# Appendix B Commands

All WQ Module commands and descriptions follow. This page has deliberately been set to be wider than the main document so as to accommodate the detail contained within the table. Tips provided in the manual’s introduction for interacting with the table should be reviewed, especially with regard to searching and navigation. Other tips for use specific to this table include:

• Commands are coloured and although they show as underlined on mouse hover, these are not hyperlinked
• Corresponding arguments (presented as their symbols) are coloured and listed in the required order within angled parentheses following each command ==.
• Each argument is a hyperlink to its description in the relevant Appendix. This description then includes hyperlinks to the relevant science and command syntax (Section 4). This allows easy navigation between command, parameter and scientific information
• The final text of each description is ‘Simulation construction section …’ and is a link to the relevant part of Section 4 where the command syntax is presented in context. More parameter details and descriptions are subsequently available via further hyperlinks included in the construction section
• Commands that have multiple possible combinations of more than one argument are presented as separate table entries. These related entries (that share the same command) are easily navigable by use of the links provided in the right hand table column, headed “Links”
Table B.1: WQM Commands
oxygen flux ==
$$\langle$$$$F_{sed}^{O_2}$$$$\rangle$$
Used in a materials block to control the sediment flux rate of oxygen. Simulation construction section 4.6.4. $$\text{ }$$
oxygen benthic ==
$$\langle$$$$K_{sed-O_2}^{O_2}$$,$$\theta_{sed}^{O_2}$$$$\rangle$$
Used in an oxygen constituent model block to control the response of benthic oxygen flux to temperature and oxygen concentration. Simulation construction section 4.6.3.1.1. $$\text{ }$$
oxygen model ==
$$\langle$$O2$$\rangle$$
Used to commence an oxygen constituent model block via specification of a constituent model from the oxygen constituent model class. Simulation construction section 4.6.3.1. $$\text{ }$$
oxygen min max ==
$$\langle$$$$\left[DO\right]_{min}^{O_2}$$,$$\left[DO\right]_{max}^{O_2}$$$$\rangle$$
Used in an oxygen constituent model block to set minimum and maximum dissolved oxygen concentrations. Simulation construction section 4.6.3.1.1. $$\text{ }$$
simulation class ==
$$\langle$$DO;inorganics;organics$$\rangle$$
Used in Part 1: Simulation controls of WQM control file to specify water quality simulation class. If not specified, “DO” is assumed and all associated “DO” class default parameters are applied. Simulation construction section 4.5.1. $$\text{ }$$
end oxygen model Used to terminate an oxygen constituent model block. Must follow an oxygen model == command. Simulation construction section 4.6.3.1.1. $$\text{ }$$
wq units ==
$$\langle$$mgl;mmm$$\rangle$$
Used in Part 1: Simulation controls of WQM control file to set the units used for water quality simulation. Milligrams per litre and millimoles per cubic metre are “mgl” and “mmm”, respectively. Simulation construction section 4.5.1. $$\text{ }$$
wq dt ==
$$\langle$$$$dt$$$$\rangle$$
Used in Part 1: Simulation controls of WQM control file to set the timestep at which TUFLOW calls the WQM to undertake non-conservative water quality calculations, in seconds. Simulation construction section 4.5.1. $$\text{ }$$
silicate flux ==
$$\langle$$$$F_{sed}^{Si}$$$$\rangle$$
Used in a materials block to control the sediment flux rate of silicate. Simulation construction section 4.7.4. $$\text{ }$$
silicate benthic ==
$$\langle$$$$K_{sed-O_2}^{Si}$$,$$\theta_{sed}^{Si}$$$$\rangle$$
Used in a silicate constituent model block to control the response of benthic silicate flux to temperature and oxygen concentration. Simulation construction section 4.7.3.2.1. $$\text{ }$$
silicate min max ==
$$\langle$$$$\left[Si\right]_{min}^{Si}$$,$$\left[Si\right]_{max}^{Si}$$$$\rangle$$
Used in a silicate constituent model block to set minimum and maximum silicate concentrations. Simulation construction section 4.7.3.2.1. $$\text{ }$$
silicate model ==
$$\langle$$Si$$\rangle$$
Used to commence a silicate constituent model block via specification of a constituent model from the silicate constituent model class. Simulation construction section 4.7.3.2. $$\text{ }$$
oxygen ==
$$\langle$$on;off$$\rangle$$
Used in a silicate constituent model block to switch the dependence of silicate processes on dissolved oxygen on or off. Simulation construction section 4.7.3.2.1. $$\text{ }$$
ammonium flux ==
$$\langle$$$$F_{sed}^{NH_4}$$$$\rangle$$
Used in a materials block to control the sediment flux rate of ammonium. Simulation construction section 4.7.4. $$\text{ }$$
ammonium benthic ==
$$\langle$$$$K_{sed-O_2}^{NH_4}$$,$$\theta_{sed}^{NH_4}$$$$\rangle$$
Used in an inorganic nitrogen constituent model block to control the response of benthic ammonium flux to temperature and oxygen concentration. Simulation construction section 4.7.3.3.1. $$\text{ }$$
ammonium min max ==
$$\langle$$$$\left[NH_4\right]_{min}^{NH_4}$$,$$\left[NH_4\right]_{max}^{NH_4}$$$$\rangle$$
Used in an inorganic nitrogen constituent model block to set minimum and maximum ammonium concentrations. Simulation construction section 4.7.3.3.1. $$\text{ }$$
inorganic nitrogen model ==
$$\langle$$AmmoniumNitrate$$\rangle$$
Used to commence an inorganic nitrogen constituent model block via specification of a constituent model from the inorganic nitrogen constituent model class. Simulation construction section 4.7.3.3. $$\text{ }$$
oxygen ==
$$\langle$$on;off$$\rangle$$
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. Simulation construction section 4.7.3.3.1. $$\text{ }$$
end silicate model Used to terminate a silicate constituent model block. Must follow a silicate model == command. Simulation construction section 4.7.3.2.1. $$\text{ }$$
end inorganic nitrogen model Used to terminate an inorganic nitrogen nitrogen constituent model block. Must follow an inorganic nitrogen model == command. Simulation construction section 4.7.3.3.1. $$\text{ }$$
nitrate flux ==
$$\langle$$$$F_{sed}^{NO_3}$$$$\rangle$$
Used in a materials block to control the sediment flux rate of nitrate. Simulation construction section 4.7.4. $$\text{ }$$
nitrate benthic ==
$$\langle$$$$K_{sed-O_2}^{NO_3}$$,$$\theta_{sed}^{NO_3}$$$$\rangle$$
Used in an inorganic nitrogen constituent model block to control the response of benthic nitrate flux to temperature and oxygen concentration. Simulation construction section 4.7.3.3.1. $$\text{ }$$
nitrate min max ==
$$\langle$$$$\left[NO_3\right]_{min}^{NO_3}$$,$$\left[NO_3\right]_{max}^{NO_3}$$$$\rangle$$
Used in an inorganic nitrogen constituent model block to set minimum and maximum nitrate concentrations. Simulation construction section 4.7.3.3.1. $$\text{ }$$
nitrification ==
$$\langle$$$$R_{nitrif}^{NH_4}$$,$$K_{nitrif-O_2}^{NH_4}$$,$$\theta_{nitrif}^{NH_4}$$$$\rangle$$
Used in an inorganic nitrogen constituent model block to control nitrification and its response to oxygen concentration and temperature. Simulation construction section 4.7.3.3.1. $$\text{ }$$
denitrification ==
$$\langle$$Michaelis Menten,$$R_{denit}^{NO_3}$$,$$K_{denit-O2-MM}^{NO_3}$$,$$\theta_{denit}^{NO_3}$$$$\rangle$$
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. Simulation construction section 4.7.3.3.1. exponential
denitrification ==
$$\langle$$exponential,$$R_{denit}^{NO_3}$$,$$K_{denit-O2-exp}^{NO_3}$$,$$\theta_{denit}^{NO_3}$$$$\rangle$$
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. Simulation construction section 4.7.3.3.1. Michaelis Menten
atmospheric deposition ==
$$\langle$$$$\left[{TN}\right]_{rain}$$,$$R_{atm-dry}^{TN}$$,$$f_{TN}^{NO_3}$$$$\rangle$$
Used in an inorganic nitrogen constituent model block to control the wet and dry atmospheric deposition of inorganic nitrogen. Simulation construction section 4.7.3.3.1. $$\text{ }$$
inorganic phosphorus model ==
$$\langle$$FRPhs,FRPhsads$$\rangle$$
Used to commence an inorganic phosphorus constituent model block via specification of a constituent model from the inorganic phosphorus constituent model class. Simulation construction section 4.7.3.4. $$\text{ }$$
end inorganic phosphorus model Used to terminate an inorganic phosphorus phosphorus constituent model block. Must follow a inorganic phosphorus model == command. Simulation construction section 4.7.3.4.1. $$\text{ }$$
FRP min max ==
$$\langle$$$$\left[FRP\right]_{min}^{FRP}$$,$$\left[FRP\right]_{max}^{FRP}$$$$\rangle$$
Used in an inorganic phosphorus constituent model block to set minimum and maximum FRP concentrations. Simulation construction section 4.7.3.4.1. $$\text{ }$$
FRP flux ==
$$\langle$$$$F_{sed}^{FRP}$$$$\rangle$$
Used in a materials block to control the sediment flux rate of FRP. Simulation construction section 4.7.4. $$\text{ }$$
FRP benthic ==
$$\langle$$$$K_{sed-O_2}^{FRP}$$,$$\theta_{sed}^{FRP}$$$$\rangle$$
Used in an inorganic phosphorus constituent model block to control the response of benthic FRP flux to temperature and oxygen concentration. Simulation construction section 4.7.3.4.1. $$\text{ }$$
oxygen ==
$$\langle$$on;off$$\rangle$$
Used in an inorganic phosphorus constituent model block to switch the dependence of FRP processes on dissolved oxygen on or off. Simulation construction section 4.7.3.4.1. $$\text{ }$$
atmospheric deposition ==
$$\langle$$$$\left[{FRP}\right]_{rain}$$,$$R_{atm-dry}^{FRPads}$$$$\rangle$$
Used in an inorganic phosphorus constituent model block to control the wet (and dry) atmospheric deposition of FRP (adsorbed FRP). Simulation construction section 4.7.3.4.1. $$\text{ }$$
$$\langle$$$$\left[FRPads\right]_{min}^{FRPads}$$,$$\left[FRPads\right]_{max}^{FRPads}$$$$\rangle$$
Used in an inorganic phosphorus constituent model block to set minimum and maximum adsorbed FRP concentrations. Simulation construction section 4.7.3.4.2. $$\text{ }$$
$$\langle$$linear,$$K_{ads-L}^{FRP}$$$$\rangle$$
Used in an inorganic phosphorus constituent model block to set the paramters for the linear FRP adsorption model. Simulation construction section 4.7.3.4.2. quadratic
$$\langle$$quadratic,$$K_{ads-Q}^{FRP}$$,$$Q^{FRP}_{max}$$$$\rangle$$
Used in a constituent model block to set the paramters for the quadratic FRP adsorption model. Simulation construction section 4.7.3.4.2. linear
phyto model ==
$$\langle$$basic;advanced,group_name$$\rangle$$
Used to commence a phytoplankton constituent model block via specification of a model from the phytoplankton constituent model class, 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. Simulation construction section 4.7.3.5. $$\text{ }$$
min max ==
$$\langle$$$$\left[PHY\right]_{min}^{PHY}$$,$$\left[PHY\right]_{max}^{PHY}$$$$\rangle$$
Used in a phytoplankton constituent model block to set minimum and maximum phytoplankton group concentrations. Simulation construction section 4.7.3.5.1. $$\text{ }$$
temperature limitation ==
$$\langle$$none$$\rangle$$
Used in a phytoplankton constituent model block to turn off phytoplankton group temperature limitation. Simulation construction section 4.7.3.5.1.1. standard
temperature limitation ==
$$\langle$$standard,$$T_{std}^{phy}$$,$$T_{opt}^{phy}$$,$$T_{max}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set the standard phytoplankton group temperature limitation function. Simulation construction section 4.7.3.5.1.1. none
salinity limitation ==
$$\langle$$none$$\rangle$$
Used in a phytoplankton constituent model block to turn off phytoplankton group salinity limitation. Simulation construction section 4.7.3.5.1.2. fresh,marine,
mixed,estuarine
salinity limitation ==
$$\langle$$fresh,$$S_{opt-fresh}^{phy}$$,$$S_{max-fresh}^{phy}$$,$$L_{max-fresh}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to select the freshwater phytoplankton group salinity limitation. Simulation construction section 4.7.3.5.1.2. none,marine,
mixed,estuarine
salinity limitation ==
$$\langle$$marine,$$S_{opt-marine}^{phy}$$,$$L_{zero-marine}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to select the marine phytoplankton group salinity limitation. Simulation construction section 4.7.3.5.1.2. none,fresh,
mixed,estuarine
salinity limitation ==
$$\langle$$mixed,$$S_{opt-mix}^{phy}$$,$$S_{max-mix}^{phy}$$,$$L_{zero-mix}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to select the mixed phytoplankton group salinity limitation. Simulation construction section 4.7.3.5.1.2. none,marine,
mixed,estuarine
salinity limitation ==
$$\langle$$estuarine,$$S_{opt-est}^{phy}$$,$$S_{max-est}^{phy}$$,$$P_{est}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to select the estuarine phytoplankton group salinity limitation. Simulation construction section 4.7.3.5.1.2. none,fresh,
marine,mixed
nitrogen limitation ==
$$\langle$$$$\left[N\right]_{min}^{phy}$$,$$K_{lim-N}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set nitrogen limitation parameters for the basic phytoplankton model. Simulation construction section 4.7.3.5.1.4. advanced
nitrogen limitation ==
$$\langle$$$$\left[N\right]_{min}^{phy}$$,$$K_{lim-N}^{phy}$$,$$X_{N-C-min}^{phy}$$,$$X_{N-C-max}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set nitrogen limitation parameters for the advanced phytoplankton model. Simulation construction section 4.7.3.5.2.1. basic
phosphorus limitation ==
$$\langle$$$$\left[P\right]_{min}^{phy}$$,$$K_{lim-P}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set phosphorus limitation parameters for the basic phytoplankton model. Simulation construction section 4.7.3.5.1.5. advanced
phosphorus limitation ==
$$\langle$$$$\left[P\right]_{min}^{phy}$$,$$K_{lim-P}^{phy}$$,$$X_{P-C-min}^{phy}$$,$$X_{P-C-max}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set phosphorus limitation parameters for the advanced phytoplankton model. Simulation construction section 4.7.3.5.2.2. basic
silicate limitation ==
$$\langle$$$$\left[Si\right]_{min}^{phy}$$,$$K_{lim-Si}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set silicate limitation parameters for the basic phytoplankton model. Specifying this command triggers silicate uptake. Simulation construction section 4.7.3.5.1.6. $$\text{ }$$
light limitation ==
$$\langle$$basic,$$Ke^{phy}$$,$$I_{K-bas}$$$$\rangle$$
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 vlaue of $$I_K$$ specified in this command overrides any value specified using the settling == stokes , $$I_K$$ command. Simulation construction section 4.7.3.5.1.3. monod,steele,
webb,jassby,
chalker,klepper,
integrated,
light limitation ==
$$\langle$$monod,$$Ke^{phy}$$,$$I_{K-mon}$$$$\rangle$$
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 vlaue of $$I_K$$ specified in this command overrides any value specified using the settling == stokes , $$I_K$$ command. Simulation construction section 4.7.3.5.1.3. basic,steele,
webb,jassby,
chalker,klepper,
integrated,
light limitation ==
$$\langle$$steele,$$Ke^{phy}$$,$$I_{S-ste}$$$$\rangle$$
Used in a phytoplankton constituent model block to set steele light limitation parameters for the basic and advanced phytoplankton constituent models. Simulation construction section 4.7.3.5.1.3. basic,monod,
webb,jassby,
chalker,klepper,
integrated,
light limitation ==
$$\langle$$webb,$$Ke^{phy}$$,$$I_{K-web}$$$$\rangle$$
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 vlaue of $$I_K$$ specified in this command overrides any value specified using the settling == stokes , $$I_K$$ command. Simulation construction section 4.7.3.5.1.3. basic,steele,
monod,jassby,
chalker,klepper,
integrated,
light limitation ==
$$\langle$$jassby,$$Ke^{phy}$$,$$I_{K-jas}$$$$\rangle$$
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 vlaue of $$I_K$$ specified in this command overrides any value specified using the settling == stokes , $$I_K$$ command. Simulation construction section 4.7.3.5.1.3. basic,steele,
webb,monod,
chalker,klepper,
integrated,
light limitation ==
$$\langle$$chalker,$$Ke^{phy}$$,$$I_{K-cha}$$$$\rangle$$
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 == stokes , $$I_K$$ command. Simulation construction section 4.7.3.5.1.3. basic,steele,
webb,jassby,
monod,klepper,
integrated,
light limitation ==
$$\langle$$klepper,$$Ke^{phy}$$,$$I_{S-kle}$$$$\rangle$$
Used in a phytoplankton constituent model block to set klepper light limitation parameters for the basic and advanced phytoplankton constituent models. Simulation construction section 4.7.3.5.1.3. basic,steele,
webb,jassby,
chalker,monod,
integrated,
light limitation ==
$$\langle$$integrated,$$Ke^{phy}$$,$$I_{S-int}$$$$\rangle$$
Used in a phytoplankton constituent model block to set integrated light limitation parameters for the basic and advanced phytoplankton constituent models. Simulation construction section 4.7.3.5.1.3. basic,steele,
webb,jassby,
chalker,klepper,
monod,
uptake ==
$$\langle$$$$X_{N-C-con}^{phy}$$,$$X_{P-C-con}^{phy}$$,$$X_{Si-C-con}^{phy}$$$$\rangle$$
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. Simulation construction section 4.7.3.5.1.7. advanced
uptake ==
$$\langle$$$$R_{N-uptake}^{phy}$$,$$R_{P-uptake}^{phy}$$,$$X_{Si-C-con}^{phy}$$$$\rangle$$
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. Simulation construction section 4.7.3.5.2.3. basic
settling ==
$$\langle$$none$$\rangle$$
Used in a phytoplankton constituent model block to turn off settling in both basic and advanced phytoplankton constituent models. Simulation construction section 4.7.3.5.1.12. constant,thermal,
stokes,motile
settling ==
$$\langle$$constant,$$V_{settle}^{phy}$$$$\rangle$$
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 using settling == none. Simulation construction section 4.7.3.5.1.12. none,thermal,
stokes,motile
settling ==
$$\langle$$thermal,$$V_{settle}^{phy}$$$$\rangle$$
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. Simulation construction section 4.7.3.5.1.12. none,constant,
stokes,motile
settling ==
$$\langle$$stokes,$$I_{K-sto}$$$$\rangle$$
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 limitaton 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. Simulation construction section 4.7.3.5.1.12. none,constant,
thermal,motile
settling ==
$$\langle$$motile,$$V_{mot}^{phy}$$,$$I_{K-mot}$$$$\rangle$$
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 limitaton 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. Simulation construction section 4.7.3.5.2.4. none,constant,
thermal,stokes
carbon chla ratio ==
$$\langle$$$$X_{cc}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set the ratio of phytoplankton cell carbon biomass to chlorophyll a . Simulation construction section 4.7.3.5.1.10. $$\text{ }$$
end phyto model Used to terminate a phytoplankton constituent model block. Must follow a phyto model == command. Simulation construction section 4.7.3.5.1.13. $$\text{ }$$
nitrogen fixing ==
$$\langle$$$$R_{nfix}^{N_2}$$,$$f_{nfix}^{phy}$$$$\rangle$$
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. Simulation construction section 4.7.3.5.1.11. $$\text{ }$$
primary productivity ==
$$\langle$$$$R_{prod}^{phy}$$,$$\theta_{prod}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set primary productivity parameters of a phytoplankton constituent model. Simulation construction section 4.7.3.5.1.8. $$\text{ }$$
respiration ==
$$\langle$$$$R_{resp}^{phy}$$,$$\theta_{resp}^{phy}$$,$$f_{true-resp}^{phy}$$,$$f_{excr-loss}^{phy}$$,$$f_{exud}^{phy}$$$$\rangle$$
Used in a phytoplankton constituent model block to set respiration and exudation parameters of a phytoplankton constituent model. Simulation construction section 4.7.3.5.1.9. $$\text{ }$$
water quality model ==
$$\langle$$tuflow$$\rangle$$
Instruct TUFLOW FV to activate TUFLOW WQM. Simulation construction section 4.4.1. $$\text{ }$$
water quality control file ==
$$\langle$$water quality control file name$$\rangle$$
Name of WQM control file, with no path. If this file is not in the FV control file directory, then additionally use command water quality mode directory ==. Simulation construction section 4.4.1. $$\text{ }$$
water quality model directory ==
$$\langle$$water quality control file directory$$\rangle$$
Relative path from location of FV control file to the WQM control file directory, including last backslash, e.g. “..$$\backslash$$WQM$$\backslash$$”. Simulation construction section 4.4.1. $$\text{ }$$
restart ==
$$\langle$$restart file path and name$$\rangle$$
Specification of full path and name of previously saved restart file. Simulation construction section 4.4.2.1. $$\text{ }$$
initial wq concentration ==
$$\langle$$comma separated wq initial conditions$$\rangle$$
Ordered individual computed variable initial conditions. Simulation construction section 4.4.2.1. $$\text{ }$$
initial scalar profile ==
$$\langle$$initial condition file name and path$$\rangle$$
Ordered individual computed variable initial conditions in a columnar text file. Simulation construction section 4.4.2.1. $$\text{ }$$
initial condition 2d ==
$$\langle$$initial condition file name and path$$\rangle$$
Ordered individual computed variable initial conditions in a columnar text file. Simulation construction section 4.4.2.1. $$\text{ }$$
initial condition 3d ==
$$\langle$$initial condition file name and path$$\rangle$$
Ordered individual computed variable initial conditions in a columnar text file. Simulation construction section 4.4.2.1. $$\text{ }$$
material ==
$$\langle$$Up to 10 comma separated material integers$$\rangle$$
Command to initiate a materials block. Commands within this block apply to the material numbers listed in this command. Simulation construction section 4.5.3. $$\text{ }$$
end material Command to terminate a materials block. This command must be paired with a corresponding material command to initiate the block. Simulation construction section 4.5.3. $$\text{ }$$
include sediment ==
$$\langle$$include sediment transport calculations,include sediment in density calculation$$\rangle$$
TUFLOW FV command to include sediment simulation. Sediment must be simulated if adsorbed phosphorus is included in a WQM simulation. Simulation construction section 4.7.5.1.2. $$\text{ }$$
carbon min max ==
$$\langle$$$$\left[POC\right]_{min}^{POC}$$,$$\left[POC\right]_{max}^{POC}$$,$$\left[DOC\right]_{min}^{DOC}$$,$$\left[DOC\right]_{max}^{DOC}$$$$\rangle$$
Used in an organic matter constituent model block to set minimum and maximum particulate and dissolved organic carbon concentrations. Simulation construction section 4.8.3.5. $$\text{ }$$
nitrogen min max ==
$$\langle$$$$\left[PON\right]_{min}^{PON}$$,$$\left[PON\right]_{max}^{PON}$$,$$\left[DON\right]_{min}^{DON}$$,$$\left[DON\right]_{max}^{DON}$$$$\rangle$$
Used in an organic matter constituent model block to set minimum and maximum particulate and dissolved organic nitrogen concentrations. Simulation construction section 4.8.3.5. $$\text{ }$$
phosphorus min max ==
$$\langle$$$$\left[POP\right]_{min}^{POP}$$,$$\left[POP\right]_{max}^{POP}$$,$$\left[DOP\right]_{min}^{DOP}$$,$$\left[DOP\right]_{max}^{DOP}$$$$\rangle$$
Used in an organic matter constituent model block to set minimum and maximum particulate and dissolved organic phosphorus concentrations. Simulation construction section 4.8.3.5. $$\text{ }$$
organic matter model ==
$$\langle$$labile,refractory$$\rangle$$
Used to commence an organics constituent model block via specification of a model from the organics constituent model class.. Simulation construction section 4.8.3.5. $$\text{ }$$
DOC flux ==
$$\langle$$$$F_{sed}^{DOC}$$$$\rangle$$
Used in a materials block to control the sediment flux rate of DOC. Simulation construction section 4.8.4. $$\text{ }$$
DON flux ==
$$\langle$$$$F_{sed}^{DON}$$$$\rangle$$
Used in a materials block to control the sediment flux rate of DON. Simulation construction section 4.8.4. $$\text{ }$$
DOP flux ==
$$\langle$$$$F_{sed}^{DOP}$$$$\rangle$$
Used in a materials block to control the sediment flux rate of DOP. Simulation construction section 4.8.4. $$\text{ }$$
organics benthic ==
$$\langle$$$$K_{sed-O_2}^{DOM}$$,$$\theta_{sed}^{DOM}$$$$\rangle$$
Used in an organics constituent model block to control the response of benthic DOM flux to temperature and oxygen concentration. Simulation construction section 4.8.3.5.1. $$\text{ }$$
end organic matter model Used to terminate an organics constituent model block. Must follow an organic matter model == command. Simulation construction section 4.8.3.5.1. $$\text{ }$$
oxygen ==
$$\langle$$on;off$$\rangle$$
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 asnd set to ‘off’. Simulation construction section 4.8.3.5.1. $$\text{ }$$
hydrolysis ==
$$\langle$$$$R_{hyd}^{POC}$$,$$R_{hyd}^{PON}$$,$$R_{hyd}^{POP}$$,$$K_{hyd-O_2}^{POM}$$,$$\theta_{hyd}^{POM}$$$$\rangle$$
Used in an organics constituent model block to parameterise particulate organic carbon, nitrogen and phosphorus hydrolysis. Simulation construction section 4.8.3.5.1. $$\text{ }$$
mineralisation ==
$$\langle$$$$R_{miner}^{DOM}$$,$$K_{miner-O_2}^{DOM}$$,$$\theta_{miner}^{DOM}$$,$$f_{an}$$,$$K_{miner-NO_3}^{NO_3}$$$$\rangle$$
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. Simulation construction section 4.8.3.5.1. $$\text{ }$$
$$\langle$$$$Ke^{POM}$$,$$Ke^{DOM}$$$$\rangle$$
Used in an organics constituent model block to parameterise light attenuation due to the presence of particulate and dissolved organic matter. Simulation construction section 4.8.3.5.1. $$\text{ }$$
ref breakdown ==
$$\langle$$$$R_{bdn}^{RPOM}$$,$$X_N^{RPOM}$$,$$X_P^{RPOM}$$$$\rangle$$
Used in an organics constituent model block to parameterise the breakdown of refractory particulate organic matter. Simulation construction section 4.8.3.5.2. $$\text{ }$$
ref carbon min max ==
$$\langle$$$$\left[RPOM\right]_{min}^{RPOM}$$,$$\left[RPOM\right]_{max}^{RPOM}$$,$$\left[RDOC\right]_{min}^{RDOC}$$,$$\left[RDOC\right]_{max}^{RDOC}$$$$\rangle$$
Used in an organic matter constituent model block to set minimum and maximum refractory particulate organic matter and refractory dissolved organic carbon concentrations. Simulation construction section 4.8.3.5.2. $$\text{ }$$
ref nitrogen min max ==
$$\langle$$$$\left[RDON\right]_{min}^{RDON}$$,$$\left[RDON\right]_{max}^{RDON}$$$$\rangle$$
Used in an organic matter constituent model block to set minimum and maximum refractory dissolved organic nitrogen concentrations. Simulation construction section 4.8.3.5.2. $$\text{ }$$
ref phosphorus min max ==
$$\langle$$$$\left[RDOP\right]_{min}^{RDOP}$$,$$\left[RDOP\right]_{max}^{RDOP}$$$$\rangle$$
Used in an organic matter constituent model block to set minimum and maximum refractory dissolved organic phosphorus concentrations. Simulation construction section 4.8.3.5.2. $$\text{ }$$
ref activation ==
$$\langle$$$$R_{act}^{RDOM}$$$$\rangle$$
Used in an organic matter constituent model block to set the rate of activation of refractory dissolved organic carbon, nitrogen and phosphorus. Simulation construction section 4.8.3.5.2. $$\text{ }$$
$$\langle$$$$Ke^{RPOM}$$,$$R_{CDOM}^{RDOM}$$$$\rangle$$
Used in an organics constituent model block to parameterise light attenuation due to the presence of refractory particulate and dissolved organic matter. Simulation construction section 4.8.3.5.2. $$\text{ }$$
ref photolysis ==
$$\langle$$$$f_{photo}^{RDOM}$$$$\rangle$$
Used in an organics constituent model block to parameterise the proportion of photolysis of refractory dissolved organic matter that produces labile dissolved organic matter. Simulation construction section 4.8.3.5.2. $$\text{ }$$
anaerobic oxidation of ammonium ==
$$\langle$$$$k_{anmx}^{N_2}$$,$$K_{anmx-NH_4}^{N_2}$$,$$K_{anmx-NO_2}^{N_2}$$$$\rangle$$
Used in an inorganic nitrogen constituent model block to control anaerobic oxidation of ammonium and its response to ambient ammonium and nitrate concentrations. Simulation construction section 4.7.3.3.1. $$\text{ }$$
diss nitrate reduction to ammonium ==
$$\langle$$$$R_{DRNA}^{NO_3}$$,$$K_{DRNA-O_2}^{NO_3}$$$$\rangle$$
Used in an inorganic nitrogen constituent model block to control dissimilatory reduction of nitrate to ammonium and its response to ambient oxygen concentrations. Simulation construction section 4.7.3.3.1. $$\text{ }$$
settling ==
$$\langle$$$$V_{settle}^{FRP}$$$$\rangle$$
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 STM in future releases of the WQM. Simulation construction section 4.7.3.4.2. $$\text{ }$$
settling ==
$$\langle$$none$$\rangle$$
Used in an organic matter constituent model block to set the settling rate of labile particulate organic matter to zero. Simulation construction section 4.8.3.5.1. $$\text{ }$$
settling ==
$$\langle$$constant,$$V_{settle}^{lorg}$$$$\rangle$$
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 STM in future releases of the WQM. Simulation construction section 4.8.3.5.1. $$\text{ }$$
settling ==
$$\langle$$thermal,$$V_{settle}^{lorg}$$$$\rangle$$
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 STM in future releases of the WQM. Simulation construction section 4.8.3.5.1. $$\text{ }$$
settling ==
$$\langle$$stokes,$$d_{lorg}$$,$$\rho_{lorg}$$$$\rangle$$
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 STM in future releases of the WQM. Simulation construction section 4.8.3.5.1. $$\text{ }$$
ref settling ==
$$\langle$$none$$\rangle$$
Used in an organic matter constituent model block to set the settling rate of refractory particulate organic matter to zero. Simulation construction section 4.8.3.5.2. $$\text{ }$$
ref settling ==
$$\langle$$constant,$$V_{settle}^{rorg}$$$$\rangle$$
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 STM in future releases of the WQM. Simulation construction section 4.8.3.5.2. $$\text{ }$$
ref settling ==
$$\langle$$thermal,$$V_{settle}^{rorg}$$$$\rangle$$
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 STM in future releases of the WQM. Simulation construction section 4.8.3.5.2. $$\text{ }$$
ref settling ==
$$\langle$$stokes,$$d_{rorg}$$,$$\rho_{rorg}$$$$\rangle$$
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 STM in future releases of the WQM. Simulation construction section 4.8.3.5.2. $$\text{ }$$
cell water quality depth ==
$$\langle$$$$d_{min-wq}$$$$\rangle$$
Instruct TUFLOW FV to not execute water quality calculations on cells that have depths less than this specified value. Simulation construction section 4.4.1. $$\text{ }$$
disable water quality model ==
$$\langle$$$$B_{disable-wq}$$$$\rangle$$
Instruct TUFLOW FV to disable (1) or enable (0) water quality calculations on all cells. Simulation construction section 4.4.1. $$\text{ }$$
wq equilibrium substeps ==
$$\langle$$$$fess$$$$\rangle$$
Used in Part 1: Simulation controls of WQM control file to set the frequency of timesteps at which the WQM undertakes non-kinetic calculations, in number of water quality timesteps. This only applies to FRP adsorption. Simulation construction section 4.5.1. $$\text{ }$$