Tutorial M09: Difference between revisions

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{| class="wikitable" align="right"
| colspan="3" style="text-align:center;" | '''USEFUL LINKS'''
|-
| width="220pt" style="text-align:center;" | '''Wiki Links'''
| width="220pt" style="text-align:center;" | '''Help'''
| width="220pt" style="text-align:center;" | '''Downloads'''
|-
| [http://fvwiki.tuflow.com/index.php?title=Main_Page ''TUFLOW FV Wiki Main Page'']
| ''[[Contact|Products Support/Contact]]''
| [https://www.tuflow.com/downloads/ ''TUFLOW FV Downloads'']
|-
| ''[[Tutorial Model Introduction|TUFLOW FV Tutorials]]''
| ''[[Requesting a Licence]]''
| [https://www.tuflow.com/downloads/tuflow-fv-models/ ''Tutorial Module Data'']
|-
| [https://wiki.tuflow.com/index.php?title=Main_Page ''TUFLOW Classic/HPC Wiki'']
| ''[[TUFLOW FV Glossary|TUFLOW FV Glossary]]''
| [https://www.tuflow.com/downloads/ ''Manuals'']
|}
=Tutorial Description=
=Tutorial Description=
Tutorial Module 09 demonstrates the development of a 3D water quality model using the TUFLOW FV Water Quality (WQ) Module.  Starting with the final model of Tutorial 05, this tutorial will progressively increase in complexity, incorporating the simulation of dissolved oxygen, then inorganic nutrients, and finally capturing full organic nutrient cycling. Tutorial Module 09 provides a full set of working model files that can be re-run and experimented with, in a manner similar to the [https://gitlab.com/tuflow-user-group/tuflow-fv/example-models/wqm mass conservation model]. <br>
Tutorial Module 09 demonstrates the development of a 3D water quality model using the TUFLOW FV Water Quality (WQ) Module.  Starting with the final model of [https://fvwiki.tuflow.com/index.php?title=Tutorial_Module05 Tutorial 05], this tutorial will progressively increase in complexity, incorporating the simulation of dissolved oxygen, then inorganic nutrients, and finally capturing full organic nutrient cycling. Tutorial Module 09 provides a full set of working model files that can be re-run and experimented with. <br>


The tutorial is broken up into the following subsections:
The tutorial is broken up into the following subsections:
:* [[Tutorial_Module09#Set_up_TUFLOW_FV |Set up TUFLOW FV for Simulation]]
:* [[Tutorial_Module09#Set_up_TUFLOW_FV |Set up TUFLOW FV]]
:* [[Tutorial_Module09#Tutorial_Data | Overview of Provided Data Files]]
:* [[Tutorial_Module09#Tutorial_Data | Tutorial Data]]
:* [[Tutorial_Module09#TUFLOW_FV_Hydrodynamic_Model_Setups | Summary of Hydrodynamic Model Setups]]
:* [[Tutorial_Module09#TUFLOW_FV_Hydrodynamic_Model_Setups | TUFLOW FV Hydrodynamic Model Setups]]
:* [[Tutorial_Module09#TUFLOW_FV_WQ_Module_Setups | Summary of Water Quality Model Setups]]
:* [[Tutorial_Module09#TUFLOW_FV_WQ_Module_Setups | TUFLOW FV WQ Module Setups]]
:* [[Tutorial_Module09#Running_the_Models | Running the Models]]
:* [[Tutorial_Module09#Running_the_Models | Running the Models]]
:* [[Tutorial_Module09#Inspecting_Results | Inspecting Results]]
:* [[Tutorial_Module09#Inspecting_Results | Inspecting Results]]
:* [[Tutorial_Module09#Conclusion | Conclusion]]


<br>
<br>


=Set up TUFLOW FV=
=Set up TUFLOW FV=
This tutorial recommends the use of TUFLOW FV 2020.03.105, available on the [https://www.tuflow.com/downloads/#tuflow_fv TUFLOW Downloads Page]. Please download TUFLOW FV 2020.03.105 and save to '''C:\TUFLOWFV\2020.03.105\''' or another preferred location. This location will be used in building scripts to run Tutorial 09's models. <br>
This tutorial recommends the use of TUFLOW FV 2023.0 or later, available on the [https://www.tuflow.com/downloads/#tuflow_fv TUFLOW Downloads Page]. Please download TUFLOW FV 2023.0 or later, and save to '''C:\TUFLOWFV\''' or another preferred location. This location will be used in building scripts to run Tutorial 09's models. <br>


This demonstration model dynamically couples TUFLOW FV with [https://gotm.net/portfolio/ GOTM] to model vertical turbulence exchanges. To do so, please download the [https://www.dropbox.com/s/h132fs3ejo4ppot/tuflowfv_external_turb_2020.zip?dl=0 TUFLOW FV External Turbulence API]. Once downloaded, unzip the file '''.\GOTM\tuflowfv_external_turb.dll''' and replace the default '''tuflowfv_external_turb.dll''' that resides in the same directory as '''TUFLOWFV.exe''' (for example, '''C:\TUFLOWFV\2020.03.105\'''). If this step has already been undertaken as part of the running of Tutorial 05, then it need not be repeated here. <br>
This demonstration model dynamically couples TUFLOW FV with [https://gotm.net/portfolio/ GOTM] to model vertical turbulence exchanges. To do so, please download the [https://www.dropbox.com/s/h132fs3ejo4ppot/tuflowfv_external_turb_2020.zip?dl=0 TUFLOW FV External Turbulence API]. Once downloaded, unzip the file '''.\GOTM\tuflowfv_external_turb.dll''' and replace the default '''tuflowfv_external_turb.dll''' that resides in the same directory as '''TUFLOWFV.exe''' (for example, '''C:\TUFLOWFV\2023.0\'''). If this step has already been undertaken as part of the running of [https://fvwiki.tuflow.com/index.php?title=Tutorial_Module05 Tutorial 05], then it need not be repeated here. <br>


TUFLOW FV WQ uses the dynamically linked library tuflowfv_wq.dll, which ships with TUFLOW FV 2020.03.105, so no additional user set up is required to access the compiled binary necessary for water quality simulation. <br><br>
TUFLOW FV WQ uses the dynamically linked library '''tuflowfv_wq.dll''', which ships with TUFLOW FV 2023.0 or later, so no additional user set up is required to access the compiled binary necessary for water quality simulation. <br><br>


=Tutorial Data=
=Tutorial Data=
The data for Tutorial 09 is available from the TUFLOW Website [https://www.tuflow.com/downloads/tuflow-fv-models/ Tutorial Module Download]. The folders and most of their contents are the same as those within Tutorial 05’s “Complete_Model” folder, with the addition of one new folder (named “wqm”) that houses TUFLOW FV WQ control files. The initial condition and boundary condition files in Tutorial 09 are slightly altered and expanded (to account for water quality specification) versions of those provided in Tutorial 05.  <br>
The data for Tutorial 09 is available from the [https://www.tuflow.com/downloads/tuflow-fv-models/ TUFLOW Website]. The folders and most of their contents are the same as those within [https://fvwiki.tuflow.com/index.php?title=Tutorial_Module05 Tutorial 05]’s '''Complete_Model''' folder, with some additional folders. The initial condition and boundary condition files in Tutorial 09 are slightly altered and expanded (to account for water quality specification) versions of those provided in [https://fvwiki.tuflow.com/index.php?title=Tutorial_Module05 Tutorial 05].  <br>


It is recommended that Tutorial 05 be completed before this water quality tutorial is attempted.
''Everything you need to complete this tutorial is within the Tutorial Module 09 data download folder. However, if you would like to better appreciate the model setting and hydrodynamics you may want to complete [https://fvwiki.tuflow.com/index.php?title=Tutorial_Module05 Tutorial 05] first.''


===Complete Model Folder Contents===
===Complete Model Folder Contents===
Three water quality models are provided in the Complete Model folder under the '''TUFLOWFV folder''', and include:
Three water quality models are provided in the '''Complete_Model''' folder under the '''TUFLOWFV''' folder, and include:


:* .2dm model mesh file '''‘hydraul_006.2dm’''' ('''model\geo''' folder, unchanged from Tutorial 05)
:* .2dm model mesh file '''‘hydraul_006.2dm’''' ('''model\geo''' folder, unchanged from Tutorial 05)
:* 3D layer .csv file ('''model\csv folder''', unchanged from Tutorial 05)
:* 3D_Z_Layers_003.csv file ('''model\csv''' folder, unchanged from Tutorial 05)
:* Supporting GIS files for nodestring and material definition ('''model\gis''' folder)
:* Supporting GIS files for nodestring and material definition ('''model\gis''' folder)
:* GIS empty files for adding features to the model ('''model\gis\empty''' folder, unchanged from Tutorial 05)
:* GIS empty files for adding features to the model ('''model\gis\empty''' folder, unchanged from Tutorial 05)
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===Upstream And Downstream Boundary Condition Files===
===Upstream And Downstream Boundary Condition Files===
The upstream boundary condition file from Tutorial 05 is the same in this tutorial but has added columns (one for each water quality constituent simulated). The added columns have headers that are not keywords in themselves, but are used by TUFLOW FV to determine water quality boundary conditions for each constituent based on ordered listing of these same headers in “bc” blocks in each TUFLOW FV control file (see subsequent sections for a description of this ordering process). This upstream boundary’s location is set in the model mesh via association with a nodestring. <br>
The upstream boundary condition file from [https://fvwiki.tuflow.com/index.php?title=Tutorial_Module05 Tutorial 05] is the same in this tutorial but has added columns (one for each water quality constituent simulated). The added columns have headers that are not keywords in themselves, but are used by TUFLOW FV to determine water quality boundary conditions for each constituent based on ordered listing of these same headers in “bc” blocks in each TUFLOW FV control file (see subsequent sections for a description of this ordering process). This upstream boundary’s location is set in the model mesh via association with a nodestring. <br>


The downstream nodestring boundary condition of Tutorial 09’s model mesh has been removed so that it presents a barrier (such as a dam wall) to flow rather than an outflow. A new boundary condition has been created in its place that that is a polygon extraction that has outflows that approximately balance those entering the model from its upstream end. No salinity, temperature, sediment or water quality specifications (columns) are necessary for this extraction boundary condition because it represents outflows that have no influence on the model other than volumetric removal. <br>
The downstream nodestring boundary condition of Tutorial 09’s model mesh has been removed so that it presents a barrier (such as a dam wall) to flow rather than an outflow. A new boundary condition has been created in its place that is a polygon extraction that has outflows that approximately balance those entering the model from its upstream end. No salinity, temperature, sediment or water quality specifications (columns) are necessary for this extraction boundary condition because it represents outflows that have no influence on the model other than volumetric removal. <br>


For the second and third simulations, a further inflow boundary condition is added (also as an inflow polygon) to represent a high nutrient wastewater treatment plant discharge.
For the second and third simulations, a further inflow boundary condition is added (also as an inflow polygon) to represent a high nutrient wastewater treatment plant discharge.


===Model Mesh File===
===Model Mesh File===
This is the same model mesh as that used in Tutorial 05, in 3D (TUFLOW FV control file HYD_002.fvc).  
This is the same model mesh as that used in [https://fvwiki.tuflow.com/index.php?title=Tutorial_Module05 Tutorial 05].


===Meteorological NetCDF Files===
===Meteorological NetCDF Files===
The meteorological data for the model is the same as that used in Tutorial 05, in 3D (TUFLOW FV control file HYD_002.fvc).<br><br>
The meteorological data for the model is the same as that used in [https://fvwiki.tuflow.com/index.php?title=Tutorial_Module05 Tutorial 05].<br><br>


=TUFLOW FV Hydrodynamic Model Setups=
=TUFLOW FV Hydrodynamic Model Setups=
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<br>
<br>


{|class="wikitable"
{|class="wikitable" style="width: 90%;"
|-
|-
|[[WQ_000.fvc| WQ_000.fvc]]
| [[WQ_000.fvc| WQ_000.fvc]]
|The same as HYD_002.fvc but with additional commands to allow for simulation of dissolved oxygen. <br>Companion water quality control file is WQ_000.fvwq (see following section)
| The same as [https://fvwiki.tuflow.com/index.php?title=HYD_002 HYD_002.fvc] but with additional commands to allow for simulation of dissolved oxygen. <br>Companion water quality control file is WQ_000.fvwq (see following section)
|-
|-
|[[WQ_001.fvc| WQ_001.fvc]]
| [[WQ_001.fvc| WQ_001.fvc]]
|The same as HYD_002.fvc but with additional commands to allow for simulation of dissolved oxygen, inorganic nutrients and phytoplankton. <br>Companion water quality control file is WQ_001.fvwq (see following section)
| The same as [https://fvwiki.tuflow.com/index.php?title=HYD_002 HYD_002.fvc] but with additional commands to allow for simulation of dissolved oxygen, inorganic nutrients and phytoplankton. <br>Companion water quality control file is WQ_001.fvwq (see following section)
|-
|-
|[[WQ_002.fvc| WQ_002.fvc]]
| [[WQ_002.fvc| WQ_002.fvc]]
|The same as HYD_002.fvc but with additional commands to allow for simulation of dissolved oxygen, inorganic nutrients, organic nutrients and phytoplankton. <br>Companion water quality control file is WQ_002.fvwq (see following section)
| The same as [https://fvwiki.tuflow.com/index.php?title=HYD_002 HYD_002.fvc] but with additional commands to allow for simulation of dissolved oxygen, inorganic nutrients, organic nutrients and phytoplankton. <br>Companion water quality control file is WQ_002.fvwq (see following section)
|-
|-
|}
|}
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===Model 000: Dissolved oxygen===
===Model 000: Dissolved oxygen===
Dissolved oxygen simulation is often a good place to start when constructing water quality models. The model WQ_000.fvc provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing. <br>
Dissolved oxygen simulation is often a good place to start when constructing water quality models. The model [https://fvwiki.tuflow.com/index.php?title=WQ_000.fvc WQ_000.fvc] provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing. <br>


{|class="wikitable" width="1200pt"
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|
|-
|-
| width="400pt" | simulation class == do
| style="width: 50%;" | Simulation Class == do
| Sets the overall simulation class to be "DO"
| Set the overall simulation class to be "DO"


|-
|-
| wq dt == 1800.0
| WQ dt == 1800.0
| Sets the water quality module timestep. This is the frequency at which the WQ module is called from TUFLOW FV
| Set the Water Quality Module timestep. This is the frequency at which the WQ Module is called from TUFLOW FV


|-
|-
| wq units == mgl
| WQ Units == mgl
| Sets the units of simulation of the WQ module.  
| Set the units of simulation of the WQ Module.  


|}
|}


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|-
|-


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|
|-
|-
| width="400pt" | oxygen model == O2
| style="width: 50%;" | Oxygen Model == O2
| Set oxygen constituent model to be O2
| Set oxygen constituent model to be O2


|-
|-
|   oxygen benthic == 0.5, 1.08
| &emsp; &emsp; Oxygen Benthic == 0.5, 1.08
| Set sediment oxygen consumption properties
| Set sediment oxygen consumption properties


|-
|-
| end oxygen model
| End Oxygen Model
| End oxygen constituent model
| End oxygen constituent model


|}
|}


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|
|-
|-
| width="400pt" | material == default
| style="width: 50%;" | Material == default
| rowspan="3" | Set default material properties
| rowspan="3" | Set default material properties
|-
|-
|   oxygen flux == -10.0
| &emsp; &emsp; Oxygen Flux == -10.0
|-
|-
| end material
| End Material


|-
|-
| material == 1
| Material == 1
| rowspan="3" | Set sediment oxygen properties for material 1
| rowspan="3" | Set sediment oxygen properties for material 1
|-
|-
|   oxygen flux == -550.0  
| &emsp; &emsp; Oxygen Flux == -550.0  
|-
|-
| end material
| End Material


|-
|-
| material == 2 ! Mudflats
| Material == 2 ! Mudflats
| rowspan="3" | Set sediment oxygen properties for material 2
| rowspan="3" | Set sediment oxygen properties for material 2
|-
|-
|   oxygen flux == 0.0  
| &emsp; &emsp; Oxygen Flux == 0.0  
|-
|-
| end material
| End Material


|-
|-
| material == 4 ! Deep channel
| Material == 4 ! Deep channel
| rowspan="3" | Set sediment oxygen properties for material 4
| rowspan="3" | Set sediment oxygen properties for material 4
|-
|-
|   oxygen flux == -3500.0  
| &emsp; &emsp; Oxygen Flux == -3500.0  
|-
|-
| end material
| End Material


|}
|}
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===Model 001: Inorganics===
===Model 001: Inorganics===
Simulation of inorganics is often the next logical step after simulating dissolved oxygen. The model WQ_001.fvc provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing.  The constituent model block for oxygen is unchanged from model 000. One phytoplankton group is simulated.<br>
Simulation of inorganics is often the next logical step after simulating dissolved oxygen. The model [https://fvwiki.tuflow.com/index.php?title=WQ_001.fvc WQ_001.fvc] provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing.  The constituent model block for oxygen is unchanged from model 000. One phytoplankton group is simulated.<br>


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|-
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| width="400pt" | simulation class == inorganics
| style="width: 50%;" | Simulation Class == inorganics
| Set the overall simulation class to be “inorganics”
| Set the overall simulation class to be “inorganics”


|-
|-
| wq dt == 1800.0
| WQ dt == 1800.0
| Set the water quality module timestep. This is the frequency at which the WQ module is called from TUFLOW FV
| Set the Water Quality Module timestep. This is the frequency at which the WQ Module is called from TUFLOW FV


|-
|-
| wq units == mgl
| WQ Units == mgl
| Set the units of simulation of the WQ module.  
| Set the units of simulation of the WQ Module.  


|}
|}


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|  
|-
|-
| width="400pt" | silicate model == Si
| style="width: 50%;" | Silicate Model == Si
| Set silicate constituent model to be Si
| Set silicate constituent model to be Si


|-
|-
|   silicate min max == 0.0, 100.0
| &emsp; &emsp; Silicate Min Max == 0.0, 100.0
| Set min and max values for silicate
| Set min and max values for silicate


|-
|-
|   oxygen benthic == 4.2, 1.01
| &emsp; &emsp; Oxygen Benthic == 4.2, 1.01
| Set silicate sediment release properties
| Set silicate sediment release properties


|-
|-
|   oxygen == on
| &emsp; &emsp; Oxygen == on
| Include oxygen in the simulation of silicate dynamics
| Include oxygen in the simulation of silicate dynamics


|-
|-
| end silicate model
| End Silicate Model
| End silicate constituent model
| End silicate constituent model


|}
|}


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|-


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|
|-
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| width="400pt" | Inorganic nitrogen model == ammoniumnitrate
| style="width: 50%;" | Inorganic Nitrogen Model == ammoniumnitrate
| Set inorganic nitrogen constituent model to be ammoniumnitrate
| Set inorganic nitrogen constituent model to be ammoniumnitrate


|-
|-
|   ammonium min max == 0.0, 50.0
| &emsp; &emsp; Ammonium Min Max == 0.0, 50.0
| rowspan="2" | Set min and max values for ammonium and nitrate
| rowspan="2" | Set min and max values for ammonium and nitrate
|-
|-
|   ammonium min max == 0.0, 50.0
| &emsp; &emsp; Ammonium Min Max == 0.0, 50.0


|-
|-
|   ammonium benthic == 4.05, 1.06
| &emsp; &emsp; Ammonium Benthic == 4.05, 1.06
| rowspan="2" | Set ammonium and nitrate sediment release properties
| rowspan="2" | Set ammonium and nitrate sediment release properties
|-
|-
|   nitrate benthic == 4.25, 1.10
| &emsp; &emsp; Nitrate Benthic == 4.25, 1.10


|-
|-
|   nitrification == 0.05, 4.15, 1.01
| &emsp; &emsp; Nitrification == 0.05, 4.15, 1.01
| Set nitrification parameters
| Set nitrification parameters


|-
|-
|   denitrification == michaelis menten, 0.05, 4.01, 1.03
| &emsp; &emsp; Denitrification == michaelis menten, 0.05, 4.01, 1.03
| Set denitrification model and properties
| Set denitrification model and properties


|-
|-
|     oxygen == on
| &emsp; &emsp; Oxygen == on
| Include oxygen in the simulation of inorganic nitrogen dynamics
| Include oxygen in the simulation of inorganic nitrogen dynamics


|-
|-
|   atmospheric deposition == 5.0, 0.0, 0.5
| &emsp; &emsp; Atmospheric Deposition == 5.0, 0.0, 0.5
| Set atmospheric deposition of inorganic nitrogen parameters
| Set atmospheric deposition of inorganic nitrogen parameters


|-
|-
|   anaerobic oxidation of ammonium == 0.005, 2.5, 2.5
| &emsp; &emsp; Anaerobic Oxidation Of Ammonium == 0.005, 2.5, 2.5
| Set anammox parameters
| Set anammox parameters


|-
|-
|     diss nitrate reduction to ammonium == 0.005, 5.0
| &emsp; &emsp; Diss Nitrate Reduction To Ammonium == 0.005, 5.0
| Set DRNA parameters
| Set DRNA parameters


|-
|-
| end inorganic nitrogen model
| End Inorganic Nitrogen Model
| End inorganic nitrogen constituent model
| End inorganic nitrogen constituent model


|}
|}


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|
|-
|-
| width="400pt" | Inorganic phosphorus model == frphsads
| style="width: 50%;" | Inorganic Phosphorus Model == frphsads
| Set inorganic phosphorus constituent model to be frphads, which includes simulation of free and adsorbed inorganic phosphorus
| Set inorganic phosphorus constituent model to be frphads, which includes simulation of free and adsorbed inorganic phosphorus


|-
|-
|   FRP min max == 0.0, 5.0
| &emsp; &emsp; FRP Min Max == 0.0, 5.0
| rowspan="2" | Set min and max values for inorganic phosphorus and adsorbed inorganic phosphorus
| rowspan="2" | Set min and max values for inorganic phosphorus and adsorbed inorganic phosphorus
|-
|-
|   FRP ads min max == 0.0, 5.0
| &emsp; &emsp; FRP Ads Min Max == 0.0, 5.0


|-
|-
|   FRP benthic == 4.3, 1.095
| &emsp; &emsp; FRP Benthic == 4.3, 1.095
| Set inorganic phosphorus sediment release properties
| Set inorganic phosphorus sediment release properties


|-
|-
|   oxygen == on
| &emsp; &emsp; Oxygen == on
| Include oxygen in the simulation of inorganic phosphorus dynamics
| Include oxygen in the simulation of inorganic phosphorus dynamics


|-
|-
|   atmospheric deposition == 0.5, 0.0
| &emsp; &emsp; Atmospheric Deposition == 0.5, 0.0
| Set atmospheric deposition of inorganic phosphorus parameters
| Set atmospheric deposition of inorganic phosphorus parameters


|-
|-
|   adsorption == linear, 0.005
| &emsp; &emsp; Adsorption == linear, 0.005
| Set adsorption model and parameter
| Set adsorption model and parameter


|-
|-
|   settling == 0.000
| &emsp; &emsp; Settling == 0.000
| Set settling rate of adsorbed inorganic phosphorus
| Set settling rate of adsorbed inorganic phosphorus


|-
|-
| end inorganic phosphorus model
| End Inorganic Phosphorus Model
| End inorganic phosphorus constituent model
| End inorganic phosphorus constituent model


|}
|}


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|-
|-
| width="400pt" | phyto model == basic, green
| style="width: 50%;" | Phyto Model == basic, green
| Set phytoplankton constituent model to be the basic model (i.e. assumed constant internal carbon to nutrient ratios), and named as “green”  
| Set phytoplankton constituent model to be the basic model (i.e. assumed constant internal carbon to nutrient ratios), and named as “green”  


|-
|-
|   min max == 0.05, 50.0
| &emsp; &emsp; Min Max == 0.05, 50.0
| Set min and max values the phytoplankton group
| Set min and max values the phytoplankton group


|-
|-
|   temperature limitation == none
| &emsp; &emsp; Temperature Limitation == none
| Set the temperature limitation model to none. Users may want to trail other models
| Set the temperature limitation model to none. Users may want to trial other models


|-
|-
|   salinity limitation == none
| &emsp; &emsp; Salinity Limitation == none
| Set the salinity limitation model to be off
| Set the salinity limitation model to be off


|-
|-
|   light limitation == basic, 0.0, 20.0
| &emsp; &emsp; Light Limitation == basic, 0.0, 20.0
| Set the light limitation model and parameters
| Set the light limitation model and parameters


|-
|-
|   nitrogen limitation == 0.01, 2.5
| &emsp; &emsp; Nitrogen Limitation == 0.01, 2.5
| Set the nitrogen limitation model and parameters
| Set the nitrogen limitation model and parameters


|-
|-
|   phosphorus limitation == 0.005, 0.01
| &emsp; &emsp; Phosphorus Limitation == 0.005, 0.01
| Set the phosphorus limitation model and parameters
| Set the phosphorus limitation model and parameters


|-
|-
|   uptake == 3.0, 0.6, 8.0
| &emsp; &emsp; Uptake == 3.0, 0.6, 8.0
| Set nutrient uptake parameters
| Set nutrient uptake parameters


|-
|-
|   primary productivity == 2.4, 1.2  
| &emsp; &emsp; Primary Productivity == 2.4, 1.2  
| Set primary productivity parameters
| Set primary productivity parameters


|-
|-
|   respiration == 0.01, 1.0, 0.3, 0.4, 0.5  
| &emsp; &emsp; Respiration == 0.01, 1.0, 0.3, 0.4, 0.5  
| Set respiration parameters
| Set respiration parameters


|-
|-
|   carbon chla ratio == 27.8
| &emsp; &emsp; Carbon Chla Ratio == 27.8
| Set the carbon to chlorophyll a ratio
| Set the carbon to chlorophyll a ratio


|-
|-
|   nitrogen fixing == 0.001, 0.5
| &emsp; &emsp; Nitrogen Fixing == 0.001, 0.5
| Turn of nitrogen fixing and set its parameters
| Turn on nitrogen fixing and set its parameters


|-
|-
|   settling == constant, -0.05
| &emsp; &emsp; Settling == constant, -0.05
| Set a constant settling rate model and its parameter
| Set a constant settling rate model and its parameter


|-
|-
| end phyto model
| End Phyto Model
| End phytoplankton constituent model
| End phytoplankton constituent model


|}
|}


{|class="wikitable" width="1200pt"
{|class="wikitable" style="width: 90%;"
|-
|-


Line 383: Line 404:
|
|
|-
|-
| width="400pt" | material == default
| style="width: 50%;" | Material == default
| rowspan="7" | Set default material properties for all constituents that are allowed sediment fluxes
| rowspan="7" | Set default material properties for all constituents that are allowed sediment fluxes
|-
|-
|   oxygen flux == -10.0  
| &emsp; &emsp; Oxygen Flux == -10.0  
|-
|-
|   silicate flux == 10.0
| &emsp; &emsp; Silicate Flux == 10.0
|-
|-
|   ammonium flux == 20.0
| &emsp; &emsp; Ammonium Flux == 20.0
|-
|-
|   nitrate flux == 30.0  
| &emsp; &emsp; Nitrate Flux == 30.0  
|-
|-
|   frp flux == 5.0  
| &emsp; &emsp; FRP Flux == 5.0  
|-
|-
| end material
| End Material


|-
|-
| material == 1
| Material == 1
| rowspan="3" | Set sediment oxygen properties for material 1 (unchanged from model 000)
| rowspan="3" | Set sediment oxygen properties for material 1 (unchanged from model 000)
|-
|-
|   oxygen flux == -550.0  
| &emsp; &emsp; Oxygen Flux == -550.0  
|-
|-
| end material
| End Material


|-
|-
| material == 2 ! Mudflats
| Material == 2 ! Mudflats
| rowspan="3" | Set sediment oxygen properties for material 2 (unchanged from model 000)
| rowspan="3" | Set sediment oxygen properties for material 2 (unchanged from model 000)
|-
|-
|   oxygen flux == 0.0  
| &emsp; &emsp; Oxygen Flux == 0.0  
|-
|-
| end material
| End Material


|-
|-
| material == 4 ! Deep channel
| Material == 4 ! Deep channel
| rowspan="3" | Set sediment oxygen properties for material 4 (unchanged from model 000)
| rowspan="3" | Set sediment oxygen properties for material 4 (unchanged from model 000)
|-
|-
|   oxygen flux == -3500.0  
| &emsp; &emsp; Oxygen Flux == -3500.0  
|-
|-
| end material
| End Material


|}
|}
Line 432: Line 453:
:** Free reactive phosphorus (mg/L)
:** Free reactive phosphorus (mg/L)
:** Adsorbed free reactive phosphorus (mg/L)
:** Adsorbed free reactive phosphorus (mg/L)
:** One phytoplankton group called “green”
:** One phytoplankton group called “green” (&mu;g/L)
:*    Uses the milligrams per litre units system, with TUFLOW FV calling the WQ Module every 30 minutes
:*    Uses the milligrams per litre units system, with TUFLOW FV calling the WQ Module every 30 minutes
:* Has sediment oxygen demand that varies spatially across various material types, but constant behaviour for all other sediment releases.
:* Has sediment oxygen demand that varies spatially across various material types, but constant behaviour for all other sediment releases.


===Model 002: Organics===
===Model 002: Organics===
Simulation of organics is often the next logical step after simulating inorganics. The model WQ_002.fvc provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing. Constituent model blocks for oxygen, silicate, inorganic nitrogen, inorganic phosphorus and phytoplankton are unchanged from model 001. <br>
Simulation of organics is often the next logical step after simulating inorganics. The model [https://fvwiki.tuflow.com/index.php?title=WQ_002.fvc WQ_002.fvc] provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing. Constituent model blocks for oxygen, silicate, inorganic nitrogen, inorganic phosphorus and phytoplankton are unchanged from model 001. <br>


{|class="wikitable" width="1200pt"
{|class="wikitable" style="width: 90%;"
|-
|-


Line 445: Line 466:
|
|
|-
|-
| width="400pt" | simulation class == organics
| style="width: 50%;" | Simulation Class == organics
| Set the overall simulation class to be “organics”
| Set the overall simulation class to be “organics”


|-
|-
| wq dt == 1800.0
| WQ dt == 1800.0
| Set the water quality module timestep. This is the frequency at which the WQ module is called from TUFLOW FV
| Set the Water Quality Module timestep. This is the frequency at which the WQ Module is called from TUFLOW FV


|-
|-
| wq units == mgl
| WQ units == mgl
| Set the units of simulation of the WQ module.  
| Set the units of simulation of the WQ Module.  


|}
|}


{|class="wikitable" width="1200pt"
{|class="wikitable" style="width: 90%;"
|-
|-


Line 468: Line 489:
|
|
|-
|-
| width="400pt" | organic matter model == refractory
| style="width: 50%;" | Organic Matter Model == refractory
| Set organics constituent model to be both labile and refractory
| Set organics constituent model to be both labile and refractory


|-
|-
|   carbon min max == 0.0, 10.0, 0.0, 10.0
| &emsp; &emsp; Carbon Min Max == 0.0, 10.0, 0.0, 10.0
| rowspan="3" | Set min and max values for labile particulate and labile dissolved organic carbon, nitrogen and phosphorus  
| rowspan="3" | Set min and max values for labile particulate and labile dissolved organic carbon, nitrogen and phosphorus  
|-
|-
|   nitrogen min max == 0.0, 10.0, 0.0, 10.0
| &emsp; &emsp; Nitrogen Min Max == 0.0, 10.0, 0.0, 10.0
|-
|-
|   phosphorus min max == 0.0, 10.0, 0.0, 10.0
| &emsp; &emsp; Phosphorus Min Max == 0.0, 10.0, 0.0, 10.0


|-
|-
|   organics benthic == 1.0, 1.08
| &emsp; &emsp; Organics Benthic == 1.0, 1.08
| Set labile organic matter hydrolysis parameters
| Set labile organic matter hydrolysis parameters


|-
|-
|   mineralisation == 0.01, 1.2, 1.03, 0.5, 0.5  
| &emsp; &emsp; Mineralisation == 0.01, 1.2, 1.03, 0.5, 0.5  
| Set labile organic matter mineralisation parameters
| Set labile organic matter mineralisation parameters


|-
|-
|   self shading == 0.0, 0.0
| &emsp; &emsp; Self Shading == 0.0, 0.0
| Set labile organic matter self shading parameters
| Set labile organic matter self shading parameters


|-
|-
|   settling == stokes, 0.00000035, 2450.8
| &emsp; &emsp; Settling == stokes, 0.00000035, 2450.8
| Set labile particulate settling model and parameters
| Set labile particulate settling model and parameters


|-
|-
|   ref carbon min max == 0.0, 10.0, 0.0, 10.0
| &emsp; &emsp; Ref Carbon Min Max == 0.0, 10.0, 0.0, 10.0
| rowspan="3" | Set min and max values for refractory particulate and refractory dissolved organic carbon, nitrogen and phosphorus  
| rowspan="3" | Set min and max values for refractory particulate and refractory dissolved organic carbon, nitrogen and phosphorus  
|-
|-
|   ref nitrogen min max == 0.0, 10.0, 0.0, 10.0
| &emsp; &emsp; Ref Nitrogen Min Max == 0.0, 10.0, 0.0, 10.0
|-
|-
|   ref phosphorus min max == 0.0, 9.0, 0.0, 9.0
| &emsp; &emsp; Ref Phosphorus Min Max == 0.0, 9.0, 0.0, 9.0


|-
|-
|   ref breakdown == 0.001, 0.1, 0.01
| &emsp; &emsp; Ref Breakdown == 0.001, 0.1, 0.01
| Set refractory organic matter breakdown parameters
| Set refractory organic matter breakdown parameters


|-
|-
|   ref activation == 0.01
| &emsp; &emsp; Ref Activation == 0.01
| Set refractory organic matter activation parameters
| Set refractory organic matter activation parameters


|-
|-
|   ref photolysis == 0.5
| &emsp; &emsp; Ref Photolysis == 0.5
| Set refractory organic matter photolysis parameter
| Set refractory organic matter photolysis parameter


|-
|-
|   ref self shading == 0.0, 0.0
| &emsp; &emsp; Ref Self Shading == 0.0, 0.0
| Set refractory organic matter self shading parameters
| Set refractory organic matter self shading parameters


|-
|-
|   ref settling == stokes, 0.00000045, 2450.8
| &emsp; &emsp; Ref Settling == stokes, 0.00000045, 2450.8
| Set refractory particulate settling model and parameters
| Set refractory particulate settling model and parameters


|-
|-
| end organic matter model
| End Organic Matter Model
| End organics constituent model  
| End organics constituent model  


|}
|}


{|class="wikitable" width="1200pt"
{|class="wikitable" style="width: 90%;"
|-
|-


Line 536: Line 557:
|
|
|-
|-
| width="400pt" | material == default
| style="width: 50%;" | Material == default
| rowspan="10" | Set default material properties for all constituents that are allowed sediment fluxes
| rowspan="10" | Set default material properties for all constituents that are allowed sediment fluxes
|-
|-
|   oxygen flux == -10.0
| &emsp; &emsp; Oxygen Flux == -10.0
|-
|-
|   silicate flux == 10.0
| &emsp; &emsp; Silicate Flux == 10.0
|-
|-
|   ammonium flux == 20.0
| &emsp; &emsp; Ammonium Flux == 20.0
|-
|-
|   nitrate flux == 30.0
| &emsp; &emsp; Nitrate Flux == 30.0
|-
|-
|   frp flux == 5.0
| &emsp; &emsp; FRP Flux == 5.0
|-
|-
|   doc flux == 20.0
| &emsp; &emsp; DOC Flux == 20.0
|-
|-
|   don flux == 10.0
| &emsp; &emsp; DON Flux == 10.0
|-
|-
|   dop flux == 5.0
| &emsp; &emsp; DOP Flux == 5.0
|-
|-
| end material
| End Material


|-
|-
| material == 1
| Material == 1
| rowspan="3" | Set sediment oxygen properties for material 1 (unchanged from model 000)
| rowspan="3" | Set sediment oxygen properties for material 1 (unchanged from model 000)
|-
|-
|   oxygen flux == -550.0  
| &emsp; &emsp; Oxygen Flux == -550.0  
|-
|-
| end material
| End Material


|-
|-
| material == 2 ! Mudflats
| Material == 2 ! Mudflats
| rowspan="3" | Set sediment oxygen properties for material 2 (unchanged from model 000)
| rowspan="3" | Set sediment oxygen properties for material 2 (unchanged from model 000)
|-
|-
|   oxygen flux == 0.0  
| &emsp; &emsp; Oxygen Flux == 0.0  
|-
|-
| end material
| End Material


|-
|-
| material == 4 ! Deep channel
| Material == 4 ! Deep channel
| rowspan="3" | Set sediment oxygen properties for material 4 (unchanged from model 000)
| rowspan="3" | Set sediment oxygen properties for material 4 (unchanged from model 000)
|-
|-
|   oxygen flux == -3500.0  
| &emsp; &emsp; Oxygen Flux == -3500.0  
|-
|-
| end material
| End Material


|}
|}
Line 597: Line 618:
:** Particulate and dissolved refractory organic nitrogen (mg/L)
:** Particulate and dissolved refractory organic nitrogen (mg/L)
:** Particulate and dissolved refractory organic phosphorus (mg/L)
:** Particulate and dissolved refractory organic phosphorus (mg/L)
:** One phytoplankton group called “green”
:** One phytoplankton group called “green” (&mu;g/L)
:* Uses the milligrams per litre units system, with TUFLOW FV calling the WQ Module every 30 minutes
:* Uses the milligrams per litre units system, with TUFLOW FV calling the WQ Module every 30 minutes
:* Has sediment oxygen demand that varies spatially across various material types, but constant behaviour for all other sediment releases.
:* Has sediment oxygen demand that varies spatially across various material types, but constant behaviour for all other sediment releases.
Line 619: Line 640:
===Model 000: Dissolved Oxygen===
===Model 000: Dissolved Oxygen===


All results from this simulation can be viewed and interrogated in QGIS using TUFLOW Viewer. To start this process: <br>
All results from this simulation can be viewed and interrogated in QGIS using the TUFLOW Viewer Plugin. To start this process: <br>


:* Open QGIS
'''1.''' Open QGIS <br>
:* Make sure the [https://wiki.tuflow.com/index.php?title=TUFLOW_Viewer TUFLOW Viewer Plugin] is installed
'''2.''' Make sure the [https://wiki.tuflow.com/index.php?title=TUFLOW_Viewer TUFLOW Viewer Plugin] is installed <br>
::[[File:T09_7.0.0.01.png | 300px]]<br>
::[[File:T09_7.0.0.01.png | 300px]]<br>
:* Load the water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. Initially, this tutorial will use WQ_000_WQ.nc
'''3.''' Within the TUFLOW Viewer Plugin, load the water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. This tutorial will initially use WQ_000_WQ.nc <br>
::[[File:T09_7.0.0.02.png | 300px]]<br>
::[[File:T09_7.0.0.02.png | 300px]]<br>
:* Once loaded, click once on the WQ_DISS_OXYGEN_MG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset
'''4.''' Once loaded, click once on the WQ_DISS_OXYGEN_MG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset <br>
::[[File:T09_7.0.0.03.png | 300px]]<br>
::[[File:T09_7.0.0.03.png | 300px]]<br>


::[[File:T09_7.0.0.04.png | 300px]]<br>
::[[File:T09_7.0.0.04.png | 300px]]<br>
:* Click the TUFLOW Viewer mesh rendering button, if desired [[File:T09_7.0.0.05.png | 100px]]. This will show the mesh, but is not required to be displayed
'''5.''' Click the TUFLOW Viewer Mesh Rendering button, if desired [[File:T09_7.0.0.05.png | 100px]]. This will show the mesh, but is not required to be displayed <br>
::[[File:T09_7.0.0.06.png | 375px]]<br>
::[[File:T09_7.0.0.06.png | 375px]]<br>
   
   
Line 639: Line 660:
The three dimensional netcdf dataset can be interrogated at a single x/y coordinate location, and a vertical profile over the water column at that location then plotted. This output is a line, and the time at which this line is plotted can be adjusted using the TUFLOW Viewer time controls. To do this: <br>
The three dimensional netcdf dataset can be interrogated at a single x/y coordinate location, and a vertical profile over the water column at that location then plotted. This output is a line, and the time at which this line is plotted can be adjusted using the TUFLOW Viewer time controls. To do this: <br>


:* Make sure the WQ_DISS_OXYGEN_MG_L field is selected as above
'''1.''' Make sure the WQ_DISS_OXYGEN_MG_L field is selected as above <br>
:* Click the down arrow next to the TUFLOW Viewer Vertical Profile button and select the WQ_DISS_OXYGEN_MG_L field checkbox  
'''2.''' Click the down arrow next to the TUFLOW Viewer Vertical Profile button and select the WQ_DISS_OXYGEN_MG_L field checkbox <br>
::[[File:T09_7.0.1.01.png|300px]]<br>
::[[File:T09_7.0.1.01.png|300px]]<br>
:* Click again on the same down arrow to exit the drop down menu
'''3.''' Click again on the same down arrow to exit the drop down menu <br>
:* Click once on the TUFLOW Viewer Vertical Profile button itself
'''4.''' Click once on the TUFLOW Viewer Vertical Profile button itself <br>
::[[File:T09_7.0.1.02.png|300px]]<br>
::[[File:T09_7.0.1.02.png|300px]]<br>
:* Click once anywhere within the model domain – somewhere near the deeper northern end of the model will be more interesting than the shallow areas. A pink dot will appear on the clicked location, and a profile of dissolved oxygen concentration at that location will appear in the TUFLOW Viewer Plot window, within the Vertical Profile tab. The initial profile will be uniform with depth because the water quality model was initialised with a single dissolved oxygen concentration everywhere within the domain
'''5.''' Click once anywhere within the model domain – somewhere near the deeper northern end of the model will be more interesting than the shallow areas. A pink dot will appear on the clicked location, and a profile of dissolved oxygen concentration at that location will appear in the TUFLOW Viewer Plot window, within the Vertical Profile tab. The initial profile will be uniform with depth because the water quality model was initialised with a single dissolved oxygen concentration everywhere within the domain <br>
::[[File:T09_7.0.1.03.png|100px]]<br>
::[[File:T09_7.0.1.03.png|100px]]<br>


::[[File:T09_7.0.1.04.png|700px]]<br>
::[[File:T09_7.0.1.04.png|700px]]<br>
:* Right click on the Plot window and select Customise  
'''6.''' Right click on the Plot window and select Customise <br>
::[[File:T09_7.0.1.05.png|700px]]<br>
::[[File:T09_7.0.1.05.png|700px]]<br>
:* Select the desired depth (y-axis) and dissolved oxygen (x-axis) ranges, and rename axes labels if desired, and click OK. Make sure the ranges include all the data to be displayed, otherwise the plot will disappear off the axes. The ranges shown below are satisfactory in this example
'''7.''' Select the desired depth (y-axis) and dissolved oxygen (x-axis) ranges, and rename axes labels if desired, and click OK. Make sure the ranges include all the data to be displayed, otherwise the plot will disappear off the axes. The ranges shown below are satisfactory in this example <br>
::[[File:T09_7.0.1.06.png|300px]]<br>
::[[File:T09_7.0.1.06.png|300px]]<br>
:* The Plot window should appear similar to the below. The vertical dimension (depth) is shown in the y-axis and dissolved oxygen concentration on the x-axis. The green line is the dissolved oxygen concentration at all model depths at the X/Y location previously chosen, at the initial timestep of the model simulation.
'''8.''' The Plot window should appear similar to the below. The vertical dimension (depth) is shown in the y-axis and dissolved oxygen concentration on the x-axis. The green line is the dissolved oxygen concentration at all model depths at the X/Y location previously chosen, at the initial timestep of the model simulation <br>
::[[File:T09_7.0.1.07.png|700px]]<br>
::[[File:T09_7.0.1.07.png|700px]]<br>
:* Click on the Freeze axis limits button to keep the ranges selected throughout time
'''9.''' Click on the Freeze Axis Limits button to keep the ranges selected throughout time <br>
::[[File:T09_7.0.1.08.png|300px]]<br>
::[[File:T09_7.0.1.08.png|300px]]<br>
:* Use the TUFLOW Viewer time navigation buttons to see how the (green line) vertical profile of dissolved oxygen at the chosen X/Y location changes in time. Check the Show as dates box to have the model time presented as dates
'''10.''' Use the TUFLOW Viewer Time Navigation buttons to see how the (green line) vertical profile of dissolved oxygen at the chosen X/Y location changes in time. Check the Show as dates box to have the model time presented as dates <br>
::[[File:T09_7.0.1.09.png|700px]]<br>
::[[File:T09_7.0.1.09.png|700px]]<br>
:* It is expected that dissolved oxygen will decrease at depth (due to sediment consumption), and increase at the surface (due to atmospheric reaeration), to show profiles similar to the below. Overturning events where the water column vertically mixes are also expected
'''11.''' It is expected that dissolved oxygen will decrease at depth (due to sediment consumption), and increase at the surface (due to atmospheric reaeration), to show profiles similar to the below. Overturning events where the water column vertically mixes are also expected <br>
::[[File:T09_7.0.1.10.png|700px]]<br>
::[[File:T09_7.0.1.10.png|700px]]<br>


Line 666: Line 687:
The three dimensional netcdf dataset can be interrogated concurrently at multiple x/y coordinate locations, and a continuous vertical curtain profile over the water column at those locations plotted. This is essentially a vertical slice through the three dimensional dataset, at a series of X/Y points that form a line over the model domain when viewed in plan. This output is a colour contoured curtain, and the time at which this curtain is plotted can be adjusted using the TUFLOW Viewer time controls. To do this: <br>
The three dimensional netcdf dataset can be interrogated concurrently at multiple x/y coordinate locations, and a continuous vertical curtain profile over the water column at those locations plotted. This is essentially a vertical slice through the three dimensional dataset, at a series of X/Y points that form a line over the model domain when viewed in plan. This output is a colour contoured curtain, and the time at which this curtain is plotted can be adjusted using the TUFLOW Viewer time controls. To do this: <br>


:* Make sure the WQ_DISS_OXYGEN_MG_L field is selected as above
'''1.''' Make sure the WQ_DISS_OXYGEN_MG_L field is selected as above <br>
:* Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_DISS_OXYGEN_MG_L field checkbox  
'''2.''' Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_DISS_OXYGEN_MG_L field checkbox <br>
::[[File:T09_7.0.2.01.png | 300px ]] <br>
::[[File:T09_7.0.2.01.png | 300px ]] <br>
:* Click again on the same down arrow to exit the drop down menu
'''3.''' Click again on the same down arrow to exit the drop down menu <br>
:* Click on the TUFLOW Viewer Curtain Plot button itself
'''4.''' Click on the TUFLOW Viewer Curtain Plot button itself <br>
::[[File:T09_7.0.2.02.png | 300px ]] <br>
::[[File:T09_7.0.2.02.png | 300px ]] <br>
:* Click a path along the desired curtain X/Y location within the model domain – somewhere along the deeper drowned river thalweg from the northern end of the model to the south will be more interesting than the shallow areas. Double click to end the curtain path definition. A green line will appear along the clicked locations, and a curtain profile of dissolved oxygen concentration along that path will appear in the TUFLOW Viewer Plot window, within the Cross Section / Long Profile tab. The left hand end of the curtain colour contour will be the first location clicked in the green path
'''5.''' Click a path along the desired curtain X/Y location within the model domain – somewhere along the deeper drowned river thalweg from the northern end of the model to the south will be more interesting than the shallow areas. Double click to end the curtain path definition. A green line will appear along the clicked locations, and a curtain profile of dissolved oxygen concentration along that path will appear in the TUFLOW Viewer Plot window, within the Cross Section / Long Profile tab, as shown below. The left hand end of the curtain colour contour will be the first location clicked in the green path <br>
::[[File:T09_7.0.2.03.png | 400px ]] <br>
::[[File:T09_7.0.2.03.png | 400px ]] <br>


::[[File:T09_7.0.2.04.png | 700px ]] <br>
::[[File:T09_7.0.2.04.png | 700px ]] <br>
:* Customise the plot as previously described, and click OK
'''6.''' Customise the plot as previously described, and click OK <br>
::[[File:T09_7.0.2.05.png | 300px ]] <br>
::[[File:T09_7.0.2.05.png | 300px ]] <br>
:* The colourbar scale, name and map can be adjusted by clicking on the Images, etc. tab
'''7.''' The colourbar scale, name and map can be adjusted by clicking on the Images, etc. tab <br>
::[[File:T09_7.0.2.06.png | 300px ]] <br>
::[[File:T09_7.0.2.06.png | 300px ]] <br>
:* The curtain plot should then look similar to the following (it will have different data depending on the time selected)
'''8.''' The curtain plot should then look similar to the following (it will have different data depending on the time selected) <br>
::[[File:T09_7.0.2.07.png | 700px ]] <br>
::[[File:T09_7.0.2.07.png | 700px ]] <br>
:* Use the TUFLOW Viewer time navigation buttons to see how the vertical curtain of dissolved oxygen along the chosen X/Y path changes in time. Check the Show as dates box to have the model time presented as dates
'''9.''' Use the TUFLOW Viewer Time Navigation buttons to see how the vertical curtain of dissolved oxygen along the chosen X/Y path changes in time. Check the Show as dates box to have the model time presented as dates <br>
::[[File:T09_7.0.2.08.png | 700px ]] <br>
::[[File:T09_7.0.2.08.png | 700px ]] <br>
:* It is expected that dissolved oxygen will decrease at depth (due to sediment consumption), and increase at the surface (due to atmospheric reaeration). Overturning events where the water column vertically mixes are also expected
'''10.''' It is expected that dissolved oxygen will decrease at depth (due to sediment consumption), and increase at the surface (due to atmospheric reaeration). Overturning events where the water column vertically mixes are also expected <br>


====Vertical curtain profiles – GIS location====
====Vertical curtain profiles – GIS location====
Line 690: Line 711:
Whilst the three dimensional netcdf dataset can be interrogated along a manually defined curtain as above, it is sometimes more convenient to use a predefined and repeatable curtain transect path. This can be achieved by using a shapefile to set the transect location rather than manual digitising. To do this: <br>
Whilst the three dimensional netcdf dataset can be interrogated along a manually defined curtain as above, it is sometimes more convenient to use a predefined and repeatable curtain transect path. This can be achieved by using a shapefile to set the transect location rather than manual digitising. To do this: <br>


:* Make sure the WQ_000_WQ.nc dataset is loaded into the TUFLOW Viewer as above, and the WQ_DISS_OXYGEN_MG_L field is selected
'''1.''' Make sure the WQ_000_WQ.nc dataset is loaded into the TUFLOW Viewer as above, and the WQ_DISS_OXYGEN_MG_L field is selected <br>
:* Drag the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" onto the QGIS map window. The location of the transect will appear on top of the WQ_DISS_OXYGEN_MGL contours as a line
'''2.''' Drag the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" onto the QGIS Map window. The location of the transect will appear on top of the WQ_DISS_OXYGEN_MGL contours as a line <br>
::[[File:T09_7.0.3.01.png | 400px ]] <br>
::[[File:T09_7.0.3.01.png | 400px ]] <br>
:* Click on the QGIS selection tool
'''3.''' Click on the QGIS Selection tool <br>
::[[File:T09_7.0.3.02.png | 200px ]] <br>
::[[File:T09_7.0.3.02.png | 200px ]] <br>
:* Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour
'''4.''' Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour <br>
::[[File:T09_7.0.3.03.png | 300px ]] <br>
::[[File:T09_7.0.3.03.png | 300px ]] <br>
:* Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_DISS_OXYGEN_MG_L field checkbox  
'''5.''' Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_DISS_OXYGEN_MG_L field checkbox <br>
::[[File:T09_7.0.3.04.png | 300px ]] <br>
::[[File:T09_7.0.3.04.png | 300px ]] <br>
:* Click again on the same down arrow to exit the drop down menu
'''6.''' Click again on the same down arrow to exit the drop down menu <br>
:* Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting
'''7.''' Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting <br>
::[[File:T09_7.0.3.05.png | 400px ]] <br>
::[[File:T09_7.0.3.05.png | 400px ]] <br>
:* Click on the Curtain button
'''8.''' Click on the Curtain button <br>
::[[File:T09_7.0.3.07.png | 300px ]] <br>
::[[File:T09_7.0.3.07.png | 300px ]] <br>
:* A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows
'''9.''' A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows <br>
::[[File:T09_7.0.3.08.png | 700px ]] <br>
::[[File:T09_7.0.3.08.png | 700px ]] <br>
:* Make any changes to the plot axes or colour bar as required (see above)
'''10.''' Make any changes to the plot axes or colour bar as required (see above) <br>
:* As above, use the TUFLOW Viewer time navigation buttons to see how the vertical curtain of dissolved oxygen along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, dissolved oxygen will decrease at depth, as expected
'''11.''' As above, use the TUFLOW Viewer Time Navigation buttons to see how the vertical curtain of dissolved oxygen along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, dissolved oxygen will decrease at depth, as expected <br>
::[[File:T09_7.0.3.09.png | 700px ]] <br>
::[[File:T09_7.0.3.09.png | 700px ]] <br>
:* Overturning events will also occur during the simulation to return the lower depth dissolved oxygen concentrations in part
'''12.''' Overturning events will also occur during the simulation to restore dissolved oxygen concentrations at depth <br>
::[[File:T09_7.0.3.10.png | 700px ]] <br>
::[[File:T09_7.0.3.10.png | 700px ]] <br>


Line 716: Line 737:
The same curtain interrogation techniques can be used to examine the inorganics (001) simulation results. Using the same interrogation techniques described above, the inorganic phosphorus concentrations can be examined along the same curtain, especially in the location of the wastewater treatment plant. To do this: <br>
The same curtain interrogation techniques can be used to examine the inorganics (001) simulation results. Using the same interrogation techniques described above, the inorganic phosphorus concentrations can be examined along the same curtain, especially in the location of the wastewater treatment plant. To do this: <br>


:* Load the inorganics water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. In this case, WQ_001_WQ.nc will be loaded
'''1.''' Load the inorganics water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. In this case, WQ_001_WQ.nc will be loaded <br>
::[[File:T09_7.1.01.png | 300 px]] <br>
::[[File:T09_7.1.01.png | 300 px]] <br>
:* Once loaded, click once on the WQ_FRP_MG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset
'''2.''' Once loaded, click once on the WQ_FRP_MG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset <br>
::[[File:T09_7.1.02.png | 300 px]] <br>
::[[File:T09_7.1.02.png | 300 px]] <br>
:* Make sure the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" is loaded into the QGIS map window as above
'''3.''' Make sure the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" is loaded into the QGIS Map window as above <br>
:* Click on the QGIS selection tool
'''4.''' Click on the QGIS Selection tool <br>
::[[File:T09_7.1.03.png | 200 px]] <br>
::[[File:T09_7.1.03.png | 200 px]] <br>
:* Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour
'''5.''' Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour <br>
::[[File:T09_7.1.04.png | 300 px]] <br>
::[[File:T09_7.1.04.png | 300 px]] <br>
:* Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_FRP_MG_L field checkbox  
'''6.''' Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_FRP_MG_L field checkbox <br>
::[[File:T09_7.1.05.png | 300 px]] <br>
::[[File:T09_7.1.05.png | 300 px]] <br>
:* Click again on the same down arrow to exit the drop down menu
'''7.''' Click again on the same down arrow to exit the drop down menu <br>
:* Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting
'''8.''' Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting <br>
::[[File:T09_7.1.06.png | 400 px]] <br>
::[[File:T09_7.1.06.png | 400 px]] <br>
:* Click on the Curtain button
'''9.''' Click on the Curtain button <br>
::[[File:T09_7.1.07.png | 300 px]] <br>
::[[File:T09_7.1.07.png | 300 px]] <br>
:* A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows  
'''10.''' A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows <br>
::[[File:T09_7.1.08.png | 700 px]] <br>
::[[File:T09_7.1.08.png | 700 px]] <br>
:* Make any changes to the plot axes or colourbar as required (see above)
'''11.''' Make any changes to the plot axes or colourbar as required (see above) <br>
:* As above, use the TUFLOW Viewer time navigation buttons to see how the vertical curtain of FRP along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, FRP will increase at the location of the wastewater treatment plant discharge, as expected
'''12.''' As above, use the TUFLOW Viewer Time Navigation buttons to see how the vertical curtain of FRP along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, FRP will increase at the location of the wastewater treatment plant discharge, as expected <br>
::[[File:T09_7.1.09.png | 700 px]] <br>
::[[File:T09_7.1.09.png | 700 px]] <br>


Line 742: Line 763:
The same curtain interrogation techniques can be used to examine the organics (002) simulation results. Using the same interrogation techniques described above, the phytoplankton concentrations can be examined along the same curtain, especially in the location of the wastewater treatment plant. To do this: <br>
The same curtain interrogation techniques can be used to examine the organics (002) simulation results. Using the same interrogation techniques described above, the phytoplankton concentrations can be examined along the same curtain, especially in the location of the wastewater treatment plant. To do this: <br>


:* Load the organics water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. In this case, WQ_002_WQ.nc will be loaded
'''1.''' Load the organics water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. In this case, WQ_002_WQ.nc will be loaded <br>
::[[File:T09_7.2.01.png | 300px]] <br>
::[[File:T09_7.2.01.png | 300px]] <br>
:* Once loaded, click once on the WQ_PHYTO_GREEN_CONC_MICG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset
'''2.''' Once loaded, click once on the WQ_PHYTO_GREEN_CONC_MICG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset <br>
::[[File:T09_7.2.02.png | 300px]] <br>
::[[File:T09_7.2.02.png | 300px]] <br>
:* Make sure the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" is loaded into the QGIS map window as above
'''3.''' Make sure the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" is loaded into the QGIS Map window as above <br>
:* Click on the QGIS selection tool
'''4.''' Click on the QGIS Selection tool
::[[File:T09_7.2.03.png | 200px]] <br>
::[[File:T09_7.2.03.png | 200px]] <br>
:* Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour
'''5.''' Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour <br>
::[[File:T09_7.2.04.png | 300px]] <br>
::[[File:T09_7.2.04.png | 300px]] <br>
:* Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_PHYTO_GREEN_CONC_MICG_L field checkbox.
'''6.''' Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_PHYTO_GREEN_CONC_MICG_L field checkbox <br>
::[[File:T09_7.2.05.png | 300px]] <br>
::[[File:T09_7.2.05.png | 300px]] <br>
:* Click again on the same down arrow to exit the drop down menu
'''7.''' Click again on the same down arrow to exit the drop down menu <br>
:* Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting
'''8.''' Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting <br>
::[[File:T09_7.2.06.png | 400px]] <br>
::[[File:T09_7.2.06.png | 400px]] <br>
:* Click on the Curtain button
'''9.''' Click on the Curtain button <br>
::[[File:T09_7.2.07.png | 300px]] <br>
::[[File:T09_7.2.07.png | 300px]] <br>
:* A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows
'''10.''' A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows <br>
::[[File:T09_7.2.08.png | 700px]] <br>
::[[File:T09_7.2.08.png | 700px]] <br>
:* Make any changes to the plot axes or colourbar as required (see above)
'''11.''' Make any changes to the plot axes or colourbar as required (see above) <br>
:* As above, use the TUFLOW Viewer time navigation buttons to see how the vertical curtain of phytoplankton concentration along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, phytoplankton grows and concentrations increase at the location of the wastewater treatment plant discharge (and elsewhere through advection), as expected
'''12.''' As above, use the TUFLOW Viewer Time Navigation buttons to see how the vertical curtain of phytoplankton concentration along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, phytoplankton grows and concentrations increase at the location of the wastewater treatment plant discharge (and elsewhere through advection), as expected <br>
::[[File:T09_7.0.3.06.png | 700px]] <br>
::[[File:T09_7.0.3.06.png | 700px]] <br>
:* Try plotting other TUFLOW FV WQ Module variables to see how they evolve in time
'''13.''' Try plotting other TUFLOW FV WQ Module variables to see how they evolve in time <br>
<br>
<br>


=Conclusion=
=Conclusion=


This tutorial has covered the basics of setting up, executing and interrogating a TUFLOW FV water quality module simulation. To complete more tutorials or learn more tips and tricks, please return to the [[Main Page|TUFLOW FV Wiki Mainpage]].
This tutorial has covered the basics of setting up, executing and interrogating a TUFLOW FV WQ Module simulation. To complete more tutorials or learn more tips and tricks (including how to take advantage of the [[Use of Water Quality Module Diagnostics | WQ Module's diagnostic variables]] in your model calibration process), please return to the [[Main Page|TUFLOW FV Wiki Mainpage]].

Revision as of 12:32, 28 March 2023

USEFUL LINKS
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TUFLOW Classic/HPC Wiki TUFLOW FV Glossary Manuals

Tutorial Description

Tutorial Module 09 demonstrates the development of a 3D water quality model using the TUFLOW FV Water Quality (WQ) Module. Starting with the final model of Tutorial 05, this tutorial will progressively increase in complexity, incorporating the simulation of dissolved oxygen, then inorganic nutrients, and finally capturing full organic nutrient cycling. Tutorial Module 09 provides a full set of working model files that can be re-run and experimented with.

The tutorial is broken up into the following subsections:


Set up TUFLOW FV

This tutorial recommends the use of TUFLOW FV 2023.0 or later, available on the TUFLOW Downloads Page. Please download TUFLOW FV 2023.0 or later, and save to C:\TUFLOWFV\ or another preferred location. This location will be used in building scripts to run Tutorial 09's models.

This demonstration model dynamically couples TUFLOW FV with GOTM to model vertical turbulence exchanges. To do so, please download the TUFLOW FV External Turbulence API. Once downloaded, unzip the file .\GOTM\tuflowfv_external_turb.dll and replace the default tuflowfv_external_turb.dll that resides in the same directory as TUFLOWFV.exe (for example, C:\TUFLOWFV\2023.0\). If this step has already been undertaken as part of the running of Tutorial 05, then it need not be repeated here.

TUFLOW FV WQ uses the dynamically linked library tuflowfv_wq.dll, which ships with TUFLOW FV 2023.0 or later, so no additional user set up is required to access the compiled binary necessary for water quality simulation.

Tutorial Data

The data for Tutorial 09 is available from the TUFLOW Website. The folders and most of their contents are the same as those within Tutorial 05’s Complete_Model folder, with some additional folders. The initial condition and boundary condition files in Tutorial 09 are slightly altered and expanded (to account for water quality specification) versions of those provided in Tutorial 05.

Everything you need to complete this tutorial is within the Tutorial Module 09 data download folder. However, if you would like to better appreciate the model setting and hydrodynamics you may want to complete Tutorial 05 first.

Complete Model Folder Contents

Three water quality models are provided in the Complete_Model folder under the TUFLOWFV folder, and include:

  • .2dm model mesh file ‘hydraul_006.2dm’ (model\geo folder, unchanged from Tutorial 05)
  • 3D_Z_Layers_003.csv file (model\csv folder, unchanged from Tutorial 05)
  • Supporting GIS files for nodestring and material definition (model\gis folder)
  • GIS empty files for adding features to the model (model\gis\empty folder, unchanged from Tutorial 05)
  • Boundary condition data, in .csv and .nc format (bc_dbase and bc_dbase\met\ folders, with the latter unchanged from Tutorial 05)
  • Meteorology FVC file (bc_dbase\met\ folder, unchanged from Tutorial 05)
  • Sediment file FVSED for modelling sediment transport (stm folder, unchanged from Tutorial 05)
  • Water quality control files (wqm folder)
  • Results are not provided as part of this tutorial data package. The simulations need to run to produce results.

Upstream And Downstream Boundary Condition Files

The upstream boundary condition file from Tutorial 05 is the same in this tutorial but has added columns (one for each water quality constituent simulated). The added columns have headers that are not keywords in themselves, but are used by TUFLOW FV to determine water quality boundary conditions for each constituent based on ordered listing of these same headers in “bc” blocks in each TUFLOW FV control file (see subsequent sections for a description of this ordering process). This upstream boundary’s location is set in the model mesh via association with a nodestring.

The downstream nodestring boundary condition of Tutorial 09’s model mesh has been removed so that it presents a barrier (such as a dam wall) to flow rather than an outflow. A new boundary condition has been created in its place that is a polygon extraction that has outflows that approximately balance those entering the model from its upstream end. No salinity, temperature, sediment or water quality specifications (columns) are necessary for this extraction boundary condition because it represents outflows that have no influence on the model other than volumetric removal.

For the second and third simulations, a further inflow boundary condition is added (also as an inflow polygon) to represent a high nutrient wastewater treatment plant discharge.

Model Mesh File

This is the same model mesh as that used in Tutorial 05.

Meteorological NetCDF Files

The meteorological data for the model is the same as that used in Tutorial 05.

TUFLOW FV Hydrodynamic Model Setups

The TUFLOW FV control files for the models covered in this tutorial are located in the Complete_Model\TUFLOWFV\runs (TUFLOW FV control files) and Complete_Model\TUFLOWFV\wqm (TUFLOW FV WQ Module control files) directories. Descriptions are listed below.

WQ_000.fvc The same as HYD_002.fvc but with additional commands to allow for simulation of dissolved oxygen.
Companion water quality control file is WQ_000.fvwq (see following section)
WQ_001.fvc The same as HYD_002.fvc but with additional commands to allow for simulation of dissolved oxygen, inorganic nutrients and phytoplankton.
Companion water quality control file is WQ_001.fvwq (see following section)
WQ_002.fvc The same as HYD_002.fvc but with additional commands to allow for simulation of dissolved oxygen, inorganic nutrients, organic nutrients and phytoplankton.
Companion water quality control file is WQ_002.fvwq (see following section)


TUFLOW FV WQ Module Setups

The commands and syntax of the fvwq control files are provided below. Copy and paste commands into the search facility of the TUFLOW FV Water Quality Module manual for detailed descriptions of each.

Model 000: Dissolved oxygen

Dissolved oxygen simulation is often a good place to start when constructing water quality models. The model WQ_000.fvc provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing.

! SIMULATION CONTROLS
Simulation Class == do Set the overall simulation class to be "DO"
WQ dt == 1800.0 Set the Water Quality Module timestep. This is the frequency at which the WQ Module is called from TUFLOW FV
WQ Units == mgl Set the units of simulation of the WQ Module.
! CONSTITUENT MODEL SETTINGS
! Oxygen
Oxygen Model == O2 Set oxygen constituent model to be O2
    Oxygen Benthic == 0.5, 1.08 Set sediment oxygen consumption properties
End Oxygen Model End oxygen constituent model
! MATERIAL SPECIFICATIONS
Material == default Set default material properties
    Oxygen Flux == -10.0
End Material
Material == 1 Set sediment oxygen properties for material 1
    Oxygen Flux == -550.0
End Material
Material == 2 ! Mudflats Set sediment oxygen properties for material 2
    Oxygen Flux == 0.0
End Material
Material == 4 ! Deep channel Set sediment oxygen properties for material 4
    Oxygen Flux == -3500.0
End Material

The fvwq file has a set up that:

  • Deploys the “DO” Simulation Class, so therefore includes the water quality computed variables:
    • Dissolved oxygen (mg/L)
  • Uses the milligrams per litre units system, with TUFLOW FV calling the WQ Module every 30 minutes
  • Has sediment oxygen demand that varies spatially across various material types. These demands are greatest in the drowned river thalweg (material 4), and zero in the shallows

Model 001: Inorganics

Simulation of inorganics is often the next logical step after simulating dissolved oxygen. The model WQ_001.fvc provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing. The constituent model block for oxygen is unchanged from model 000. One phytoplankton group is simulated.

! SIMULATION CONTROLS
Simulation Class == inorganics Set the overall simulation class to be “inorganics”
WQ dt == 1800.0 Set the Water Quality Module timestep. This is the frequency at which the WQ Module is called from TUFLOW FV
WQ Units == mgl Set the units of simulation of the WQ Module.
! CONSTITUENT MODEL SETTINGS
! Silicate
Silicate Model == Si Set silicate constituent model to be Si
    Silicate Min Max == 0.0, 100.0 Set min and max values for silicate
    Oxygen Benthic == 4.2, 1.01 Set silicate sediment release properties
    Oxygen == on Include oxygen in the simulation of silicate dynamics
End Silicate Model End silicate constituent model
! Inorganic Nitrogen
Inorganic Nitrogen Model == ammoniumnitrate Set inorganic nitrogen constituent model to be ammoniumnitrate
    Ammonium Min Max == 0.0, 50.0 Set min and max values for ammonium and nitrate
    Ammonium Min Max == 0.0, 50.0
    Ammonium Benthic == 4.05, 1.06 Set ammonium and nitrate sediment release properties
    Nitrate Benthic == 4.25, 1.10
    Nitrification == 0.05, 4.15, 1.01 Set nitrification parameters
    Denitrification == michaelis menten, 0.05, 4.01, 1.03 Set denitrification model and properties
    Oxygen == on Include oxygen in the simulation of inorganic nitrogen dynamics
    Atmospheric Deposition == 5.0, 0.0, 0.5 Set atmospheric deposition of inorganic nitrogen parameters
    Anaerobic Oxidation Of Ammonium == 0.005, 2.5, 2.5 Set anammox parameters
    Diss Nitrate Reduction To Ammonium == 0.005, 5.0 Set DRNA parameters
End Inorganic Nitrogen Model End inorganic nitrogen constituent model
! Inorganic Phosphorus
Inorganic Phosphorus Model == frphsads Set inorganic phosphorus constituent model to be frphads, which includes simulation of free and adsorbed inorganic phosphorus
    FRP Min Max == 0.0, 5.0 Set min and max values for inorganic phosphorus and adsorbed inorganic phosphorus
    FRP Ads Min Max == 0.0, 5.0
    FRP Benthic == 4.3, 1.095 Set inorganic phosphorus sediment release properties
    Oxygen == on Include oxygen in the simulation of inorganic phosphorus dynamics
    Atmospheric Deposition == 0.5, 0.0 Set atmospheric deposition of inorganic phosphorus parameters
    Adsorption == linear, 0.005 Set adsorption model and parameter
    Settling == 0.000 Set settling rate of adsorbed inorganic phosphorus
End Inorganic Phosphorus Model End inorganic phosphorus constituent model
! Phytoplankton
Phyto Model == basic, green Set phytoplankton constituent model to be the basic model (i.e. assumed constant internal carbon to nutrient ratios), and named as “green”
    Min Max == 0.05, 50.0 Set min and max values the phytoplankton group
    Temperature Limitation == none Set the temperature limitation model to none. Users may want to trial other models
    Salinity Limitation == none Set the salinity limitation model to be off
    Light Limitation == basic, 0.0, 20.0 Set the light limitation model and parameters
    Nitrogen Limitation == 0.01, 2.5 Set the nitrogen limitation model and parameters
    Phosphorus Limitation == 0.005, 0.01 Set the phosphorus limitation model and parameters
    Uptake == 3.0, 0.6, 8.0 Set nutrient uptake parameters
    Primary Productivity == 2.4, 1.2 Set primary productivity parameters
    Respiration == 0.01, 1.0, 0.3, 0.4, 0.5 Set respiration parameters
    Carbon Chla Ratio == 27.8 Set the carbon to chlorophyll a ratio
    Nitrogen Fixing == 0.001, 0.5 Turn on nitrogen fixing and set its parameters
    Settling == constant, -0.05 Set a constant settling rate model and its parameter
End Phyto Model End phytoplankton constituent model
! MATERIAL SPECIFICATIONS
Material == default Set default material properties for all constituents that are allowed sediment fluxes
    Oxygen Flux == -10.0
    Silicate Flux == 10.0
    Ammonium Flux == 20.0
    Nitrate Flux == 30.0
    FRP Flux == 5.0
End Material
Material == 1 Set sediment oxygen properties for material 1 (unchanged from model 000)
    Oxygen Flux == -550.0
End Material
Material == 2 ! Mudflats Set sediment oxygen properties for material 2 (unchanged from model 000)
    Oxygen Flux == 0.0
End Material
Material == 4 ! Deep channel Set sediment oxygen properties for material 4 (unchanged from model 000)
    Oxygen Flux == -3500.0
End Material

The fvwq file has a set up that:

  • Deploys the “inorganics” Simulation Class, so therefore includes the water quality computed variables:
    • Dissolved oxygen (mg/L)
    • Silicate (mg/L)
    • Ammonium (mg/L)
    • Nitrate (mg/L)
    • Free reactive phosphorus (mg/L)
    • Adsorbed free reactive phosphorus (mg/L)
    • One phytoplankton group called “green” (μg/L)
  • Uses the milligrams per litre units system, with TUFLOW FV calling the WQ Module every 30 minutes
  • Has sediment oxygen demand that varies spatially across various material types, but constant behaviour for all other sediment releases.

Model 002: Organics

Simulation of organics is often the next logical step after simulating inorganics. The model WQ_002.fvc provides this simulation capability, in 3D, and includes density effects, atmospheric heat exchange and meteorological forcing. Constituent model blocks for oxygen, silicate, inorganic nitrogen, inorganic phosphorus and phytoplankton are unchanged from model 001.

! SIMULATION CONTROLS
Simulation Class == organics Set the overall simulation class to be “organics”
WQ dt == 1800.0 Set the Water Quality Module timestep. This is the frequency at which the WQ Module is called from TUFLOW FV
WQ units == mgl Set the units of simulation of the WQ Module.
! CONSTITUENT MODEL SETTINGS
! Organics
Organic Matter Model == refractory Set organics constituent model to be both labile and refractory
    Carbon Min Max == 0.0, 10.0, 0.0, 10.0 Set min and max values for labile particulate and labile dissolved organic carbon, nitrogen and phosphorus
    Nitrogen Min Max == 0.0, 10.0, 0.0, 10.0
    Phosphorus Min Max == 0.0, 10.0, 0.0, 10.0
    Organics Benthic == 1.0, 1.08 Set labile organic matter hydrolysis parameters
    Mineralisation == 0.01, 1.2, 1.03, 0.5, 0.5 Set labile organic matter mineralisation parameters
    Self Shading == 0.0, 0.0 Set labile organic matter self shading parameters
    Settling == stokes, 0.00000035, 2450.8 Set labile particulate settling model and parameters
    Ref Carbon Min Max == 0.0, 10.0, 0.0, 10.0 Set min and max values for refractory particulate and refractory dissolved organic carbon, nitrogen and phosphorus
    Ref Nitrogen Min Max == 0.0, 10.0, 0.0, 10.0
    Ref Phosphorus Min Max == 0.0, 9.0, 0.0, 9.0
    Ref Breakdown == 0.001, 0.1, 0.01 Set refractory organic matter breakdown parameters
    Ref Activation == 0.01 Set refractory organic matter activation parameters
    Ref Photolysis == 0.5 Set refractory organic matter photolysis parameter
    Ref Self Shading == 0.0, 0.0 Set refractory organic matter self shading parameters
    Ref Settling == stokes, 0.00000045, 2450.8 Set refractory particulate settling model and parameters
End Organic Matter Model End organics constituent model
! MATERIAL SPECIFICATIONS
Material == default Set default material properties for all constituents that are allowed sediment fluxes
    Oxygen Flux == -10.0
    Silicate Flux == 10.0
    Ammonium Flux == 20.0
    Nitrate Flux == 30.0
    FRP Flux == 5.0
    DOC Flux == 20.0
    DON Flux == 10.0
    DOP Flux == 5.0
End Material
Material == 1 Set sediment oxygen properties for material 1 (unchanged from model 000)
    Oxygen Flux == -550.0
End Material
Material == 2 ! Mudflats Set sediment oxygen properties for material 2 (unchanged from model 000)
    Oxygen Flux == 0.0
End Material
Material == 4 ! Deep channel Set sediment oxygen properties for material 4 (unchanged from model 000)
    Oxygen Flux == -3500.0
End Material

The fvwq file has a set up that:

  • Deploys the “organics” Simulation Class, so therefore includes the water quality computed variables:
    • Dissolved oxygen (mg/L)
    • Silicate (mg/L)
    • Ammonium (mg/L)
    • Nitrate (mg/L)
    • Free reactive phosphorus (mg/L)
    • Adsorbed free reactive phosphorus (mg/L)
    • Particulate and dissolved labile organic carbon (mg/L)
    • Particulate and dissolved labile organic nitrogen (mg/L)
    • Particulate and dissolved labile organic phosphorus (mg/L)
    • Particulate and dissolved refractory organic carbon (mg/L)
    • Particulate and dissolved refractory organic nitrogen (mg/L)
    • Particulate and dissolved refractory organic phosphorus (mg/L)
    • One phytoplankton group called “green” (μg/L)
  • Uses the milligrams per litre units system, with TUFLOW FV calling the WQ Module every 30 minutes
  • Has sediment oxygen demand that varies spatially across various material types, but constant behaviour for all other sediment releases.


Running the Models

Results have not been provided with the data download package and you will need to run each model to obtain them. To do this, you can refer to Running TUFLOW FV for a detailed description of the various methods for running a TUFLOW FV simulation. A template batch file is provided in the Complete_Model\TUFLOWFV\runs folder. Within this batch file, you will need to repath to the version of TUFLOW FV you have downloaded and updated as defined in Set up TUFLOW FV.

Results are written to three netcdf files, where XXX is either 000 (“DO”), 001 (“inorganics”) or 002 (“organics”):

  • WQ_XXX_HD.nc (Hydrodynamics and sediment)
  • WQ_XXX_WQ.nc (All water quality variables)
  • WQ_XXX_WQ_diag.nc (All water quality diagnostic variables)


Inspecting Results

Model 000: Dissolved Oxygen

All results from this simulation can be viewed and interrogated in QGIS using the TUFLOW Viewer Plugin. To start this process:

1. Open QGIS
2. Make sure the TUFLOW Viewer Plugin is installed

T09 7.0.0.01.png

3. Within the TUFLOW Viewer Plugin, load the water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. This tutorial will initially use WQ_000_WQ.nc

T09 7.0.0.02.png

4. Once loaded, click once on the WQ_DISS_OXYGEN_MG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset

T09 7.0.0.03.png
T09 7.0.0.04.png

5. Click the TUFLOW Viewer Mesh Rendering button, if desired T09 7.0.0.05.png. This will show the mesh, but is not required to be displayed

T09 7.0.0.06.png

Given that the model is a stationary waterway, the dimension of primary interest is the vertical. It therefore makes sense to examine the dissolved oxygen predictions using vertical interrogation techniques. Different ways of doing this are presented below.

Vertical line profiles

The three dimensional netcdf dataset can be interrogated at a single x/y coordinate location, and a vertical profile over the water column at that location then plotted. This output is a line, and the time at which this line is plotted can be adjusted using the TUFLOW Viewer time controls. To do this:

1. Make sure the WQ_DISS_OXYGEN_MG_L field is selected as above
2. Click the down arrow next to the TUFLOW Viewer Vertical Profile button and select the WQ_DISS_OXYGEN_MG_L field checkbox

T09 7.0.1.01.png

3. Click again on the same down arrow to exit the drop down menu
4. Click once on the TUFLOW Viewer Vertical Profile button itself

T09 7.0.1.02.png

5. Click once anywhere within the model domain – somewhere near the deeper northern end of the model will be more interesting than the shallow areas. A pink dot will appear on the clicked location, and a profile of dissolved oxygen concentration at that location will appear in the TUFLOW Viewer Plot window, within the Vertical Profile tab. The initial profile will be uniform with depth because the water quality model was initialised with a single dissolved oxygen concentration everywhere within the domain

T09 7.0.1.03.png
T09 7.0.1.04.png

6. Right click on the Plot window and select Customise

T09 7.0.1.05.png

7. Select the desired depth (y-axis) and dissolved oxygen (x-axis) ranges, and rename axes labels if desired, and click OK. Make sure the ranges include all the data to be displayed, otherwise the plot will disappear off the axes. The ranges shown below are satisfactory in this example

T09 7.0.1.06.png

8. The Plot window should appear similar to the below. The vertical dimension (depth) is shown in the y-axis and dissolved oxygen concentration on the x-axis. The green line is the dissolved oxygen concentration at all model depths at the X/Y location previously chosen, at the initial timestep of the model simulation

T09 7.0.1.07.png

9. Click on the Freeze Axis Limits button to keep the ranges selected throughout time

T09 7.0.1.08.png

10. Use the TUFLOW Viewer Time Navigation buttons to see how the (green line) vertical profile of dissolved oxygen at the chosen X/Y location changes in time. Check the Show as dates box to have the model time presented as dates

T09 7.0.1.09.png

11. It is expected that dissolved oxygen will decrease at depth (due to sediment consumption), and increase at the surface (due to atmospheric reaeration), to show profiles similar to the below. Overturning events where the water column vertically mixes are also expected

T09 7.0.1.10.png

Vertical curtain profiles – manual location

The three dimensional netcdf dataset can be interrogated concurrently at multiple x/y coordinate locations, and a continuous vertical curtain profile over the water column at those locations plotted. This is essentially a vertical slice through the three dimensional dataset, at a series of X/Y points that form a line over the model domain when viewed in plan. This output is a colour contoured curtain, and the time at which this curtain is plotted can be adjusted using the TUFLOW Viewer time controls. To do this:

1. Make sure the WQ_DISS_OXYGEN_MG_L field is selected as above
2. Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_DISS_OXYGEN_MG_L field checkbox

T09 7.0.2.01.png

3. Click again on the same down arrow to exit the drop down menu
4. Click on the TUFLOW Viewer Curtain Plot button itself

T09 7.0.2.02.png

5. Click a path along the desired curtain X/Y location within the model domain – somewhere along the deeper drowned river thalweg from the northern end of the model to the south will be more interesting than the shallow areas. Double click to end the curtain path definition. A green line will appear along the clicked locations, and a curtain profile of dissolved oxygen concentration along that path will appear in the TUFLOW Viewer Plot window, within the Cross Section / Long Profile tab, as shown below. The left hand end of the curtain colour contour will be the first location clicked in the green path

T09 7.0.2.03.png
T09 7.0.2.04.png

6. Customise the plot as previously described, and click OK

T09 7.0.2.05.png

7. The colourbar scale, name and map can be adjusted by clicking on the Images, etc. tab

T09 7.0.2.06.png

8. The curtain plot should then look similar to the following (it will have different data depending on the time selected)

T09 7.0.2.07.png

9. Use the TUFLOW Viewer Time Navigation buttons to see how the vertical curtain of dissolved oxygen along the chosen X/Y path changes in time. Check the Show as dates box to have the model time presented as dates

T09 7.0.2.08.png

10. It is expected that dissolved oxygen will decrease at depth (due to sediment consumption), and increase at the surface (due to atmospheric reaeration). Overturning events where the water column vertically mixes are also expected

Vertical curtain profiles – GIS location

Whilst the three dimensional netcdf dataset can be interrogated along a manually defined curtain as above, it is sometimes more convenient to use a predefined and repeatable curtain transect path. This can be achieved by using a shapefile to set the transect location rather than manual digitising. To do this:

1. Make sure the WQ_000_WQ.nc dataset is loaded into the TUFLOW Viewer as above, and the WQ_DISS_OXYGEN_MG_L field is selected
2. Drag the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" onto the QGIS Map window. The location of the transect will appear on top of the WQ_DISS_OXYGEN_MGL contours as a line

T09 7.0.3.01.png

3. Click on the QGIS Selection tool

T09 7.0.3.02.png

4. Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour

T09 7.0.3.03.png

5. Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_DISS_OXYGEN_MG_L field checkbox

T09 7.0.3.04.png

6. Click again on the same down arrow to exit the drop down menu
7. Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting

T09 7.0.3.05.png

8. Click on the Curtain button

T09 7.0.3.07.png

9. A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows

T09 7.0.3.08.png

10. Make any changes to the plot axes or colour bar as required (see above)
11. As above, use the TUFLOW Viewer Time Navigation buttons to see how the vertical curtain of dissolved oxygen along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, dissolved oxygen will decrease at depth, as expected

T09 7.0.3.09.png

12. Overturning events will also occur during the simulation to restore dissolved oxygen concentrations at depth

T09 7.0.3.10.png

Model 001: Inorganics

The same curtain interrogation techniques can be used to examine the inorganics (001) simulation results. Using the same interrogation techniques described above, the inorganic phosphorus concentrations can be examined along the same curtain, especially in the location of the wastewater treatment plant. To do this:

1. Load the inorganics water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. In this case, WQ_001_WQ.nc will be loaded

T09 7.1.01.png

2. Once loaded, click once on the WQ_FRP_MG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset

T09 7.1.02.png

3. Make sure the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" is loaded into the QGIS Map window as above
4. Click on the QGIS Selection tool

T09 7.1.03.png

5. Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour

T09 7.1.04.png

6. Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_FRP_MG_L field checkbox

T09 7.1.05.png

7. Click again on the same down arrow to exit the drop down menu
8. Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting

T09 7.1.06.png

9. Click on the Curtain button

T09 7.1.07.png

10. A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows

T09 7.1.08.png

11. Make any changes to the plot axes or colourbar as required (see above)
12. As above, use the TUFLOW Viewer Time Navigation buttons to see how the vertical curtain of FRP along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, FRP will increase at the location of the wastewater treatment plant discharge, as expected

T09 7.1.09.png

Model 002: Organics

The same curtain interrogation techniques can be used to examine the organics (002) simulation results. Using the same interrogation techniques described above, the phytoplankton concentrations can be examined along the same curtain, especially in the location of the wastewater treatment plant. To do this:

1. Load the organics water quality netcdf results file, by navigating to the results folder of your simulation and selecting the netcdf file you wish to view. In this case, WQ_002_WQ.nc will be loaded

T09 7.2.01.png

2. Once loaded, click once on the WQ_PHYTO_GREEN_CONC_MICG_L field in the Result Type window, and a plan view of the results will appear in the main map window. This is automatically set to be the surface layer of the three dimensional dataset

T09 7.2.02.png

3. Make sure the shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp" is loaded into the QGIS Map window as above
4. Click on the QGIS Selection tool

T09 7.2.03.png

5. Select the line from the loaded shapefile "TUFLOWFV\model\gis\2d_zln_Curtain_000_L.shp". The line will change colour

T09 7.2.04.png

6. Click the down arrow next to the TUFLOW Viewer Curtain Plot button, and select the WQ_PHYTO_GREEN_CONC_MICG_L field checkbox

T09 7.2.05.png

7. Click again on the same down arrow to exit the drop down menu
8. Select ‘Layer Selection’ from the dropdown menu under Map Output Plotting

T09 7.2.06.png

9. Click on the Curtain button

T09 7.2.07.png

10. A curtain plot should appear in the ‘Cross Section / Long Profile’ plot window as follows

T09 7.2.08.png

11. Make any changes to the plot axes or colourbar as required (see above)
12. As above, use the TUFLOW Viewer Time Navigation buttons to see how the vertical curtain of phytoplankton concentration along the chosen X/Y path changes in time. Check the Show as dates box (as above) to have the model time presented as dates. As the timeseries is clicked through, phytoplankton grows and concentrations increase at the location of the wastewater treatment plant discharge (and elsewhere through advection), as expected

T09 7.0.3.06.png

13. Try plotting other TUFLOW FV WQ Module variables to see how they evolve in time

Conclusion

This tutorial has covered the basics of setting up, executing and interrogating a TUFLOW FV WQ Module simulation. To complete more tutorials or learn more tips and tricks (including how to take advantage of the WQ Module's diagnostic variables in your model calibration process), please return to the TUFLOW FV Wiki Mainpage.