Appendix Q Parameters

Following are parameters that can be specified within the WQ Module via user commands.

Tips for use:

  • Use the search box to dynamically filter the table
  • Sort the filtered (or unfiltered) table by clicking the arrows at the top of each column
  • Use “s” on your keyboard to toggle the contents pane on and off to provide more screen width if needed
  • UD = user defined
  • N/A = not applicable
  • For each parameter, use the links in the final column to navigate to either:
    • A description of the corresponding control file command that includes the parameter (these links are all suffixed with ‘==’)
    • The section describing the relevant science and/or equations (these links are all called ‘science’)
  • Where numerical limits are provided for phytoplankton simulation parameters, the conversion bewteen \(\mu\)g/L Clh a and mmol/m\(^3\) or carbon is assumed to be 27.0 mg C/mg Chl a

Where parameter ranges are provided, these are not to be taken as fixed, but as indicative only. Some environmental settings may require parameterisation outside the ranges specified in this manual.

Table Q.1: WQM parameters
Parameter Notation Units Range Default Description Links
Sediment oxygen flux \(F_{sed}^{O_2}\) mg O\(_2\)/m\(^2\)/d

mmol O\(_2\)/m\(^2\)/d
(-6400, 0)

(-200, 0)
0

0
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 oxygen flux ==

science
Sediment half saturation oxygen concentration for oxygen flux \(K_{sed-O_2}^{O_2}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 oxygen benthic ==

science
Sediment oxygen flux temperature coefficient \(\theta_{sed}^{O_2}\) [-] (1, 1.1) 1 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 benthic ==

science
Minimum dissolved oxygen concentration \(\left[DO\right]_{min}^{O_2}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 0.5)

(0, 15.6)
NA

NA
The minimum allowable dissolved oxygen concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 oxygen min max ==

science
Maximum dissolved oxygen concentration \(\left[DO\right]_{max}^{O_2}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(6, 20)

(187.5, 625)
NA

NA
The maximum allowable dissolved oxygen concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 min max ==

science
Timestep \(dt\) seconds (UD, UD) 900 The timestep at which the WQM is called from the hydrodynamic model wq dt ==

Sediment silicate flux \(F_{sed}^{Si}\) mg Si/m\(^2\)/d

mmol Si/m\(^2\)/d
(0, 140)

(0, 5)
0

0
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 silicate flux ==

science
Sediment half saturation oxygen concentration for silicate flux \(K_{sed-O_2}^{Si}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 silicate benthic ==

science
Sediment silicate flux temperature coefficient \(\theta_{sed}^{Si}\) [-] (1, 1.1) 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 benthic ==

science
Minimum silicate concentration \(\left[Si\right]_{min}^{Si}\) mg/L Si

mmol/m\(^3\) Si
(0, 2.8)

(0, 100)
NA

NA
The minimum allowable silicate concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 silicate min max ==

science
Maximum silicate concentration \(\left[Si\right]_{max}^{Si}\) mg/L Si

mmol/m\(^3\) Si
(0, 140)

(0, 5000)
NA

NA
The maximum allowable silicate concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 min max ==

science
Sediment ammonium flux \(F_{sed}^{NH_4}\) mg NH\(_4\)-N/m\(^2\)/d

mmol NH\(_4\)-N/m\(^2\)/d
(0, 140)

(0, 10)
0

0
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 ammonium flux ==

science
Sediment half saturation oxygen concentration for ammonium flux \(K_{sed-O_2}^{NH_4}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 ammonium benthic ==

science
Sediment ammonium flux temperature coefficient \(\theta_{sed}^{NH_4}\) [-] (1, 1.1) 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 benthic ==

science
Minimum ammonium concentration \(\left[NH_4\right]_{min}^{NH_4}\) mg/L NH\(_4\)-N

mmol/m\(^3\) NH\(_4\)-N
(0, 0.098)

(0, 7)
NA

NA
The minimum allowable ammonium concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 ammonium min max ==

science
Maximum ammonium concentration \(\left[NH_4\right]_{max}^{NH_4}\) mg/L NH\(_4\)-N

mmol/m\(^3\) NH\(_4\)-N
(0, 98)

(0, 7000)
NA

NA
The maximum allowable ammonium concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 min max ==

science
Sediment nitrate flux \(F_{sed}^{NO_3}\) mg NO\(_3\)-N/m\(^2\)/d

mmol NO\(_3\)-N/m\(^2\)/d
(0, 140)

(0, 10)
0

0
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 nitrate flux ==

science
Sediment half saturation oxygen concentration for nitrate flux \(K_{sed-O_2}^{NO_3}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 nitrate benthic ==

science
Sediment nitrate flux temperature coefficient \(\theta_{sed}^{NO_3}\) [-] (1, 1.1) 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 benthic ==

science
Minimum nitrate concentration \(\left[NO_3\right]_{min}^{NO_3}\) mg/L NO\(_3\)-N

mmol/m\(^3\) NO\(_3\)-N
(0, 0.098)

(0, 7)
NA

NA
The minimum allowable nitrate concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 nitrate min max ==

science
Maximum nitrate concentration \(\left[NO_3\right]_{max}^{NO_3}\) mg/L NO\(_3\)-N

mmol/m\(^3\) NO\(_3\)-N
(0, 98)

(0, 7000)
NA

NA
The maximum allowable nitrate concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 nitrate min max ==

science
Nitrification rate \(R_{nitrif}^{NH_4}\) /d (0, 1) 0

0
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 nitrification ==

science
Half saturation oxygen concentration for nitrification \(K_{nitrif-O_2}^{NH_4}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
The dissolved oxygen concentration for which the computed nitrification rate is half the user specified rate, at 20\(^o\)C nitrification ==

science
Nitrification temperature coefficient \(\theta_{nitrif}^{NH_4}\) [-] (1, 1.1) 1 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 nitrification ==

science
Denitrification rate \(R_{denit}^{NO_3}\) /d (0, 0.5) 0

0
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 denitrification ==

science
Half saturation oxygen concentration for denitrification \(K_{denit-O2-MM}^{NO_3}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 denitrification ==

science
Normalising oxygen concentration for denitrification \(K_{denit-O2-exp}^{NO_3}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 denitrification ==

science
Denitrification temperature coefficient \(\theta_{denit}^{NO_3}\) [-] (1, 1.1) 1 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 ==

science
Half saturation nitrate concentration for denitrification \(K_{denit-NO3}^{NO_3}\) mg/L NO\(_3\)-N

mmol/m\(^3\) NO\(_3\)-N
(0, 5)

(0, 357.1)
0.07

5
The nitrate concentration for which the computed denitrification rate is half the user specified rate, at 20\(^o\)C and with no influence of ambient dissolved oxygen concentration. This is not user specifiable and is set to the default value denitrification ==

science
Denitrification model Michaelis Menten;exponential 0 (, ) 0 The model used to simulate denitrification denitrification ==

science
Wet atmospheric inorganic nitrogen deposition \(\left[{TN}\right]_{rain}\) mg/L N

mmol/m\(^3\) N
(0, 98)

(0, 7000)
0

0
The concentration of total inorganic nitrogen in rainfall. This is the sum of ammonium and nitrate N and is applied as a multiplicative factor to rainfall depth to compute a mass flux atmospheric deposition ==

science
Dry atmospheric inorganic nitrogen deposition \(R_{atm-dry}^{TN}\) mg/m\(^2\)/d N

mmol/m\(^2\)/d N
(0, 98)

(0, 7000)
0

0
The rate of atmopsheric fallout of dry inorganic nitrogen. This is the sum of ammonium and nitrate N and is applied as a spatial and temporal constant value to compute a mass flux atmospheric deposition ==

science
Fraction of atmospheric nitrogen deposition that is nitrate \(f_{TN}^{NO_3}\) [-] (0, 1) 0 The fraction of N that is nitrate in atmospheric deposition. The same factor is applied to both wet and dry deposition of N. A value of 1 (0) will set wet and dry deposition to be purely nitrate (ammonium) atmospheric deposition ==

science
Minimum FRP concentration \(\left[FRP\right]_{min}^{FRP}\) mg/L PO\(_4\)-P

mmol/m\(^3\) PO\(_4\)-P
(0, 0.01)

(0, 0.32)
NA

NA
The minimum allowable FRP concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 FRP min max ==

science
Maximum FRP concentration \(\left[FRP\right]_{max}^{FRP}\) mg/L PO\(_4\)-P

mmol/m\(^3\) PO\(_4\)-P
(0, 10)

(0, 320)
NA

NA
The maximum allowable FRP concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 FRP min max ==

science
Sediment FRP flux \(F_{sed}^{FRP}\) mg FRP-P/m\(^2\)/d

mmol FRP-P/m\(^2\)/d
(0, 155)

(0, 5)
0

0
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 FRP flux ==

science
Sediment half saturation oxygen concentration for FRP flux \(K_{sed-O_2}^{FRP}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 FRP benthic ==

science
Sediment FRP flux temperature coefficient \(\theta_{sed}^{FRP}\) [-] (1, 1.1) 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 benthic ==

science
Wet atmospheric FRP deposition \(\left[{FRP}\right]_{rain}\) mg/L P

mmol/m\(^3\) P
(0, 10)

(0, 320)
0

0
The concentration of FRP in rainfall. This is only FRP P and is applied as a multiplicative factor to rainfall depth to compute a mass flux atmospheric deposition ==

science
Dry atmospheric FRP deposition \(R_{atm-dry}^{FRPads}\) mg/m\(^2\)/d P

mmol/m\(^2\)/d P
(0, 10)

(0, 320)
0

0
The rate of atmopsheric fallout of adsorbed FRP. This is only applied to adsorbed FRP P. If adsorbed FRP is not simulated then this value is ignored. If used, it is applied as a spatial and temporal constant value to compute a mass flux atmospheric deposition ==

science
Minimum adsorbed FRP concentration \(\left[FRPads\right]_{min}^{FRPads}\) mg/L PO\(_4\)-P

mmol/m\(^3\) PO\(_4\)-P
(0, 0.01)

(0, 0.32)
NA

NA
The minimum allowable adsorbed FRP concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 FRPads min max ==

science
Maximum adsorbed FRP concentration \(\left[FRPads\right]_{max}^{FRPads}\) mg/L PO\(_4\)-P

mmol/m\(^3\) PO\(_4\)-P
(0, 10)

(0, 320)
NA

NA
The maximum allowable adsorbed FRP concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 ==

science
Linear FRP sorption partitioning coefficient \(K_{ads-L}^{FRP}\) L/mg (0.01, 0.3) 0.01 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 ==

science
Quadratic FRP sorption partitioning coefficient \(K_{ads-Q}^{FRP}\) L/mg (0.6, 0.8) 0.7 The ratio of adsorption and desorption rate coefficients for phosphorus adsorption ==

science
Maximum adsorption capacity of phosphorus \(Q^{FRP}_{max}\) mg FRP-P/mg TSS (0.005, 0.006) 0.0051 The maximum mass of P that can be adsorbed onto ambient suspended sediment, per unit mass of suspended sediment adsorption ==

science
Maximum adsorption particle size \(D50_{ads-max}^{FRP}\) m (, ) 0 Not yet used. Will be activated in future releases of the WQM

Minimum phyto concentration \(\left[PHY\right]_{min}^{PHY}\) \(\mu\)g/L Chl a

mmol/m\(^3\) C
(0.01, 0.1)

(0.023, 0.225)
0.01

0.0225
The minimum allowable group phytoplankton concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 minuimum 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 oncentration for subsequent timesteps min max ==

science
Maximum phyto concentration \(\left[PHY\right]_{max}^{PHY}\) \(\mu\)g/L Chl a

mmol/m\(^3\) C
(0.01, 50)

(0.0025, 112.5)
NA

NA
The maximum allowable group phytoplankton concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 min max ==

science
Standard temperature \(T_{std}^{phy}\) \(^o\)C (5, 25) 10 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} temperature limitation ==

science
Optimum temperature \(T_{opt}^{phy}\) \(^o\)C (5, 25) 20 Used to compute shape of temperature limitation function between T\(_{std}\) and T\(_{max}\). Must always be less than the specified T$_{max} temperature limitation ==

science
Maximum temperature \(T_{max}^{phy}\) \(^o\)C (25, 35) 30 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}$ temperature limitation ==

science
Optimum freshwater salinity \(S_{opt-fresh}^{phy}\) g/L (0, 45) 0 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 salinity limitation ==

science
Maximum freshwater salinity \(S_{max-fresh}^{phy}\) g/L (0, 45) 5 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 \(L_{max-fresh}^{phy}\) salinity limitation ==

science
Limitation function at maximum freshwater salinity \(L_{max-fresh}^{phy}\) [-] (0, -) 0 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 ==

science
Optimum marine salinity \(S_{opt-marine}^{phy}\) g/L (0, 45) 0 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 salinity limitation ==

science
Limitation function at zero marine salinity \(L_{zero-marine}^{phy}\) [-] (0, -) 0 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 ==

science
Optimum mixed salinity \(S_{opt-mix}^{phy}\) g/L (0, 45) 0 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 salinity limitation ==

science
Maximum mixed salinity \(S_{max-mix}^{phy}\) g/L (0, 45) 5 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 salinity limitation ==

science
Limitation function at zero and (\(S_{opt-mix}^{phy} + S_{max-mix}^{phy}\)) mixed salinity \(L_{zero-mix}^{phy}\) [-] (0, -) 0 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 ==

science
Optimum estuarine salinity \(S_{opt-est}^{phy}\) g/L (0, 45) 0 Used to compute the estuarine salinity limitation function. It is the salinity at which the estuarine salinity limitation function has a value of 1 salinity limitation ==

science
Maximum estuarine salinity \(S_{max-est}^{phy}\) g/L (0, 45) 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 salinity limitation ==

science
Power coefficient for estuarine salinity limitation \(P_{est}^{phy}\) [-] (0, 5) 0 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 ==

science
Minimum concentration of N for phytoplankton uptake \(\left[N\right]_{min}^{phy}\) mg/L N

mmol/m\(^3\) N
(0, 0.1)

(0.00, 7.14)
0.01

0.71
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 nitrogen limitation ==

science
Half saturation N concentration for phytoplankton uptake of N \(K_{lim-N}^{phy}\) mg/L N

mmol/m\(^3\) N
(1, 5)

(71.4, 357.14)
1

71.43
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 ==

science
Minimum ratio of internal phytoplankton N to biomass \(X_{N-C-min}^{phy}\) mg N/mg Chl a

mmol N/mmol C
(2.97, 4.75)

(0.09, 0.15)
2.97

0.09
Used to compute the nitrogen limitation function in the advanced phytoplankton model if internal nitrogen stores are not exhausted. 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 nitrogen limitation ==

science
Maximum ratio of internal phytoplankton N to biomass \(X_{N-C-max}^{phy}\) mg N/mg Chl a

mmol N/mmol C
(4.75, 6.54)

(0.15, 0.21)
6.54

0.21
Used to compute the nitrogen limitation function in the advanced phytoplankton model if internal nitrogen stores are not exhausted. 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 nitrogen limitation ==

science
Minimum concentration of P for phytoplankton uptake \(\left[P\right]_{min}^{phy}\) mg/L P

mmol/m\(^3\) P
(0, 0.1)

(0.0, 3.23)
0.001

0.03
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 phosphorus limitation ==

science
Half saturation P concentration for phytoplankton uptake of P \(K_{lim-P}^{phy}\) mg/L P

mmol/m\(^3\) P
(0.1, 0.5)

(3.23, 16.13)
0.1

3.23
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 ==

science
Minimum ratio of internal phytoplankton P to biomass \(X_{P-C-min}^{phy}\) mg P/mg Chl a

mmol P/mmol C
(0.33, 0.66)

(0.005, 0.009)
0.33

0.005
Used to compute the phosphorus limitation function in the advanced phytoplankton model if internal phosphorus stores are not exhausted. 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 phosphorus limitation ==

science
Maximum ratio of internal phytoplankton P to biomass \(X_{P-C-max}^{phy}\) mg P/mg Chl a

mmol P/mmol C
(0.66, 0.99)

(0.009, 0.014)
0.99

0.014
Used to compute the phosphorus limitation function in the advanced phytoplankton model if internal phosphorus stores are not exhausted. 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 phosphorus limitation ==

science
Minimum concentration of silicate for phytoplankton uptake \(\left[Si\right]_{min}^{phy}\) mg/L Si

mmol/m\(^3\) Si
(0, 0.1)

(0.00, 3.57)
0.01

0.36
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 silicate limitation ==

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Half saturation silicate concentration for phytoplankton uptake of silicate \(K_{lim-Si}^{phy}\) mg/L Si

mmol/m\(^3\) Si
(1, 10)

(35.71, 357.14)
1

35.71
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 limitation ==

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Half saturation constant for basic model light growth limitation \(I_{K-bas}\) W/m\(^2\) (1, 1500) 20 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 ==

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Half saturation constant for monod model light growth limitation \(I_{K-mon}\) W/m\(^2\) (1, 1500) 20 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 ==

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Saturating light intensity for the steele model light growth limitation \(I_{S-ste}\) W/m\(^2\) (1, 1500) 20 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 ==

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Half saturation constant for webb model light growth limitation \(I_{K-web}\) W/m\(^2\) (1, 1500) 20 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 light limitation ==

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Half saturation constant for jassby model light growth limitation \(I_{K-jas}\) W/m\(^2\) (1, 1500) 20 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 ==

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Half saturation constant for chalker model light growth limitation \(I_{K-cha}\) W/m\(^2\) (1, 1500) 20 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 ==

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Saturating light intensity for the klepper model light growth limitation \(I_{S-kle}\) W/m\(^2\) (1, 1500) 20 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 ==

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Saturating light intensity for the integrated model light growth limitation \(I_{S-int}\) W/m\(^2\) (1, 1500) 20 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 ==

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Constant ratio of internal phytoplankton N to biomass \(X_{N-C-con}^{phy}\) mg N/mg Chl a

mmol N/mmol C
(2.97, 6.54)

(0.09, 0.21)
4.75

0.15
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 uptake ==

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Constant ratio of internal phytoplankton P to biomass \(X_{P-C-con}^{phy}\) mg P/mg Chl a

mmol P/mmol C
(0.33, 0.99)

(0.009, 0.014)
0.66

0.009
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 uptake ==

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Constant ratio of internal phytoplankton silicate to biomass \(X_{Si-C-con}^{phy}\) mg Si/mg Chl a

mmol Si/mmol C
(5.94, 11.89)

(0.09, 0.19)
8.92

0.14
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 ==

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Rate of inorganic nitrogen uptake by phytoplankton \(R_{N-uptake}^{phy}\) mg N/mg Chl a/d

mmol N/mmol C/d
(0.080, 2.704)

(0.0025, 0.086)
0

0
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 uptake ==

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Rate of inorganic phosphorus uptake by phytoplankton \(R_{P-uptake}^{phy}\) mg P/mg Chl a/d

mmol P/mmol C/d
(0.011, 0.374)

(0.0002, 0.005)
0

0
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 uptake ==

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Constant rate of phytoplankton settling \(V_{settle}^{phy}\) m/d (0, 50) 0 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 ==

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Stokes settling light half saturation light intensity \(I_{K-sto}\) W/m\(^2\) (0, 1500) 20 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 ==

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Motile settling velocity \(V_{mot}^{phy}\) m/d (0, 50) 0 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 settling ==

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Motile settling light half saturation light intensity \(I_{K-mot}\) W/m\(^2\) (0, 1500) 20 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 ==

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Carbon to chlorophyll a ratio \(X_{cc}^{phy}\) mg carbon / mg chlorophyll a (20, 40) 27 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 \(\mu\)g. This value is constant for a given phytoplankton group carbon chla ratio ==

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Nitrogen fixing rate \(R_{nfix}^{N_2}\) mg N / mg Chl a / d

mmol N / mmol C /d
(0, 5)

(0, 0.16)
0

0
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 nitrogen fixing ==

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Penalty function of nitrogen fixing on primary productivity \(f_{nfix}^{phy}\) [-] (0, 1) 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 fixing ==

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Phytoplankton primary productivity rate \(R_{prod}^{phy}\) /d (0, 3.5) 0 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 primary productivity ==

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Phytoplankton primary productivity temperature coefficient \(\theta_{prod}^{phy}\) [-] (1, 1.1) 1 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 primary productivity ==

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Phytoplankton respiration rate \(R_{resp}^{phy}\) /d (0, 0.1) 0 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 respiration ==

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Phytoplankton respiration temperature coefficient \(\theta_{resp}^{phy}\) [-] (1, 1.1) 1 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 respiration ==

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Fraction of phytoplankton respiration that is true respiration \(f_{true-resp}^{phy}\) [-] (0, 1) 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 respiration ==

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Fraction of phytoplanton loss that is excretion \(f_{excr-loss}^{phy}\) [-] (0, 1) 0 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. respiration ==

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Fraction of primary production lost to exudation \(f_{exud}^{phy}\) [-] (0, 1) 0 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 respiration ==

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Phytoplankton specific shading coefficient \(Ke^{phy}\) /(\(\mu\)g Chl a/L)/m

/(mmol C/m\(^3\))/m
(0, 0.0225)

(0, 0.01)
0

0
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. This parameter is used in all light limitation == commands, but only the reference to the basic model is included in this table. Use the navigation in the commands Appendix to see linkages with other light limitation commands light limitation ==

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Minimum POC concentration \(\left[POC\right]_{min}^{POC}\) mg/L C

mmol/m\(^3\) C
(0, 0.1)

(0, 8.33)
NA

NA
The minimum allowable labile particulate organic carbon concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 carbon min max ==

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Maximum POC concentration \(\left[POC\right]_{max}^{POC}\) mg/L C

mmol/m\(^3\) C
(0, 100)

(0, 8333)
NA

NA
The maximum allowable labile particulate organic carbon concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 carbon min max ==

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Minimum DOC concentration \(\left[DOC\right]_{min}^{DOC}\) mg/L C

mmol/m\(^3\) C
(0, 0.1)

(0, 8.33)
NA

NA
The minimum allowable labile dissolved organic carbon concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 carbon min max ==

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Maximum DOC concentration \(\left[DOC\right]_{max}^{DOC}\) mg/L C

mmol/m\(^3\) C
(0, 100)

(0, 8333)
NA

NA
The maximum allowable labile dissolved organic carbon concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 carbon min max ==

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Minimum PON concentration \(\left[PON\right]_{min}^{PON}\) mg/L N

mmol/m\(^3\) N
(0, 0.1)

(0, 7.14)
NA

NA
The minimum allowable labile particulate organic nitrogen concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 nitrogen min max ==

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Maximum PON concentration \(\left[PON\right]_{max}^{PON}\) mg/L N

mmol/m\(^3\) N
(0, 100)

(0, 7143)
NA

NA
The maximum allowable labile particulate organic nitrogen concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 nitrogen min max ==

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Minimum DON concentration \(\left[DON\right]_{min}^{DON}\) mg/L N

mmol/m\(^3\) N
(0, 0.1)

(0, 7.14)
NA

NA
The minimum allowable labile dissolved organic nitrogen concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 nitrogen min max ==

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Maximum DON concentration \(\left[DON\right]_{max}^{DON}\) mg/L N

mmol/m\(^3\) N
(0, 100)

(0, 7143)
NA

NA
The maximum allowable labile dissolved organic nitrogen concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 nitrogen min max ==

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Minimum POP concentration \(\left[POP\right]_{min}^{POP}\) mg/L P

mmol/m\(^3\) P
(0, 0.01)

(0, 0.32)
NA

NA
The minimum allowable labile particulate organic phosphorus concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 phosphorus min max ==

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Maximum POP concentration \(\left[POP\right]_{max}^{POP}\) mg/L P

mmol/m\(^3\) P
(0, 10)

(0, 323)
NA

NA
The maximum allowable labile particulate organic phosphorus concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 phosphorus min max ==

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Minimum DOP concentration \(\left[DOP\right]_{min}^{DOP}\) mg/L P

mmol/m\(^3\) P
(0, 0.01)

(0, 0.32)
NA

NA
The minimum allowable labile dissolved organic phosphorus concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 phosphorus min max ==

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Maximum DOP concentration \(\left[DOP\right]_{max}^{DOP}\) mg/L P

mmol/m\(^3\) P
(0, 10)

(0, 323)
NA

NA
The maximum allowable labile dissolved organic phosphorus concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 phosphorus min max ==

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Sediment DOC flux \(F_{sed}^{DOC}\) mg C/m\(^2\)/d

mmol C/m\(^2\)/d
(0, 120)

(0, 10)
0

0
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 DOC flux ==

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Sediment DON flux \(F_{sed}^{DON}\) mg N/m\(^2\)/d

mmol N/m\(^2\)/d
(0, 21.126)

(0, 1.509)
0

0
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 DON flux ==

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Sediment DOP flux \(F_{sed}^{DOP}\) mg P/m\(^2\)/d

mmol P/m\(^2\)/d
(0, 2.914)

(0, 0.094)
0

0
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 DOP flux ==

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Sediment half saturation oxygen concentration for DOM flux \(K_{sed-O_2}^{DOM}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 organics benthic ==

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Sediment DOM flux temperature coefficient \(\theta_{sed}^{DOM}\) [-] (1, 1.1) 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 organics benthic ==

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POC hydrolysis rate \(R_{hyd}^{POC}\) /d (0, 0.1) 0

0
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 hydrolysis ==

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PON hydrolysis rate \(R_{hyd}^{PON}\) /d (0, 0.015) 0

0
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 hydrolysis ==

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POP hydrolysis rate \(R_{hyd}^{POP}\) /d (0, 0.0009) 0

0
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 hydrolysis ==

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Half saturation oxygen concentration for POM hydrolysis \(K_{hyd-O_2}^{POM}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 hydrolysis ==

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POM hydrolysis temperature coefficient \(\theta_{hyd}^{POM}\) [-] (1, 1.1) 1 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 hydrolysis ==

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DOM mineralisation rate \(R_{miner}^{DOM}\) /d (0, 0.1) 0

0
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) mineralisation ==

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Half saturation oxygen concentration for DOM mineralisation \(K_{miner-O_2}^{DOM}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 4.8)

(0, 150)
4

125
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 mineralisation ==

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DOM mineralisation temperature coefficient \(\theta_{miner}^{DOM}\) [-] (1, 1.1) 1 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 mineralisation ==

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Anaerobic mineralisation multiplier \(f_{an}\) [-] (0, 1) 0 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 mineralisation ==

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Half saturation nitrate concentration for nitrate consumption via anaerobic mineralisation of dissolved organic carbon \(K_{miner-NO_3}^{NO_3}\) mg/L NO\(_3\)-N

mmol/m\(^3\) NO\(_3\)-N
(0, 2.1)

(0, 150)
1.75

125
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 mineralisation ==

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POM specific shading coefficient \(Ke^{POM}\) /(mg POC/L)/m

/(mmol POC/m\(^3\))/m
(0, 8.33)

(0, 0.1)
0

0
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 self shading ==

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DOM specific shading coefficient \(Ke^{DOM}\) /(mg DOC/L)/m

/(mmol DOC/m\(^3\))/m
(0, 8.33)

(0, 0.1)
0

0
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 self shading ==

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RPOM breakdown rate \(R_{bdn}^{RPOM}\) /d (0, 0.1) 0

0
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 ref breakdown ==

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Ratio of N to C in refractory particulate organic matter \(X_N^{RPOM}\) [-] (0.094, 0.19) 0.15 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 ref breakdown ==

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Ratio of P to C in refractory particulate organic matter \(X_P^{RPOM}\) [-] (0.00094, 0.019) 0.0094 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 breakdown ==

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Minimum RPOM concentration \(\left[RPOM\right]_{min}^{RPOM}\) mg/L C

mmol/m\(^3\) C
(0, 0.1)

(0, 8.33)
NA

NA
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 WQM. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 ref carbon min max ==

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Maximum RPOM concentration \(\left[RPOM\right]_{max}^{RPOM}\) mg/L C

mmol/m\(^3\) C
(0, 100)

(0, 8333)
NA

NA
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 WQM. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 carbon min max ==

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Minimum RDOC concentration \(\left[RDOC\right]_{min}^{RDOC}\) mg/L C

mmol/m\(^3\) C
(0, 0.1)

(0, 8.33)
NA

NA
The minimum allowable refractory dissolved organic carbon concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 ref carbon min max ==

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Maximum RDOC concentration \(\left[RDOC\right]_{max}^{RDOC}\) mg/L C

mmol/m\(^3\) C
(0, 100)

(0, 8333)
NA

NA
The maximum allowable refractory dissolved organic carbon concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 carbon min max ==

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Minimum RDON concentration \(\left[RDON\right]_{min}^{RDON}\) mg/L N

mmol/m\(^3\) N
(0, 0.1)

(0, 7.14)
NA

NA
The minimum allowable refractory dissolved organic nitrogen concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 ref nitrogen min max ==

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Maximum RDON concentration \(\left[RDON\right]_{max}^{RDON}\) mg/L N

mmol/m\(^3\) N
(0, 100)

(0, 7143)
NA

NA
The maximum allowable refractory dissolved organic nitrogen concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 ==

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Minimum RDOP concentration \(\left[RDOP\right]_{min}^{RDOP}\) mg/L P

mmol/m\(^3\) P
(0, 0.01)

(0, 0.32)
NA

NA
The minimum allowable refractory dissolved organic phosphorus concentration. If the WQM detects a concentration less than this, then it will be reset to this value, and reported in the WQM 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 ref phosphorus min max ==

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Maximum RDOP concentration \(\left[RDOP\right]_{max}^{RDOP}\) mg/L P

mmol/m\(^3\) P
(0, 10)

(0, 323)
NA

NA
The maximum allowable refractory dissolved organic phosphorus concentration. If the WQM detects a concentration greater than this, then it will be reset to this value, and reported in the WQM 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 ==

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RDOM activation rate \(R_{act}^{RDOM}\) /d (0, 0.1) 0

0
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 activation ==

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RPOM specific shading coefficient \(Ke^{RPOM}\) /(mg RPOM/L)/m

/(mmol RPOM/m\(^3\))/m
(0, 8.33)

(0, 0.1)
0

0
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 ref self shading ==

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CDOM multiplier \(R_{CDOM}^{RDOM}\) [-] (0, 2) 0 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 self shading ==

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RDOM photolysis fraction \(f_{photo}^{RDOM}\) [-] (0, 1) 0 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 photolysis ==

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Anaerobic oxidation of ammonium rate \(k_{anmx}^{N_2}\) mg N/L/d

mmol N/m\(^3\)/d
(0, 0.5)

(0, 0.036)
0

0
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 anaerobic oxidation of ammonium ==

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Half saturation ammonium concentration for anammox \(K_{anmx-NH_4}^{N_2}\) mg/L NH\(_4\)-N

mmol/m\(^3\) NH\(_4\)-N
(0, 10)

(0, 714)
1.75

125
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 anaerobic oxidation of ammonium ==

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Half saturation nitrite concentration for anammox \(K_{anmx-NO_2}^{N_2}\) mg/L NO\(_2\)-N

mmol/m\(^3\) NO\(_2\)-N
(0, 10)

(0, 714)
1.75

125
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 anaerobic oxidation of ammonium ==

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Dissimilatory reduction of nitrate to ammonium rate \(R_{DRNA}^{NO_3}\) /d (0, 0.05) 0

0
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 diss nitrate reduction to ammonium ==

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Half saturation oxygen concentration for DRNA \(K_{DRNA-O_2}^{NO_3}\) mg/L O\(_2\)

mmol/m\(^3\) O\(_2\)
(0, 10)

(0, 312.5)
4

125
The oxygen concentration for which the computed reduction of nitrate to ammonium would be half the corresponding rate. Cannot be varied spatially diss nitrate reduction to ammonium ==

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Constant rate of adsorbed FRP settling \(V_{settle}^{FRP}\) m/d (0, 50) 0 The constant settling velocity applied to adsorbed FRP. Future releases of the WQM will dynamically link this settling velocity to calculations made by the TUFLOW FV STM. A negative value is a downwards velocity settling ==

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Labile organic matter stokes diameter \(d_{lorg}\) m (1 e-09, 1 e -06) 1 e-09 The conceptual diameter of labile particulate organic matter applied in stokes calculations of settling velocity. Future releases of the WQM will dynamically link settling velocity to calculations made by the TUFLOW FV STM settling ==

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Labile organic matter stokes density \(\rho_{lorg}\) kg/m\(^3\) (1000, 3000) 2000 The density of labile particulate organic matter applied in stokes calculations of settling velocity. Future releases of the WQM will dynamically link settling velocity to calculations made by the TUFLOW FV STM settling ==

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Labile organic matter settling velocity \(V_{settle}^{lorg}\) m/d (0, 50) 0 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 WQM will dynamically link settling velocity to calculations made by the TUFLOW FV STM settling ==

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Refractory organic matter stokes diameter \(d_{rorg}\) m (1 e-09, 1 e -06) 1 e-09 The conceptual diameter of refractory particulate organic matter applied in stokes calculations of settling velocity. Future releases of the WQM will dynamically link settling velocity to calculations made by the TUFLOW FV STM ref settling ==

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Refractory organic matter stokes density \(\rho_{rorg}\) kg/m\(^3\) (1000, 3000) 2000 The density of refractory particulate organic matter applied in stokes calculations of settling velocity. Future releases of the WQM will dynamically link settling velocity to calculations made by the TUFLOW FV STM ref settling ==

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Refractory organic matter settling velocity \(V_{settle}^{rorg}\) m/d (0, 50) 0 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 WQM will dynamically link settling velocity to calculations made by the TUFLOW FV STM ref settling ==

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Minimum water quality calculation depth \(d_{min-wq}\) m (0, UD) 0.01 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 cell water quality depth ==

Disable water quality calculation \(B_{disable-wq}\) [-] (0, 1) 0 A Boolean flag to disable (1) or enable (0) water quality calculations. The flag is specified in the TUFLOW FV control file disable water quality model ==

Non-kinetic equilibrium substep frequency \(fess\) number of wqm timesteps (1, UD) 1 The frequency (in WQ timesteps) at which the WQM 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 equilibrium substeps ==