A.2 FVWQ Commands
Adsorption
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Adsorption == Linear, \(K_{ads-L}^{FRP}\)
Model Construction: Section 4.7.3.4.2
Used in an inorganic phosphorus constituent model block to set the paramters for the linear FRP adsorption model.
For further information on the linear adsorption model, refer to Section F.4.1.
\(K_{ads-L}^{FRP}\) - Linear FRP Sorption Partitioning Coefficient
Default: 0.01
Units: L/mg
Range: (0.01, 0.3)
Science: Section F.4
The coefficient that determines the partitioning of FRP between free and adsorbed states. Can be estimated by dividing adsorbed FRP by free FRP and the concentration of suspended sediment, if these three quantities are known
Adsorption == Quadratic, \(K_{ads-Q}^{FRP}\), \(Q^{FRP}_{max}\)
Model Construction: Section 4.7.3.4.2
Used in a constituent model block to set the paramters for the quadratic FRP adsorption model.
For further information on the quadratic adsorption model, refer to Section F.4.2.
\(K_{ads-Q}^{FRP}\) - Quadratic FRP Sorption Partitioning Coefficient
Default: 0.7
Units: L/mg
Range: (0.6, 0.8)
Science: Section F.4
The ratio of adsorption and desorption rate coefficients for phosphorus
\(Q^{FRP}_{max}\) - Maximum Adsorption Capacity of Phosphorus
Default: 0.0051
Units: mg FRP-P/mg TSS
Range: (0.005, 0.006)
Science: Section F.4
The maximum mass of P that can be adsorbed onto ambient suspended sediment, per unit mass of suspended sediment
Alive Min Max == \(\left[PTH_a\right]_{min}^{pth}\), \(\left[PTH_a\right]_{max}^{pth}\)
Model Construction: Section 4.6.3.2.1
Used in an (optional) pathogens constituent model block to set minimum and maximum alive (free) pathogen concentrations.
\(\left[PTH_a\right]_{min}^{pth}\) - Minimum Alive Pathogen Concentration
Default: NA
Units: CFU/100mL
Range: (0, 0)
Science: Appendix N
The minimum allowable alive (free) pathogen concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[PTH_a\right]_{max}^{pth}\) - Maximum Alive Pathogen Concentration
Default: NA
Units: CFU/100mL
Range: (0, 1 e 12)
Science: Appendix N
The maximum allowable alive (free) pathogen concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Ammonium Benthic == \(K_{sed-O_2}^{NH_4}\), \(\theta_{sed}^{NH_4}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to control the response of benthic ammonium flux to temperature and oxygen concentration.
\(K_{sed-O_2}^{NH_4}\) - Sediment Half Saturation Oxygen Concentration for Ammonium Flux
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section E.1
The dissolved oxygen concentration for which the computed sediment ammonium flux is half the user specified rate, at 20\(^o\)C. Cannot be varied spatially
\(\theta_{sed}^{NH_4}\) - Sediment Ammonium Flux Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section E.1
The factor to which (\(T\)-20) is raised to account for temperature effects on ammonium sediment flux. A value of 1.0 will remove the effect of temperature
Ammonium Flux == \(F_{sed}^{NH_4}\)
Model Construction: Section 4.7.4
Used in a materials block to control the sediment flux rate of ammonium.
\(F_{sed}^{NH_4}\) - Sediment Ammonium Flux
Units Range Default mg NH\(_4\)-N/m\(^2\)/d (0, 140) 0 mmol NH\(_4\)-N/m\(^2\)/d (0, 10) 0 Science: Section E.1
The rate at which ammonium is exchanged between the sediments and overlying water column at 20\(^o\)C excluding the influence of overlying dissolved oxygen concentration. Can be varied spatially via use of model mesh material types. This is not the maxuimum rate of ammonium sediment flux.
This parameter is output as a diagnostic variable. For further information, refer to Ammonium User Defined Sediment Flux.
Ammonium Min Max == \(\left[NH_4\right]_{min}^{NH_4}\), \(\left[NH_4\right]_{max}^{NH_4}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to set minimum and maximum ammonium concentrations.
\(\left[NH_4\right]_{min}^{NH_4}\) - Minimum Ammonium Concentration
Units Range Default mg/L NH\(_4\)-N (0, 0.098) NA mmol/m\(^3\) NH\(_4\)-N (0, 7) NA Science: Appendix E
The minimum allowable ammonium concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[NH_4\right]_{max}^{NH_4}\) - Maximum Ammonium Concentration
Units Range Default mg/L NH\(_4\)-N (0, 98) NA mmol/m\(^3\) NH\(_4\)-N (0, 7000) NA Science: Appendix E
The maximum allowable ammonium concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Anaerobic Oxidation Of Ammonium == \(k_{anmx}^{N_2}\), \(K_{anmx-NH_4}^{N_2}\), \(K_{anmx-NO_2}^{N_2}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to control anaerobic oxidation of ammonium and its response to ambient ammonium and nitrate concentrations.
\(k_{anmx}^{N_2}\) - Anaerobic Oxidation of Ammonium Rate
Units Range Default mg N/L/d (0, 0.5) 0 mmol N/m\(^3\)/d (0, 0.036) 0 Science: Section E.4
The rate at which ammonium is oxidised (consuming nitrite) to nitrogen gas N\(_2\) at 20\(^o\)C excluding the influence of ambient ammonium and nitrite concentrations. This is not solely a per day rate, but is the mass (or mmol) rate of production of nitrogen in free nitrogen gas, per unit volume, per day. Anammox only operates when ambient dissolved oxygen concentrations are less than 0.1 mg/L. A value of 0.0 will switch off anammox
\(K_{anmx-NH_4}^{N_2}\) - Half Saturation Ammonium Concentration for Anammox
Units Range Default mg/L NH\(_4\)-N (0, 10) 1.75 mmol/m\(^3\) NH\(_4\)-N (0, 714) 125 Science: Section E.4
The ammonium concentration for which the computed consumption of ammonium due to anaerobic oxidation would be half the corresponding anaerobic oxidation rate, excluding the influence of nitrite. Cannot be varied spatially
\(K_{anmx-NO_2}^{N_2}\) - Half Saturation Nitrite Concentration for Anammox
Units Range Default mg/L NO\(_2\)-N (0, 10) 1.75 mmol/m\(^3\) NO\(_2\)-N (0, 714) 125 Science: Section E.4
The nitrite concentration for which the computed consumption of ammonium due to anaerobic oxidation would be half the corresponding anaerobic oxidation rate, excluding the influence of ammonium. Cannot be varied spatially
Atmospheric Deposition
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Atmospheric Deposition == \(\left[{FRP}\right]_{rain}\), \(R_{atm-dry}^{FRPads}\)
Model Construction: Section 4.7.3.4.1
Used in an inorganic phosphorus constituent model block to control the wet (and dry) atmospheric deposition of FRP (adsorbed FRP).
\(\left[{FRP}\right]_{rain}\) - FRP Concentration in Rainfall
Units Range Default mg/L P (0, 0.01) 0 mmol/m\(^3\) P (0, 0.32) 0 Science: Section 4.7.3.4.1
The concentration of FRP in rainfall which is directly deposited into the surface layer cells. If rainfall is modeled within TUFLOW FV, this will be computed from the mass flux values of rainfall
\(R_{atm-dry}^{FRPads}\) - Dry Atmospheric Deposition Rate for Adsorbed FRP
Units Range Default mg/m\(^2\)/d P (0, 0.001) 0 mmol/m\(^2\)/d P (0, 0.00003) 0 Science: Section 4.7.3.4.1
The dry atmospheric deposition rate of adsorbed FRP expressed as a flux per unit area per day. This flux is applied to the surface layer cells
Atmospheric Deposition == \(\left[{TN}\right]_{rain}\), \(R_{atm-dry}^{TN}\), \(f_{TN}^{NO_3}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to control the wet and dry atmospheric deposition of inorganic nitrogen.
\(\left[{TN}\right]_{rain}\) - Total Nitrogen Concentration in Rainfall
Units Range Default mg/L N (0, 1) 0 mmol/m\(^3\) N (0, 71) 0 Science: Section 4.7.3.3.1
The concentration of total nitrogen (NO3 + NH4) in rainfall which is directly deposited into the surface layer cells. The split between NO3 and NH4 is determined by \(f_{TN}^{NO_3}\)
\(R_{atm-dry}^{TN}\) - Dry Atmospheric Deposition Rate for Total Nitrogen
Units Range Default mg/m\(^2\)/d N (0, 0.1) 0 mmol/m\(^2\)/d N (0, 0.007) 0 Science: Section 4.7.3.3.1
The dry atmospheric deposition rate of total nitrogen (NO3 + NH4) expressed as a flux per unit area per day. This flux is applied to the surface layer cells. The split between NO3 and NH4 is determined by \(f_{TN}^{NO_3}\)
\(f_{TN}^{NO_3}\) - Fraction of Atmospheric Total Nitrogen Deposited as Nitrate
Default: 0.5
Units: NA
Range: (0, 1)
Science: Section 4.7.3.3.1
The fraction of atmospheric nitrogen deposition (wet and dry) that is in the form of nitrate (NO3), as opposed to ammonium (NH4). The remainder is deposited as ammonium
Carbon Chla Ratio == \(X_{cc}^{phy}\)
Model Construction: Section 4.7.3.5.1.10
Used in a phytoplankton constituent model block to set the mass of carbon per unit of chlorophyll a (Chl a).
\(X_{cc}^{phy}\) - Carbon to Chlorophyll A Ratio
Default: 40
Units: mg C/mg Chl a
Range: (1, 100)
Science: Section G.2
The ratio of carbon to chlorophyll a in the cellular biomass of a phytoplankton group. The units of chlorophyll a in this ratio are milligrams (mg), not μg. This value is constant for a given phytoplankton group
Carbon Min Max == \(\left[POC\right]_{min}^{POC}\), \(\left[POC\right]_{max}^{POC}\), \(\left[DOC\right]_{min}^{DOC}\), \(\left[DOC\right]_{max}^{DOC}\)
Model Construction: Section 4.8.3.5
Used in an organic matter constituent model block to set minimum and maximum particulate and dissolved organic carbon concentrations.
\(\left[POC\right]_{min}^{POC}\) - Minimum POC Concentration
Units Range Default mg/L C (0, 0.1) NA mmol/m\(^3\) C (0, 8.33) NA Science: Appendix M
The minimum allowable labile particulate organic carbon concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[POC\right]_{max}^{POC}\) - Maximum POC Concentration
Units Range Default mg/L C (0, 100) NA mmol/m\(^3\) C (0, 8333) NA Science: Appendix M
The maximum allowable labile particulate organic carbon concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
\(\left[DOC\right]_{min}^{DOC}\) - Minimum DOC Concentration
Units Range Default mg/L C (0, 0.1) NA mmol/m\(^3\) C (0, 8.33) NA Science: Appendix M
The minimum allowable labile dissolved organic carbon concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[DOC\right]_{max}^{DOC}\) - Maximum DOC Concentration
Units Range Default mg/L C (0, 100) NA mmol/m\(^3\) C (0, 8333) NA Science: Appendix M
The maximum allowable labile dissolved organic carbon concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Cell Water Quality Depth == \(d_{min-wq}\)
Status: Optional
Model Construction: Section 4.4.1
Instruct TUFLOW FV to not execute water quality calculations on cells that have depths less than this specified value.
\(d_{min-wq}\) - Minimum Water Quality Calculation Depth
Default: 0.01
Units: m
Range: (0, UD)
The minimum depth at which water calculations will be computed. This depth is the depth of the entire computational column that immediately overlies the sediment (bed) for a given 2D cell. The depth is specified in the TUFLOW FV control file
Denitrification
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Denitrification == Exponential, \(R_{denit}^{NO_3}\), \(K_{denit-O2-exp}^{NO_3}\), \(\theta_{denit}^{NO_3}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to activate the exponential model and control denitrification and its response to ambient oxygen concentrations and temperature.
For further information on the exponential denitrification model, refer to Section E.3.
\(R_{denit}^{NO_3}\) - Denitrification Rate
Units Range Default d (0, 0.5) 0 0 Science: Section E.3
The rate at which nitrate is denitrified to nitrogen gas N\(_2\) at 20\(^o\)C excluding the influence of ambient dissolved oxygen and nitrate concentrations. A value of 0.0 will switch off denitrification
\(K_{denit-O2-exp}^{NO_3}\) - Normalising Oxygen Concentration for Denitrification
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section E.3
The dissolved oxygen concentration that divides (normalises) the ambient dissolved oxygen concentration in the exponent term of the exponential denitrification model, at 20\(^o\)C and with no influence of ambient nitrate concentration. This value is used if the ‘exponential’ denitrification model is speciifed as the first argument of the Denitrification command
\(\theta_{denit}^{NO_3}\) - Denitrification Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section E.3
The factor to which (\(T\)-20) is raised to account for temperature effects on denitrification. A value of 1.0 will remove the effect of temperature
Denitrification == Michaelis Menten, \(R_{denit}^{NO_3}\), \(K_{denit-O2-MM}^{NO_3}\), \(\theta_{denit}^{NO_3}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to activate the Michaelis Menten model and control denitrification and its response to ambient oxygen concentrations and temperature.
For further information on the Michaelis Menten denitrification model, refer to Section E.3.
\(R_{denit}^{NO_3}\) - Denitrification Rate
Units Range Default d (0, 0.5) 0 0 Science: Section E.3
The rate at which nitrate is denitrified to nitrogen gas N\(_2\) at 20\(^o\)C excluding the influence of ambient dissolved oxygen and nitrate concentrations. A value of 0.0 will switch off denitrification
\(K_{denit-O2-MM}^{NO_3}\) - Half Saturation Oxygen Concentration for Denitrification
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section E.3
The dissolved oxygen concentration for which the computed denitrification rate is half the user specified rate, at 20\(^o\)C and with no influence of ambient nitrate concentration. This value is used if the ‘Michaelis Menten’ denitrification model is speciifed as the first argument of the Denitrification command
\(\theta_{denit}^{NO_3}\) - Denitrification Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section E.3
The factor to which (\(T\)-20) is raised to account for temperature effects on denitrification. A value of 1.0 will remove the effect of temperature
Disable Water Quality Model == \(B_{disable-wq}\)
Status: Optional
Model Construction: Section 4.4.1
Instruct TUFLOW FV to disable (1) or enable (0) water quality calculations on all cells.
\(B_{disable-wq}\) - Disable Water Quality Calculation
Default: 0
Units: NA
Range: (0, 1)
A Boolean flag to disable (1) or enable (0) water quality calculations. The flag is specified in the TUFLOW FV control file
Diss Nitrate Reduction To Ammonium == \(R_{DRNA}^{NO_3}\), \(K_{DRNA-O_2}^{NO_3}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to control dissimilatory reduction of nitrate to ammonium and its response to ambient oxygen concentrations.
\(R_{DRNA}^{NO_3}\) - Dissimilatory Reduction of Nitrate to Ammonium Rate
Units Range Default /d (0, 0.05) 0 0 Science: Section E.5
The rate at which nitrate is reduced to ammonium at 20\(^o\)C excluding the influence of ambient nitrate concentrations. A value of 0.0 will switch off DRNA
\(K_{DRNA-O_2}^{NO_3}\) - Half Saturation Oxygen Concentration for DRNA
Units Range Default mg/L O\(_2\) (0, 10) 4 mmol/m\(^3\) O\(_2\) (0, 312.5) 125 Science: Section E.5
The oxygen concentration for which the computed reduction of nitrate to ammonium would be half the corresponding rate. Cannot be varied spatially
DOC Flux == \(F_{sed}^{DOC}\)
Model Construction: Section 4.8.4
Used in a materials block to control the sediment flux rate of DOC.
\(F_{sed}^{DOC}\) - Sediment DOC Flux
Units Range Default mg C/m\(^2\)/d (0, 120) 0 mmol C/m\(^2\)/d (0, 10) 0 Science: Section M.1
The rate at which labile dissolved organic carbon is exchanged between the sediments and overlying water column at 20\(^o\)C excluding the influence of overlying dissolved oxygen concentration. Can be varied spatially via use of model mesh material types. This is not the maxuimum rate of labile DOC sediment flux.
This parameter is output as a diagnostic variable. For further information, refer to DOC User Defined Sediment Flux.
DON Flux == \(F_{sed}^{DON}\)
Model Construction: Section 4.8.4
Used in a materials block to control the sediment flux rate of DON.
\(F_{sed}^{DON}\) - Sediment DON Flux
Units Range Default mg N/m\(^2\)/d (0, 21.126) 0 mmol N/m\(^2\)/d (0, 1.509) 0 Science: Section M.1
The rate at which labile dissolved organic nitrogen is exchanged between the sediments and overlying water column at 20\(^o\)C excluding the influence of overlying dissolved oxygen concentration. Can be varied spatially via use of model mesh material types. This is not the maxuimum rate of labile DON sediment flux.
This parameter is output as a diagnostic variable. For further information, refer to DON User Defined Sediment Flux.
DOP Flux == \(F_{sed}^{DOP}\)
Model Construction: Section 4.8.4
Used in a materials block to control the sediment flux rate of DOP.
\(F_{sed}^{DOP}\) - Sediment DOP Flux
Units Range Default mg P/m\(^2\)/d (0, 2.914) 0 mmol P/m\(^2\)/d (0, 0.094) 0 Science: Section M.1
The rate at which labile dissolved organic phosphorus is exchanged between the sediments and overlying water column at 20\(^o\)C excluding the influence of overlying dissolved oxygen concentration. Can be varied spatially via use of model mesh material types. This is not the maxuimum rate of labile DOP sediment flux.
This parameter is output as a diagnostic variable. For further information, refer to DOP User Defined Sediment Flux.
End Inorganic Nitrogen Model
Model Construction: Section 4.7.3.3.1
Used to terminate an inorganic nitrogen nitrogen constituent model block. Must follow an Inorganic Nitrogen Model command.
End Inorganic Phosphorus Model
Model Construction: Section 4.7.3.4.1
Used to terminate an inorganic phosphorus phosphorus constituent model block. Must follow a Inorganic Phosphorus Model command.
End Material
Model Construction: Section 4.5.3
Command to terminate a materials block. This command must be paired with a corresponding Material command to initiate the block.
End Organic Matter Model
Model Construction: Section 4.8.3.5.1
Used to terminate an organics constituent model block. Must follow an Organic Matter Model command.
End Oxygen Model
Model Construction: Section 4.6.3.1.1
Used to terminate an oxygen constituent model block. Must follow an Oxygen Model command.
End Pathogen Model
Status: Conditional - Required if a pathogen constituent model is implemented via Pathogen Model
Model Construction: Section 4.6.3.2.1, Section 4.6.3.2.2
Required Dependent Command(s): Pathogen Model
Used to terminate a pathogen constituent model block. Must follow a Pathogen Model command.
End Phyto Model
Model Construction: Section 4.7.3.5.1.13
Used to terminate a phytoplankton constituent model block. Must follow a Phyto Model command.
End Silicate Model
Model Construction: Section 4.7.3.2.1
Used to terminate a silicate constituent model block. Must follow a Silicate Model command.
FRP Benthic == \(K_{sed-O_2}^{FRP}\), \(\theta_{sed}^{FRP}\)
Model Construction: Section 4.7.3.4.1
Used in an inorganic phosphorus constituent model block to control the response of benthic FRP flux to temperature and oxygen concentration.
\(K_{sed-O_2}^{FRP}\) - Sediment Half Saturation Oxygen Concentration for FRP Flux
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section F.1
The dissolved oxygen concentration for which the computed sediment FRP flux is half the user specified rate, at 20\(^o\)C. Cannot be varied spatially
\(\theta_{sed}^{FRP}\) - Sediment FRP Flux Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section F.1
The factor to which (\(T\)-20) is raised to account for temperature effects on FRP sediment flux. A value of 1.0 will remove the effect of temperature
FRP Flux == \(F_{sed}^{FRP}\)
Model Construction: Section 4.7.4
Used in a materials block to control the sediment flux rate of FRP.
\(F_{sed}^{FRP}\) - Sediment FRP Flux
Units Range Default mg FRP-P/m\(^2\)/d (0, 155) 0 mmol FRP-P/m\(^2\)/d (0, 5) 0 Science: Section F.1
The rate at which FRP is exchanged between the sediments and overlying water column at 20\(^o\)C excluding the influence of overlying dissolved oxygen concentration. Can be varied spatially via use of model mesh material types. This is not the maxuimum rate of FRP sediment flux.
This parameter is output as a diagnostic variable. For further information, refer to FRP User Defined Sediment Flux.
FRP Min Max == \(\left[FRP\right]_{min}^{FRP}\), \(\left[FRP\right]_{max}^{FRP}\)
Model Construction: Section 4.7.3.4.1
Used in an inorganic phosphorus constituent model block to set minimum and maximum FRP concentrations.
\(\left[FRP\right]_{min}^{FRP}\) - Minimum FRP Concentration
Units Range Default mg/L PO\(_4\)-P (0, 0.01) NA mmol/m\(^3\) PO\(_4\)-P (0, 0.32) NA Science: Appendix F
The minimum allowable FRP concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[FRP\right]_{max}^{FRP}\) - Maximum FRP Concentration
Units Range Default mg/L PO\(_4\)-P (0, 10) NA mmol/m\(^3\) PO\(_4\)-P (0, 320) NA Science: Appendix F
The maximum allowable FRP concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
FRPads Min Max == \(\left[FRPads\right]_{min}^{FRPads}\), \(\left[FRPads\right]_{max}^{FRPads}\)
Model Construction: Section 4.7.3.4.2
Used in an inorganic phosphorus constituent model block to set minimum and maximum adsorbed FRP concentrations.
\(\left[FRPads\right]_{min}^{FRPads}\) - Minimum Adsorbed FRP Concentration
Units Range Default mg/L P (0, 0.01) NA mmol/m\(^3\) P (0, 0.32) NA Science: Section 4.7.3.4.2
The minimum allowable adsorbed FRP concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file
\(\left[FRPads\right]_{max}^{FRPads}\) - Maximum Adsorbed FRP Concentration
Units Range Default mg/L P (0, 1) NA mmol/m\(^3\) P (0, 32) NA Science: Section 4.7.3.4.2
The maximum allowable adsorbed FRP concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file
Hydrolysis == \(R_{hyd}^{POC}\), \(R_{hyd}^{PON}\), \(R_{hyd}^{POP}\), \(K_{hyd-O_2}^{POM}\), \(\theta_{hyd}^{POM}\)
Model Construction: Section 4.8.3.5.1
Used in an organics constituent model block to parameterise particulate organic carbon, nitrogen and phosphorus hydrolysis.
\(R_{hyd}^{POC}\) - POC Hydrolysis Rate
Units Range Default /d (0, 0.1) 0 0 Science: Section M.2
The rate at which labile particulate organic carbon is hydrolysed to dissolved organic carbon at 20\(^o\)C excluding the influence of ambient dissolved oxygen concentration. This is not the maxuimum rate of POC hydrolysis
\(R_{hyd}^{PON}\) - PON Hydrolysis Rate
Units Range Default /d (0, 0.015) 0 0 Science: Section M.2
The rate at which labile particulate organic nitrogen is hydrolysed to dissolved organic nitrogen at 20\(^o\)C excluding the influence of ambient dissolved oxygen concentration. This is not the maxuimum rate of PON hydrolysis
\(R_{hyd}^{POP}\) - POP Hydrolysis Rate
Units Range Default /d (0, 0.0009) 0 0 Science: Section M.2
The rate at which labile particulate organic phosphorus is hydrolysed to dissolved organic phosphorus at 20\(^o\)C excluding the influence of ambient dissolved oxygen concentration. This is not the maxuimum rate of POP hydrolysis
\(K_{hyd-O_2}^{POM}\) - Half Saturation Oxygen Concentration for POM Hydrolysis
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section M.2
The dissolved oxygen concentration for which the computed hydrolysis of labile POM is half the user specified rate, at 20\(^o\)C. Cannot be varied spatially. The same value is applied to all labile particulate organic constituents (carbon, nitrogen and phosphorus), and also to the breakdown of refractory particulate organic matter
\(\theta_{hyd}^{POM}\) - POM Hydrolysis Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section M.2
The factor to which (\(T\)-20) is raised to account for temperature effects on labile POM hydrolysis. A value of 1.0 will remove the effect of temperature. The same value is applied to all labile particulate organic constituents (carbon, nitrogen and phosphorus), and also to the breakdown of refractory particulate organic matter
Include Sediment == Include sediment transport calculations, Include sediment in density calculation
Status: Optional
Model Construction: Section 4.7.5.1.2
TUFLOW FV command to include sediment simulation. Sediment must be simulated if adsorbed phosphorus is included in a WQ Module simulation.
Initial Condition 2D == Initial condition file name and path.csv
Status: Optional
Model Construction: Section 4.4.2.1
Ordered individual computed variable initial conditions in a columnar text file.
Initial Condition 3D == Initial condition file name and path.csv
Status: Optional
Model Construction: Section 4.4.2.1
Ordered individual computed variable initial conditions in a columnar text file.
Initial Scalar Profile == Initial condition file name and path.csv
Status: Optional
Model Construction: Section 4.4.2.1
Ordered individual computed variable initial conditions in a columnar text file.
Initial WQ Concentration == Comma separated WQ initial conditions
Status: Optional
Model Construction: Section 4.4.2.1
Ordered individual computed variable initial conditions.
Inorganic Nitrogen Model == AmmoniumNitrate
Model Construction: Section 4.7.3.3
Used to commence an inorganic nitrogen constituent model block via specification of a constituent model from the inorganic nitrogen constituent model class (Section 4.7.3.3).
Inorganic Phosphorus Model == FRPhs | FRPhsAds
Model Construction: Section 4.7.3.4
Used to commence an inorganic phosphorus constituent model block via specification of a constituent model (FRPhs or FRPhsAds) from the inorganic phosphorus constituent model class.
Light Limitation
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Light Limitation == Basic, \(Ke^{phy}\), \(I_{K-bas}\)
Model Construction: Section 4.7.3.5.1.3
Used in a phytoplankton constituent model block to set basic light limitation parameters for the basic and advanced phytoplankton constituent models. If Stokes Settling is used, then the value of \(I_K\) specified in this command overrides any value specified using the Settling command.
For further information on the basic light limitation model, refer to Section I.6.1.
\(Ke^{phy}\) - Phytoplankton Specific Shading Coefficient
Units Range Default (\(\mu\)g Chl a/L)/m (0, 0.0225) 0 (mmol C/m\(^3\))/m (0, 0.01) 0 Science: Section L.1
The rate at which light is attenuated by phytoplankton. This coefficient is per unit concentration of phytoplankton, per metre (depth). It is multiplied by phytoplankton concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients.
\(I_{K-bas}\) - Half Saturation Constant for Basic Model Light Growth Limitation
Default: 20
Units: W/m\(^2\)
Range: (1, 1500)
Science: Section I.6.1
Used to compute the basic light limitation function for both basic and advanced phytoplankton constituent models. It divides (normalises) the photosynthetically available radiation incident on the top and bottom of a computational cell and forms the lower limit of the exponential integral
Light Limitation == Chalker, \(Ke^{phy}\), \(I_{K-cha}\)
Model Construction: Section 4.7.3.5.1.3
Used in a phytoplankton constituent model block to set Chalker light limitation parameters for the basic and advanced phytoplankton constituent models. If Stokes Settling is used then the vlaue of \(I_K\) specified in this command overrides any value specified using the Settling command.
For further information on the chalker light limitation model, refer to Section I.6.6.
\(Ke^{phy}\) - Phytoplankton Specific Shading Coefficient
Units Range Default (\(\mu\)g Chl a/L)/m (0, 0.0225) 0 (mmol C/m\(^3\))/m (0, 0.01) 0 Science: Section L.1
The rate at which light is attenuated by phytoplankton. This coefficient is per unit concentration of phytoplankton, per metre (depth). It is multiplied by phytoplankton concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients.
\(I_{K-cha}\) - Half Saturation Constant for Chalker Model Light Growth Limitation
Default: 20
Units: W/m\(^2\)
Range: (1, 1500)
Science: Section I.6.6
Used to compute the chalker light limitation function for both basic and advanced phytoplankton constituent models. It divides (normalises) the photosynthetically available radiation incident at the centre of a computational cell
Light Limitation == Integrated, \(Ke^{phy}\), \(I_{S-int}\)
Model Construction: Section 4.7.3.5.1.3
Used in a phytoplankton constituent model block to set integrated light limitation parameters for the basic and advanced phytoplankton constituent models.
For further information on the integrated light limitation model, refer to Section I.6.8.
\(Ke^{phy}\) - Phytoplankton Specific Shading Coefficient
Units Range Default /(\(\mu\)g Chl a/L)/m (0, 0.0225) 0 /(mmol C/m\(^3\))/m (0, 0.01) 0 Science: Section L.1
The rate at which light is attenuated by phytoplankton. This coefficient is per unit concentration of phytoplankton, per metre (depth). It is multiplied by phytoplankton concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients.
\(I_{S-int}\) - Saturating Light Intensity for The Integrated Model Light Growth Limitation
Default: 20
Units: W/m\(^2\)
Range: (1, 1500)
Science: Section I.6.8
Used to compute the integrated light limitation function for both basic and advanced phytoplankton constituent models. It divides (normalises) the photosynthetically available radiation incident on the top and bottom of a computational cell. This limitation function includes photoinhibition
Light Limitation == Jassby, \(Ke^{phy}\), \(I_{K-jas}\)
Model Construction: Section 4.7.3.5.1.3
Used in a phytoplankton constituent model block to set Jassby light limitation parameters for the basic and advanced phytoplankton constituent models. If Stokes Settling is used then the value of \(I_K\) specified in this command overrides any value specified using the Settling command.
For further information on the Jassby light limitation model, refer to Section I.6.5.
\(Ke^{phy}\) - Phytoplankton Specific Shading Coefficient
Units Range Default (\(\mu\)g Chl a/L)/m (0, 0.0225) 0 (mmol C/m\(^3\))/m (0, 0.01) 0 Science: Section L.1
The rate at which light is attenuated by phytoplankton. This coefficient is per unit concentration of phytoplankton, per metre (depth). It is multiplied by phytoplankton concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients.
\(I_{K-jas}\) - Half Saturation Constant for Jassby Model Light Growth Limitation
Default: 20
Units: W/m\(^2\)
Range: (1, 1500)
Science: Section I.6.5
Used to compute the jassby light limitation function for both basic and advanced phytoplankton constituent models. It divides (normalises) the photosynthetically available radiation incident at the centre of a computational cell
Light Limitation == Klepper, \(Ke^{phy}\), \(I_{S-kle}\)
Model Construction: Section 4.7.3.5.1.3
Used in a phytoplankton constituent model block to set Klepper light limitation parameters for the basic and advanced phytoplankton constituent models.
For further information on the Klepper light limitation model, refer to Section I.6.7.
\(Ke^{phy}\) - Phytoplankton Specific Shading Coefficient
Units Range Default (\(\mu\)g Chl a/L)/m (0, 0.0225) 0 (mmol C/m\(^3\))/m (0, 0.01) 0 Science: Section L.1
The rate at which light is attenuated by phytoplankton. This coefficient is per unit concentration of phytoplankton, per metre (depth). It is multiplied by phytoplankton concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients.
\(I_{S-kle}\) - Saturating Light Intensity for The Klepper Model Light Growth Limitation
Default: 20
Units: W/m\(^2\)
Range: (1, 1500)
Science: Section I.6.7
Used to compute the klepper light limitation function for both basic and advanced phytoplankton constituent models. It divides (normalises) the photosynthetically available radiation incident at the centre of a computational cell. This limitation function includes photoinhibition
Light Limitation == Monod, \(Ke^{phy}\), \(I_{K-mon}\)
Model Construction: Section 4.7.3.5.1.3
Used in a phytoplankton constituent model block to set Monod light limitation parameters for the basic and advanced phytoplankton constituent models. If Stokes Settling is used, then the value of \(I_K\) specified in this command overrides any value specified using the Settling command.
For further information on the Monod light limitation model, refer to Section I.6.2.
\(Ke^{phy}\) - Phytoplankton Specific Shading Coefficient
Units Range Default (\(\mu\)g Chl a/L)/m (0, 0.0225) 0 (mmol C/m\(^3\))/m (0, 0.01) 0 Science: Section L.1
The rate at which light is attenuated by phytoplankton. This coefficient is per unit concentration of phytoplankton, per metre (depth). It is multiplied by phytoplankton concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients.
\(I_{K-mon}\) - Half Saturation Constant for Monod Model Light Growth Limitation
Default: 20
Units: W/m\(^2\)
Range: (1, 1500)
Science: Section I.6.2
Used to compute the monod light limitation function for both basic and advanced phytoplankton constituent models. It divides (normalises) the photosynthetically available radiation incident at the centre of a computational cell
Light Limitation == Steele, \(Ke^{phy}\), \(I_{S-ste}\)
Model Construction: Section 4.7.3.5.1.3
Used in a phytoplankton constituent model block to set Steele light limitation parameters for the basic and advanced phytoplankton constituent models.
For further information on the Steele light limitation model, refer to Section I.6.3.
\(Ke^{phy}\) - Phytoplankton Specific Shading Coefficient
Units Range Default (\(\mu\)g Chl a/L)/m (0, 0.0225) 0 (mmol C/m\(^3\))/m (0, 0.01) 0 Science: Section L.1
The rate at which light is attenuated by phytoplankton. This coefficient is per unit concentration of phytoplankton, per metre (depth). It is multiplied by phytoplankton concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients.
\(I_{S-ste}\) - Saturating Light Intensity for The Steele Model Light Growth Limitation
Default: 20
Units: W/m\(^2\)
Range: (1, 1500)
Science: Section I.6.3
Used to compute the steele light limitation function for both basic and advanced phytoplankton constituent models. It divides (normalises) the photosynthetically available radiation incident at the centre of a computational cell. This limitation function includes photoinhibition
Light Limitation == Webb, \(Ke^{phy}\), \(I_{K-web}\)
Model Construction: Section 4.7.3.5.1.3
Used in a phytoplankton constituent model block to set Webb light limitation parameters for the basic and advanced phytoplankton constituent models. If Stokes Settling is used then the value of \(I_K\) specified in this command overrides any value specified using the Settling command.
For further information on the Webb light limitation model, refer to Section I.6.4.
\(Ke^{phy}\) - Phytoplankton Specific Shading Coefficient
Units Range Default (\(\mu\)g Chl a/L)/m (0, 0.0225) 0 (mmol C/m\(^3\))/m (0, 0.01) 0 Science: Section L.1
The rate at which light is attenuated by phytoplankton. This coefficient is per unit concentration of phytoplankton, per metre (depth). It is multiplied by phytoplankton concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients.
\(I_{K-web}\) - Half Saturation Constant for Webb Model Light Growth Limitation
Default: 20
Units: W/m\(^2\)
Range: (1, 1500)
Science: Section I.6.4
Used to compute the webb light limitation function for both basic and advanced phytoplankton constituent models. It divides (normalises) the photosynthetically available radiation incident at the centre of a computational cell
Material == Up to 10 comma separated material integers
Model Construction: Section 4.5.3
Command to initiate a materials block. Commands within this block apply to the material numbers listed in this command.
Min Max == \(\left[PHY\right]_{min}^{PHY}\), \(\left[PHY\right]_{max}^{PHY}\)
Model Construction: Section 4.7.3.5.1
Used in a phytoplankton constituent model block to set minimum and maximum phytoplankton group concentrations.
\(\left[PHY\right]_{min}^{PHY}\) - Minimum Phyto Concentration
Units Range Default \(\mu\)g/L Chl a (0.01, 0.1) 0.01 mmol/m\(^3\) C (0.023, 0.225) 0.0225 Science: Appendix G
The minimum allowable group phytoplankton concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. It is also important the this minimum value not be set to zero. If phytoplankton concentrations are allowed to reduce to zero then the numerical scheme will not allow the group to regrow because growth is applied as a multiplicative factor from one timestep to the next. Multiplying any growth rate by a previous timestep’s zero group concentration will therefore always result in zero group concentration for subsequent timesteps
\(\left[PHY\right]_{max}^{PHY}\) - Maximum Phyto Concentration
Units Range Default \(\mu\)g/L Chl a (0.01, 50) NA mmol/m\(^3\) C (0.0025, 112.5) NA Science: Appendix G
The maximum allowable group phytoplankton concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Mineralisation == \(R_{miner}^{DOM}\), \(K_{miner-O_2}^{DOM}\), \(\theta_{miner}^{DOM}\), \(f_{an}\), \(K_{miner-NO_3}^{NO_3}\)
Model Construction: Section 4.8.3.5.1
Used in an organics constituent model block to parameterise dissolved organic matter (carbon, nitrogen and phosphorus) mineralisation. It includes the parameters that govern anaerobic mineralisation, that is, the consumption of nitrate in the dissolved organic matter mineralisation process.
\(R_{miner}^{DOM}\) - DOM Mineralisation Rate
Units Range Default /d (0, 0.1) 0 0 Science: Section M.4
The rate at which labile dissolved organic carbon, nitrogen and phosphorus are mineralised to their corresponding dissolved inorganic constituents at 20\(^o\)C excluding the influence of ambient dissolved oxygen concentration. This is not the maxuimum rate of mineralisation. The same rate is applied to all labile dissolved organic constituents (carbon, nitrogen and phosphorus)
\(K_{miner-O_2}^{DOM}\) - Half Saturation Oxygen Concentration for DOM Mineralisation
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section M.4
The dissolved oxygen concentration for which the computed aerobic and anaerobic mineralisation of labile DOM is half the user specified rate, at 20\(^o\)C, and with \(f_{an}\) equal to 1.0. If \(f_{an}\) is equal to zero then this half saturation oxygen concentration is the dissolved oxygen concentration for which the computed aerobic mineralisation of labile DOM is half the user specified rate, again at 20\(^o\)C. Cannot be varied spatially. The same value is applied to all labile dissolved organic constituents (carbon, nitrogen and phosphorus), and also to the activation of refractory dissolved organic carbon, nitrogen and phosporus
\(\theta_{miner}^{DOM}\) - DOM Mineralisation Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section M.4
The factor to which (\(T\)-20) is raised to account for temperature effects on labile DOM mineralisation. A value of 1.0 will remove the effect of temperature. The same value is applied to all labile dissolved organic constituents (carbon, nitrogen and phosphorus), and also to the activation of refractory dissolved organic carbon, nitrogen and phosporus
\(f_{an}\) - Anaerobic Mineralisation Multiplier
Default: 0
Units: NA
Range: (0, 1)
Science: Section M.4
The factor applied to the compenent of mineralisation of labile dissolved organic matter that does not consume dissolved oxygen. A value of 0.0 will entirely suppress the Michaelis-Menten weighting that non dissolved oxygen based processes have in calculating overall mineralisation of labile dissolved organic matter. Setting this parameter to zero does not suppress non dissolved oxygen mineralisation. This same factor is also applied to the activation of refractory dissolved organic carbon, nitrogen and phosphorus to their labile equivalents. If activation is to be simulated then the command Mineralisation will need to be issued to set \(f_{an}\). In this case, and if the simulation of dissolved organic matter mineralisation is not desired, then set \(R_{miner}^{DOM}\) to be zero in the same mineralisation command
\(K_{miner-NO_3}^{NO_3}\) - Half Saturation Nitrate Concentration for Nitrate Consumption Via Anaerobic Mineralisation of Dissolved Organic Carbon
Units Range Default mg/L NO\(_3\)-N (0, 2.1) 1.75 mmol/m\(^3\) NO\(_3\)-N (0, 150) 125 Science: Section M.4
The nitrate concentration for which the computed consumption of nitrate due to anaerobic mineralisation is half the corresponding anaerobic mineralisation of labile dissolved organic carbon. If this paramter is set to zero, then the consumption of nitrate as a source of oxygen as part of organic matter mineralisation is switched off. Cannot be varied spatially
Mortality == \(k_d^{pth}\), \(C_{SM}^{pth}\), \(\alpha\), \(\beta\), \(\theta_{mor}^{pth}\)
Model Construction: Section 4.6.3.2.1
Used in an (optional) pathogens constituent model block to control the mortality of pathogens. The fourth parameter \(\beta\) is unused but must be kept as a placeholder in this command so that five arguments are specified.
\(k_d^{pth}\) - Pathogen Dark Death Rate
Default: 0
Units: /d
Range: (0, 1)
Science: Section N.1
The natural mortality rate in freshwater at 20 \(^o\)C. Also referred to as the dark death rate
\(C_{SM}^{pth}\) - Salinity Effect On Mortality
Default: 0
Units: /d /psu
Range: (0, 0.1)
Science: Section N.1
The salinity effect on mortality. Set this to zero to remove salinity effects on mortality
\(\alpha\) - Parameter Controlling Salinity Mortality Dependence
Default: 1
Units: NA
Range: (0, 10)
Science: Section N.1
An exponentially applied controller of the mortality response to salinity. Set this to 1.0 to make salinity dependence linear. Do not set this and \(C_{SM}^{pth}\) to both be zero
\(\beta\) - Parameter Controlling DOC Trophic Mortality Dependence
Default: 1
Units: NA
Range: (0, 0)
Science: Section N.1
An exponentially applied controller of the mortality response to DOC. Not implemented
\(\theta_{mor}^{pth}\) - Pathogen Mortality Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.2)
Science: Section N.1
The factor to which (\(T\)-20) is raised to account for temperature effects on pathogen mortality. A value of 1.0 will remove the effect of temperature
Nitrate Benthic == \(K_{sed-O_2}^{NO_3}\), \(\theta_{sed}^{NO_3}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to control the response of benthic nitrate flux to temperature and oxygen concentration.
\(K_{sed-O_2}^{NO_3}\) - Sediment Half Saturation Oxygen Concentration for Nitrate Flux
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section E.1
The dissolved oxygen concentration for which the computed sediment nitrate flux is half the user specified rate, at 20\(^o\)C. Cannot be varied spatially
\(\theta_{sed}^{NO_3}\) - Sediment Nitrate Flux Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section E.1
The factor to which (\(T\)-20) is raised to account for temperature effects on nitrate sediment flux. A value of 1.0 will remove the effect of temperature
Nitrate Flux == \(F_{sed}^{NO_3}\)
Model Construction: Section 4.7.4
Used in a materials block to control the sediment flux rate of nitrate.
\(F_{sed}^{NO_3}\) - Sediment Nitrate Flux
Units Range Default mg NO\(_3\)-N/m\(^2\)/d (0, 140) 0 mmol NO\(_3\)-N/m\(^2\)/d (0, 10) 0 Science: Section E.1
The rate at which nitrate is exchanged between the sediments and overlying water column at 20\(^o\)C excluding the influence of overlying dissolved oxygen concentration. Can be varied spatially via use of model mesh material types. This is not the maxuimum rate of nitrate sediment flux.
This parameter is output as a diagnostic variable. For further information, refer to Nitrate User Defined Sediment Flux.
Nitrate Min Max == \(\left[NO_3\right]_{min}^{NO_3}\), \(\left[NO_3\right]_{max}^{NO_3}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to set minimum and maximum nitrate concentrations.
\(\left[NO_3\right]_{min}^{NO_3}\) - Minimum Nitrate Concentration
Units Range Default mg/L NO\(_3\)-N (0, 0.098) NA mmol/m\(^3\) NO\(_3\)-N (0, 7) NA Science: Appendix E
The minimum allowable nitrate concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[NO_3\right]_{max}^{NO_3}\) - Maximum Nitrate Concentration
Units Range Default mg/L NO\(_3\)-N (0, 98) NA mmol/m\(^3\) NO\(_3\)-N (0, 7000) NA Science: Appendix E
The maximum allowable nitrate concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Nitrification == \(R_{nitrif}^{NH_4}\), \(K_{nitrif-O_2}^{NH_4}\), \(\theta_{nitrif}^{NH_4}\)
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to control nitrification and its response to oxygen concentration and temperature.
\(R_{nitrif}^{NH_4}\) - Nitrification Rate
Units Range Default /d (0, 1) 0 0 Science: Section E.2
The rate at which ammonium is nitrified to nitrate at 20\(^o\)C excluding the influence of ambient dissolved oxygen concentration. A value of 0.0 will switch off nitrification
\(K_{nitrif-O_2}^{NH_4}\) - Half Saturation Oxygen Concentration for Nitrification
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section E.2
The dissolved oxygen concentration for which the computed nitrification rate is half the user specified rate, at 20\(^o\)C
\(\theta_{nitrif}^{NH_4}\) - Nitrification Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section E.2
The factor to which (\(T\)-20) is raised to account for temperature effects on nitrification. A value of 1.0 will remove the effect of temperature
Nitrogen Fixing == \(R_{nfix}^{N_2}\), \(f_{nfix}^{phy}\)
Model Construction: Section 4.7.3.5.1.11
Used in a phytoplankton constituent model block to set the nitrogen fixing parameters of a phytoplankton constituent model. The first parameter sets the rate of nitrogen fixing and the second dictates the influence of nitrogen fixing on primary productivity.
\(R_{nfix}^{N_2}\) - Nitrogen Fixing Rate
Units Range Default mg N / mg Chl a / d (0, 5) 0 mmol N / mmol C /d (0, 0.16) 0 Science: Section J.2.3
The rate at which nitrogen N is fixed from the atmosphere to complement nitrogen uptake from the water column. This rate excludes the influence of nitrogen limitation due to water column nutrient scarcity. It is the mass (or molar) rate of uptake of nitrogen N from the atmopshere, not N\(_2\). Note the units of chlorophyll a are in mg, not \(\mu\)g
\(f_{nfix}^{phy}\) - Penalty Function of Nitrogen Fixing On Primary Productivity
Default: 1
Units: NA
Range: (0, 1)
Science: Section H.1
A rate modifier that accounts for the metabolic cost of nitrogen fixing on primary productivity. This modifier can be thought of as a penalty function, with values of zero and one corresponding to no and maximum penalties, respectively. A penalty of 1 (the default) will always set primary productivity to zero
Nitrogen Limitation
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Nitrogen Limitation == \(\left[N\right]_{min}^{phy}\), \(K_{lim-N}^{phy}\)
Model Construction: Section 4.7.3.5.1.4
Used in a phytoplankton constituent model block to set nitrogen limitation parameters for the basic phytoplankton model.
\(\left[N\right]_{min}^{phy}\) - Minimum Concentration of N for Phytoplankton Uptake
Units Range Default mg/L N (0, 0.1) 0.01 mmol/m\(^3\) N (0.00, 7.14) 0.71 Science: Section I.3.1
Used to compute the nitrogen limitation function in the basic phytoplankton model. Also used by the advanced phytoplankton model if internal nitrogen stores are exhausted. It is the minimum N concentration (as NH\(_4\)-N + NO\(_3\)-N) at which uptake of nitrogen by phytoplankton can occur
\(K_{lim-N}^{phy}\) - Half Saturation N Concentration for Phytoplankton Uptake of N
Units Range Default mg/L N (1, 5) 1 mmol/m\(^3\) N (71.4, 357.14) 71.43 Science: Section I.3.1
Used to compute the nitrogen limitation function in the basic phytoplankton model. Also used by the advanced phytoplankton model if internal nitrogen stores are exhausted. It is the concentration of N (NH\(_4\)-N + NO\(_3\)-N) that when added to the specified minimum \(\left[N\right]_{min}^{phy}\) sets the nitrogen limitation function to a value of 0.5. A value of zero for this parameter will set the nitrogen limitation function to always be 1
Nitrogen Limitation == \(\left[N\right]_{min}^{phy}\), \(K_{lim-N}^{phy}\), \(X_{N-C-min}^{phy}\), \(X_{N-C-max}^{phy}\)
Model Construction: Section 4.7.3.5.2.1
Used in a phytoplankton constituent model block to set nitrogen limitation parameters for the advanced phytoplankton model.
\(\left[N\right]_{min}^{phy}\) - Minimum Concentration of N for Phytoplankton Uptake
Units Range Default mg/L N (0, 0.1) 0.01 mmol/m\(^3\) N (0.00, 7.14) 0.71 Science: Section I.3.1
Used to compute the nitrogen limitation function in the basic phytoplankton model. Also used by the advanced phytoplankton model if internal nitrogen stores are exhausted. It is the minimum N concentration (as NH\(_4\)-N + NO\(_3\)-N) at which uptake of nitrogen by phytoplankton can occur
\(K_{lim-N}^{phy}\) - Half Saturation N Concentration for Phytoplankton Uptake of N
Units Range Default mg/L N (1, 5) 1 mmol/m\(^3\) N (71.4, 357.14) 71.43 Science: Section I.3.1
Used to compute the nitrogen limitation function in the basic phytoplankton model. Also used by the advanced phytoplankton model if internal nitrogen stores are exhausted. It is the concentration of N (NH\(_4\)-N + NO\(_3\)-N) that when added to the specified minimum \(\left[N\right]_{min}^{phy}\) sets the nitrogen limitation function to a value of 0.5. A value of zero for this parameter will set the nitrogen limitation function to always be 1
\(X_{N-C-min}^{phy}\) - Minimum Internal Nitrogen to Carbon Ratio of Phytoplankton
Default: 0.05
Units: mg N/mg C
Range: (0.02, 0.21)
Science: Section I.3.2
The minimum internal nitrogen to carbon ratio of phytoplankton before growth becomes limited by nitrogen. This forms the quota that is used to trigger increased nitrogen uptake
\(X_{N-C-max}^{phy}\) - Maximum Internal Nitrogen to Carbon Ratio of Phytoplankton
Default: 0.20
Units: mg N/mg C
Range: (0.05, 0.30)
Science: Section I.3.2
The maximum internal nitrogen to carbon ratio of phytoplankton after which no further nitrogen uptake is allowed until growth dilutes the concentration
Nitrogen Min Max == \(\left[PON\right]_{min}^{PON}\), \(\left[PON\right]_{max}^{PON}\), \(\left[DON\right]_{min}^{DON}\), \(\left[DON\right]_{max}^{DON}\)
Model Construction: Section 4.8.3.5
Used in an organic matter constituent model block to set minimum and maximum particulate and dissolved organic nitrogen concentrations.
\(\left[PON\right]_{min}^{PON}\) - Minimum PON Concentration
Units Range Default mg/L N (0, 0.01) NA mmol/m\(^3\) N (0, 0.71) NA Science: Appendix M
The minimum allowable labile particulate organic nitrogen concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file
\(\left[PON\right]_{max}^{PON}\) - Maximum PON Concentration
Units Range Default mg/L N (0, 10) NA mmol/m\(^3\) N (0, 714) NA Science: Appendix M
The maximum allowable labile particulate organic nitrogen concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file
\(\left[DON\right]_{min}^{DON}\) - Minimum DON Concentration
Units Range Default mg/L N (0, 0.01) NA mmol/m\(^3\) N (0, 0.71) NA Science: Appendix M
The minimum allowable labile dissolved organic nitrogen concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file
\(\left[DON\right]_{max}^{DON}\) - Maximum DON Concentration
Units Range Default mg/L N (0, 10) NA mmol/m\(^3\) N (0, 714) NA Science: Appendix M
The maximum allowable labile dissolved organic nitrogen concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file
Organic Matter Model == Labile | Refractory
Model Construction: Section 4.8.3.5.1, Section 4.8.3.5.2
Used to commence an organics constituent model block via specification of a model from the organics constituent model class.
Organics Benthic == \(K_{sed-O_2}^{DOM}\), \(\theta_{sed}^{DOM}\)
Model Construction: Section 4.8.3.5.1
Used in an organics constituent model block to control the response of benthic DOM flux to temperature and oxygen concentration.
\(K_{sed-O_2}^{DOM}\) - Sediment Half Saturation Oxygen Concentration for DOM Flux
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section M.1
The dissolved oxygen concentration for which the computed sediment labile DOM flux is half the user specified rate, at 20\(^o\)C. Cannot be varied spatially. This value is applied equally to labile dissolved organic carbon, nitrogen and phosphorus
\(\theta_{sed}^{DOM}\) - Sediment DOM Flux Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section M.1
The factor to which (\(T\)-20) is raised to account for temperature effects on labile DOM sediment flux. A value of 1.0 will remove the effect of temperature. This value is applied equally to labile dissolved organic carbon, nitrogen and phosphorus
Oxygen
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Oxygen == ON | OFF
Model Construction: Section 4.7.3.3.1
Used in an inorganic nitrogen constituent model block to switch the dependence of all nitrogen (ammonium and nitrate) processes on dissolved oxygen ON or OFF.
For further information on the science of this command, refer to Section E.1.
Oxygen == ON | OFF
Model Construction: Section 4.8.3.5.1
Used in an organics constituent model block to switch the dependence of all processes on dissolved oxygen ON or OFF. Anammox and DRNA processes will be switched off entirely if this command is issued and set to OFF.
For further information on the science of this command, refer to Section M.1.
Oxygen == ON | OFF
Model Construction: Section 4.7.3.4.1
Used in an inorganic phosphorus constituent model block to switch the dependence of FRP processes on dissolved oxygen ON or OFF.
For further information on the science of this command, refer to Section F.1.
Oxygen == ON | OFF
Model Construction: Section 4.7.3.2.1
Used in a silicate constituent model block to switch the dependence of silicate processes on dissolved oxygen ‘ON’ or ‘OFF’.
For further information on the science of this command, refer to Section D.1.
Oxygen Benthic == \(K_{sed-O_2}^{O_2}\), \(\theta_{sed}^{O_2}\)
Model Construction: Section 4.6.3.1.1
Used in an oxygen constituent model block to control the response of benthic oxygen flux to temperature and oxygen concentration.
\(K_{sed-O_2}^{O_2}\) - Sediment Half Saturation Oxygen Concentration for Oxygen Flux
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section C.2
The dissolved oxygen concentration for which the computed sediment oxygen flux is half the user specified rate, at 20\(^o\)C. Cannot be varied spatially
\(\theta_{sed}^{O_2}\) - Sediment Oxygen Flux Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section C.2
The factor to which (\(T\)-20) is raised to account for temperature effects on oxygen sediment flux. A value of 1.0 will remove the effect of temperature
Oxygen Flux == \(F_{sed}^{O_2}\)
Model Construction: Section 4.6.4
Used in a materials block to control the sediment flux rate of oxygen.
\(F_{sed}^{O_2}\) - Sediment Oxygen Flux
Units Range Default mg O\(_2\)/m\(^2\)/d (-6400, 0) 0 mmol O\(_2\)/m\(^2\)/d (-200, 0) 0 Science: Section C.2
The rate at which dissolved oxygen is exchanged between the sediments and overlying water column at 20\(^o\)C excluding the influence of overlying dissolved oxygen concentration. Can be varied spatially via use of model mesh material types. This is not the maxuimum rate of oxygen sediment flux.
This parameter is output as a diagnostic variable. For further information, refer to Oxygen User Defined Sediment Flux.
Oxygen Min Max == \(\left[DO\right]_{min}^{O_2}\), \(\left[DO\right]_{max}^{O_2}\)
Model Construction: Section 4.6.3.1.1
Used in an oxygen constituent model block to set minimum and maximum dissolved oxygen concentrations.
\(\left[DO\right]_{min}^{O_2}\) - Minimum Dissolved Oxygen Concentration
Units Range Default mg/L O\(_2\) (0, 0.5) NA mmol/m\(^3\) O\(_2\) (0, 15.6) NA Science: Appendix C
The minimum allowable dissolved oxygen concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[DO\right]_{max}^{O_2}\) - Maximum Dissolved Oxygen Concentration
Units Range Default mg/L O\(_2\) (6, 20) NA mmol/m\(^3\) O\(_2\) (187.5, 625) NA Science: Appendix C
The maximum allowable dissolved oxygen concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Oxygen Model == O2
Model Construction: Section 4.6.3.1, sec-ConModDOO2-4
Used to commence an oxygen constituent model block via specification of a constituent model from the oxygen constituent model class.
Oxygen Piston Model
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Oxygen Piston Model == Ho16
Model Construction: Section 4.6.3.1
Used in an oxygen constituent model block to activate the Ho et al 2016 oxygen piston model.
For further information on the science of this command, refer to Section C.1.
Oxygen Piston Model == Wanninkhof92
Model Construction: Section 4.6.3.1
Used in an oxygen constituent model block to activate the Wanninkhof 1992 oxygen piston model.
For further information on the science of this command, refer to Section C.1.
Pathogen Model == Free | Attached, pathname
Status: Optional
Model Construction: Section 4.6.3.2.1, Section 4.6.3.2.2
Required Dependent Command(s): End Pathogen Model
Used to commence a pathogen model block via specification of a model from the pathogen constituent model class. pathname is any user specified pathgen group name that:
- Uses only alphanumeric characters
- Has no spaces
- Excludes the keyword ‘PATH’, and
- Is not the same as any other group name
Phosphorus Limitation == \(\left[P\right]_{min}^{phy}\), \(K_{lim-P}^{phy}\)
Model Construction: Section 4.7.3.5.1.5
Used in a phytoplankton constituent model block to set phosphorus limitation parameters for the basic phytoplankton model.
\(\left[P\right]_{min}^{phy}\) - Minimum Concentration of P for Phytoplankton Uptake
Units Range Default mg/L P (0, 0.1) 0.001 mmol/m\(^3\) P (0.0, 3.23) 0.03 Science: Section I.4.1
Used to compute the phosphorus limitation function in the basic phytoplankton model. Also used by the advanced phytoplankton model if internal phosphorus stores are exhausted. It is the minimum P concentration (as FRP-P) at which uptake of phosphorus by phytoplankton can occur
\(K_{lim-P}^{phy}\) - Half Saturation P Concentration for Phytoplankton Uptake of P
Units Range Default mg/L P (0.1, 0.5) 0.1 mmol/m\(^3\) P (3.23, 16.13) 3.23 Science: Section I.4.1
Used to compute the phosphorus limitation function in the basic phytoplankton model. Also used by the advanced phytoplankton model if internal phosphorus stores are exhausted. It is the concentration of P (FRP-P) that when added to the specified minimum \(\left[P\right]_{min}^{phy}\) sets the phosphorus limitation function to a value of 0.5. A value of zero for this parameter will set the phosphorus limitation function to always be 1
Phosphorus Limitation == \(\left[P\right]_{min}^{phy}\), \(K_{lim-P}^{phy}\), \(X_{P-C-min}^{phy}\), \(X_{P-C-max}^{phy}\)
Model Construction: Section 4.7.3.5.2.2
Used in a phytoplankton constituent model block to set phosphorus limitation parameters for the advanced phytoplankton model.
\(\left[P\right]_{min}^{phy}\) - Minimum Concentration of P for Phytoplankton Uptake
Units Range Default mg/L P (0, 0.1) 0.001 mmol/m\(^3\) P (0.0, 3.23) 0.03 Science: Section I.4.1
Used to compute the phosphorus limitation function in the basic phytoplankton model. Also used by the advanced phytoplankton model if internal phosphorus stores are exhausted. It is the minimum P concentration (as FRP-P) at which uptake of phosphorus by phytoplankton can occur
\(K_{lim-P}^{phy}\) - Half Saturation P Concentration for Phytoplankton Uptake of P
Units Range Default mg/L P (0.1, 0.5) 0.1 mmol/m\(^3\) P (3.23, 16.13) 3.23 Science: Section I.4.1
Used to compute the phosphorus limitation function in the basic phytoplankton model. Also used by the advanced phytoplankton model if internal phosphorus stores are exhausted. It is the concentration of P (FRP-P) that when added to the specified minimum \(\left[P\right]_{min}^{phy}\) sets the phosphorus limitation function to a value of 0.5. A value of zero for this parameter will set the phosphorus limitation function to always be 1
\(X_{P-C-min}^{phy}\) - Minimum Internal Phosphorus to Carbon Ratio of Phytoplankton
Default: 0.005
Units: mg P/mg C
Range: (0.003, 0.021)
Science: Section I.4.2
The minimum internal phosphorus to carbon ratio of phytoplankton before growth becomes limited by phosphorus. This forms the quota that is used to trigger increased phosphorus uptake
\(X_{P-C-max}^{phy}\) - Maximum Internal Phosphorus to Carbon Ratio of Phytoplankton
Default: 0.020
Units: mg P/mg C
Range: (0.005, 0.030)
Science: Section I.4.2
The maximum internal phosphorus to carbon ratio of phytoplankton after which no further phosphorus uptake is allowed until growth dilutes the concentration
Phosphorus Min Max == \(\left[POP\right]_{min}^{POP}\), \(\left[POP\right]_{max}^{POP}\), \(\left[DOP\right]_{min}^{DOP}\), \(\left[DOP\right]_{max}^{DOP}\)
Model Construction: Section 4.8.3.5
Used in an organic matter constituent model block to set minimum and maximum particulate and dissolved organic phosphorus concentrations.
\(\left[POP\right]_{min}^{POP}\) - Minimum POP Concentration
Units Range Default mg/L P (0, 0.001) NA mmol/m\(^3\) P (0, 0.032) NA Science: Appendix M
The minimum allowable labile particulate organic phosphorus concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file
\(\left[POP\right]_{max}^{POP}\) - Maximum POP Concentration
Units Range Default mg/L P (0, 1) NA mmol/m\(^3\) P (0, 32) NA Science: Appendix M
The maximum allowable labile particulate organic phosphorus concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file
\(\left[DOP\right]_{min}^{DOP}\) - Minimum DOP Concentration
Units Range Default mg/L P (0, 0.001) NA mmol/m\(^3\) P (0, 0.032) NA Science: Appendix M
The minimum allowable labile dissolved organic phosphorus concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file
\(\left[DOP\right]_{max}^{DOP}\) - Maximum DOP Concentration
Units Range Default mg/L P (0, 1) NA mmol/m\(^3\) P (0, 32) NA Science: Appendix M
The maximum allowable labile dissolved organic phosphorus concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file
Phyto Model == Basic | Advanced, group_name
Model Construction: Section 4.7.3.5
Used to commence a phytoplankton constituent model block via specification of a model from the phytoplankton constituent model class (Basic or Advanced), and a phytoplankton ‘group_name’. The group name can be any name required. If the advanced phytoplankton model is used then internal nitrogen and phosphorus concentrations will be simulated as computed variables and therefore must have respective initial conditions and boundary conditions specified, paying attention to ordering rules as required.
Primary Productivity == \(R_{prod}^{phy}\), \(\theta_{prod}^{phy}\)
Model Construction: Section 4.7.3.5.1.8
Used in a phytoplankton constituent model block to set primary productivity parameters of a phytoplankton constituent model.
\(R_{prod}^{phy}\) - Phytoplankton Primary Productivity Rate
Default: 0
Units: /d
Range: (0, 3.5)
Science: Section H.1
The phytoplankton primary productivity (growth) rate at 20\(^o\)C with no light, temperature, salinty, silicate or nutrient limitation. This rate is multiplied by ambient phytoplankton concentration to derive initial carbon, nutrient and silicate uptake fluxes
\(\theta_{prod}^{phy}\) - Phytoplankton Primary Productivity Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section I.2.2
The factor to which (\(T\)-20) is raised to account for temperature effects on phytoplankton growth in the standard temperature limitation function. A value of 1.0 will remove the effect of temperature
Ref Activation == \(R_{act}^{RDOM}\)
Model Construction: Section 4.8.3.5.2
Used in an organic matter constituent model block to set the rate of activation of refractory dissolved organic carbon, nitrogen and phosphorus.
\(R_{act}^{RDOM}\) - RDOM Activation Rate
Units Range Default /d (0, 0.1) 0 0 Science: Section M.5
The rate at which refractory dissolved organic carbon, nitrogen and phosphorus are activated to their corresponding labile dissolved organic constituents at 20\(^o\)C excluding the influence of ambient dissolved oxygen concentration. This is not the maxuimum rate of activation. The same rate is applied to all refractory dissolved organic constituents (carbon, nitrogen and phosphorus)
Ref Breakdown == \(R_{bdn}^{RPOM}\), \(X_N^{RPOM}\), \(X_P^{RPOM}\)
Model Construction: Section 4.8.3.5.2
Used in an organics constituent model block to parameterise the breakdown of refractory particulate organic matter.
\(R_{bdn}^{RPOM}\) - RPOM Breakdown Rate
Units Range Default /d (0, 0.1) 0 0 Science: Section M.3
The rate at which refractory particulate organic matter (a single computed variable) is broken down to labile particulate organic carbon, nitrogen and phosphorus (three computed variables) at 20\(^o\)C excluding the influence of ambient dissolved oxygen concentration. This is not the maxuimum rate of breakdown
\(X_N^{RPOM}\) - Ratio of N to C in Refractory Particulate Organic Matter
Default: 0.15
Units: NA
Range: (0.094, 0.19)
Science: Section M.3
The molar ratio of N to C in refractory particulate organic matter. This ratio should not differ significantly from the Redfield ratio of 16/106.
\(X_P^{RPOM}\) - Ratio of P to C in Refractory Particulate Organic Matter
Default: 0.0094
Units: NA
Range: (0.00094, 0.019)
Science: Section M.3
The molar ratio of P to C in refractory particulate organic matter. This ratio should not differ significantly from the Redfield ratio of 1/106.
Ref Carbon Min Max == \(\left[RPOM\right]_{min}^{RPOM}\), \(\left[RPOM\right]_{max}^{RPOM}\), \(\left[RDOC\right]_{min}^{RDOC}\), \(\left[RDOC\right]_{max}^{RDOC}\)
Model Construction: Section 4.8.3.5.2
Used in an organic matter constituent model block to set minimum and maximum refractory particulate organic matter and refractory dissolved organic carbon concentrations.
\(\left[RPOM\right]_{min}^{RPOM}\) - Minimum RPOM Concentration
Units Range Default mg/L C (0, 0.1) NA mmol/m\(^3\) C (0, 8.33) NA Science: Appendix M
The minimum allowable refractory particulate organic matter concentration. Although referred to as organic matter, it is accounted as (and in units of) carbon in the WQ Module. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[RPOM\right]_{max}^{RPOM}\) - Maximum RPOM Concentration
Units Range Default mg/L C (0, 100) NA mmol/m\(^3\) C (0, 8333) NA Science: Appendix M
The maximum allowable refractory particulate organic matter concentration. Although referred to as organic matter, it is accounted as (and in units of) carbon in the WQ Module. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
\(\left[RDOC\right]_{min}^{RDOC}\) - Minimum RDOC Concentration
Units Range Default mg/L C (0, 0.1) NA mmol/m\(^3\) C (0, 8.33) NA Science: Appendix M
The minimum allowable refractory dissolved organic carbon concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[RDOC\right]_{max}^{RDOC}\) - Maximum RDOC Concentration
Units Range Default mg/L C (0, 100) NA mmol/m\(^3\) C (0, 8333) NA Science: Appendix M
The maximum allowable refractory dissolved organic carbon concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Ref Nitrogen Min Max == \(\left[RDON\right]_{min}^{RDON}\), \(\left[RDON\right]_{max}^{RDON}\)
Model Construction: Section 4.8.3.5.2
Used in an organic matter constituent model block to set minimum and maximum refractory dissolved organic nitrogen concentrations.
\(\left[RDON\right]_{min}^{RDON}\) - Minimum RDON Concentration
Units Range Default mg/L N (0, 0.1) NA mmol/m\(^3\) N (0, 7.14) NA Science: Appendix M
The minimum allowable refractory dissolved organic nitrogen concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[RDON\right]_{max}^{RDON}\) - Maximum RDON Concentration
Units Range Default mg/L N (0, 100) NA mmol/m\(^3\) N (0, 7143) NA Science: Appendix M
The maximum allowable refractory dissolved organic nitrogen concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Ref Phosphorus Min Max == \(\left[RDOP\right]_{min}^{RDOP}\), \(\left[RDOP\right]_{max}^{RDOP}\)
Model Construction: Section 4.8.3.5.2
Used in an organic matter constituent model block to set minimum and maximum refractory dissolved organic phosphorus concentrations.
\(\left[RDOP\right]_{min}^{RDOP}\) - Minimum RDOP Concentration
Units Range Default mg/L P (0, 0.01) NA mmol/m\(^3\) P (0, 0.32) NA Science: Appendix M
The minimum allowable refractory dissolved organic phosphorus concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[RDOP\right]_{max}^{RDOP}\) - Maximum RDOP Concentration
Units Range Default mg/L P (0, 10) NA mmol/m\(^3\) P (0, 323) NA Science: Appendix M
The maximum allowable refractory dissolved organic phosphorus concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Ref Photolysis == \(f_{photo}^{RDOM}\)
Model Construction: Section 4.8.3.5.2
Used in an organics constituent model block to parameterise the proportion of photolysis of refractory dissolved organic matter that produces labile dissolved organic matter.
\(f_{photo}^{RDOM}\) - RDOM Photolysis Fraction
Default: 0
Units: NA
Range: (0, 1)
Science: Section M.6
The proportion of photolysed refractory dissolved organic matter that is is converted to labile dissolved organic matter. The remaining proportion is converted to dissolved inorganic carbon and nutrients. This multiplier is applied equally to refractory dissolved organic carbon, nitrogen and phosphorus
Ref Self Shading == \(Ke^{RPOM}\), \(R_{CDOM}^{RDOM}\)
Model Construction: Section 4.8.3.5.2
Used in an organics constituent model block to parameterise light attenuation due to the presence of refractory particulate and dissolved organic matter.
\(Ke^{RPOM}\) - RPOM Specific Shading Coefficient
Units Range Default /(mg RPOM/L)/m (0, 8.33) 0 /(mmol RPOM/m\(^3\))/m (0, 0.1) 0 Science: Section M.7
The rate at which light is attenuated by refractory particulate organic matter. This coefficient is per unit concentration of refractory particulate organic carbon (the units of RPOM) per metre (depth). It is multiplied by RPOM concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients
\(R_{CDOM}^{RDOM}\) - CDOM Multiplier
Default: 0
Units: NA
Range: (0, 2)
Science: Section M.7
The linear multiplicative factor applied to the calculated value of CDOM for use in organic matter self shading calculations. A value greater (less) than 1.0 increases (decreases) the CDOM estimate and hence increases (decreases) shading. . This coefficient is dimensionless but can be thought of as light attenuation per unit of CDOM, which are both in units of /m. Multiplying this parameter by CDOM in each computational cell therefore leaves a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients
Ref Settling
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Ref Settling == Constant, \(V_{settle}^{rorg}\)
Model Construction: Section 4.8.3.5.2
Used in an organic matter constituent model block to control the settling rate of refractory particulate organic matter. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
For further information on the constant settling model, refer to Section M.8.2.
\(V_{settle}^{rorg}\) - Refractory Organic Matter Settling Velocity
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section M.8.2
The settling velocity applied to refractory particulate organic matter for constant or density related settling calculations. A negative value is a downwards velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
Ref Settling == None
Model Construction: Section 4.8.3.5.2
Used in an organic matter constituent model block to set the settling rate of refractory particulate organic matter to zero.
For further information on the science of this command, refer to Section M.8.1.
Ref Settling == Stokes, \(d_{rorg}\), \(\rho_{rorg}\)
Model Construction: Section 4.8.3.5.2
Used in an organic matter constituent model block to control the settling rate of refractory particulate organic matter. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
For further information on the stokes settling model, refer to Section M.8.4.
\(d_{rorg}\) - Refractory Organic Matter Stokes Diameter
Default: 1 e-09
Units: m
Range: (1 e-09, 1 e -06)
Science: Section M.8.4
The conceptual diameter of refractory particulate organic matter applied in stokes calculations of settling velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
\(\rho_{rorg}\) - Refractory Organic Matter Stokes Density
Default: 2000
Units: kg/m\(^3\)
Range: (1000, 3000)
Science: Section M.8.4
The density of refractory particulate organic matter applied in stokes calculations of settling velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
Ref Settling == Thermal, \(V_{settle}^{rorg}\)
Model Construction: Section 4.8.3.5.2
Used in an organic matter constituent model block to control the settling rate of refractory particulate organic matter. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
For further information on the thermal settling model, refer to Section M.8.3.
\(V_{settle}^{rorg}\) - Refractory Organic Matter Settling Velocity
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section M.8.2
The settling velocity applied to refractory particulate organic matter for constant or density related settling calculations. A negative value is a downwards velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
Report Min Max Warnings == ON | OFF
Model Construction: Section 4.5.1
Used in Part 1: Simulation controls of WQ Module control file to suppress writing concentration limit exceedance warnings to the WQ log file. If not specified it is set to on. This command should not be used as a way to ignore concentration exceedances, and has only been included in the WQ Module to allow for the rare occassions when known and expected exceedances occurr regularly - writing of these to the log file can cause very large log files to be written and result in system instability.
Respiration == \(R_{resp}^{phy}\), \(\theta_{resp}^{phy}\), \(f_{true-resp}^{phy}\), \(f_{excr-loss}^{phy}\), \(f_{exud}^{phy}\)
Model Construction: Section 4.7.3.5.1.9
Used in a phytoplankton constituent model block to set respiration and exudation parameters of a phytoplankton constituent model.
\(R_{resp}^{phy}\) - Phytoplankton Respiration Rate
Default: 0
Units: /d
Range: (0, 0.1)
Science: Section H.2
The phytoplankton respiration rate at 20\(^o\)C with no temperature or salinty limitation. This rate is multiplied by ambient phytoplankton concentration to derive excretion and mortality fluxes. It is added to the parallel primary productivity and exudation rates and then multiplied by ambient phytoplankton concentration to compute biomass flux
\(\theta_{resp}^{phy}\) - Phytoplankton Respiration Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section H.2
The factor to which (\(T\)-20) is raised to account for temperature effects on phytoplankton respiration. A value of 1.0 will remove the effect of temperature
\(f_{true-resp}^{phy}\) - Fraction of Phytoplankton Respiration That Is True Respiration
Default: 1
Units: NA
Range: (0, 1)
Science: Section K.1
The proportion of consumed carbohydrates (that were generated during photosynthesis) that are converted to energy, as opposed to waste matter. A value of one (zero) has all consumed carbohydrates converted to energy (waste), and will minimise (maximise) excretive losses
\(f_{excr-loss}^{phy}\) - Fraction of Phytoplanton Loss That Is Excretion
Default: 0
Units: NA
Range: (0, 1)
Science: Section K.1
The proportion of combined excretive and mortality losses that are excretive. If \(f_{true-resp}^{phy}\) is set to one (zero) then this parameter has no (maximum) effect.
\(f_{exud}^{phy}\) - Fraction of Primary Production Lost to Exudation
Default: 0
Units: NA
Range: (0, 1)
Science: Section H.3
The proportion of primary production that does not generate retained cellular carbon biomass, but is lost through exudation (and hence excretion). Exudation losses are summed with potentially modified respiration losses to compute excretion
Restart == Restart file path and name.rst
Status: Optional
Model Construction: Section 4.4.2.1
Specification of full path and name of previously saved restart file.
Salinity Limitation
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Salinity Limitation == Estuarine, \(S_{opt-est}^{phy}\), \(S_{max-est}^{phy}\), \(P_{est}^{phy}\)
Model Construction: Section 4.7.3.5.1.2
Used in a phytoplankton constituent model block to select the estuarine phytoplankton group salinity limitation.
For further information on the estuarine salinity limitation model, refer to Section I.7.5.
\(S_{opt-est}^{phy}\) - Optimum Estuarine Salinity
Default: 0
Units: g/L
Range: (0, 45)
Science: Section I.7.5
Used to compute the estuarine salinity limitation function. It is the salinity at which the estuarine salinity limitation function has a value of 1
\(S_{max-est}^{phy}\) - Maximum Estuarine Salinity
Default: 5
Units: g/L
Range: (0, 45)
Science: Section I.7.5
Used to compute the estuarine salinity limitation function. It is the maximum salinity at which the estuarine salinity limitation function has a value greater than zero
\(P_{est}^{phy}\) - Power Coefficient for Estuarine Salinity Limitation
Default: 0
Units: NA
Range: (0, 5)
Science: Section I.7.5
Used to compute the estuarine salinity limitation function. It determines the gradient of the estuarine limitation function (with salinity) above and below \(S_{opt-est}^{phy}\). Small (large) values of this parameter provide low (high) gradients
Salinity Limitation == Fresh, \(S_{opt-fresh}^{phy}\), \(S_{max-fresh}^{phy}\), \(L_{max-fresh}^{phy}\)
Model Construction: Section 4.7.3.5.1.2
Used in a phytoplankton constituent model block to select the freshwater phytoplankton group salinity limitation.
For further information on the freshwater salinity limitation model, refer to Section I.7.2.
\(S_{opt-fresh}^{phy}\) - Optimum Freshwater Salinity
Default: 0
Units: g/L
Range: (0, 45)
Science: Section I.7.2
Used to compute the freshwater salinity limitation function. It is the maximum salinity at which the freshwater salinity limitation function has a value of 1
\(S_{max-fresh}^{phy}\) - Maximum Freshwater Salinity
Default: 5
Units: g/L
Range: (0, 45)
Science: Section I.7.2
Used to compute the freshwater salinity limitation function. It is the maximum salinity at which the freshwater salinity limitation function is greater than the vlaue of \(L_{max-fresh}^{phy}\)
\(L_{max-fresh}^{phy}\) - Limitation Function At Maximum Freshwater Salinity
Default: 0
Units: NA
Range: (0, -)
Science: Section I.7.2
Used to compute the freshwater salinity limitation function. It is the value of the freshwater limitation function at a salinity of \(S_{max-fresh}\). If this limitation function value is set to be between zero and one (greater than one), then the computed limitation will be applied as a reductive (enhancement) factor to primary productivity (respiration).
Salinity Limitation == Marine, \(S_{opt-marine}^{phy}\), \(L_{zero-marine}^{phy}\)
Model Construction: Section 4.7.3.5.1.2
Used in a phytoplankton constituent model block to select the marine phytoplankton group salinity limitation.
For further information on the marine salinity limitation model, refer to Section I.7.3.
\(S_{opt-marine}^{phy}\) - Optimum Marine Salinity
Default: 0
Units: g/L
Range: (0, 45)
Science: Section I.7.3
Used to compute the marine salinity limitation function. It is the minimum salinity at which the marine salinity limitation function has a value of 1
\(L_{zero-marine}^{phy}\) - Limitation Function At Zero Marine Salinity
Default: 0
Units: NA
Range: (0, -)
Science: Section I.7.3
Used to compute the marine salinity limitation function. It is the value of the marine limitation function at a salinity of zero. If this limitation function value is set to be between zero and one (greater than one), then the computed limitation will be applied as a reductive (enhancement) factor to primary productivity (respiration).
Salinity Limitation == Mixed, \(S_{opt-mix}^{phy}\), \(S_{max-mix}^{phy}\), \(L_{zero-mix}^{phy}\)
Model Construction: Section 4.7.3.5.1.2
Used in a phytoplankton constituent model block to select the mixed phytoplankton group salinity limitation.
For further information on the mixed salinity limitation model, refer to Section I.7.4.
\(S_{opt-mix}^{phy}\) - Optimum Mixed Salinity
Default: 0
Units: g/L
Range: (0, 45)
Science: Section I.7.4
Used to compute the mixed salinity limitation function. It is the minimum salinity at which the mixed salinity limitation function has a value of 1
\(S_{max-mix}^{phy}\) - Maximum Mixed Salinity
Default: 5
Units: g/L
Range: (0, 45)
Science: Section I.7.4
Used to compute the mixed salinity limitation function. It is the maximum salinity at which the mixed salinity limitation function has a value of 1
\(L_{zero-mix}^{phy}\) - Limitation Function At Zero And (\(S_{Opt-Mix}^{Phy} + S_{Max-Mix}^{Phy}\)) Mixed Salinity
Default: 0
Units: NA
Range: (0, -)
Science: Section I.7.4
Used to compute the mixed salinity limitation function. It is the value of the mixed limitation function at a salinity of zero and (\(S_{opt-mix}^{phy} + S_{max-mix}^{phy}\)). If this limitation function value is set to be between zero and one (greater than one), then the computed limitation will be applied as a reductive (enhancement) factor to primary productivity (respiration).
Salinity Limitation == None
Model Construction: Section 4.7.3.5.1.2
Used in a phytoplankton constituent model block to turn off phytoplankton group salinity limitation.
For more information on the science of this command, refer to Section I.7.1.
Self Shading == \(Ke^{POM}\), \(Ke^{DOM}\)
Model Construction: Section 4.8.3.5.1
Used in an organics constituent model block to parameterise light attenuation due to the presence of particulate and dissolved organic matter.
\(Ke^{POM}\) - POM Specific Shading Coefficient
Units Range Default /(mg POC/L)/m (0, 8.33) 0 /(mmol POC/m\(^3\))/m (0, 0.1) 0 Science: Section M.7
The rate at which light is attenuated by labile particulate organic matter. This coefficient is per unit concentration of particulate organic carbon (which is used as a proxy for particulate organic matter) per metre (depth). It is multiplied by POC concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients
\(Ke^{DOM}\) - DOM Specific Shading Coefficient
Units Range Default /(mg DOC/L)/m (0, 8.33) 0 /(mmol DOC/m\(^3\))/m (0, 0.1) 0 Science: Section M.7
The rate at which light is attenuated by labile dissolved organic matter. This coefficient is per unit concentration of dissolved organic carbon (which is used as a proxy for dissolved organic matter) per metre (depth). It is multiplied by DOC concentration in each computational cell to leave a value that has units of per meter, which is the same as standard extinction coefficients and therefore is able to be added to other (e.g. background) parallel extinction coefficients
Settling
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Settling == \(V_{settle}^{FRP}\)
Model Construction: Section 4.7.3.4.2
Used in an inorganic phosphorus constituent model block to control the settling rate of adsorbed FRP. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
\(V_{settle}^{FRP}\) - Constant Rate of Adsorbed FRP Settling
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section F.5
The constant settling velocity applied to adsorbed FRP. Future releases of the WQ Module will dynamically link this settling velocity to calculations made by the TUFLOW FV ST Module. A negative value is a downwards velocity
Settling == \(V_{settle}^{pth}\)
Model Construction: Section 4.6.3.2.1
Used in an (optional) pathogens constituent model block to set free pathogen settling velocities. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
\(V_{settle}^{pth}\) - Unattached Pathogen Settling Velocity
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section N.4
The settling velocity of unattached pathogens. A negative value is a downwards velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
Settling == \(V_{settle}^{pth}\), \(V_{settle}^{pth_t}\)
Model Construction: Section 4.6.3.2.2
Used in an (optional) pathogens constituent model block to set free and attached pathogen settling velocities. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
\(V_{settle}^{pth}\) - Unattached Pathogen Settling Velocity
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section N.4
The settling velocity of unattached pathogens. A negative value is a downwards velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
\(V_{settle}^{pth_t}\) - Attached Pathogen Settling Velocity
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section N.4
The settling velocity of attached pathogens. A negative value is a downwards velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
Settling == Constant, \(V_{settle}^{lorg}\)
Model Construction: Section 4.8.3.5.1
Used in an organic matter constituent model block to control the settling rate of labile particulate organic matter. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
For further information on the constant organic settling model, refer to Section M.8.2.
\(V_{settle}^{lorg}\) - Labile Organic Matter Settling Velocity
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section M.8.2
The settling velocity applied to labile particulate organic matter for constant or density related settling calculations. A negative value is a downwards velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
Settling == Constant, \(V_{settle}^{phy}\)
Model Construction: Section 4.7.3.5.1.12
Used in a phytoplankton constituent model block to set a constant settling velocity in both basic and advanced phytoplankton constituent models. A negative value specified in this command is a downwards velocity. Setting the settling velocity to zero in this model is the same as setting Settling to None.
For further information on the constant phytoplankton settling model, refer to Section H.4.2.
\(V_{settle}^{phy}\) - Constant Rate of Phytoplankton Settling
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section H.4.2
The constant settling velocity applied to phytoplankton using either the basic or advanced phytoplankton constituent model. It is applied as a constant (in the constant settling model) or modified by density (using the density correction model). A negative value is a downwards velocity
Settling == Motile, \(V_{mot}^{phy}\), \(I_{K-mot}\)
Model Construction: Section 4.7.3.5.2.4
Used in a phytoplankton constituent model block to compute settling velocity via motility functions that depend on ambient conditions, in only the advanced phytoplankton constituent model. The specification of \(I_K\) is not mandatory in this command. If it is not specified then the \(I_K\) specified in the phytoplankton constituent model’s light limitation model will be used. If a light limitation model is not specified, or uses \(I_S\) instead of \(I_K\), then the library default value of \(I_K\) is used. If \(I_K\) is specified both in this motile settling command and a phytoplankton constituent model light limitation function, then the value specified in the Light Limitation command is used, and the value specified in this command is ignored.
For further information on the motile phytoplankton settling model, refer to Section H.4.5.
\(V_{mot}^{phy}\) - Motile Settling Velocity
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section H.4.5
The motile settling velocity applied to phytoplankton, that is then modified by local light conditions. It can be applied to only to the advanced phytoplankton constituent model. A negative value is a downwards velocity
\(I_{K-mot}\) - Motile Settling Light Half Saturation Light Intensity
Default: 20
Units: W/m\(^2\)
Range: (0, 1500)
Science: Section H.4.5
The half saturation light intensity used to compute direction of motility. It can be applied only to the advanced phytoplankton constituent model. This value is ignored if \(I_K\) has been specified in a light limitation model within the same phytoplankton constituent model block
Settling == None
Model Construction: Section 4.8.3.5.1
Used in an organic matter constituent model block to set the settling rate of labile particulate organic matter to zero.
For further information on the science of this command, refer to Section M.8.1.
Settling == None
Model Construction: Section 4.7.3.5.1.12
Used in a phytoplankton constituent model block to turn off settling in both basic and advanced phytoplankton constituent models.
For more information on the science of this command, refer to Section H.4.1.
Settling == Stokes, \(d_{lorg}\), \(\rho_{lorg}\)
Model Construction: Section 4.8.3.5.1
Used in an organic matter constituent model block to control the settling rate of labile particulate organic matter. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
For further information on the stokes organic settling model, refer to Section M.8.4.
\(d_{lorg}\) - Labile Organic Matter Stokes Diameter
Default: 1 e-09
Units: m
Range: (1 e-09, 1 e -06)
Science: Section M.8.4
The conceptual diameter of labile particulate organic matter applied in stokes calculations of settling velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
\(\rho_{lorg}\) - Labile Organic Matter Stokes Density
Default: 2000
Units: kg/m\(^3\)
Range: (1000, 3000)
Science: Section M.8.4
The density of labile particulate organic matter applied in stokes calculations of settling velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
Settling == Stokes, \(I_{K-sto}\)
Model Construction: Section 4.7.3.5.1.12
Used in a phytoplankton constituent model block to compute settling velocity via stokes settling laws in both basic and advanced phytoplankton constituent models. Density must be simulated as a computed variable for each phytoplankton group that uses this model, so must have cell density initial conditions and boundary conditions specified as per ordering rules. The specification of \(I_K\) is not mandatory in this command. If it is not specified then the \(I_K\) specified in the phytoplankton constituent model’s light limitation model will be used. If a light limitation model is not specified, or uses \(I_S\) instead of \(I_K\), then the library default value of \(I_K\) is used. If \(I_K\) is specified both in this stokes settling command and a phytoplankton constituent model light limitation function, then the value specified in the Light Limitation command is used, and the value specified in this command is ignored.
For further information on the stokes phytoplankton settling model, refer to Section H.4.4.
\(I_{K-sto}\) - Stokes Settling Light Half Saturation Light Intensity
Default: 20
Units: W/m\(^2\)
Range: (0, 1500)
Science: Section H.4.4
The half saturation light intensity used to compute cell density, which is in turn required for calculation of Stokes settling velocity. It can be applied to either the basic or advanced phytoplankton constituent model. This value is ignored if \(I_K\) has been specified in a light limitation model within the same phytoplankton constituent model block
Settling == Thermal, \(V_{settle}^{lorg}\)
Model Construction: Section 4.8.3.5.1
Used in an organic matter constituent model block to control the settling rate of labile particulate organic matter. This will be linked directly to the TUFLOW FV ST Module in future releases of the WQ Module.
For further information on the thermal organic settling model, refer to Section M.8.3.
\(V_{settle}^{lorg}\) - Labile Organic Matter Settling Velocity
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section M.8.2
The settling velocity applied to labile particulate organic matter for constant or density related settling calculations. A negative value is a downwards velocity. Future releases of the WQ Module will dynamically link settling velocity to calculations made by the TUFLOW FV ST Module
Settling == Thermal, \(V_{settle}^{phy}\)
Model Construction: Section 4.7.3.5.1.12
Used in a phytoplankton constituent model block to set a constant settling velocity in both basic and advanced phytoplankton constituent models, allowing for temperature effects to settling. A negative value specified in this command is a downwards velocity.
For further information on the thermal phytoplankton settling model, refer to Section H.4.3.
\(V_{settle}^{phy}\) - Constant Rate of Phytoplankton Settling
Default: 0
Units: m/d
Range: (-50, 0)
Science: Section H.4.2
The constant settling velocity applied to phytoplankton using either the basic or advanced phytoplankton constituent model. It is applied as a constant (in the constant settling model) or modified by density (using the density correction model). A negative value is a downwards velocity
Silicate Benthic == \(K_{sed-O_2}^{Si}\), \(\theta_{sed}^{Si}\)
Model Construction: Section 4.7.3.2.1
Used in a silicate constituent model block to control the response of benthic silicate flux to temperature and oxygen concentration.
\(K_{sed-O_2}^{Si}\) - Sediment Half Saturation Oxygen Concentration for Silicate Flux
Units Range Default mg/L O\(_2\) (0, 4.8) 4 mmol/m\(^3\) O\(_2\) (0, 150) 125 Science: Section D.1
The dissolved oxygen concentration for which the computed sediment silicate flux is half the user specified rate, at 20\(^o\)C. Cannot be varied spatially
\(\theta_{sed}^{Si}\) - Sediment Silicate Flux Temperature Coefficient
Default: 1
Units: NA
Range: (1, 1.1)
Science: Section D.1
The factor to which (\(T\)-20) is raised to account for temperature effects on silicate sediment flux. A value of 1.0 will remove the effect of temperature
Silicate Flux == \(F_{sed}^{Si}\)
Model Construction: Section 4.7.4
Used in a materials block to control the sediment flux rate of silicate.
\(F_{sed}^{Si}\) - Sediment Silicate Flux
Units Range Default mg Si/m\(^2\)/d (0, 140) 0 mmol Si/m\(^2\)/d (0, 5) 0 Science: Section D.1
The rate at which silicate is exchanged between the sediments and overlying water column at 20\(^o\)C excluding the influence of overlying dissolved oxygen concentration. Can be varied spatially via use of model mesh material types. This is not the maxuimum rate of silicate sediment flux.
This parameter is output as a diagnostic variable. For further information, refer to Silicate User Defined Sediment Flux.
Silicate Limitation == \(\left[Si\right]_{min}^{phy}\), \(K_{lim-Si}^{phy}\)
Model Construction: Section 4.7.3.5.1.6
Used in a phytoplankton constituent model block to set silicate limitation parameters for the basic phytoplankton model. Specifying this command triggers silicate uptake.
\(\left[Si\right]_{min}^{phy}\) - Minimum Concentration of Silicate for Phytoplankton Uptake
Units Range Default mg/L Si (0, 0.1) 0.01 mmol/m\(^3\) Si (0.00, 3.57) 0.36 Science: Section I.5
Used to compute the silicate limitation function in the basic and advanced phytoplankton model. It is the minimum silicate concentration at which uptake of silicate by phytoplankton can occur
\(K_{lim-Si}^{phy}\) - Half Saturation Silicate Concentration for Phytoplankton Uptake of Silicate
Units Range Default mg/L Si (1, 10) 1 mmol/m\(^3\) Si (35.71, 357.14) 35.71 Science: Section I.5
Used to compute the silicate limitation function in the basic and advanced phytoplankton model. It is the concentration of silicate that when added to the specified minimum \(\left[Si\right]_{min}^{phy}\) sets the silicate limitation function to a value of 0.5. A value of zero for this parameter will set the silicate limitation function to always be 1
Silicate Min Max == \(\left[Si\right]_{min}^{Si}\), \(\left[Si\right]_{max}^{Si}\)
Model Construction: Section 4.7.3.2.1
Used in a silicate constituent model block to set minimum and maximum silicate concentrations.
\(\left[Si\right]_{min}^{Si}\) - Minimum Silicate Concentration
Units Range Default mg/L Si (0, 2.8) NA mmol/m\(^3\) Si (0, 100) NA Science: Appendix D
The minimum allowable silicate concentration. If the WQ Module detects a concentration less than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues. A value other than zero for this parameter would be unusual
\(\left[Si\right]_{max}^{Si}\) - Maximum Silicate Concentration
Units Range Default mg/L Si (0, 140) NA mmol/m\(^3\) Si (0, 5000) NA Science: Appendix D
The maximum allowable silicate concentration. If the WQ Module detects a concentration greater than this, then it will be reset to this value, and reported in the WQ Module log file. The root cause for requiring this reset should be addressed as this resetting is not intended to be a permanent solution and will cause mass conservation issues
Silicate Model == Si
Model Construction: Section 4.7.3.2, sec-ConModSiSi-4
Used to commence a silicate constituent model block via specification of a constituent model from the silicate constituent model class.
Simulation Class == DO | Inorganics | Organics
Model Construction: Section 4.5.1
Used in Part 1: Simulation controls of WQ Module control file to specify water quality simulation class. If not specified, “DO” is assumed and all associated “DO” class default parameters are applied.
For further information on each simulation class, refer to Section 3.1 (DO), Section 3.2 (Inorganics) and Section 3.3 (Organics).
Target Attached Fraction == \(f_{att}^{pth}\)
Model Construction: Section 4.6.3.2.2
Used in an (optional) pathogens constituent model block to set the target attached pathogen fraction.
\(f_{att}^{pth}\) - Target Pathogen Attachment Fraction
Default: 0
Units: NA
Range: (0, 1)
Science: Section N.3
The target fraction of attached pathogens. It is computed as the concentration of attached pathogens, divided by the sum of attached and alive pathogens for each computational.
Temperature Limitation
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Temperature Limitation == None
Model Construction: Section 4.7.3.5.1.1
Used in a phytoplankton constituent model block to turn off phytoplankton group temperature limitation.
For further information on the science of this command, refer to Section I.2.1.
Temperature Limitation == Standard, \(T_{std}^{phy}\), \(T_{opt}^{phy}\), \(T_{max}^{phy}\)
Model Construction: Section 4.7.3.5.1.1
Used in a phytoplankton constituent model block to set the standard phytoplankton group temperature limitation function.
For further information on the standard temperature limitation model, refer to Section I.2.2.
\(T_{std}^{phy}\) - Standard Temperature
Default: 10
Units: \(^o\)C
Range: (5, 25)
Science: Section I.2.2
Used to compute shape of temperature limitation function between T\(_{std}\) and T\(_{max}\). Below T\(_{std}\), the phytoplankton temperature limitation function is a simple Arrhenius relationship. Must always be less than the specified T\(_{max}\)
\(T_{opt}^{phy}\) - Optimum Temperature
Default: 20
Units: \(^o\)C
Range: (5, 25)
Science: Section I.2.2
Used to compute shape of temperature limitation function between \(T_{std}\) and T\(_{max}\). Must always be less than the specified T\(_{max}\)
\(T_{max}^{phy}\) - Maximum Temperature
Default: 30
Units: \(^o\)C
Range: (25, 35)
Science: Section I.2.2
Used to compute shape of temperature limitation function between T\(_{std}\) and T\(_{max}\). Above T\(_{max}\), the phytoplankton temperature limitation function is 0. Must always be greater than the specified T\(_{std}\) and T\(_{opt}\)
Uptake
Navigation row for this command. Argument syntax depends on the selected implementation. Refer to the implementation specific sections immediately below.
Uptake == \(R_{N-uptake}^{phy}\), \(R_{P-uptake}^{phy}\), \(X_{Si-C-con}^{phy}\)
Model Construction: Section 4.7.3.5.2.3
Used in a phytoplankton constituent model block to set nitrogen and phosphorus (and optionally silicate) uptake rates for the advanced phytoplankton constituent model only. The silicate internal concentration ratio is ignored if silicate uptake is not activated.
\(R_{N-uptake}^{phy}\) - Rate of Inorganic Nitrogen Uptake By Phytoplankton
Units Range Default mg N/mg Chl a/d (0.080, 2.704) 0 mmol N/mmol C/d (0.0025, 0.086) 0 Science: Section J.2.2
Used to compute the uptake of nitrogen during growth in the advanced phytoplankton constituent model only. It is the nitrogen uptake rate per unit of phytoplankton (per day) without any influence of temperature or nutrient limitation. The unit of phytoplankton is either mg (not \(\mu\)g) Chl a or mmol C, depending on the units system used
\(R_{P-uptake}^{phy}\) - Rate of Inorganic Phosphorus Uptake By Phytoplankton
Units Range Default mg P/mg Chl a/d (0.011, 0.374) 0 mmol P/mmol C/d (0.0002, 0.005) 0 Science: Section J.3.2
Used to compute the uptake of phosphorus during growth in the advanced phytoplankton constituent model only. It is the phosphorus uptake rate per unit of phytoplankton (per day) without any influence of temperature or nutrient limitation. The unit of phytoplankton is either mg (not \(\mu\)g) Chl a or mmol C, depending on the units system used
\(X_{Si-C-con}^{phy}\) - Constant Ratio of Internal Phytoplankton Silicate to Biomass
Units Range Default mg Si/mg Chl a (5.94, 11.89) 8.92 mmol Si/mmol C (0.09, 0.19) 0.14 Science: Section J.4
Used to compute the uptake of silicate during growth in the basic and advanced phytoplankton constituent models. It should be based on the extended Redfield ratio of 106:16:1:15 or C:N:P:Si (or Chla a equivalent). Note the units of mg of Chl a rather than \(\mu\)g
Uptake == \(X_{N-C-con}^{phy}\), \(X_{P-C-con}^{phy}\), \(X_{Si-C-con}^{phy}\)
Model Construction: Section 4.7.3.5.1.7
Used in a phytoplankton constituent model block to set constant nitrogen, phosphorus and optionally silicate to biomass ratios for the basic phytoplankton constituent model only.
\(X_{N-C-con}^{phy}\) - Constant Ratio of Internal Phytoplankton N to Biomass
Units Range Default mg N/mg Chl a (2.97, 6.54) 4.75 mmol N/mmol C (0.09, 0.21) 0.15 Science: Section J.2.1
Used to compute the uptake of nitrogen during growth in the basic phytoplankton constituent model only. It should be based on the Redfield ratio of 106:16:1 or C:N:P (or Chla a equivalent). Note the units of mg of Chl a rather than \(\mu\)g
\(X_{P-C-con}^{phy}\) - Constant Ratio of Internal Phytoplankton P to Biomass
Units Range Default mg P/mg Chl a (0.33, 0.99) 0.66 mmol P/mmol C (0.009, 0.014) 0.009 Science: Section J.3.1
Used to compute the uptake of phosphorus during growth in the basic phytoplankton constituent model only. It should be based on the Redfield ratio of 106:16:1 or C:N:P (or Chla a equivalent). Note the units of mg of Chl a rather than \(\mu\)g
\(X_{Si-C-con}^{phy}\) - Constant Ratio of Internal Phytoplankton Silicate to Biomass
Units Range Default mg Si/mg Chl a (5.94, 11.89) 8.92 mmol Si/mmol C (0.09, 0.19) 0.14 Science: Section J.4
Used to compute the uptake of silicate during growth in the basic and advanced phytoplankton constituent models. It should be based on the extended Redfield ratio of 106:16:1:15 or C:N:P:Si (or Chla a equivalent). Note the units of mg of Chl a rather than \(\mu\)g
UVA Inactivation == \(k_{uva}^{pth}\), \(c_{S_{uva}}^{pth}\), \(K_{DO_{uva}}^{pth}\)
Model Construction: Section 4.6.3.2.1
Used in an (optional) pathogens constituent model block to control the inactivation of pathogens due to UV-A light.
\(k_{uva}^{pth}\) - Pathogen Freshwater Inactivation Rate Coefficient for Exposure to UV-A Light
Default: 0
Units: m\(^2\) /MJ
Range: (0, 20)
Science: Section N.2
Inactivation effect of UV-A radiation. Excludes the effect of salinity and oxygen on inactivation
\(c_{S_{uva}}^{pth}\) - Coefficient That Enhances The Inactivation Effect of UV-A Light Under Saline Conditions
Default: 0
Units: m\(^2\) /MJ /psu
Range: (0, 0.007)
Science: Section N.2
Enhancement of inactivation of UV-A radiation due to salinity. A value of 0.0 will remove the effect of salinity
\(K_{DO_{uva}}^{pth}\) - Half Saturation Oxygen Concentration for UV-A Light Inactivation
Units Range Default mg/L O\(_2\) (0, 8) 4 (0, 250) 125 Science: Section N.2
The dissolved oxygen concentration for which the computed inactivation rate under UV-A light is half that which would occur without oxygen limitation. A value of 0.0 will remove the effect of oxygen
UVB Inactivation == \(k_{uvb}^{pth}\), \(c_{S_{uvb}}^{pth}\), \(K_{DO_{uvb}}^{pth}\)
Model Construction: Section 4.6.3.2.1
Used in an (optional) pathogens constituent model block to control the inactivation of pathogens due to UV-B light.
\(k_{uvb}^{pth}\) - Pathogen Freshwater Inactivation Rate Coefficient for Exposure to UV-B Light
Default: 0
Units: m\(^2\) /MJ
Range: (0, 100)
Science: Section N.2
Inactivation effect of UV-B radiation. Excludes the effect of salinity and oxygen on inactivation
\(c_{S_{uvb}}^{pth}\) - Coefficient That Enhances The Inactivation Effect of UV-B Light Under Saline Conditions
Default: 0
Units: m\(^2\) /MJ /psu
Range: (0, 0.007)
Science: Section N.2
Enhancement of inactivation of UV-B radiation due to salinity. A value of 0.0 will remove the effect of salinity
\(K_{DO_{uvb}}^{pth}\) - Half Saturation Oxygen Concentration for UV-B Light Inactivation
Units Range Default mg/L O\(_2\) (0, 8) 4 (0, 250) 125 Science: Section N.2
The dissolved oxygen concentration for which the computed inactivation rate under UV-B light is half that which would occur without oxygen limitation. A value of 0.0 will remove the effect of oxygen
Visible Inactivation == \(k_{vis}^{pth}\), \(c_{S_{vis}}^{pth}\), \(K_{DO_{vis}}^{pth}\)
Model Construction: Section 4.6.3.2.1
Used in an (optional) pathogens constituent model block to control the inactivation of pathogens due to visible light.
\(k_{vis}^{pth}\) - Pathogen Freshwater Inactivation Rate Coefficient for Exposure to Visible Light
Default: 0
Units: m\(^2\) /MJ
Range: (0, 1)
Science: Section N.2
Inactivation effect of visible radiation. Excludes the effect of salinity and oxygen on inactivation
\(c_{S_{vis}}^{pth}\) - Coefficient That Enhances The Inactivation Effect of Visible Light Under Saline Conditions
Default: 0
Units: m\(^2\) /MJ /psu
Range: (0, 0.007)
Science: Section N.2
Enhancement of inactivation of visible radiation due to salinity. A value of 0.0 will remove the effect of salinity
\(K_{DO_{vis}}^{pth}\) - Half Saturation Oxygen Concentration for Visible Light Inactivation
Units Range Default mg/L O\(_2\) (0, 8) 4 (0, 250) 125 Science: Section N.2
The dissolved oxygen concentration for which the computed inactivation rate under visible light is half that which would occur without oxygen limitation. A value of 0.0 will remove the effect of oxygen
Water Quality Control File == Water quality control file name.fvwq
Status: Required
Model Construction: Section 4.4.1
Name of WQ Module control file, with no path. If this file is not in the FV control file directory, then additionally use command Water Quality Model Directory.
Water Quality Model == TUFLOW
Status: Required
Model Construction: Section 4.4.1
Instruct TUFLOW FV to activate TUFLOW WQ Module.
Water Quality Model Directory == Water quality control file directory
Status: Optional
Model Construction: Section 4.4.1
Relative path from location of FV control file to the WQ Module control file directory, including last backslash, e.g. “..\(\backslash\)WQM\(\backslash\)”.
WQ dt == \(dt\)
Model Construction: Section 4.5.1
Used in Part 1: Simulation controls of WQ Module control file to set the timestep at which TUFLOW calls the WQ Module to undertake non-conservative water quality calculations, in seconds.
\(dt\) - Timestep
Default: 900
Units: seconds
Range: (UD, UD)
The timestep at which the WQ Module is called from the hydrodynamic model
WQ Equilibrium Substeps == \(fess\)
Model Construction: Section 4.5.1
Used in Part 1: Simulation controls of WQ Module control file to set the frequency of timesteps at which the WQ Module undertakes non-kinetic calculations, in number of water quality timesteps. This only applies to FRP adsorption.
\(fess\) - Non-Kinetic Equilibrium Substep Frequency
Default: 1
Units: Number of WQ Module timesteps
Range: (1, UD)
The frequency (in WQ timesteps) at which the WQ Module calls non-kinetic equilibrium calculations. for example, a value of 12 will call non-kinetic calculations every twelfth time the WQ module is called
WQ Units == mgL | mmm
Model Construction: Section 4.5.1
Used in Part 1: Simulation controls of WQ Module control file to set the units used for water quality simulation. Milligrams per litre and millimoles per cubic metre are “mgL” and “mmm”, respectively.
For further information on units, refer to Section 4.2.
