# Appendix P Diagnostic variables

The WQM’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.

WQM water quality 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 WQM, 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 selected.

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 zero indicates that a 2D cell (and associated 3D column) is dry. Water quality diagnostic variables are reported as zero when 2D cells are dry, so using the stat field to filter out these dry cells is required when post processing results from models where cells wet and dry. Similarly, 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.

Table P.1: WQ Module diagnostic variables
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.3)
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.4)
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.2)
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 $$F_{atm-din\langle computed \rangle}^{N}$$ 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 $$F_{atm-dip\langle computed \rangle}^{P}$$ 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_M2_S

WQ_DIAG_POC_SEDMTN_FLUX_MMOL_M2_S
POC sedimentation flux $$F_{sedmtn\langle computed\rangle}^{POC}$$ mg/m$$^2$$/d

mmol/m$$^2$$/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 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.31)
WQ_DIAG_PON_SEDMTN_FLUX_MG_M2_S

WQ_DIAG_PON_SEDMTN_FLUX_MMOL_M2_S
PON sedimentation flux $$F_{sedmtn\langle computed\rangle}^{PON}$$ mg/m$$^2$$/d

mmol/m$$^2$$/d
The flux of settling labile particulate organic nitrogen that leaves the water column and enters the sediment. This is not flux of PO from the sediments. 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.31)
WQ_DIAG_POP_SEDMTN_FLUX_MG_M2_S

WQ_DIAG_POP_SEDMTN_FLUX_MMOL_M2_S
POP sedimentation flux $$F_{sedmtn\langle computed\rangle}^{POP}$$ mg/m$$^2$$/d

mmol/m$$^2$$/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 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.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_M2_S

WQ_DIAG_RPOM_SEDMTN_FLUX_MMOL_M2_S
RPOM sedimentation flux $$F_{sedmtn\langle computed\rangle}^{RPOM}$$ mg/m$$^2$$/d

mmol/m$$^2$$/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 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:
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 $$R_{IN-IP}^{phy}$$ [-] 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 1 (no limitation) Phytoplankton:
Basic
Section J.2
WQ_DIAG_PHY_NAME_SAL_LIM_ND Salinity limitation function $$L_{sal-r}^{phy}$$ [-] 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 $$L_{sal-pp}^{phy}$$ [-] 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_M2_D

WQ_DIAG_PHY_NAME_SEDMTN_MMOL_M2_D
Phytoplankton sedimentation $$F_{sedmtn\langle computed\rangle}^{phy}$$ $$\mu$$g/m$$^2$$/d

mmol/m$$^2$$/d
The flux of phytoplankton carbon into the sediments as a result of settling for a phytoplankton group. Values are only losss and are only negative. Multiply by cell area (m$$^2$$) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost to settling in that interval 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_M2_D

WQ_DIAG_PHYTO_COM_SEDMTN_MMOL_M2_D
Community phytoplankton sedimentation $$F_{sedmtn\langle computed\rangle}^{comm}$$ $$\mu$$g/m$$^2$$/d

mmol/m$$^2$$/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 losss and are only negative. Multiply by cell area (m$$^2$$) and time interval of interest (seconds/86400) to compute the mass (or moles) that would be lost to settling in that interval 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 $$R_{PP-resp}^{comm}$$ [-] 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 $$R_{NPP-resp}^{comm}$$ [-] 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 $$F_{nit-uptake\langle computed\rangle}^{comm}$$ 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 $$F_{amm-uptake\langle computed\rangle}^{comm}$$ 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 $$F_{P-uptake\langle computed\rangle}^{comm}$$ 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 $$F_{C-uptake\langle computed\rangle}^{comm}$$ $$\mu$$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 $$\left[Chla\right]^{comm}$$ $$\mu$$g/L

mmol/m$$^3$$
The concentration of phytoplankton, summed over all phytoplankton groups (i.e. a simulation’s phytoplankton community). This will be the same numerical value as Community chlorophyll a if the MGL simulation units are used 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.4)
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_RESUS_MICG_M2_D

WQ_DIAG_PHYTO_COM_RESUS_MMOL_M2_D
Community resuspension $$F_{resus}^{comm}$$ $$\mu$$g/m$$^2$$/d

mmol/m$$^2$$
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 $$F_{N-fix}^{comm}$$ 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 ammonium-N and nitrate-N 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 nitrate-N to ammonium-N (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 $$F_{resp-N\langle computed\rangle}^{phy}$$ 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 $$F_{resp-P\langle computed\rangle}^{phy}$$ 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 $$F_{N-uptake}^{phy}$$ 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:
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 $$F_{P-uptake}^{phy}$$ 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:
Equation (K.7)

Equation (K.8)
WQ_DIAG_PHY_NAME_SEDMTN_N_MG_M2_D

WQ_DIAG_PHY_NAME_SEDMTN_N_MMOL_M2_D
Phytoplankton sedimentation - nitrogen $$F_{sedmtn-N\langle computed\rangle}^{phy}$$ mg/m$$^2$$/d

mmol/m$$^2$$/d
The flux of phytoplankton nitrogen into the sediments as a result of settling for a phytoplankton group. Values are only losss and are only negative. Multiply by cell area (m$$^2$$) 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 Phytoplankton:
Basic

Phytoplankton:
Equation (I.14)

Equation (I.15)
WQ_DIAG_PHY_NAME_SEDMTN_P_MG_M2_D

WQ_DIAG_PHY_NAME_SEDMTN_P_MMOL_M2_D
Phytoplankton sedimentation - phosphorus $$F_{sedmtn-P\langle computed\rangle}^{phy}$$ mg/m$$^2$$/d

mmol/m$$^2$$/d
The flux of phytoplankton phosphorus into the sediments as a result of settling for a phytoplankton group. Values are only losss and are only negative. Multiply by cell area (m$$^2$$) 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 Phytoplankton:
Basic

Phytoplankton:
Equation (I.16)

Equation (I.17)
WQ_DIAG_PHY_NAME_EXCR_MICG_L_D

WQ_DIAG_PHY_NAME_EXCR_MMOL_M3_D
Phytoplankton excretion $$F_{C-excr}^{phy}$$ 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 $$F_{C-mort}^{phy}$$ 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 $$F_{N-excr}^{phy}$$ 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 $$F_{N-mort}^{phy}$$ 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 $$F_{P-excr}^{phy}$$ 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 $$F_{P-mort}^{phy}$$ 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)

Adsorbed FRP sedimentation rate $$F_{sed\langle computed\rangle}^{FRPAds}$$ mg/m$$^2$$/d

mmol/m$$^2$$/d
Currently unused and reported as zero. Will be activated in future releases
Adsorbed FRP resuspension rate $$F_{resus}^{FRPads}$$ mg/m$$^2$$/d
mmol/m$$^2$$/d
FRP adsorption rate $$F_{ads\langle computed\rangle}^{FRP}$$ mg/L/d
mmol/m$$^3$$/d