Appendix Q Diagnostic variables
The WQ Module’s diagnostic output variables, and the core (lowest order) constituent model class and instance where each is deployed are listed below. With regard to naming:
 Units are included in the diagnostic variable names, with “ND” signifying “no dimension”
 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 actually be named “WQ_PHYTO_GREEN_INT_N_MGL” if a user defined phytoplankton group name was “green”
 The text “PHYTO_COM” indicates summed (community level) diagnostics and is not changed by user specification of individual phytoplankton group names
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 diagnostic 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.
WQ Module calculations are not performed on computational columns of cells that are shallow. In such instances, the reported diagnostic variables are carried from the previous water quality timestep and as such may not reflect actual diagnostics at the reported time. This matter will be addressed in future releases of the WQ Module, however in the interim, caution should be used in the interpretation of diagnostic variables in cells that are known to regularly wet and dry.
In order to preserve shape consistency across all outputs, sheet style diagnostics such as benthic or atmospheric fluxes are reported as fully three dimensional fields. In all cases, these fluxes are reported in the bottom (bed) cell of each computational column (including surface atmospheric fluxes). All other three dimensional cell values are reported as zeros. Therefore, when viewing or interrogating these flux outputs in QGIS, python or MATLAB, the bottom layer of each diagnostic variable should be queried.
When interrogating three dimensional diagnostic 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 0 indicates that a 2D cell (and associated 3D column) is dry. Water quality diagnostic variables are reported as 0 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.
In addition, and because diagnostic variables are not tracked or advected and dispersed between timesteps (like computed variables are), they are also set to 0 when water quality calculations are turned off in a given cell due to either the cell being dry, or it having a water depth less than \(d_{minwq}\) (set via the cell water quality depth == command). Therefore, care must be taken when interpreting diagnostic variable outputs in cells that are shallower than the specified or default water quality depth.
It is also noted that the first timestep reported in diagnostic variable outputs has a value of zero for all cells. This is because the diagnostic array is initialised at zero before each suite of water quality calculations, including before the first water quality timestep, and so when the diagnostic values are written at output file initialisation, all diagnostic values are zero. This contrasts with computed variables written at the same initialisation of output files  these variables are set to the user specified initial conditions. Diagnostic variables do not have corresponding initial conditions and are therefore set to zero on first writing of results. This should be noted in post processing analyses.
If viewing netcdf water quality diagnostic 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 diagnostic 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.
Output diagnostic variable name  Common name  Symbol  Units  Description  Core constituent model  Links 

WQ_DIAG_O2_SAT_PCT  Oxygen saturation  \(\left[DO\right]_{psat}\)  %  Dissolved oxygen percentage saturation that is the equivalent of the dissolved oxygen concentration at current temperature, salinity and pressure conditions 
Oxygen: O2 
Equation (D.5) 
WQ_DIAG_ACTUAL_O2_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_O2_SED_FLUX_MMOL_M2_D 
Oxygen sediment flux  \(F_{sed\langle computed\rangle}^{O_2}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The dynamically computed flux of oxygen across the sediment water interface. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Oxygen: O2 
Equation (D.6) 
WQ_DIAG_O2_ATMOS_EXCHANGE_MG_M2_D WQ_DIAG_O2_ATMOS_EXCHANGE_MMOL_M2_D 
Oxygen atmospheric flux  \(F_{atm}^{O_2}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The flux of atmospheric oxygen entering the water column. Positive (negative) values are fluxes to (from) the water column from (to) the atmosphere. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Oxygen: O2 
Equation (D.4) 
WQ_DIAG_ACTUAL_SI_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_SI_SED_FLUX_MMOL_M2_D 
Silicate sediment flux  \(F_{sed\langle computed\rangle}^{Si}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The dynamically computed flux of silicate across the sediment water interface. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Silicate: Si 
Equation (E.1) 
WQ_DIAG_ACTUAL_NH4_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_NH4_SED_FLUX_MMOL_M2_D 
Ammonium sediment flux  \(F_{sed\langle computed\rangle}^{NH_4}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The dynamically computed flux of ammonium across the sediment water interface. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.1) 
WQ_DIAG_ACTUAL_NO3_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_NO3_SED_FLUX_MMOL_M2_D 
Nitrate sediment flux  \(F_{sed\langle computed\rangle}^{NO_3}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The dynamically computed flux of nitrate across the sediment water interface. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.1) 
WQ_DIAG_NITRIFICATION_MG_L_D WQ_DIAG_NITRIFICATION_MMOL_M3_D 
Nitrification flux  \(F_{nitrif\langle computed\rangle}^{NH_4}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of ammonium N to nitrate N due to nitrification. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.4) 
WQ_DIAG_DENITRIFICATION_MG_L_D WQ_DIAG_DENITRIFICATION_MMOL_M3_D 
Denitrification flux  \(F_{denit\langle computed\rangle}^{NO_3}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of nitrate N to nitrogen gas N due to denitrification. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.7) 
WQ_DIAG_DIN_ATMOS_EXCHANGE_MG_M2_D WQ_DIAG_DIN_ATMOS_EXCHANGE_MMOL_M2_D 
Nitrogen atmospheric flux  \(F_{atmdin\langle computed \rangle}^{N}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The combined wet (rainfall) and dry deposition of inorganic nitrogen across the atmosphere water interface. Positive values are fluxes to the water column from the atmosphere. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.21) 
WQ_DIAG_ACTUAL_FRP_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_FRP_SED_FLUX_MMOL_M2_D 
FRP sediment flux  \(F_{sed\langle computed\rangle}^{FRP}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The dynamically computed flux of FRP across the sediment water interface. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Inorganic phosphorus: FRPhs 
Equation (G.1) 
WQ_DIAG_DIP_ATMOS_EXCHANGE_MG_M2_D WQ_DIAG_DIP_ATMOS_EXCHANGE_MMOL_M2_D 
Phosphorus atmospheric flux  \(F_{atmdip\langle computed \rangle}^{P}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The combined wet (rainfall) and dry deposition of inorganic phosphorus across the atmosphere water interface. Only FRP (FRPads) contributes to wet (dry) deposition. Positive values are fluxes to the water column from the atmosphere. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Inorganic phosphorus: FRPhs 
Equation (G.4) 
WQ_DIAG_POC_SEDMTN_FLUX_MG_L_D WQ_DIAG_POC_SEDMTN_FLUX_MMOL_M3_D 
POC sedimentation flux  \(F_{sedmtn\langle computed\rangle}^{POC}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of settling labile particulate organic carbon that leaves the water column and enters the sediment. This is not flux of POC from the sediments. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell volume (L or m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic (per L or m\(^3\)) have been chosen deliberately for consistency with other analogous volumetric losses such as hydrolysis. This is intended to assist in simplifying post processing 
Organic matter: Labile 
Equation (N.31) 
WQ_DIAG_PON_SEDMTN_FLUX_MG_L_D WQ_DIAG_PON_SEDMTN_FLUX_MMOL_M3_D 
PON sedimentation flux  \(F_{sedmtn\langle computed\rangle}^{PON}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of settling labile particulate organic nitrogen that leaves the water column and enters the sediment. This is not flux of PON from the sediments. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell volume (L or m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic (per L or m\(^3\)) have been chosen deliberately for consistency with other analogous volumetric losses such as hydrolysis. This is intended to assist in simplifying post processing 
Organic matter: Labile 
Equation (N.31) 
WQ_DIAG_POP_SEDMTN_FLUX_MG_L_D WQ_DIAG_POP_SEDMTN_FLUX_MMOL_M3_D 
POP sedimentation flux  \(F_{sedmtn\langle computed\rangle}^{POP}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of settling labile particulate organic phosphorus that leaves the water column and enters the sediment. This is not flux of POP from the sediments. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell volume (L or m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic (per L or m\(^3\)) have been chosen deliberately for consistency with other analogous volumetric losses such as hydrolysis. This is intended to assist in simplifying post processing 
Organic matter: Labile 
Equation (N.31) 
WQ_DIAG_CHRMPHIC_DISS_ORGS_M  CDOM  \(CDOM_{\langle computed \rangle}\)  /m  Chromorphic dissolved organic matter. It is the equivalent extinction coefficient for absorption of radiation at 440 nm. It is computed from DOC (and RDOC if refractory organic matter is simulated) and uses the relationship of Equation (N.22) 
Organic matter: Refractory 
Equation (N.22) 
WQ_DIAG_ACTUAL_DOC_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_DOC_SED_FLUX_MMOL_M2_D 
DOC sediment flux  \(F_{sed\langle computed\rangle}^{DOC}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The dynamically computed flux of DOC across the sediment water interface. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Organic matter: Labile 
Equation (N.1) 
WQ_DIAG_ACTUAL_DON_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_DON_SED_FLUX_MMOL_M2_D 
DON sediment flux  \(F_{sed\langle computed\rangle}^{DON}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The dynamically computed flux of DON across the sediment water interface. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Organic matter: Labile 
Equation (N.1) 
WQ_DIAG_ACTUAL_DOP_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_DOP_SED_FLUX_MMOL_M2_D 
DOP sediment flux  \(F_{sed\langle computed\rangle}^{DOP}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The dynamically computed flux of DOP across the sediment water interface. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell area (m\(^2\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval 
Organic matter: Labile 
Equation (N.1) 
WQ_DIAG_POC_HYDROL_MG_L_D WQ_DIAG_POC_HYDROL_MMOL_M3_D 
POC hydrolysis flux  \(F_{hyd\langle computed\rangle}^{POC}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of labile POC to labile DOC due to hydrolysis. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be hydrolysed in that interval 
Organic matter: Labile 
Equation (N.3) 
WQ_DIAG_DOC_MINERL_MG_L_D WQ_DIAG_DOC_MINERL_MMOL_M3_D 
DOC mineralisation flux  \(F_{miner\langle computed\rangle}^{DOC}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of labile DOC to DIC due to mineralisation. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be mineralised in that interval 
Organic matter: Labile 
Equation (N.9) 
WQ_DIAG_PON_HYDROL_MG_L_D WQ_DIAG_PON_HYDROL_MMOL_M3_D 
PON hydrolysis flux  \(F_{hyd\langle computed\rangle}^{PON}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of labile PON to labile DON due to hydrolysis. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be hydrolysed in that interval 
Organic matter: Labile 
Equation (N.3) 
WQ_DIAG_DON_MINERL_MG_L_D WQ_DIAG_DON_MINERL_MMOL_M3_D 
DON mineralisation flux  \(F_{miner\langle computed\rangle}^{DON}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of labile DON to ammonium due to mineralisation. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be mineralised in that interval 
Organic matter: Labile 
Equation (N.9) 
WQ_DIAG_POP_HYDROL_MG_L_D WQ_DIAG_POP_HYDROL_MMOL_M3_D 
POP hydrolysis flux  \(F_{hyd\langle computed\rangle}^{POP}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of labile POP to labile DOP due to hydrolysis. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be hydrolysed in that interval 
Organic matter: Labile 
Equation (N.3) 
WQ_DIAG_DOP_MINERL_MG_L_D WQ_DIAG_DOP_MINERL_MMOL_M3_D 
DOP mineralisation flux  \(F_{miner\langle computed\rangle}^{DOP}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of labile DOP to FRP due to mineralisation. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be mineralised in that interval 
Organic matter: Labile 
Equation (N.9) 
WQ_DIAG_DOC_MINERL_AN_MG_L_D WQ_DIAG_DOC_MINERL_AN_MMOL_M3_D 
DOC anaerobic mineralisation flux  \(F_{miner\langle computed\rangle}^{an}\) 
mg/L/d mmol/m\(^3\)/d 
The component of the mineralisation flux of labile dissolved organic carbon that is anaerobic, i.e. the mineralisation that occurs after oxygen has been consumed from both diatomic dissolved oxygen and nitrate. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) of carbon that would be anaerobically mineralised in that interval. Reporting units of this diagnostic are carbon 
Organic matter: Labile 
Equation (N.15) 
WQ_DIAG_DOC_MINERL_DENIT_MG_L_D WQ_DIAG_DOC_MINERL_DENIT_MMOL_M3_D 
DOC denitification mineralisation  \(F_{miner\langle computed\rangle}^{NO_3}\) 
mg/L/d mmol/m\(^3\)/d 
The component of the mineralisation flux of labile dissolved organic carbon that occurs following consumption of dissolved oxygen, and that sources its oxygen from stripping (denitrifying) nitrate. It is the mineralisation that occurs after oxygen has been consumed from diatomic dissolved oxygen but before anaerobic mineralisation occurs. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) of carbon that would be aerobically mineralised in that interval. The same number of moles of nitrate N will be consumed. Reporting units of this diagnostic are carbon 
Organic matter: Labile 
Equation (N.14) 
WQ_DIAG_DOC_BOD5_MG_L  BOD5  \(BOD5_{\langle computed\rangle}^{O_2}\)  mg/L  The reduction in the concentration of dissolved oxygen that would result by the action of aerobic mineralisation of dissolved organic carbon over a period of 5 days. It is computed at the instantaneous oxygen consumption rate 
Organic matter: Labile 
Equation (N.13) 
WQ_DIAG_POM_VERT_VEL_M_S  Labile particulate organic matter settling velocity  \(V_{settle\langle computed \rangle}^{lorg}\)  m/s  The computed settling velocity of labile particulate organic carbon, nitrogen and phosphorus (which all have the same velocity). Positive (negative) values are upwards (downwards) 
Organic matter: Labile 
Section N.8 
WQ_DIAG_RPOM_SEDMTN_FLUX_MG_L_D WQ_DIAG_RPOM_SEDMTN_FLUX_MMOL_M3_D 
RPOM sedimentation flux  \(F_{sedmtn\langle computed\rangle}^{RPOM}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of settling refractory particulate organic matter that leaves the water column and enters the sediment. This is not flux of RPOM from the sediments. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. Multiply by cell volume (L or m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be exchanged in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic (per L or m\(^3\)) have been chosen deliberately for consistency with other analogous volumetric losses such as photolysis. This is intended to assist in simplifying post processing 
Organic matter: Refractory 
Equation (N.32) 
WQ_DIAG_PHOTOLYSIS_MG_L_D WQ_DIAG_PHOTOLYSIS_MMOL_M3_D 
RPOM Photolysis  \(F_{photo\langle computed\rangle}^{RDOC}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of refractory dissolved organic carbon to labile dissolved organic carbon and potentially DIC (if \(f_{photo}^{DOM}\) is not 1.0). This flux is always positive and is the carbon fraction only. Equivalent nitrogen and phosphorus fraction fluxes can be computed as per Equation (N.23) 
Organic matter: Refractory 
Equation (N.23) 
WQ_DIAG_RPOM_VERT_VEL_M_S  Refractory particulate organic matter settling velocity  \(V_{settle\langle computed \rangle}^{rorg}\)  m/s  The computed settling velocity of refractory particulate organic matter. Positive (negative) values are upwards (downwards) 
Organic matter: Refractory 
Section N.8 
WQ_DIAG_PHY_NAME_INT_NUTR_RATIO_ND  Ratio of internal nutrients  \(R_{INIP}^{phy}\)  []  The ratio of internal nitrogen to internal phosphorus for a phytoplankton group. This quantity is reported for both the basic and advanced phytoplankton constituent models, with the former being the constant quotient of user (or default) internal nitrogen and phosphorus to carbon ratios. If the latter, this diagnostic will vary between the quotients of the user defined (or default) minimum and maximum limits of internal nitrogen and phosphorus to carbon ratios. Although noted here as being dimensionless, this quantity can be thought of as having units of (N concentration) / (P concentration) 
Phytoplankton: Basic 

WQ_DIAG_PHY_NAME_LGHT_LIM_ND  Light limitation function  \(L_{lght}^{phy}\)  0  The dynamically computed light limitation function for a phytoplankton group. It varies between 0 (complete limitation) and 1 (no limitation) 
Phytoplankton: Basic 
Section J.6 
WQ_DIAG_PHY_NAME_N_LIM_ND  Nitrogen limitation function  \(L_{nit}^{phy}\)  []  The dynamically computed nitrogen limitation function for a phytoplankton group. It varies between 0 (complete limitation) and 1 (no limitation) 
Phytoplankton: Basic 
Section J.3 
WQ_DIAG_PHY_NAME_P_LIM_ND  Phosphorus limitation function  \(L_{phs}^{phy}\)  []  The dynamically computed phosphorus limitation function for a phytoplankton group. It varies between 0 (complete limitation) and 1 (no limitation) 
Phytoplankton: Basic 
Section J.4 
WQ_DIAG_PHY_NAME_SI_LIM_ND  Silicate limitation function  \(L_{sil}^{phy}\)  []  The dynamically computed silicate limitation function for a phytoplankton group. It varies between 0 (complete limitation) and 1 (no limitation) 
Phytoplankton: Basic 
Section J.5 
WQ_DIAG_PHY_NAME_TMPTR_LIM_ND  Temperature limitation function  \(L_T^{phy}\)  []  The dynamically computed temperature limitation function for a phytoplankton group. It varies between 0 (complete limitation) and a positive number. This limitation function value can be greater than 1, and in such instances this represents an opportunity for augmented phytoplankton growth (subject to the values of other related limitation functions) 
Phytoplankton: Basic 
Section J.2 
WQ_DIAG_PHY_NAME_SAL_LIM_ND  Salinity limitation function  \(L_{salr}^{phy}\)  []  The dynamically computed salinity limitation function applied to respiration of a phytoplankton group. It is always greater than 1 (no limitation). The same diagnostic variable name is used for the corollary primary productivity salinity limitation function because the two limitation functions are mutually exclusive 
Phytoplankton: Basic 
Section J.7 
WQ_DIAG_PHY_NAME_SAL_LIM_ND  Salinity limitation function  \(L_{salpp}^{phy}\)  []  The dynamically computed salinity limitation function applied to primary production of a phytoplankton group. It varies between 0 (complete limitation) and 1 (no limitation). The same diagnostic variable name is used for the corollary respiration salinity limitation function because the two limitation functions are mutually exclusive 
Phytoplankton: Basic 
Section J.7 
WQ_DIAG_PHY_NAME_PRIM_PROD_MICG_L_D WQ_DIAG_PHY_NAME_PRIM_PROD_MMOL_M3_D 
Phytoplankton primary productivity  \(F_{prod\langle computed\rangle}^{phy}\) 
\(\mu\)g/L/d mmol/m\(^3\)/d 
The flux of carbon to phytoplankton as a result of productivity, without accounting for respiration, for a phytoplankton group. Also referred to as growth or gross primary productivity, and typically associated with daytime phytoplankton photosynthesis. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up via productivity in that interval 
Phytoplankton: Basic 
Equation (I.5) 
WQ_DIAG_PHY_NAME_SEDMTN_MICG_L_D WQ_DIAG_PHY_NAME_SEDMTN_MMOL_M3_D 
Phytoplankton sedimentation  \(F_{sedmtn\langle computed\rangle}^{phy}\) 
\(\mu\)g/L/d mmol/m\(^3\)/d 
The flux of phytoplankton chlorophyll a (or carbon) into the sediments as a result of settling for a phytoplankton group. Values are only losses and are only negative. Multiply by cell volume (L or m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost to settling in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic (per L or m\(^3\)) have been chosen deliberately for consistency with other analogous volumetric losses such as mortality. This is intended to assist in simplifying post processing 
Phytoplankton: Basic 
Equation (I.13) 
WQ_DIAG_PHY_NAME_VERT_VEL_M_S  Phytoplankton settling velocity  \(V_{settle}^{phy}\)  m/s  Phytoplankton settling velocity, as computed from the user specified (or default) method, for a phytoplankton group. Upwards (downwards) is negaitve (positive) 
Phytoplankton: Basic 
Section I.4 
WQ_DIAG_PHYTO_COM_SEDMTN_MICG_L_D WQ_DIAG_PHYTO_COM_SEDMTN_MMOL_M3_D 
Community phytoplankton sedimentation  \(F_{sedmtn\langle computed\rangle}^{comm}\) 
\(\mu\)g/L/d mmol/m\(^3\)/d 
The flux of phytoplankton into the sediments as a result of settling, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Values are only losses and are only negative. Multiply by cell volume (L or m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost to settling in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic (per L or m\(^3\)) have been chosen deliberately for consistency with other analogous losses such as individual phytoplankton group sedimentation rates. This is intended to assist in simplifying post processing 
Phytoplankton: Basic 
Equation (I.13) 
WQ_DIAG_PHYTO_COM_PRIM_PROD_MICG_L_D WQ_DIAG_PHYTO_COM_PRIM_PROD_MMOL_M3_D 
Community primary productivity  \(F_{prod\langle computed\rangle}^{comm}\) 
\(\mu\)g/L/d mmol/m\(^3\)/d 
The flux of carbon (and nutrients) to phytoplankton as a result of productivity, without accounting for respiration, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Also referred to as growth, and typically associated with daytime phytoplankton photosynthesis. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up via productivity in that interval 
Phytoplankton: Basic 
Equation (I.5) 
WQ_DIAG_PHYTO_COM_NET_PROD_MICG_L_D WQ_DIAG_PHYTO_COM_NET_PROD_MMOL_M3_D 
Community net primary productivity  \(F_{netprod\langle computed\rangle}^{comm}\) 
\(\mu\)g/L/d mmol/m\(^3\)/d 
The flux of carbon (and nutrients) to phytoplankton as a result of productivity, accounting for respiration losses due only to the consumption of stored energy, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Also referred to as net primary productivity. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up via net productivity in that interval 
Phytoplankton: Basic 
Equation (I.9) 
WQ_DIAG_PHYTO_COM_PROD_RESP_R_  Community primary productivity ratio  \(R_{PPresp}^{comm}\)  []  Ratio of primary productivity to true respiration, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Currently inactive and reported as 999 
Phytoplankton: 

WQ_DIAG_PHYTO_COM_NET_RESP_R_  Community net primary productivity ratio  \(R_{NPPresp}^{comm}\)  []  Ratio of net primary productivity to true respiration, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Currently inactive and reported as 999 
Phytoplankton: 

WQ_DIAG_PHYTO_COM_NO3_UPTAKE_MG_L_D WQ_DIAG_PHYTO_COM_NO3_UPTAKE_MMOL_M3_D 
Community nitrate uptake  \(F_{nituptake\langle computed\rangle}^{comm}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of nitrate to phytoplankton as a result of productivity, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up in that interval. Although computed differently for the basic and advanced phytoplankton constituent models, the interpretation of this quantity is the same for both 
Phytoplankton: Basic 
Equation (K.3) 
WQ_DIAG_PHYTO_COM_NH4_UPTAKE_MG_L_D WQ_DIAG_PHYTO_COM_NH4_UPTAKE_MMOL_M3_D 
Community ammonium uptake  \(F_{ammuptake\langle computed\rangle}^{comm}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of ammonium to phytoplankton as a result of productivity, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up in that interval. Although computed differently for the basic and advanced phytoplankton constituent models, the interpretation of this quantity is the same for both 
Phytoplankton: Basic 
Equation (K.3) 
WQ_DIAG_PHYTO_COM_P_UPTAKE_MG_L_D WQ_DIAG_PHYTO_COM_P_UPTAKE_MMOL_M3_D 
Community FRP uptake  \(F_{Puptake\langle computed\rangle}^{comm}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of FRP to phytoplankton as a result of productivity, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up in that interval. Although computed differently for the basic and advanced phytoplankton constituent models, the interpretation of this quantity is the same for both 
Phytoplankton: Basic 
Equation (K.7) 
WQ_DIAG_PHYTO_COM_C_UPTAKE_MG_L_D WQ_DIAG_PHYTO_COM_C_UPTAKE_MMOL_M3_D 
Community carbon uptake  \(F_{Cuptake\langle computed\rangle}^{comm}\) 
\(\mu\)g/L/d mmol/m\(^3\)/d 
The flux of carbon (and nutrients) to phytoplankton as a result of productivity, without accounting for respiration, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Also referred to as growth, and typically associated with daytime phytoplankton photosynthesis. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up via productivity in that interval. This is numerically the same as primary productivity 
Phytoplankton: Basic 
Equation (K.1) 
WQ_DIAG_PHYTO_COM_PAR_W_M2  Community PAR  PAR  W/m\(^2\)  The ambient PAR field in each computational cell, as set by the hydrodynamic model 
Phytoplankton: Basic 
Section 2.3.2 
WQ_DIAG_PHYTO_COM_TCHLA_MICG_L  Community chlorophyll a  \(\left[Chla\right]^{comm}\)  \(\mu\)g/L  The total chlorophyll a summed across all phytoplankton groups 
Phytoplankton: Basic 

WQ_DIAG_PHYTO_COM_TPHY_MMOL_C_M3 WQ_DIAG_PHYTO_COM_TPHY_MMOL_C_M3 
Community phytoplankton concentration  \(\left[Chla\right]^{comm}\) 
mmol/m\(^3\) mmol/m\(^3\) 
The concentration of phytoplankton in mmols of carbon, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). Multiplying this number by 12 and dividing (on a cell by cell basis) by the equivalent Community chlorophyll a value (as reported, i.e. in \(\mu\)g/L) will result in an array of the average carbon to chlorophyll a ratio of the community for each cell. This is effectively a concentration weighted average of the individual phytoplankton group carbon to chlorophyll a ratios at any given time and in any given cell 
Phytoplankton: Basic 

WQ_DIAG_PHYTO_COM_T_IN_N_MG_L WQ_DIAG_PHYTO_COM_T_IN_N_MMOL_M3 
Community internal nitrogen concentration  \(\left[N\right]_{in}^{comm}\) 
\(\mu\)g/L mmol/m\(^3\) 
The internal nitrogen concentration of phytoplankton, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community), for both the basic and advanced phytoplankton constituent models 
Phytoplankton: Basic 
Section K.2.2 
WQ_DIAG_PHYTO_COM_T_IN_P_MG_L WQ_DIAG_PHYTO_COM_T_IN_P_MMOL_M3 
Community internal phosphorus concentration  \(\left[P\right]_{in}^{comm}\) 
\(\mu\)g/L mmol/m\(^3\) 
The internal phosphorus concentration of phytoplankton, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community), for both the basic and advanced phytoplankton constituent models 
Phytoplankton: Basic 
Section K.3.2 
WQ_DIAG_INPUT_O2_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_O2_SED_FLUX_MMOL_M2_D 
Oxygen user defined sediment flux  \(F_{sed}^{O_2}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The user defined (or model default) flux of oxygen across the sediment water interface. This value is reported for completeness and should not change in time for a given cell. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. This diagnostic cannot be used in mass balance or other related calculations 
Oxygen: O2 
Equation (D.6) 
WQ_DIAG_INPUT_SI_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_SI_SED_FLUX_MMOL_M2_D 
Silicate user defined sediment flux  \(F_{sed}^{Si}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The user defined (or model default) flux of silicate across the sediment water interface. This value is reported for completeness and should not change in time for a given cell. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. This diagnostic cannot be used in mass balance or other related calculations 
Silicate: Si 
Equation (E.1) 
WQ_DIAG_INPUT_NH4_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_NH4_SED_FLUX_MMOL_M2_D 
Ammonium user defined sediment flux  \(F_{sed}^{NH_4}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The user defined (or model default) flux of ammonium across the sediment water interface. This value is reported for completeness and should not change in time for a given cell. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. This diagnostic cannot be used in mass balance or other related calculations 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.1) 
WQ_DIAG_INPUT_NO3_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_NO3_SED_FLUX_MMOL_M2_D 
Nitrate user defined sediment flux  \(F_{sed}^{NO_3}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The user defined (or model default) flux of nitrate across the sediment water interface. This value is reported for completeness and should not change in time for a given cell. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. This diagnostic cannot be used in mass balance or other related calculations 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.1) 
WQ_DIAG_INPUT_FRP_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_FRP_SED_FLUX_MMOL_M2_D 
FRP user defined sediment flux  \(F_{sed}^{FRP}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The user defined (or model default) flux of FRP across the sediment water interface. This value is reported for completeness and should not change in time for a given cell. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. This diagnostic cannot be used in mass balance or other related calculations 
Inorganic phosphorus: FRPhs 
Equation (G.1) 
WQ_DIAG_INPUT_DOC_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_DOC_SED_FLUX_MMOL_M2_D 
DOC user defined sediment flux  \(F_{sed}^{DOC}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The user defined (or model default) flux of DOC across the sediment water interface. This value is reported for completeness and should not change in time for a given cell. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. This diagnostic cannot be used in mass balance or other related calculations 
Organic matter: Labile 
Equation (N.1) 
WQ_DIAG_INPUT_DON_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_DON_SED_FLUX_MMOL_M2_D 
DON user defined sediment flux  \(F_{sed}^{DON}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The user defined (or model default) flux of DON across the sediment water interface. This value is reported for completeness and should not change in time for a given cell. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. This diagnostic cannot be used in mass balance or other related calculations 
Organic matter: Labile 
Equation (N.1) 
WQ_DIAG_INPUT_DOP_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_DOP_SED_FLUX_MMOL_M2_D 
DOP user defined sediment flux  \(F_{sed}^{DOP}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
The user defined (or model default) flux of DOP across the sediment water interface. This value is reported for completeness and should not change in time for a given cell. Positive (negative) values are fluxes to (from) the water column from (to) the sediment. This diagnostic cannot be used in mass balance or other related calculations 
Organic matter: Labile 
Equation (N.1) 
WQ_DIAG_TOTAL_NITROGEN_MG_L WQ_DIAG_TOTAL_NITROGEN_MMOL_M3 
Total nitrogen  \(TN\) 
mg/L mmol/m\(^3\) 
The sum of relevant nitrogen species. These are: Simulation class DO: none Simulation class inorganics: ammonium, nitrate, phytoplankton internal nitrogen (whether it is a simulated variable or not it still contributes to total nitrogen) Simulation class organics: ammonium, nitrate, phytoplankton internal nitrogen, DON, PON and RDON if refractory organic constituent model is used 

WQ_DIAG_TOTAL_PHOSPHORUS_MG_L WQ_DIAG_TOTAL_PHOSPHORUS_MMOL_M3 
Total phosphorus  \(TP\) 
mg/L mmol/m\(^3\) 
The sum of relevant phosphorus species. These are: Simulation class DO: none Simulation class inorganics: FRP, adsorbed FRP if simulated, phytoplankton internal phosphorus (whether it is a simulated variable or not it still contributes to total phosphorus) Simulation class organics: FRP, adsorbed FRP if simulated, phytoplankton internal phosphorus, DOP, POP and RDOP if refractory organic constituent model is used 

WQ_DIAG_TOTAL_KJELDAHL_NITROGEN_MG_L WQ_DIAG_TOTAL_KJELDAHL_NITROGEN_MMOL_M3 
Total Kjeldahl nitrogen  \(TKN\) 
mg/L mmol/m\(^3\) 
The sum of relevant nitrogen species. These are: Simulation class DO: none Simulation class inorganics: ammonium, phytoplankton internal nitrogen (whether it is a simulated variable or not it still contributes to total nitrogen) Simulation class organics: ammonium, phytoplankton internal nitrogen, DON, PON and RDON if refractory organic constituent model is used 

WQ_DIAG_TOTAL_ORGANIC_CARBON_MG_L WQ_DIAG_TOTAL_ORGANIC_CARBON_MMOL_M3 
Total organic carbon  \(TOC\) 
mg/L mmol/m\(^3\) 
The sum of relevant carbon species. These are: Simulation class DO: none Simulation class inorganics: phytoplankton carbon Simulation class organics: phytoplankton carbon, DOC, POC, and RDOC and RPOM if refractory organic constituent model is used 

WQ_DIAG_INPUT_POC_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_POC_SED_FLUX_MMOL_M2_D 
POC user defined sediment flux  \(F_{sed}^{POC}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_INPUT_PON_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_PON_SED_FLUX_MMOL_M2_D 
PON user defined sediment flux  \(F_{sed}^{PON}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_INPUT_POP_SED_FLUX_MG_M2_D WQ_DIAG_INPUT_POP_SED_FLUX_MMOL_M2_D 
POP user defined sediment flux  \(F_{sed}^{POP}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_ACTUAL_POC_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_POC_SED_FLUX_MMOL_M2_D 
POC sediment flux  \(F_{sed\langle computed\rangle}^{POC}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as the same as WQ_DIAG_POC_SEDMTN_FLUX_MG_M2_D. Will be activated in future releases  
WQ_DIAG_ACTUAL_PON_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_PON_SED_FLUX_MMOL_M2_D 
PON sediment flux  \(F_{sed\langle computed\rangle}^{PON}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as the same as WQ_DIAG_PON_SEDMTN_FLUX_MG_M2_D. Will be activated in future releases  
WQ_DIAG_ACTUAL_POP_SED_FLUX_MG_M2_D WQ_DIAG_ACTUAL_POP_SED_FLUX_MMOL_M2_D 
POP sediment flux  \(F_{sed\langle computed\rangle}^{POP}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as the same as WQ_DIAG_POP_SEDMTN_FLUX_MG_M2_D. Will be activated in future releases  
WQ_DIAG_SEDIMENT_ORGC_MASS_MG_M2 WQ_DIAG_SEDIMENT_ORGC_MASS_MMOL_M2 
Organic carbon sediment mass  \(M_{sed}^{OC}\) 
mg/m\(^2\) mmol/m\(^2\) 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_SEDIMENT_ORGN_MASS_MG_M2 WQ_DIAG_SEDIMENT_ORGN_MASS_MMOL_M2 
Organic nitrogen sediment mass  \(M_{sed}^{ON}\) 
mg/m\(^2\) mmol/m\(^2\) 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_SEDIMENT_ORGP_MASS_MG_M2 WQ_DIAG_SEDIMENT_ORGP_MASS_MMOL_M2 
Organic phosphorus sediment mass  \(M_{sed}^{OP}\) 
mg/m\(^2\) mmol/m\(^2\) 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_POC_RESUS_MG_M2_D WQ_DIAG_POC_RESUS_MMOL_M2_D 
POC resuspension flux  \(F_{resus}^{POC}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_PON_RESUS_MG_M2_D WQ_DIAG_PON_RESUS_MMOL_M2_D 
PON resuspension flux  \(F_{resus}^{PON}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_POP_RESUS_MG_M2_D WQ_DIAG_POP_RESUS_MMOL_M2_D 
POP resuspension flux  \(F_{resus}^{POP}\) 
mg/m\(^2\)/d mmol/m\(^2\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_PHYTO_COM_N2_UPTAKE_MG_L_D WQ_DIAG_PHYTO_COM_N2_UPTAKE_MMOL_M3_D 
Community nitrogen fixing uptake  \(F_{Nfix}^{comm}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of atmospheric nitrogen fixed by phytoplankton, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community), for both the basic and advanced phytoplankton constituent models  
WQ_DIAG_ANAER_NH4_OX_MG_L_D WQ_DIAG_ANAER_NH4_OX_MMOL_M3_D 
Anaerobic oxidation of ammonium  \(F_{anmx\langle computed\rangle}^{N_2}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of ammoniumN and nitrateN to free diatomic nitrogen gas (also referred to as anammox). Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) on N that would be lost via anammox in that interval. The diagnostic variable is the production of nitrogen gas N (not N\(_2\)) 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.10) 
WQ_DIAG_DISS_NO3_RED_MG_L_D WQ_DIAG_DISS_NO3_RED_MMOL_M3_D 
Dissimilatory reduction of nitrate to ammonium  \(F_{DRNA\langle computed\rangle}^{NO_3}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of nitrateN to ammoniumN (also referred to as DRNA). Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) on N that would be lost via DRNA in that interval 
Inorganic nitrogen: AmmoniumNitrate 
Equation (F.12) 
WQ_DIAG_RPOM_BREAKDOWN_MG_L_D WQ_DIAG_RPOM_BREAKDOWN_MMOL_M3_D 
RPOM breakdown  \(F_{bdn\langle computed\rangle}^{RPOM}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of refractory particulate organic matter to labile particulate organic matter under microbial activity. This flux is always positive and is applied directly to the carbon fraction of RPOM. Equivalent nitrogen and phosphorus fraction fluxes are computed proportionately as per Equation (N.7) 
Organic matter: Refractory 
Equation (N.6) 
WQ_DIAG_RDOC_ACTV_MG_L_D WQ_DIAG_RDOC_ACTV_MMOL_M3_D 
RDOC activation  \(F_{act\langle computed\rangle}^{RDOC}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of refractory dissolved organic carbon to labile dissolved organic carbon under microbial activity. This flux is always positive 
Organic matter: Refractory 
Equation (N.18) 
WQ_DIAG_RDON_ACTV_MG_L_D WQ_DIAG_RDON_ACTV_MMOL_M3_D 
RDON activation  \(F_{act\langle computed\rangle}^{RDON}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of refractory dissolved organic nitrogen to labile dissolved organic nitrogen under microbial activity. This flux is always positive 
Organic matter: Refractory 
Equation (N.18) 
WQ_DIAG_RDOP_ACTV_MG_L_D WQ_DIAG_RDOP_ACTV_MMOL_M3_D 
RDOP activation  \(F_{act\langle computed\rangle}^{RDOP}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of refractory dissolved organic phosphorus to labile dissolved organic phosphorus under microbial activity. This flux is always positive 
Organic matter: Refractory 
Equation (N.18) 
WQ_DIAG_PHY_NAME_RESP_MICG_L_D WQ_DIAG_PHY_NAME_RESP_MMOL_M3_D 
Phytoplankton respiration  \(F_{resp\langle computed\rangle}^{phy}\) 
\(\mu\)g/L/d mmol/m\(^3\)/d 
The flux of carbon from phytoplankton as a result of energy consumption (referred to as true respiration). It is typically seen as a night time phytoplanktonic process but can also occur during the day. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via true respiration in that interval 
Phytoplankton: Basic 
Equation (I.8) 
WQ_DIAG_PHY_NAME_RESP_N_MG_L_D WQ_DIAG_PHY_NAME_RESP_N_MMOL_M3_D 
Phytoplankton respiration  nitrogen  \(F_{respN\langle computed\rangle}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of nitrogen from phytoplankton as a result of energy consumption (referred to as true respiration). It is typically seen as a night time phytoplanktonic process but can also occur during the day. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via true respiration in that interval 
Phytoplankton: Basic 
Equation (I.10) 
WQ_DIAG_PHY_NAME_RESP_P_MG_L_D WQ_DIAG_PHY_NAME_RESP_P_MMOL_M3_D 
Phytoplankton respiration  phosphorus  \(F_{respP\langle computed\rangle}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of phosphorus from phytoplankton as a result of energy consumption (referred to as true respiration). It is typically seen as a night time phytoplanktonic process but can also occur during the day. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via true respiration in that interval 
Phytoplankton: Basic 
Equation (I.11) 
WQ_DIAG_PHY_NAME_PRIM_PROD_N_MG_L_D WQ_DIAG_PHY_NAME_PRIM_PROD_N_MMOL_M3_D 
Phytoplankton primary productivity  nitrogen  \(F_{Nuptake}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of nitrogen to phytoplankton as a result of productivity, without accounting for respiration, for a phytoplankton group. Also referred to as growth or gross primary productivity, and typically associated with daytime phytoplankton photosynthesis. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up via productivity in that interval. This diagnostic varible name is used for both basic and advanced phytoplankton groups, even though the method to compute uptake differs between the two 
Phytoplankton: Basic Phytoplankton: Advanced 
Equation (K.2) Equation (K.4) 
WQ_DIAG_PHY_NAME_PRIM_PROD_P_MG_L_D WQ_DIAG_PHY_NAME_PRIM_PROD_P_MMOL_M3_D 
Phytoplankton primary productivity  phosphorus  \(F_{Puptake}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of phosphorus to phytoplankton as a result of productivity, without accounting for respiration, for a phytoplankton group. Also referred to as growth or gross primary productivity, and typically associated with daytime phytoplankton photosynthesis. Values are only positive. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be taken up via productivity in that interval. This diagnostic varible name is used for both basic and advanced phytoplankton groups, even though the method to compute uptake differs between the two 
Phytoplankton: Basic Phytoplankton: Advanced 
Equation (K.7) Equation (K.8) 
WQ_DIAG_PHY_NAME_SEDMTN_N_MG_L_D WQ_DIAG_PHY_NAME_SEDMTN_N_MMOL_M3_D 
Phytoplankton sedimentation  nitrogen  \(F_{sedmtnN\langle computed\rangle}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of phytoplankton nitrogen into the sediments as a result of settling for a phytoplankton group. Values are only losses and are only negative. Multiply by cell volume (L or m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost to settling in that interval. This diagnostic varible name is used for both basic and advanced phytoplankton groups, even though the method to compute uptake differs between the two. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic (per L or m\(^3\)) have been chosen deliberately for consistency with other analogous volumetric losses such as mortality. This is intended to assist in simplifying post processing 
Phytoplankton: Basic Phytoplankton: Advanced 
Equation (I.14) Equation (I.15) 
WQ_DIAG_PHY_NAME_SEDMTN_P_MG_L_D WQ_DIAG_PHY_NAME_SEDMTN_P_MMOL_M3_D 
Phytoplankton sedimentation  phosphorus  \(F_{sedmtnP\langle computed\rangle}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of phytoplankton phosphorus into the sediments as a result of settling for a phytoplankton group. Values are only losses and are only negative. Multiply by cell volume (L or m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost to settling in that interval. This diagnostic varible name is used for both basic and advanced phytoplankton groups, even though the method to compute uptake differs between the two. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic (per L or m\(^3\)) have been chosen deliberately for consistency with other analogous volumetric losses such as mortality. This is intended to assist in simplifying post processing 
Phytoplankton: Basic Phytoplankton: Advanced 
Equation (I.16) Equation (I.17) 
WQ_DIAG_PHY_NAME_EXCR_MICG_L_D WQ_DIAG_PHY_NAME_EXCR_MMOL_M3_D 
Phytoplankton excretion  \(F_{Cexcr}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of carbon from phytoplankton as a result of excretion for a phytoplankton group. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via excretion in that interval 
Phytoplankton: Basic 
Equation (L.1) 
WQ_DIAG_PHY_NAME_MORT_MICG_L_D WQ_DIAG_PHY_NAME_MORT_MMOL_M3_D 
Phytoplankton mortality  \(F_{Cmort}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of carbon from phytoplankton as a result of mortality for a phytoplankton group. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via mortality in that interval 
Phytoplankton: Basic 
Equation (L.2) 
WQ_DIAG_PHY_NAME_EXCR_N_MG_L_D WQ_DIAG_PHY_NAME_EXCR_N_MMOL_M3_D 
Phytoplankton excretion  nitrogen  \(F_{Nexcr}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of nitrogen from phytoplankton as a result of excretion for a phytoplankton group. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via excretion in that interval 
Phytoplankton: Basic 
Equation (L.3) 
WQ_DIAG_PHY_NAME_MORT_N_MG_L_D WQ_DIAG_PHY_NAME_MORT_N_MMOL_M3_D 
Phytoplankton mortality  nitrogen  \(F_{Nmort}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of nitrogen from phytoplankton as a result of mortality for a phytoplankton group. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via mortality in that interval 
Phytoplankton: Basic 
Equation (L.4) 
WQ_DIAG_PHY_NAME_EXCR_P_MG_L_D WQ_DIAG_PHY_NAME_EXCR_P_MMOL_M3_D 
Phytoplankton excretion  phosphorus  \(F_{Pexcr}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of phosphorus from phytoplankton as a result of excretion for a phytoplankton group. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via excretion in that interval 
Phytoplankton: Basic 
Equation (L.5) 
WQ_DIAG_PHY_NAME_MORT_P_MG_L_D WQ_DIAG_PHY_NAME_MORT_P_MMOL_M3_D 
Phytoplankton mortality  phosphorus  \(F_{Pmort}^{phy}\) 
mg/L/d mmol/m\(^3\)/d 
The flux of phosphorus from phytoplankton as a result of mortality for a phytoplankton group. Values are only negative. Multiply by cell volume (m\(^3\)) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost via mortality in that interval 
Phytoplankton: Basic 
Equation (L.6) 
WQ_DIAG_FRP_ADS_SEDMTN_FLUX_MG_L_D WQ_DIAG_FRP_ADS_SEDMTN_FLUX_MMOL_M3_D 
Adsorbed FRP sedimentation rate  \(F_{sed\langle computed\rangle}^{FRPAds}\) 
mg/L/d mmol/m\(^3\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_FRP_ADS_RESUS_FLUX_MG_L_D WQ_DIAG_FRP_ADS_RESUS_FLUX_MMOL_M3_D 
Adsorbed FRP resuspension rate  \(F_{resus}^{FRPads}\) 
mg/L/d mmol/m\(^3\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_FRP_ADSORPTION_RATE_MG_L_D WQ_DIAG_FRP_ADSORPTION_RATE_MMOL_M3_D 
FRP adsorption rate  \(F_{ads\langle computed\rangle}^{FRP}\) 
mg/L/d mmol/m\(^3\)/d 
Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_PATH_NAME_MORTALITY_CFU_100ML_D  Pathogen mortality  \(F_{mor}^{pth}\)  CFU/100mL/d  The flux of pathogens from alive to dead, as a result of natural (dark death) mortality. This flux includes the mortality of attached pathogens, if they are simulated. This is not the inactivation flux due to irradiation. 
Pathogen: Free 
Equation (O.1) 
WQ_DIAG_PATH_NAME_LIGHT_CFU_100ML_D  Pathogen inactivation  \(F_{invn}^{pth}\)  CFU/100mL/d  The flux of pathogens from alive to dead, as a result of irradiation. This flux includes the inactivation of attached pathogens, if they are simulated. This is not the dark death flux due to mortality. 
Pathogen: Free 
Equation (O.3) 
WQ_DIAG_PATH_NAME_ATTACHMENT_CFU_100ML_D  Pathogen attachment  \(F_{att}^{pth}\)  CFU/100mL/d  The flux of pathogens from free to attached, if attached pathogens are simulated. A positive (negative) flux is attachment (detachment) 
Pathogen: Attached 
Equation (O.4) 
WQ_DIAG_PATH_NAME_ALIVE_SEDMTN_CFU_100ML_D  Pathogen alive sedimentation  \(F_{sedmtn\langle computed\rangle}^{pth_a}\)  CFU/100mL/d  The flux of alive pathogens into the sediments as a result of settling for a pathogen group. Values are only losses and are only negative. Multiply by volume and time interval of interest (seconds/86400) to compute the CFU that would be lost to settling in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic have been chosen deliberately for consistency with other analogous volumetric losses such as mortality. This is intended to assist in simplifying post processing 
Pathogen: Free 
Equation (O.6) 
WQ_DIAG_PATH_NAME_DEAD_SEDMTN_CFU_100ML_D  Pathogen alive sedimentation  \(F_{sedmtn\langle computed\rangle}^{pth_d}\)  CFU/100mL/d  The flux of dead pathogens into the sediments as a result of settling for a pathogen group. Values are only losses and are only negative. Multiply by volume and time interval of interest (seconds/86400) to compute the CFU that would be lost to settling in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic have been chosen deliberately for consistency with other analogous volumetric losses such as mortality. This is intended to assist in simplifying post processing 
Pathogen: Free 
Equation (O.6) 
WQ_DIAG_PATH_NAME_ATTCHD_SEDMTN_CFU_100ML_D  Pathogen attached sedimentation  \(F_{sedmtn\langle computed\rangle}^{pth_t}\)  CFU/100mL/d  The flux of attached pathogens into the sediments as a result of settling for a pathogen group. Values are only losses and are only negative. Multiply by volume and time interval of interest (seconds/86400) to compute the CFU that would be lost to settling in that interval. Although often thought of as being a per area (per m\(^2\)) loss, the volumetric units of this diagnostic have been chosen deliberately for consistency with other analogous volumetric losses such as mortality. This is intended to assist in simplifying post processing 
Pathogen: Attached 
Equation (O.7) 
WQ_DIAG_PATH_NAME_GROWTH_CFU_100ML_D  Pathogen growth  \(F_{growth\langle computed\rangle}^{pth_a}\)  CFU/100mL/d  Currently unused and reported as zero. Will be activated in future releases  
WQ_DIAG_PATH_NAME_TOTAL_CFU_100ML_D  Total pathogens  \(\left[ PTH\right]^{TOT}\)  CFU/100mL  The sum of alive, dead and attached (if the latter is simulated) pathogens for a pathogen group 
Pathogen: Free 
Equation (O.8) 