdot\blockindent$Cell density $\cdot\blockindent$Internal nitrogen

The three processes that govern phytoplankton behaviour are:

Primary productivity (the photosynthetic conversion of light and carbon to stored energy and oxygen, also referred to as growth)
Respiration (the expenditure of stored energy and oxygen), and
Settling

Simulation of phytoplankton dynamics in the organics simulation class directly modifies the concentrations of a range of other computed variables. These are listed in Table 3.20. Silicate interactions only apply if phytoplankton is set to uptake silicate.

Table 3.20: **Complementary lower order computed variables: Advanced**
Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Ammonium $\cdot\blockindent$Nitrate $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
		Respiration	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light
Ammonium	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
Nitrate	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Ammonium $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$FRP $\cdot\blockindent$Silicate (if activated)
FRP	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Ammonium $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
Silicate (if activated)	mg/L or mmol/m$^3$	Primary productivity	$\cdot\blockindent$Water temperature $\cdot\blockindent$Salinity $\cdot\blockindent$Light $\cdot\blockindent$Nitrate $\cdot\blockindent$Ammonium $\cdot\blockindent$FRP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
		Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$DOP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
		Mortality	$\cdot\blockindent$POC $\cdot\blockindent$PON $\cdot\blockindent$POP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus
Labile particulate organic carbon	mg/L or mmol/m$^3$	Mortality	$\cdot\blockindent$PON $\cdot\blockindent$POP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
Labile particulate organic nitrogen	mg/L or mmol/m$^3$	Mortality	$\cdot\blockindent$POC $\cdot\blockindent$POP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
Labile particulate organic phosphorus	mg/L or mmol/m$^3$	Mortality	$\cdot\blockindent$POC $\cdot\blockindent$PON $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
Labile dissolved organic carbon	mg/L or mmol/m$^3$	Excretion	$\cdot\blockindent$DON $\cdot\blockindent$DOP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
Labile dissolved organic nitrogen	mg/L or mmol/m$^3$	Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DOP $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)
Labile dissolved organic phosphorus	mg/L or mmol/m$^3$	Excretion	$\cdot\blockindent$DOC $\cdot\blockindent$DON $\cdot\blockindent$Internal nitrogen $\cdot\blockindent$Internal phosphorus $\cdot\blockindent$Silicate (if activated)

3.3.8 Model Class: Pathogens (optional)

This model class is the same as that described in Section 3.1.3.

3.3.9 Computed variables

The relationships between all available computed variables and processes is this simulation class are presented in Figure 3.18. Depending on the constituent model classes deployed, not all of the computed variables and processes shown in the figure will necessarily be active. All network link labels have been removed (other than denoting the relevant phytoplankton model), and optional non-interacting model classes (e.g. pathogens) omitted, for clarity.

Figure 3.18: Simulation class: Organics

Computed Variables	Units	Processes	Interacting Quantities
Dissolved oxygen	mg/L or mmol/m\(^3\)	Atmospheric aeration	\(\cdot\blockindent\)Wind speed \(\cdot\blockindent\)Dissolved oxygen
		Sediment flux	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)Sediment properties

Computed Variables	Units	Processes	Interacting Quantities
Phytoplankton	\(\mu\)g Chl a/L or mmol C/m\(^3\)	Primary productivity	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Salinity \(\cdot\blockindent\)Light \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)Ammonium \(\cdot\blockindent\)Nitrate \(\cdot\blockindent\)FRP \(\cdot\blockindent\)Silicate (if activated)
		Respiration	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Salinity \(\cdot\blockindent\)Light \(\cdot\blockindent\)Dissolved oxygen
		Excretion	\(\cdot\blockindent\)Ammonium \(\cdot\blockindent\)FRP \(\cdot\blockindent\)Silicate (if activated)
		Mortality	\(\cdot\blockindent\)Ammonium \(\cdot\blockindent\)FRP \(\cdot\blockindent\)Silicate (if activated)
		Settling	\(\cdot\blockindent\)Settling model \(\cdot\blockindent\)Cell density

Computed Variables	Units	Processes	Interacting Quantities
Labile particulate organic carbon	mg C/L or mmol C/m\(^3\)	Hydrolysis	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen
		Settling	\(\cdot\blockindent\)Settling model
Labile particulate organic nitrogen	mg N/L or mmol N/m\(^3\)	Hydrolysis	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen
		Settling	\(\cdot\blockindent\)Settling model
Labile particulate organic phosphorus	mg P/L or mmol P/m\(^3\)	Hydrolysis	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen
		Settling	\(\cdot\blockindent\)Settling model
Labile dissolved organic carbon	mg C/L or mmol C/m\(^3\)	Sediment flux	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)Sediment properties
		Hydrolysis	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)POC
		Mineralisation	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)Nitrate
Labile dissolved organic nitrogen	mg N/L or mmol N/m\(^3\)	Sediment flux	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)Sediment properties
		Hydrolysis	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)PON
		Mineralisation	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)Nitrate
Labile dissolved organic phosphorus	mg P/L or mmol P/m\(^3\)	Sediment flux	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)Sediment properties
		Hydrolysis	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)POP
		Mineralisation	\(\cdot\blockindent\)Water temperature \(\cdot\blockindent\)Dissolved oxygen \(\cdot\blockindent\)Nitrate