Appendix P Computed variables
The WQ Module’s computed variables, and the core (lowest order) constituent model class and instance where each is deployed are listed below. Output variable names are also included for cross referencing. Some TUFLOW FV variables are included in the table for completeness. With regard to naming:
- The text “NAME” in variable names is a placeholder for the user defined phytoplankton group name. “WQ_PHYTO_NAME_INT_N_MGL” list in the table would be named “WQ_PHYTO_CYLINDRO_INT_N_MGL” if a user defined phytoplankton group name was “cylindro”
- The TUFLOW FV MATLAB toolbox:
- Offers several post processing tools which rely on output phytoplankton group names. These are defined in ‘..\TUFLOWFV_Matlab_Utilities_001\toolbox\tuflowfv\fv_variables.m’ with default names: ‘BLUEGREEN’, ‘BGA’, ‘FDIAT’, ‘MDIAT’, ‘DIATOM’, ‘GREEN’, ‘PHY01’, ‘PHY02’, ‘PHY03’, ‘PHY04’, ‘PHY05’, ‘PHY06’, ‘PHY07’, ‘PHY08’, ‘PHY09’, ‘PHY10’ and ‘PHY11’. Users may choose to deploy any of these names and therefore use the MATLAB post processing tools unchanged. If not, then users will need to extend the ‘fvwq_mgl’ or ‘fvwq_mmm’ name lists provided in ‘fv_variables.m’. A template is provided in that mfile, with instructions on what to change.
- Uses dissolved oxygen in the following example scripts. It has been assumed that the MGL units system has been used so that the variable name of the interrogated data set is ‘WQ_DISS_OXYGEN_MG_L’. Users can change this if desired. Other ancillaries such as plot labels, colour limits and scale factors will also need to be changed for correct presentation of data if oxygen in the MGL units system is not processed:
- ‘..\TUFLOWFV_Matlab_Utilities_001\tutorial\visual\3.sheets\sh_006_impact_sheet_multiple_models.m’
- ‘..\TUFLOWFV_Matlab_Utilities_001\tutorial\visual\4.curtains\cu_000_plot_curtain_WQ.m’
- ‘..\TUFLOWFV_Matlab_Utilities_001\tutorial\visual\5.combined_plots\co_000_plot_multiple_ways_WQ.m’
It is recommended that this Appendix be viewed with the left hand pane table of contents hidden. Use the ‘s’ key to toggle this pane on and off. Output computed variable names are exact, and can therefore be copied and pasted directly into output blocks of control files, for example. The exception is phytoplankton variables, where the user specified group name is included within the variable name, so will need to be inserted by the user.
When interrogating three dimensional computed variable results in netcdf format, the stat field of each output file indicates whether or not a 2D cell (and hence its associated 3D column) is wet or dry. The stat field is of dimension [number of 2D cells \(\times\) number of timesteps] and a value of zero indicates that a 2D cell (and associated 3D column) is dry. Water quality computed variables are reported as zero when 2D cells are dry, so using the stat field to filter out these dry cells is essential when post processing results from models where cells wet and dry. Similarly, if viewing netcdf water quality computed variables in QGIS using the TUFLOW Viewer, QGIS’s automatic colour bar (displayed in the layer legend and properties tab) will extend to zero if the model considered includes cells that wet and dry - QGIS does not use the stat field to filter out dry cells when automatically determining colour bar ranges. The user can manually adjust this colour bar range as required. The stat field is, however, used when water quality computed variable results are viewed in plan or curtain mode in the map window when using the TUFLOW Viewer: dry cells are set to be transparent, even though their ‘zero’ values may influence the automatic setting of the colour bar range.
| Common name | Notation | Units | Relevant element | Atomic number (Z) | Atomic weight (M) | Output variable name | Core constituent model |
|---|---|---|---|---|---|---|---|
| Dissolved oxygen | \(\left[DO\right]\) |
mg/L mmol/m\(^3\) |
\(O_2\) | 16 | 32 |
WQ_DISS_OXYGEN_MG_L WQ_DISS_OXYGEN_MM_M3 |
Oxygen: O2 |
| Silicate | \(\left[Si\right]\) |
mg/L mmol/m\(^3\) |
\(Si\) | 14 | 28 |
WQ_SILICATE_MG_L WQ_SILICATE_MM_M3 |
Silicate: Si |
| Ammonium | \(\left[NH_4\right]\) |
mg/L mmol/m\(^3\) |
\(N\) | 7 | 14 |
WQ_AMMONIUM_MG_L WQ_AMMONIUM_MM_M3 |
Inorganic nitrogen: AmoniumNitrate |
| Nitrate | \(\left[NO_3\right]\) |
mg/L mmol/m\(^3\) |
\(N\) | 7 | 14 |
WQ_NITRATE_MG_L WQ_NITRATE_MM_M3 |
Inorganic nitrogen: AmoniumNitrate |
| Filterable reactive phosphorus | \(\left[FRP\right]\) |
mg/L mmol/m\(^3\) |
\(P\) | 15 | 31 |
WQ_FRP_MG_L WQ_FRP_MM_M3 |
Inorganic phosphorus: FRPhs |
| Filterable reactive phosphorus adsorbed | \(\left[FRPads\right]\) |
mg/L mmol/m\(^3\) |
\(P\) | 15 | 31 |
WQ_FRP_ADS_MG_L WQ_FRP_ADS_MM_M3 |
Inorganic phosphorus: FRPhsads |
| Dissolved organic carbon | \(\left[DOC\right]\) |
mg/L mmol/m\(^3\) |
\(C\) | 6 | 12 |
WQ_DOC_MG_L WQ_DOC_MM_M3 |
Organic matter: Labile |
| Particulate organic carbon | \(\left[POC\right]\) |
mg/L mmol/m\(^3\) |
\(C\) | 6 | 12 |
WQ_POC_MG_L WQ_POC_MM_M3 |
Organic matter: Labile |
| Dissolved organic nitrogen | \(\left[DON\right]\) |
mg/L mmol/m\(^3\) |
\(N\) | 7 | 14 |
WQ_DON_MG_L WQ_DON_MM_M3 |
Organic matter: Labile |
| Particulate organic nitrogen | \(\left[PON\right]\) |
mg/L mmol/m\(^3\) |
\(N\) | 7 | 14 |
WQ_PON_MG_L WQ_PON_MM_M3 |
Organic matter: Labile |
| Dissolved organic phosphorus | \(\left[DOP\right]\) |
mg/L mmol/m\(^3\) |
\(P\) | 15 | 31 |
WQ_DOP_MG_L WQ_DOP_MM_M3 |
Organic matter: Labile |
| Particulate organic phosphorus | \(\left[POP\right]\) |
mg/L mmol/m\(^3\) |
\(P\) | 15 | 31 |
WQ_POP_MG_L WQ_POP_MM_M3 |
Organic matter: Labile |
| Refractory dissolved organic carbon | \(\left[RDOC\right]\) |
mg/L mmol/m\(^3\) |
\(C\) | 6 | 12 |
WQ_RDOC_MG_L WQ_RDOC_MM_M3 |
Organic matter: Refractory |
| Refractory dissolved organic nitrogen | \(\left[RDON\right]\) |
mg/L mmol/m\(^3\) |
\(N\) | 7 | 14 |
WQ_RDON_MG_L WQ_RDON_MM_M3 |
Organic matter: Refractory |
| Refractory dissolved organic phosphorus | \(\left[RDOP\right]\) |
mg/L mmol/m\(^3\) |
\(P\) | 15 | 31 |
WQ_RDOP_MG_L WQ_RDOP_MM_M3 |
Organic matter: Refractory |
| Refractory particulate organic matter | \(\left[RPOM\right]\) |
mg/L mmol/m\(^3\) |
\(C\) | 6 | 12 |
WQ_RPOM_MG_L WQ_RPOM_MM_M3 |
Organic matter: Refractory |
| Phytoplankton | \(\left[PHY\right]\) |
\(\mu\)g/L mmol/m\(^3\) |
\(C\) (or Chl a) | 6 | 12 |
WQ_PHYTO_NAME_CONC_MICG_L WQ_PHYTO_NAME_CONC_MM_M3 |
Phytoplankton: Basic |
| Cell density | \(\rho_{PHY}\) | kg/m\(^3\) | WQ_PHYTO_NAME_DENS_KG_M3 |
Phytoplankton: Basic |
|||
| Internal nitrogen | \(\left[IN\right]\) |
mg/L mmol/m\(^3\) |
\(N\) | 7 | 14 |
WQ_PHYTO_NAME_INT_N_MG_L WQ_PHYTO_NAME_INT_N_MM_M3 |
Phytoplankton: Advanced |
| Internal phosphorus | \(\left[IP\right]\) |
mg/L mmol/m\(^3\) |
\(P\) | 15 | 31 |
WQ_PHYTO_NAME_INT_P_MG_L WQ_PHYTO_NAME_INT_P_MM_M3 |
Phytoplankton: Advanced |
| Suspended sediment | \(\left[SS\right]\) | mg/L | SED_N | ||||
| Water temperature | T | \(^o\)C | TEMP | ||||
| Water salinity | S | g/L | SAL | ||||
| Nitrite | \(\left[NO_2\right]\) |
mg/L mmol/m\(^3\) |
\(N\) | 7 | 14 | ||
| Alive pathogen | \(\left[PTH_a\right]\) | CFU/100mL |
WQ_PATH_NAME_ALIVE_CFU_100ML WQ_PATH_NAME_ALIVE_CFU_100ML |
Pathogens: Free |
|||
| Dead pathogen | \(\left[PTH_d\right]\) | CFU/100mL |
WQ_PATH_NAME_DEAD_CFU_100ML WQ_PATH_NAME_DEAD_CFU_100ML |
Pathogens: Free |
|||
| Attached pathogen | \(\left[PTH_t\right]\) | CFU/100mL |
WQ_PATH_NAME_ATTCHD_CFU_100ML WQ_PATH_NAME_ATTCHD_CFU_100ML |
Pathogens: Attached |