Introduction
About this manual
How to use this manual
Navigation
Searching
Tables
Figures
Networks
Commands
Parameter notation
Concentration nomenclature
Feedback
1
Overview
1.1
Context
1.2
Features
1.2.1
Usability
1.2.2
Constituents and processes
1.3
Science
1.4
Versioning
1.5
Support
2
Architecture
2.1
Context
2.2
Simulation Tiers
2.2.1
Tier 1: Simulation Class
2.2.2
Tier 2: Model Class
2.2.3
Tier 3: Constituent Model
2.2.4
Tier 4: Computed Variables
2.3
Linkage with TUFLOW FV
2.3.1
Process
2.3.2
Treatment of light
2.4
Linkage with Other Hydrodynamic Models
3
Process Descriptions
3.1
Simulation Class: DO
3.1.1
Overview
3.1.2
Model Class: Oxygen
3.1.2.1
Constituent Model: O2
3.1.3
Model Class: Pathogens (optional)
3.1.3.1
Constituent Model: Free
3.1.3.2
Constituent Model: Attached
3.1.4
Computed variables
3.2
Simulation Class: Inorganics
3.2.1
Overview
3.2.2
Model Class: Oxygen
3.2.3
Model Class: Silicate
3.2.3.1
Constituent Model: Si
3.2.4
Model Class: Inorganic nitrogen
3.2.4.1
Constituent Model: AmmoniumNitrate
3.2.5
Model Class: Inorganic phosphorus
3.2.5.1
Constituent Model: FRPhs
3.2.5.2
Constituent Model: FRPhsAds
3.2.6
Model Class: Phytoplankton
3.2.6.1
Constituent Model: Basic
3.2.6.2
Constituent Model: Advanced
3.2.7
Model Class: Pathogens (optional)
3.2.8
Computed variables
3.3
Simulation Class: Organics
3.3.1
Overview
3.3.2
Model Class: Oxygen
3.3.3
Model Class: Silicate
3.3.4
Model Class: Inorganic nitrogen
3.3.5
Model Class: Inorganic phosphorus
3.3.6
Model Class: Organic matter
3.3.6.1
Constituent Model: Labile
3.3.6.2
Constituent Model: Refractory
3.3.7
Model Class: Phytoplankton
3.3.7.1
Constituent Model: Basic
3.3.7.2
Constituent Model: Advanced
3.3.8
Model Class: Pathogens (optional)
3.3.9
Computed variables
4
Simulation Construction
4.1
Context
4.2
Units
4.3
General arrangement
4.4
TUFLOW FV control file commands
4.4.1
WQ Module activation
4.4.2
Initial and boundary conditions
4.4.2.1
Initial conditions
4.4.2.2
Boundary conditions
4.4.2.3
Ordering
4.5
Water quality control file commands
4.5.1
Part 1: Simulation controls
4.5.2
Part 2: Constituent model settings
4.5.3
Part 3: Material specifications
4.5.4
Summary
4.5.5
Log files
4.6
Simulation Class: DO
4.6.1
Prerequisites
4.6.2
Part 1: Simulation specification
4.6.3
Part 2: Constituent model specification
4.6.3.1
Model class: Oxygen
4.6.3.2
Model class: Pathogens (optional)
4.6.4
Part 3: Material specification
4.6.5
Constituent ordering
4.6.5.1
Pathogens (optional)
4.6.6
Example
4.7
Simulation Class: Inorganics
4.7.1
Prerequisites
4.7.2
Part 1: Simulation specification
4.7.3
Part 2: Constituent model specification
4.7.3.1
Model class: Oxygen
4.7.3.2
Model class: Silicate
4.7.3.3
Model class: Inorganic nitrogen
4.7.3.4
Model class: Inorganic phosphorus
4.7.3.5
Model class: Phytoplankton
4.7.3.6
Model class: Pathogens (optional)
4.7.4
Part 3: Material specification
4.7.5
Constituent ordering
4.7.5.1
Excluding phytoplankton
4.7.5.2
Including phytoplankton
4.7.5.3
Including pathogens (optional)
4.7.6
Example
4.8
Simulation Class: Organics
4.8.1
Prerequisites
4.8.2
Part 1: Simulation specification
4.8.3
Part 2: Constituent model specification
4.8.3.1
Model class: Oxygen
4.8.3.2
Model class: Silicate
4.8.3.3
Model class: Inorganic nitrogen
4.8.3.4
Model class: Inorganic phosphorus
4.8.3.5
Model class: Organic matter
4.8.3.6
Model class: Phytoplankton
4.8.3.7
Model class: Pathogens (optional)
4.8.4
Part 3: Material specification
4.8.5
Constituent ordering
4.8.5.1
Labile
4.8.5.2
Refractory
4.8.5.3
Including pathogens (optional)
4.8.6
Example
4.9
Outputs
4.9.1
WQ Module outputs
4.9.2
TUFLOW FV outputs
4.9.3
Units
Appendix
A
Syntax of command descriptions
Commands
Arguments
Defaults
B
Commands
C
Demonstration model
D
Processes: oxygen
D.1
Atmospheric oxygen flux
D.2
Sediment oxygen flux
E
Processes: silicate
E.1
Sediment silicate flux
F
Processes: inorganic nitrogen
F.1
Sediment ammonium and nitrate flux
F.2
Nitrification
F.3
Denitrification
F.4
Anaerobic oxidation of ammonium
F.5
Dissimilatory reduction of nitrate to ammonium
F.6
Wet deposition of inorganic nitrogen
F.7
Dry deposition of inorganic nitrogen
G
Processes: inorganic phosphorus
G.1
Sediment FRP flux
G.2
Wet deposition of inorganic phosphorus
G.3
Dry deposition of inorganic phosphorus
G.4
Adsorption and desorption
G.4.1
Linear model
G.4.2
Quadratic model
G.5
Settling
H
Processes: phyto general
H.1
General
H.2
Units
I
Processes: phyto biomass rates
I.1
Primary productivity
I.2
Respiration
I.3
Exudation
I.4
Settling
I.4.1
None
I.4.2
Constant
I.4.3
Constant with density correction
I.4.4
Stokes
I.4.5
Motile
J
Processes: phyto limitation
J.1
General
J.2
Temperature
J.2.1
None
J.2.2
Standard
J.3
Nitrogen
J.3.1
Basic phytoplankton constituent model
J.3.2
Advanced phytoplankton constituent model
J.4
Phosphorus
J.4.1
Basic phytoplankton constituent model
J.4.2
Advanced phytoplankton constituent model
J.5
Silicate
J.6
Light
J.6.1
Basic
J.6.2
Monod
J.6.3
Steele
J.6.4
Webb
J.6.5
Jassby
J.6.6
Chalker
J.6.7
Klepper
J.6.8
Integrated
J.7
Salinity
J.7.1
None
J.7.2
Freshwater
J.7.2.1
Primary productivity
J.7.2.2
Respiration
J.7.3
Marine
J.7.3.1
Primary productivity
J.7.3.2
Respiration
J.7.4
Mixed
J.7.4.1
Primary productivity
J.7.4.2
Respiration
J.7.5
Estuarine
K
Processes: phyto uptake
K.1
Carbon
K.2
Nitrogen
K.2.1
Basic phytoplankton constituent model
K.2.2
Advanced phytoplankton constituent model
K.2.3
Nitrogen fixing
K.3
Phosphorus
K.3.1
Basic phytoplankton constituent model
K.3.2
Advanced phytoplankton constituent model
K.4
Silicate
L
Processes: phyto losses
L.1
Carbon
L.2
Nitrogen
L.3
Phosphorus
L.4
Silicate
M
Processes: phyto other
M.1
Self shading
M.2
Cell density
N
Processes: organic matter
N.1
Sediment flux
N.2
Hydrolysis
N.2.1
Consumption
N.2.2
Production
N.3
Breakdown
N.3.1
Consumption
N.3.2
Production
N.4
Mineralisation
N.4.1
Consumption
N.4.2
Production
N.5
Activation
N.5.1
Consumption
N.5.2
Production
N.6
Photolysis
N.6.1
Consumption
N.6.2
Production
N.7
Self shading
N.8
Settling
N.8.1
None
N.8.2
Constant
N.8.3
Constant with density correction
N.8.4
Stokes
O
Processes: pathogens
O.1
Mortality
O.2
Inactivation
O.3
Attachment
O.4
Settling
O.5
Other
O.5.1
Total pathogens
P
Computed variables
Q
Diagnostic variables
R
Parameters
S
Mass Conservation Model
S.1
Intent
S.2
Description
S.3
Model suite
S.4
Calculations
S.5
Access and execution
S.5.1
Access
S.5.2
Execution
S.6
Example results
TUFLOW FV Water Quality (WQ) Module User Manual Release Candiate 2025.2
Appendix E
Processes: silicate
E
Processes: silicate
E.1
Sediment silicate flux