4.8 Simulation Class: Organics

If the organics simulation class is specified with no subsequent constituent model blocks, then a simulation will be automatically constructed using this organics class, and populated with library defaults for all parameters. Computed variables will be:

• Dissolved oxygen
• Silicate
• Ammonium
• Nitrate
• Filterable reactive phosphorus
• Dissolved organic carbon
• Particulate organic carbon
• Dissolved organic nitrogen
• Particulate organic nitrogen
• Dissolved organic phosphorus
• Particulate organic phosphorus
• One phytoplankton group named ‘dummy’ that uses the basic phytoplankton constituent model

For clarity, this section uses acronyms for some computed variable names, and these acronyms are expanded in Appendix P. All references below to “organic matter” are to labile organic computed variables, unless specifically termed as refractory.

4.8.1 Prerequisites

The organics simulation class requires simulation of the following in TUFLOW FV:

• Hydrodynamics, in either two or three dimensions (including any internal one dimensional structures if present)
• Salinity
• Temperature
• Heat module on (i.e. meteorological forcing is required)

Simulation of suspended sediment (via TUFLOW FV’s sediment transport module) is required only if adsorbed phosphorus is to be simulated by the WQ Module.

4.8.2 Part 1: Simulation specification

The organics simulation class is set via

Simulation Class == Organics

The other commands in this part are not specific to this simulation class. See section 4.5.1.

4.8.3 Part 2: Constituent model specification

As per Tables 2.2 and 2.3, there are several constituent model classes available within the organics simulation class. The commands for each are described following. To avoid repetition, cross references to explanations are provided for commands that are included in previous simulation classes and remain the same for this class.

4.8.3.1 Model class: Oxygen

4.8.3.1.1 Constituent model: O2

The commands for this constituent model are described in Section 4.7.3.1.1.

4.8.3.2 Model class: Silicate

4.8.3.2.1 Constituent model: Si

The commands for this constituent model are described in Section 4.7.3.2.1.

4.8.3.3 Model class: Inorganic nitrogen

4.8.3.3.1 Constituent model: AmmoniumNitrate

The commands for this constituent model are described in Section 4.7.3.3.1.

4.8.3.4 Model class: Inorganic phosphorus

4.8.3.4.1 Constituent model: FRPhs

The commands for this constituent model are described in Section 4.7.3.4.1.

4.8.3.4.2 Constituent model: FRPhsAds

The commands for this constituent model are described in Section 4.7.3.4.2.

4.8.3.5 Model class: Organic matter

4.8.3.5.1 Constituent model: Labile

This constituent model is specified as:

Organic Matter Model == Labile

Minimum and maximum concentrations are specified as:

Carbon Min Max == \(\left[POC\right]_{min}^{POC}\), \(\left[POC\right]_{max}^{POC}\), \(\left[DOC\right]_{min}^{DOC}\), \(\left[DOC\right]_{max}^{DOC}\)

Nitrogen Min Max == \(\left[PON\right]_{min}^{PON}\), \(\left[PON\right]_{max}^{PON}\), \(\left[DON\right]_{min}^{DON}\), \(\left[DON\right]_{max}^{DON}\)

Phosphorus Min Max == \(\left[POP\right]_{min}^{POP}\), \(\left[POP\right]_{max}^{POP}\), \(\left[DOP\right]_{min}^{DOP}\), \(\left[DOP\right]_{max}^{DOP}\)

Global benthic flux parameters (used in Equation (N.1)) are specified as:

Organics Benthic == \(K_{sed-O_2}^{DOM}\), \(\theta_{sed}^{DOM}\)

Although not strictly necessary, the use of “organics” to prefix the above block command is deliberate so as to maintain consistency of command style with other constituent model blocks that include more than one computed variable, such as nitrogen and phosphorus. The command will also be accepted simply as Benthic ==.

Particulate organic hydrolysis parameters (used in (N.2) and therefore (N.3)) are set in a single command as:

Hydrolysis == \(R_{hyd}^{POC}\), \(R_{hyd}^{PON}\), \(R_{hyd}^{POP}\), \(K_{hyd-O_2}^{POM}\), \(\theta_{hyd}^{POM}\)

Dissolved organic mineralisation parameters (used in (N.8) and therefore (N.9)) are set in a single command, together with the corresponding denitrification parameters describing associated consumption of nitrate due to mineralisation (used in Equations (N.10) and (N.14)) as:

Mineralisation == \(R_{miner}^{DOM}\), \(K_{miner-O_2}^{DOM}\), \(\theta_{miner}^{DOM}\), \(f_{an}\), \(K_{miner-NO_3}^{NO_3}\)

If \(K_{miner-NO_3}^{NO_3}\) is set to 0.0, then the consumption of nitrate due to mineralisation of organic matter is switched off.

Settling of labile particulate organic matter can be specified by one of the following models:

• None

  Settling == None

  or

• Constant

  Settling == Constant, \(V_{settle}^{lorg}\)

  or

• Constant with density correction (as per Equation (N.28))

  Settling == Thermal, \(V_{settle}^{lorg}\)

  or

• Stokes (used in Equation (N.29))

  Settling == Stokes, \(d_{lorg}\), \(\rho_{lorg}\)

Self shading due to the presence of labile organics (used in Equation (N.26)) parameters are set as:

Self Shading == \(Ke^{POM}\), \(Ke^{DOM}\)

This constituent model block must be terminated using the command:

End Organic Matter Model

4.8.3.5.2 Constituent model: Refractory

This constituent model encompasses all the functionality (and commands) of the labile organic matter constituent model, but offers further commands to simulate refractory organic processes, and their interaction with labile organic and inorganic computed variables.

This constituent model is specified as:

Organic Matter Model == Refractory

Minimum and maximum concentrations are specified as follows. The carbon command includes the specification of refractory particulate organic matter minimums and maximums, as well as dissolved refractories.

Ref Carbon Min Max == \(\left[RPOM\right]_{min}^{RPOM}\), \(\left[RPOM\right]_{max}^{RPOM}\), \(\left[RDOC\right]_{min}^{RDOC}\), \(\left[RDOC\right]_{max}^{RDOC}\)

Ref Nitrogen Min Max == \(\left[RDON\right]_{min}^{RDON}\), \(\left[RDON\right]_{max}^{RDON}\)

Ref Phosphorus Min Max == \(\left[RDOP\right]_{min}^{RDOP}\), \(\left[RDOP\right]_{max}^{RDOP}\)

The breakdown of refractory particulate organic matter into labile particulate organic matter (used in Equations (N.5) and (N.6)) parameters are set as:

Ref Breakdown == \(R_{bdn}^{RPOM}\), \(X_N^{RPOM}\), \(X_P^{RPOM}\)

The activation of refractory dissolved organic matter to labile dissolved organic matter (used in Equations (N.17) and (N.18)) parameter is set as:

Ref Activation == \(R_{act}^{RDOM}\)

The photolysis of refractory organics (used in Equation (N.27)) is not turned on unless the following command is issued. It sets the parameter that proportions the split of photolysed refractory dissolved organics to labile dissolved organics and inorganics:

Ref Photolysis == \(f_{photo}^{RDOM}\)

Settling of refractory particulate organic matter can be specified by one of the following models:

• None

  Ref Settling == None

  or

• Constant

  Ref Settling == Constant, \(V_{settle}^{rorg}\)

  or

• Constant with density correction (as per Equation (N.28))

  Ref Settling == Thermal, \(V_{settle}^{rorg}\)

  or

• Stokes (used in Equation (N.29))

  Ref Settling == Stokes, \(d_{rorg}\), \(\rho_{rorg}\)

The settling model selected for the refractory particulate organic matter model must be the same as that of the labile particulate organic matter. The input parameters to this model may be different.

Self shading due to the presence of refractory organics (used in Equation (N.27)) parameters are set as:

Ref Self Shading == \(Ke^{RPOM}\), \(R_{CDOM}^{RDOM}\)

This constituent model block must be terminated using the command:

End Organic Matter Model

4.8.3.6 Model class: Phytoplankton

4.8.3.6.1 Constituent model: Basic

The commands for this constituent model are described in Section 4.7.3.5.1.

4.8.3.6.2 Constituent model: Advanced

The commands for this constituent model are described in Section 4.7.3.5.2.

4.8.3.7 Model class: Pathogens (optional)

This model class is optional.

4.8.3.7.1 Constituent model: Free

The commands for this constituent model are described in Section 4.6.3.2.1.

4.8.3.7.2 Constituent model: Attached

The commands for this constituent model are described in Section 4.6.3.2.2.

4.8.4 Part 3: Material specification

Oxygen, silicate, ammonium, nitrate FRP, dissolved organic carbon, dissolved organic nitrogen and dissolved organic phosphorus benthic fluxes are specified within both default and numbered material blocks as:

Oxygen Flux == \(F_{sed}^{O_2}\)
Silicate Flux == \(F_{sed}^{sil}\)
Ammonium Flux == \(F_{sed}^{NH_4}\)
Nitrate Flux == \(F_{sed}^{NO_3}\)
FRP Flux == \(F_{sed}^{FRP}\)
DOC Flux == \(F_{sed}^{DOC}\)
DON Flux == \(F_{sed}^{DON}\)
DOP Flux == \(F_{sed}^{DOP}\)

No adsorbed FRP, phytoplankton or particulate organic fluxes are required.

4.8.5 Constituent ordering

As for the inorganics simulation class (see Section 4.7.5) different organic matter constituent model selections require different orderings in specifying computed variable initial conditions and BC Header == commands. Notwithstanding this, all the ordering information presented in Section 4.7.5 for the inorganics simulation class applies equally to the organics simulation class, other than for insertions related to the simulation of organics (described below). As such, that section should be reviewed with regard to ordering of the following:

• Dissolved oxygen
• Silicate
• Inorganic nitrogen
• Inorganic phosphorus (including the optional simulation of adsorbed FRP), and
• Phytoplankton groups (including the basic and advanced phytoplankton constituent models, with and without simulation of cell density)

The additional initial condition and BC Header == fields related to the organics simulation class do not change the order of computed variable fields presented in Section 4.7.5 other than to insert organic matter constituent model computed variables immediately after FRP computed variables and immediately prior to required phytoplankton fields. This insertion and ordering is presented following for the labile and refractory organic matter constituent models.

4.8.5.1 Labile

The computed variables required to be specified within the labile organic matter constituent model are, in order:

• Dissolved organic carbon
• Particulate organic carbon
• Dissolved organic nitrogen
• Particulate organic nitrogen
• Dissolved organic phosphorus
• Particulate organic phosphorus

All columnar and list style initial condition computed variables are therefore expected in the following order (and map to “WQ_1” etc accordingly)

Initial WQ Concentration == \(\left[ DO \right]\), \(\left[ Si \right]\), \(\left[ NH_4 \right]\), \(\left[ NO_3 \right]\), \(\left[ FRP \right]\), (optionally \(\left[ FRPads \right]\)), \(\left[ DOC \right]\), \(\left[ POC \right]\), \(\left[ DON \right]\), \(\left[ PON \right]\), \(\left[ DOP \right]\), \(\left[ POP \right]\), \(\ldots\) {phytoplankton placeholder/s}

Similarly, in a BC Header == command within a BC block, the following order of computed variables is expected after hydrodynamic (HD BCs) boundary conditions (and map to “WQ_1” etc accordingly):

BC Header == {HD BCs} \(\ldots\) DO_mgL, Si_mgL, Amm_mgL, Nit_mgL, FRP_mgL, (optionally FRPads_mgL), DOC_mgL, POC_mgL, DON_mgL, PON_mgL, DOP_mgL, POP_mgL, \(\ldots\) {phytoplankton placeholder/s}

With regard to the above BC Header == command:

• DO_mgL, Si_mgL, Amm_mgL, Nit_mgL, FRP_mgL (optionally FRPads_mgL), DOC_mgL, POC_mgL, DON_mgL, PON_mgL, DOP_mgL and POP_mgL are the headers used to designate oxygen, silicate, ammonium, nitrate, FRP (optionally adsorbed FRP), dissolved organic carbon, particulate organic carbon, dissolved organic nitrogen, particulate organic nitrogen, dissolved organic phosphorus and particulate organic phosphorus in the related boundary condition file, respectively
• Whilst this ordering in the command is fixed, the corresponding columnar data can appear in any order in the associated boundary condition file
• The header texts “DO_mgL”, “Si_mgL”, “Amm_mgL”, “Nit_mgL”, “FRP_mgL” (optionally “FRPads_mgL”), “DOC_mgL”, “POC_mgL”, “DON_mgL”, “PON_mgL”, “DOP_mgL” and “POP_mgL” are not special keywords. They can be any headers desired, as long as they match the correct respective boundary condition file column headers

4.8.5.2 Refractory

The computed variables required to be specified within the labile organic matter constituent model are, in order:

• Dissolved organic carbon
• Particulate organic carbon
• Dissolved organic nitrogen
• Particulate organic nitrogen
• Dissolved organic phosphorus
• Particulate organic phosphorus
• Refractory dissolved organic carbon
• Refractory dissolved organic nitrogen
• Refractory dissolved organic phosphorus
• Refractory particulate organic matter

All columnar and list style initial condition computed variables are therefore expected in the following order (and map to “WQ_1” etc accordingly)

Initial WQ Concentration == \(\left[ DO \right]\), \(\left[ Si \right]\), \(\left[ NH_4 \right]\), \(\left[ NO_3 \right]\), \(\left[ FRP \right]\), (optionally \(\left[ FRPads \right]\)), \(\left[ DOC \right]\), \(\left[ POC \right]\), \(\left[ DON \right]\), \(\left[ PON \right]\), \(\left[ DOP \right]\), \(\left[ POP \right]\), \(\left[ RDOC \right]\), \(\left[ RDON \right]\), \(\left[ RDOP \right]\), \(\left[ RPOM \right]\), \(\ldots\) {phytoplankton placeholder/s}

Similarly, in a BC Header == command within a BC block, the following order of computed variables is expected after hydrodynamic (HD BCs) boundary conditions (and map to “WQ_1” etc accordingly):

BC Header == {HD BCs} \(\ldots\) DO_mgL, Si_mgL, Amm_mgL, Nit_mgL, FRP_mgL, (optionally FRPads_mgL), DOC_mgL, POC_mgL, DON_mgL, PON_mgL, DOP_mgL, POP_mgL, RDOC_mgL, RDON_mgL, RDOP_mgL, RPOM_mgL, \(\ldots\) {phytoplankton placeholder/s}

With regard to the above BC Header == command:

• DO_mgL, Si_mgL, Amm_mgL, Nit_mgL, FRP_mgL (optionally FRPads_mgL), DOC_mgL, POC_mgL, DON_mgL, PON_mgL, DOP_mgL, POP_mgL, RDOC_mgL, RDON_mgL, RDOP_mgL and RPOM_mgL are the headers used to designate oxygen, silicate, ammonium, nitrate, FRP (optionally adsorbed FRP), dissolved organic carbon, particulate organic carbon, dissolved organic nitrogen, particulate organic nitrogen, dissolved organic phosphorus, particulate organic phosphorus, refractory dissolved organic carbon, refractory dissolved nitrogen, refractory dissolved phosphorus and refractory particulate organic matter in the related boundary condition file, respectively
• Whilst this ordering in the command is fixed, the corresponding columnar data can appear in any order in the associated boundary condition file
• The header texts “DO_mgL”, “Si_mgL”, “Amm_mgL”, “Nit_mgL”, “FRP_mgL” (optionally “FRPads_mgL”), “DOC_mgL”, “POC_mgL”, “DON_mgL”, “PON_mgL”, “DOP_mgL”, “POP_mgL”, “RDOC_mgL”, “RDON_mgL”, “RDOP_mgL” and “RPOM_mgL” are not special keywords. They can be any headers desired, as long as they match the correct respective boundary condition file column headers.

4.8.5.3 Including pathogens (optional)

The ordering requirements for pathogens are the same as those described in Section 4.6.5.1. Pathogen headers are always included last (i.e. after phytoplankton in the organics simulation class).

4.8.6 Example

Following is an example of all the available WQ Module Simulation Class == Organics commands, with a single material applied as zeros everywhere as the default, and then modified by a further specification for materials 3 and 7. Two phytoplankton groups (one each of the basic and advanced models) are set, and the refractory organic matter constituent model deployed. Pathogens have been omitted for clarity, but could be added as per Section 4.6.6.

Simulation Class == Organics
WQ dt == 900
WQ Units == mgL

Oxygen Model == O2
  Oxygen Benthic == 4.0, 1.05
  Oxygen Min Max == 0.0, 25.0
End Oxygen Model

Silicate Model == Si
  Silicate Benthic == 4.0, 1.05
  Silicate Min Max == 0.0, 2500.0
  Oxygen == ON
End Silicate Model

Inorganic Nitrogen Model == AmmoniumNitrate
  Ammonium Benthic == 4.0, 1.05
  Nitrate Benthic == 4.0, 1.05
  Ammonium Min Max == 0.0, 50.0
  Nitrate Min Max == 0.0, 50.0
  Nitrification == 0.1, 4.0, 1.05
  Denitrification == Exponential, 0.5, 8.0, 1.05
  Atmospheric Deposition == 10.0, 2.4, 0.15
  Oxygen == ON
End Inorganic Nitrogen Model

Inorganic Phosphorus Model == FRPhsAds
  FRP Benthic == 4.0, 1.05
  FRP Min Max == 0.0, 35.0
  FRPads Min Max == 0.0, 35.0
  Atmospheric Deposition == 5.0, 1.4
  Adsorption == Quadratic, 1.5, 0.5
  Oxygen == ON
End Inorganic Phosphorus Model

Phyto Model == Basic, Green
  Min Max == 0.01, 40.0
  Temperature Limitation == Standard, 11.0, 14.0, 30.0
  Salinity Limitation == None
  Light Limitation == Monod, 0.3, 70.0
  Settling == Constant, 0.01
  Nitrogen Limitation == 0.01, 1.5
  Phosphorus Limitation == 0.001, 0.03
  Silicate Limitation == 0.5, 7.0
  Uptake == 4.7, 0.6, 8.9
  Carbon Chla Ratio == 32.0
  Primary Productivity == 2.0, 1.06
  Respiration == 0.02, 1.04, 0.1, 0.05, 0.6
End Phyto Model

Phyto Model == Advanced, Bluegreen
  Min Max == 0.5, 50.0
  Temperature Limitation == Standard, 10.0, 15.0, 25.0
  Salinity Limitation == Estuarine, 22.0, 35.0, 0.0
  Light Limitation == Monod, 0.5, 51.0
  Settling == Motile, 0.5
  Nitrogen Limitation == 0.05, 2.5, 4.0, 5.0
  Phosphorus Limitation == 0.01, 0.05, 0.64, 0.67
  Silicate Limitation == 1.0, 5.0
  Uptake == 0.05, 0.05, 8.9
  Carbon Chla Ratio == 27.0
  Nitrogen Fixing == 0.100, 0.100
  Primary Productivity == 1.0, 1.08
  Respiration == 0.01, 1.01, 0.2, 0.0, 0.4
End Phyto Model

Organic Matter Model == Refractory
  Carbon Min Max == 0.0, 35.0, 0.0, 35.0, 0.0, 50.0
  Nitrogen Min Max == 0.0, 25.0, 0.0, 25.0
  Phosphorus Min Max == 0.0, 5.0, 0.0, 5.0
  Organics Benthic == 4.5, 1.03
  Hydrolysis == 1.2, 0.19, 0.031, 4.2, 1.1
  Mineralisation == 0.053, 4.1, 1.02, 0.6, 1.2
  Self Shading == 0.0003, 0.00025
  Ref Carbon Min Max == 0.0, 40.0, 0.0, 35.0
  Ref Nitrogen Min Max == 0.0, 25.0
  Ref Phosphorus Min Max == 0.0, 5.0
  Ref Breakdown == 0.002, 0.15, 0.0094
  Ref Activation == 0.02
  Ref Photolysis == 0.03
  Ref Self Shading == 0.00031, 0.00022
End Organic Matter Model

Material == Default
  Oxygen Flux == 0.0
  Silicate Flux == 0.0
  Ammonium Flux == 0.0
  Nitrate Flux == 0.0
  FRP Flux == 0.0
  DOC Flux == 0.0
  DON Flux == 0.0
  DOP Flux == 0.0
End Material

Material == 3, 7
  Oxygen Flux == -400.0
  Silicate Flux == 12.0
  Ammonium Flux == 33.0
  Nitrate Flux == 3.7
  FRP Flux == 1.4
  DOC Flux == 12.0
  DON Flux == 1.81
  DOP Flux == 0.29
End Material