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Line 1: Line 1:
 
==MOHID Base 1==
 
==MOHID Base 1==
  
=== Module Benthos===
+
===Module Benthos===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleBenthos.F90 Source Code]
 +
 
 
{| class="wikitable"
 
{| class="wikitable"
  
 
|-
 
|-
! scope="col" |Project
 
! scope="col" |Module
 
 
! scope="col" |Keyword
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Options
 
! scope="col" |Option description
 
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|BIOSI_DECAY_RATE
 
|BIOSI_DECAY_RATE
 
|Biogenic silica dissolution rate
 
|Biogenic silica dissolution rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|DIATOMS
 
|DIATOMS
 
|Compute diatoms mortality
 
|Compute diatoms mortality
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|DIATOMS_MORTALITY
 
|DIATOMS_MORTALITY
 
|Diatoms mortality rate when deposited
 
|Diatoms mortality rate when deposited
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|DIATOMS_NC_RATIO
 
|DIATOMS_NC_RATIO
 
|Diatoms Nitrogen/Carbon ratio
 
|Diatoms Nitrogen/Carbon ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|DIATOMS_PC_RATIO
 
|DIATOMS_PC_RATIO
 
|Diatoms Phosphorus/Carbon ratio
 
|Diatoms Phosphorus/Carbon ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|DIATOMS_SIC_RATIO
 
|DIATOMS_SIC_RATIO
 
|Diatoms Silica/Carbon ratio
 
|Diatoms Silica/Carbon ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|DT
 
|DT
 
|Time step to compute benthic biogeochemical processes
 
|Time step to compute benthic biogeochemical processes
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|MIN_OXYGEN
 
|MIN_OXYGEN
 
|Minimum oxygen concentration for mineralization to occur
 
|Minimum oxygen concentration for mineralization to occur
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|NC_RATIO
 
|NC_RATIO
 
|Nitrogen/Carbon ratio of organic matter
 
|Nitrogen/Carbon ratio of organic matter
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|NITROGEN
 
|NITROGEN
 
|Compute nitrogen processes
 
|Compute nitrogen processes
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|OXYGEN
 
|OXYGEN
 
|Compute oxygen processes
 
|Compute oxygen processes
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|PC_RATIO
 
|PC_RATIO
 
|Phosphorus/Carbon ratio of organic matter
 
|Phosphorus/Carbon ratio of organic matter
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
+
| rowspan="2" |PELAGIC_MODEL
|Benthos
+
| rowspan="2" |Pelagic model name to which Module Benthos will be coupled
|PELAGIC_MODEL
+
|LifeModel
|Pelagic model name to which ModuleBenthos will be coupled
 
|WaterQuality
 
 
|
 
|
 +
| rowspan="2" |
 +
| rowspan="2" |
 
|-
 
|-
| Base 1
+
|WaterQuality
|Benthos
 
|PELAGIC_MODEL
 
|Pelagic model name to which ModuleBenthos will be coupled
 
|LifeModel
 
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|PHOSPHORUS
 
|PHOSPHORUS
 
|Compute phosphorus processes
 
|Compute phosphorus processes
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|PHYTO
 
|PHYTO
 
|Compute phytoplankton mortality
 
|Compute phytoplankton mortality
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|PHYTO_MORTALITY
 
|PHYTO_MORTALITY
|Phytoplankton
+
|Phytoplankton mortality rate when deposited
mortality rate when deposited
+
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|PHYTO_NC_RATIO
 
|PHYTO_NC_RATIO
 
|Phytoplankton Nitrogen/Carbon ratio
 
|Phytoplankton Nitrogen/Carbon ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|PHYTO_PC_RATIO
 
|PHYTO_PC_RATIO
 
|Phytoplankton Nitrogen/Carbon ratio
 
|Phytoplankton Nitrogen/Carbon ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|PON_DECAY_RATE
 
|PON_DECAY_RATE
 
|Particulate organic nitrogen mineralization rate
 
|Particulate organic nitrogen mineralization rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|PON_DECAY_TFACTOR
 
|PON_DECAY_TFACTOR
 
|Particulate Organic Nitrogen temperature influence factor in mineralization Rate
 
|Particulate Organic Nitrogen temperature influence factor in mineralization Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|POP_DECAY_RATE
 
|POP_DECAY_RATE
 
|Particulate organic phosphorus mineralization rate  
 
|Particulate organic phosphorus mineralization rate  
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|POP_DECAY_TFACTOR
 
|POP_DECAY_TFACTOR
 
|Particulate Organic Phosphorus temperature influence factor in mineralization Rate
 
|Particulate Organic Phosphorus temperature influence factor in mineralization Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
 
|Benthos
 
 
|SILICA
 
|SILICA
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|
 
|
 
|}
 
|}
 +
 
=== Module CEQUALW2===
 
=== Module CEQUALW2===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleCEQUALW2.F90 Source Code]
 
{| class="wikitable"
 
{| class="wikitable"
 
 
|-
 
|-
 
! scope="col" |Project
 
! scope="col" |Project
Line 191: Line 212:
 
! scope="col" |Options
 
! scope="col" |Options
 
! scope="col" |Option description
 
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 196: Line 220:
 
|DTSECONDS
 
|DTSECONDS
 
|time step, in seconds, between two CEQUALW2 calls
 
|time step, in seconds, between two CEQUALW2 calls
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 203: Line 230:
 
|NAME
 
|NAME
 
|Algae Property name as defined on Module GlobalData
 
|Algae Property name as defined on Module GlobalData
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|}
 
|}
 +
 
=== Module Discharges===
 
=== Module Discharges===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleDischarges.F90 Source Code]
 
{| class="wikitable"
 
{| class="wikitable"
 
 
|-
 
|-
 
! scope="col" |Project
 
! scope="col" |Project
Line 216: Line 247:
 
! scope="col" |Options
 
! scope="col" |Options
 
! scope="col" |Option description
 
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 221: Line 255:
 
|ALTERNATIVE_LOCATIONS
 
|ALTERNATIVE_LOCATIONS
 
|Activates the automatic search for alternative locations, when the discharge point is not a covered point
 
|Activates the automatic search for alternative locations, when the discharge point is not a covered point
 +
|0/1
 +
|Inactive/Active
 +
|0
 +
|
 +
|Boolean
 +
|-
 +
| Base 1
 +
|Discharges
 +
|COORD_X
 +
|Longitude of the discharge in geographic coordinates
 +
|
 +
|
 +
|
 +
|
 +
|Real
 +
|-
 +
| Base 1
 +
|Discharges
 +
|COORD_Y
 +
|Activates the automatic search for alternative locations, when the discharge point is not a covered point
 +
|Latitude of the discharge in geographic coordinates
 +
|
 
|
 
|
 
|
 
|
 +
|Real
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 228: Line 285:
 
|CREST_HEIGTH
 
|CREST_HEIGTH
 
|Crest Height. Parameter needed in the case of the option FLOW_OVER is active (spill flow).
 
|Crest Height. Parameter needed in the case of the option FLOW_OVER is active (spill flow).
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 234: Line 294:
 
|Discharges
 
|Discharges
 
|DATA_BASE_FILE
 
|DATA_BASE_FILE
|Definition of the data base timeserie file. If there is one, model assumes that the discharge is time variable
+
|Definition of the data base time series file. If there is one, model assumes that the discharge is time variable
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 242: Line 305:
 
|DEFAULT_FLOW_VALUE
 
|DEFAULT_FLOW_VALUE
 
|Default flow value
 
|Default flow value
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 249: Line 315:
 
|DEFAULT_VELOCITY_VALUE
 
|DEFAULT_VELOCITY_VALUE
 
|Default velocity associated with the discharge. Important to compute momentum fluxes
 
|Default velocity associated with the discharge. Important to compute momentum fluxes
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 256: Line 325:
 
|DEFAULTVALUE
 
|DEFAULTVALUE
 
|Water property value
 
|Water property value
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 263: Line 335:
 
|DESCRIPTION
 
|DESCRIPTION
 
|Discharge description
 
|Discharge description
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 269: Line 344:
 
|Discharges
 
|Discharges
 
|FLOW_COLUMN
 
|FLOW_COLUMN
|Column where the flow is defined in the data base timeserie file
+
|Column where the flow is defined in the data base time series file
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| rowspan="3" |Base 1
 +
| rowspan="3" |Discharges
 +
| rowspan="3" |FLOW_DISTRIBUTION
 +
| rowspan="3" |Chooses the hydrodynamic approximation to be solved in the momentum equation
 +
|by cell
 +
|
 +
| rowspan="3" |
 +
| rowspan="3" |
 +
| rowspan="3" |
 +
|-
 +
|by water column
 
|
 
|
 +
|-
 +
|by volume
 
|
 
|
 
|-
 
|-
Line 279: Line 373:
 
|
 
|
 
|
 
|
 +
|
 +
|
 +
|
 +
|-
 +
| Base 1
 +
|Discharges
 +
|IGNORE_ON
 +
|This keyword must be active for MOHID MPI runs
 +
|0/1
 +
|Inactive/Active
 +
|0
 +
|
 +
|Boolean
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 286: Line 393:
 
|
 
|
 
|
 
|
 +
|
 +
|
 +
|Integer
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 293: Line 403:
 
|
 
|
 
|
 
|
 +
|
 +
|
 +
|Integer
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 300: Line 413:
 
|
 
|
 
|
 
|
 +
|
 +
|
 +
|Integer
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 305: Line 421:
 
|NAME
 
|NAME
 
|Discharge name
 
|Discharge name
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 312: Line 431:
 
|NODE_ID
 
|NODE_ID
 
|ID of the discharge, when it isn't grid-based
 
|ID of the discharge, when it isn't grid-based
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 318: Line 440:
 
|Discharges
 
|Discharges
 
|TIME_SERIE_COLUMN
 
|TIME_SERIE_COLUMN
|This keyword is used to give to the model the column where the water property associated with this sub-block is defined in the timeserie.
+
|This keyword is used to give to the model the column where the water property associated with this sub-block is defined in the time series.
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 325: Line 450:
 
|Discharges
 
|Discharges
 
|U_COLUMN
 
|U_COLUMN
|This keyword is used to give to model the column where the velocity X is defined in the data base timeserie file
+
|This keyword is used to give to model the column where the velocity X is defined in the data base time series file
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 332: Line 460:
 
|Discharges
 
|Discharges
 
|V_COLUMN
 
|V_COLUMN
|This keyword is used to give to model the column where the velocity Y is defined in the data base timeserie file
+
|This keyword is used to give to model the column where the velocity Y is defined in the data base time series file
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 339: Line 470:
 
|Discharges
 
|Discharges
 
|WEIR_COEF
 
|WEIR_COEF
|Weir Coeficient. Parameter needed in the case of the option FLOW_OVER is active (spill flow).
+
|Weir Coefficient. Parameter needed in the case of the option FLOW_OVER is active (spill flow).
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 347: Line 481:
 
|WEIR_LENGTH
 
|WEIR_LENGTH
 
|Weir Length. Parameter needed in the case of the option FLOW_OVER is active (spill flow).
 
|Weir Length. Parameter needed in the case of the option FLOW_OVER is active (spill flow).
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|}
 
|}
 +
 
=== Module DrainageNetwork===
 
=== Module DrainageNetwork===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleDrainageNetwork.F90 Source Code]
 
{| class="wikitable"
 
{| class="wikitable"
 
 
|-
 
|-
 
! scope="col" |Project
 
! scope="col" |Project
Line 360: Line 498:
 
! scope="col" |Options
 
! scope="col" |Options
 
! scope="col" |Option description
 
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
 
|DrainageNetwork
 
|DrainageNetwork
 
|ADVECTION_DIFUSION
 
|ADVECTION_DIFUSION
|Compute advection and difusion of property
+
|Compute advection and diffusion of property
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
+
| rowspan="2" |Base 1
|DrainageNetwork
+
| rowspan="2" |DrainageNetwork
|ADVECTION_SCHEME
+
| rowspan="2" |ADVECTION_SCHEME
|Numerical Discretization of Advection.
+
| rowspan="2" |Numerical Discretization of Advection.
 
|1
 
|1
 
|UpwindOrder1 (Upwind scheme of 1st order)
 
|UpwindOrder1 (Upwind scheme of 1st order)
 +
| rowspan="2" |
 +
| rowspan="2" |
 +
| rowspan="2" |
 
|-
 
|-
| Base 1
+
|5
|DrainageNetwork
 
|ADVECTION_SCHEME
 
|Numerical Discretization of Advection.
 
|5
 
 
|CentralDif (Central differences scheme)
 
|CentralDif (Central differences scheme)
 
|-
 
|-
Line 386: Line 529:
 
|CHECK_NODES
 
|CHECK_NODES
 
|Check nodes consistency in the drainage network file
 
|Check nodes consistency in the drainage network file
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 393: Line 539:
 
|CHECK_REACHES
 
|CHECK_REACHES
 
|Check reaches consistency in the drainage network file (a reach connects 2 nodes)
 
|Check reaches consistency in the drainage network file (a reach connects 2 nodes)
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 400: Line 549:
 
|CONTINUOUS
 
|CONTINUOUS
 
|Computations follow from another simulation
 
|Computations follow from another simulation
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 406: Line 558:
 
|DrainageNetwork
 
|DrainageNetwork
 
|DATA_COLUMN
 
|DATA_COLUMN
|Number of column in the time serie file with the downstream water depth values
+
|Number of column in the time series file with the downstream water depth values
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 414: Line 569:
 
|DEFAULT_VALUE
 
|DEFAULT_VALUE
 
|Default value for water depth at the downstream boundary condition
 
|Default value for water depth at the downstream boundary condition
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 421: Line 579:
 
|DEFAULT_VALUE
 
|DEFAULT_VALUE
 
|Default value for this property. Also used as initial value.
 
|Default value for this property. Also used as initial value.
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 428: Line 589:
 
|DESCRIPTION
 
|DESCRIPTION
 
|Description of property
 
|Description of property
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 434: Line 598:
 
|DrainageNetwork
 
|DrainageNetwork
 
|DIFFUSION_SCHEME
 
|DIFFUSION_SCHEME
|Numerical Discretization of Difusion.
+
|Numerical Discretization of Diffusion.
 
|5
 
|5
 
|CentralDif (Central Differences discretization)
 
|CentralDif (Central Differences discretization)
 +
|
 +
|
 +
|
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 442: Line 609:
 
|DIFFUSIVITY
 
|DIFFUSIVITY
 
|Diffusivity of property
 
|Diffusivity of property
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 448: Line 618:
 
|DrainageNetwork
 
|DrainageNetwork
 
|DISCHARGES
 
|DISCHARGES
|Has water discharges into the drainage network
+
|Use module discharges
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|DrainageNetwork
 
|DISCHARGES
 
|Check if property has discharges.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
+
| rowspan="5" |Base 1
|DrainageNetwork
+
| rowspan="5" |DrainageNetwork
|DOWNSTREAM_BOUNDARY
+
| rowspan="5" |DOWNSTREAM_BOUNDARY
|Choose downstream boundary condition
+
| rowspan="5" |Choose downstream boundary condition
 
|0
 
|0
 
|Dam (flow at the outlet = 0.0)
 
|Dam (flow at the outlet = 0.0)
 +
| rowspan="5" |
 +
| rowspan="5" |
 +
| rowspan="5" |
 
|-
 
|-
| Base 1
 
|DrainageNetwork
 
|DOWNSTREAM_BOUNDARY
 
|Choose downstream boundary condition
 
 
|1
 
|1
 
|Normal (solves KynematicWave at the outlet)
 
|Normal (solves KynematicWave at the outlet)
 
|-
 
|-
| Base 1
 
|DrainageNetwork
 
|DOWNSTREAM_BOUNDARY
 
|Choose downstream boundary condition
 
 
|2
 
|2
 
|ImposedWaterDepth
 
|ImposedWaterDepth
 
|-
 
|-
| Base 1
+
|3
|DrainageNetwork
+
|ImposedWaterLevel
|FILE_IN_TIME
+
|-
|Downstream boundary condition evolution
+
|4
 +
|ImposedVelocity
 +
|-
 +
| rowspan="2" |Base 1
 +
| rowspan="2" |DrainageNetwork
 +
| rowspan="2" |FILE_IN_TIME
 +
| rowspan="2" |Downstream boundary condition evolution
 
|NONE
 
|NONE
 
|Constant evolution of downstream boundary condition (constant water depth)
 
|Constant evolution of downstream boundary condition (constant water depth)
 +
| rowspan="2" |
 +
| rowspan="2" |
 +
| rowspan="2" |
 
|-
 
|-
| Base 1
 
|DrainageNetwork
 
|FILE_IN_TIME
 
|Downstream boundary condition evolution
 
 
|TIMESERIE
 
|TIMESERIE
|Reads a time serie with water depth for downstream boundary condition
+
|Reads a time series with water depth for downstream boundary condition
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 498: Line 664:
 
|FILENAME
 
|FILENAME
 
|Path to the file with the downstream water depth time serie values
 
|Path to the file with the downstream water depth time serie values
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 504: Line 673:
 
|DrainageNetwork
 
|DrainageNetwork
 
|GLOBAL_MANNING
 
|GLOBAL_MANNING
|Assigns a Manning rugosity coeficient to all the drainage network channels
+
|Assigns a Manning rugosity coefficient to all the drainage network channels
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
+
| rowspan="3" |Base 1
|DrainageNetwork
+
| rowspan="3" |DrainageNetwork
|HYDRODYNAMIC_APROX
+
| rowspan="3" |HYDRODYNAMIC_APROX
|Chooses the hydrodynamic approximation to be solved in the momentum equation
+
| rowspan="3" |Chooses the hydrodynamic approximation to be solved in the momentum equation
 
|1
 
|1
 
|KinematicWave (friction = slope gradient)
 
|KinematicWave (friction = slope gradient)
 +
| rowspan="3" |
 +
| rowspan="3" |
 +
| rowspan="3" |
 
|-
 
|-
| Base 1
 
|DrainageNetwork
 
|HYDRODYNAMIC_APROX
 
|Chooses the hydrodynamic approximation to be solved in the momentum equation
 
 
|2
 
|2
 
|DiffusionWave (full St Venant equation except for advection)
 
|DiffusionWave (full St Venant equation except for advection)
 
|-
 
|-
| Base 1
 
|DrainageNetwork
 
|HYDRODYNAMIC_APROX
 
|Chooses the hydrodynamic approximation to be solved in the momentum equation
 
 
|3
 
|3
 
|DynamicWave (full St Venant equation)
 
|DynamicWave (full St Venant equation)
Line 532: Line 699:
 
|DrainageNetwork
 
|DrainageNetwork
 
|INITIAL_WATER_DEPTH
 
|INITIAL_WATER_DEPTH
|Assigns an initial water depth to all channels. only if continuous computation is not choosed.
+
|Assigns an initial water depth to all channels. only if continuous computation is not chosen.
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 542: Line 712:
 
|CONSTANT
 
|CONSTANT
 
|Constant initialization of property
 
|Constant initialization of property
 +
|
 +
|
 +
|
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 547: Line 720:
 
|MIN_VALUE
 
|MIN_VALUE
 
|Minimum concentration of property.
 
|Minimum concentration of property.
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 554: Line 730:
 
|MIN_WATER_DEPTH
 
|MIN_WATER_DEPTH
 
|Minimum water column for computations
 
|Minimum water column for computations
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 561: Line 740:
 
|NAME
 
|NAME
 
|Name of property
 
|Name of property
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 568: Line 750:
 
|NETWORK_FILE
 
|NETWORK_FILE
 
|Path to the file that describes nodes and reaches
 
|Path to the file that describes nodes and reaches
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 575: Line 760:
 
|TIME_SERIE
 
|TIME_SERIE
 
|Output of property values in time series files.
 
|Output of property values in time series files.
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 582: Line 770:
 
|TIME_SERIE_LOCATION
 
|TIME_SERIE_LOCATION
 
|Path to the file that has the time series location characteristics
 
|Path to the file that has the time series location characteristics
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 591: Line 782:
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|DrainageNetwork
 
|XS_CALC
 
|Method to compute trapezoidal cross section (1 - Analitic; 2 - Discretization dH)
 
 
|
 
|
 
|
 
|
 +
|
 +
|-
 +
| rowspan="2" |Base 1
 +
| rowspan="2" |DrainageNetwork
 +
| rowspan="2" |XS_CALC
 +
| rowspan="2" |Method to compute trapezoidal cross section
 +
|1
 +
|Analytic
 +
| rowspan="2" |
 +
| rowspan="2" |
 +
| rowspan="2" |
 +
|-
 +
|2
 +
|Discretization dH
 
|}
 
|}
  
 
=== Module Life===
 
=== Module Life===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleLife.F90 Source Code]
 
{| class="wikitable"
 
{| class="wikitable"
 
 
|-
 
|-
 
! scope="col" |Project
 
! scope="col" |Project
Line 610: Line 810:
 
! scope="col" |Options
 
! scope="col" |Options
 
! scope="col" |Option description
 
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
Line 615: Line 818:
 
|AFFINITY_NH4
 
|AFFINITY_NH4
 
|Affinity for NH4 uptake
 
|Affinity for NH4 uptake
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 622: Line 828:
 
|AFFINITY_NO3
 
|AFFINITY_NO3
 
|Affinity for NO3 uptake
 
|Affinity for NO3 uptake
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 629: Line 838:
 
|AFFINITY_PO4
 
|AFFINITY_PO4
 
|Affinity for PO4 uptake
 
|Affinity for PO4 uptake
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 636: Line 848:
 
|ALPHA_CHL
 
|ALPHA_CHL
 
|Chl specific initial slop of P vs I curve
 
|Chl specific initial slop of P vs I curve
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 642: Line 857:
 
|Life
 
|Life
 
|ASS_EFFIC
 
|ASS_EFFIC
|Asimilation efficiency
+
|Assimilation efficiency
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 649: Line 867:
 
|Life
 
|Life
 
|ASS_EFFIC_LOW_O2
 
|ASS_EFFIC_LOW_O2
|Asimilation efficiency @ low O2
+
|Assimilation efficiency @ low O2
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 657: Line 878:
 
|ASSIMIL_EFFIC
 
|ASSIMIL_EFFIC
 
|Assimilation efficiency
 
|Assimilation efficiency
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 664: Line 888:
 
|BIO_SI_DISS
 
|BIO_SI_DISS
 
|Biogenic silica dissolution rate
 
|Biogenic silica dissolution rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 671: Line 898:
 
|CHL_DEGRAD_RATE
 
|CHL_DEGRAD_RATE
 
|Chla degradation rate constant
 
|Chla degradation rate constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 678: Line 908:
 
|DENS_DEP_MORT
 
|DENS_DEP_MORT
 
|Density-dependence mortality rate
 
|Density-dependence mortality rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 684: Line 917:
 
|Life
 
|Life
 
|DOM_UP_KS
 
|DOM_UP_KS
|Half saturation value for DOM uptake    
+
|Half saturation value for DOM uptake
 
+
|
 
|
 
|
 
|
 
|
|-
+
|
 +
|
 +
|-
 
| Base 1
 
| Base 1
 
|Life
 
|Life
 
|DOMSL_BAC_KS
 
|DOMSL_BAC_KS
 
|Bacteria mediated DOMsl Hydrolysis
 
|Bacteria mediated DOMsl Hydrolysis
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 700: Line 938:
 
|DOMSL_BAC_VMAX
 
|DOMSL_BAC_VMAX
 
|Vmax for DOMsl Hydrolysis
 
|Vmax for DOMsl Hydrolysis
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 707: Line 948:
 
|EXC_DOM_SL_FRAC
 
|EXC_DOM_SL_FRAC
 
|DOM diverted to semi-labile pool
 
|DOM diverted to semi-labile pool
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 714: Line 958:
 
|EXCRE_UP_FRAC
 
|EXCRE_UP_FRAC
 
|Excreted fraction of uptake
 
|Excreted fraction of uptake
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 721: Line 968:
 
|EXU_NUT_STRESS
 
|EXU_NUT_STRESS
 
|Exudation under nutrient stress
 
|Exudation under nutrient stress
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 728: Line 978:
 
|GRAZ_AVAIL
 
|GRAZ_AVAIL
 
|Availability of Prey X
 
|Availability of Prey X
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 735: Line 988:
 
|GRAZ_UP_KS
 
|GRAZ_UP_KS
 
|Half saturation value for uptake
 
|Half saturation value for uptake
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 742: Line 998:
 
|LIGHT_LIM_METHOD
 
|LIGHT_LIM_METHOD
 
|Light limitation method
 
|Light limitation method
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 749: Line 1,008:
 
|LYS_REF_CON
 
|LYS_REF_CON
 
|Lysis_Ref_Con     
 
|Lysis_Ref_Con     
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 756: Line 1,018:
 
|MASS_XEK
 
|MASS_XEK
 
|Command to make a mass conservation test
 
|Command to make a mass conservation test
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 763: Line 1,028:
 
|MAX_ASSIMIL
 
|MAX_ASSIMIL
 
|Maximal assimilation rate
 
|Maximal assimilation rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 770: Line 1,038:
 
|MAX_CHLN_RATIO
 
|MAX_CHLN_RATIO
 
|Maximal Chl:N ratio
 
|Maximal Chl:N ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 777: Line 1,048:
 
|MAX_NC_RATIO
 
|MAX_NC_RATIO
 
|Maximal N:C ratio
 
|Maximal N:C ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 784: Line 1,058:
 
|MAX_PC_RATIO
 
|MAX_PC_RATIO
 
|Maximal P:C ratio
 
|Maximal P:C ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 791: Line 1,068:
 
|MAX_SPEC_UP_@10C
 
|MAX_SPEC_UP_@10C
 
|Maximum specific uptake @ 10ºC
 
|Maximum specific uptake @ 10ºC
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 798: Line 1,078:
 
|MAX_STORE_FILL
 
|MAX_STORE_FILL
 
|Maximal rate of storage filling
 
|Maximal rate of storage filling
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 805: Line 1,088:
 
|MIN_LYSIS
 
|MIN_LYSIS
 
|Minimal lysis rate
 
|Minimal lysis rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 812: Line 1,098:
 
|MIN_NC_RATIO
 
|MIN_NC_RATIO
 
|Minimal N:C ratio
 
|Minimal N:C ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 819: Line 1,108:
 
|MIN_PC_RATIO
 
|MIN_PC_RATIO
 
|Minimal P:C ratio
 
|Minimal P:C ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 825: Line 1,117:
 
|Life
 
|Life
 
|MIXOTROPHY
 
|MIXOTROPHY
|Hability to performe mixotrophy
+
|Hability to perform mixotrophy
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 833: Line 1,128:
 
|MORT_DOM_SL_FRAC
 
|MORT_DOM_SL_FRAC
 
|DOC_SL_Frac   
 
|DOC_SL_Frac   
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 840: Line 1,138:
 
|MORT_O2_DEP
 
|MORT_O2_DEP
 
|Oxygen-dependent mortality rate
 
|Oxygen-dependent mortality rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 847: Line 1,148:
 
|MORT_POM_FRAC
 
|MORT_POM_FRAC
 
|Fraction of mortality to POM
 
|Fraction of mortality to POM
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 854: Line 1,158:
 
|MORT_RATE
 
|MORT_RATE
 
|Temperature-independent mortality rate
 
|Temperature-independent mortality rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 861: Line 1,168:
 
|NH4_Ks
 
|NH4_Ks
 
|PO4 uptake affinity     
 
|PO4 uptake affinity     
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 867: Line 1,177:
 
|Life
 
|Life
 
|NIT_IN_COEF
 
|NIT_IN_COEF
|Nitrification inhibition coeficient
+
|Nitrification inhibition coefficient
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 875: Line 1,188:
 
|NIT_O_N_CONV
 
|NIT_O_N_CONV
 
|Nitrification O:N consumption ratio
 
|Nitrification O:N consumption ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 882: Line 1,198:
 
|NITRIFRADLIM
 
|NITRIFRADLIM
 
|Light radiation bellow which nitrification occurs
 
|Light radiation bellow which nitrification occurs
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 889: Line 1,208:
 
|NITRIFRATE
 
|NITRIFRATE
 
|Nitrification rate
 
|Nitrification rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 896: Line 1,218:
 
|NO3_Ks
 
|NO3_Ks
 
|NO3 uptake affinity
 
|NO3 uptake affinity
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 903: Line 1,228:
 
|NUT_STRESS_TRESHOLD
 
|NUT_STRESS_TRESHOLD
 
|Nutrient stress threshold (sedimentation)
 
|Nutrient stress threshold (sedimentation)
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 910: Line 1,238:
 
|O2_CARB_CONVERS
 
|O2_CARB_CONVERS
 
|Oxygen to carbon conversion factor
 
|Oxygen to carbon conversion factor
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 917: Line 1,248:
 
|O2_KS
 
|O2_KS
 
|Oxygen half saturation constant  
 
|Oxygen half saturation constant  
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 924: Line 1,258:
 
|O2_LOW_ASS_EFIC
 
|O2_LOW_ASS_EFIC
 
|Oxygen concentration bollow which ass efic is low  
 
|Oxygen concentration bollow which ass efic is low  
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 931: Line 1,268:
 
|PHOTOINHIBITION
 
|PHOTOINHIBITION
 
|Photoinhibition  
 
|Photoinhibition  
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 938: Line 1,278:
 
|PO4_Ks
 
|PO4_Ks
 
|PO4 uptake affinity
 
|PO4 uptake affinity
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 944: Line 1,287:
 
|Life
 
|Life
 
|POM_BAC_KS
 
|POM_BAC_KS
|Bacteria mediated POM Hydrolysis MM cosntant
+
|Bacteria mediated POM Hydrolysis MM constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 952: Line 1,298:
 
|POM_BAC_VMAX
 
|POM_BAC_VMAX
 
|Vmax for POM Hydrolysis
 
|Vmax for POM Hydrolysis
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 959: Line 1,308:
 
|Q10_VALUE
 
|Q10_VALUE
 
|Q10 value for temperature limitation
 
|Q10 value for temperature limitation
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 966: Line 1,318:
 
|REDFIELD_NC
 
|REDFIELD_NC
 
|Redfield N:C ratio
 
|Redfield N:C ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 973: Line 1,328:
 
|REDFIELD_PC
 
|REDFIELD_PC
 
|Redfield P:C ratio
 
|Redfield P:C ratio
 
+
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 981: Line 1,338:
 
|REDFIELD_SiC
 
|REDFIELD_SiC
 
|Standard Si:C ratio
 
|Standard Si:C ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 988: Line 1,348:
 
|REF_TEMP
 
|REF_TEMP
 
|Reference temperature
 
|Reference temperature
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 995: Line 1,358:
 
|REF_TEMP_Q10
 
|REF_TEMP_Q10
 
|Reference temperature for Q10 method
 
|Reference temperature for Q10 method
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,002: Line 1,368:
 
|REL_EXCESS_SI
 
|REL_EXCESS_SI
 
|Release rate of excess silicate
 
|Release rate of excess silicate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,009: Line 1,378:
 
|RESP_BASAL
 
|RESP_BASAL
 
|Basal respiration rate
 
|Basal respiration rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,016: Line 1,388:
 
|RESP_FRAC_PROD
 
|RESP_FRAC_PROD
 
|Respired fraction of production
 
|Respired fraction of production
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,023: Line 1,398:
 
|REST_RESP_@10C
 
|REST_RESP_@10C
 
|Rest respiration @ 10ºC
 
|Rest respiration @ 10ºC
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,030: Line 1,408:
 
|SED_MIN
 
|SED_MIN
 
|Minimal sedimentation rate
 
|Minimal sedimentation rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,037: Line 1,418:
 
|SED_NUT_STRESS
 
|SED_NUT_STRESS
 
|Nutrient stress sedimentation rate
 
|Nutrient stress sedimentation rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,044: Line 1,428:
 
|SEDIM_MIN
 
|SEDIM_MIN
 
|Minimal sedimentation rate
 
|Minimal sedimentation rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,051: Line 1,438:
 
|SEDIM_NUT_STRESS
 
|SEDIM_NUT_STRESS
 
|Nutrient stress threshold (sedimentation)
 
|Nutrient stress threshold (sedimentation)
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,058: Line 1,448:
 
|SI_UPTAKE_KS
 
|SI_UPTAKE_KS
 
|Silicate uptake Michaelis constant
 
|Silicate uptake Michaelis constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,065: Line 1,458:
 
|SILICA_USE
 
|SILICA_USE
 
|Set Silica use by the producer
 
|Set Silica use by the producer
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,072: Line 1,468:
 
|TEMP_LIM_METHOD
 
|TEMP_LIM_METHOD
 
|Temperature limitation method
 
|Temperature limitation method
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|}
 
|}
=== Module MacroAlgae===
+
 
 +
=== Module LightExtinction===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleLightExtinction.F90 Source Code]
 
{| class="wikitable"
 
{| class="wikitable"
 
 
|-
 
|-
 
! scope="col" |Project
 
! scope="col" |Project
Line 1,085: Line 1,485:
 
! scope="col" |Options
 
! scope="col" |Options
 
! scope="col" |Option description
 
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|BEACHED_MORT_RATE
+
|COEF_PARSONS_PORTELA
|Beached drifting macroalgae mortality rate
+
|Correct Default Coefficient for Parsons Portela SW Radiation parameterisation
 +
|Needs SW_EXTINCTION_TYPE: 4
 
|
 
|
 +
|0.04
 
|
 
|
 +
|Real
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|DEPLIM
+
|LW_EXTINCTION_COEF
|Maximum SPM deposition flux allowed for macroalgae to grow
+
|Long-wave extinction coeficient
 
|
 
|
 
|
 
|
|-
+
|0.333
| Base 1
 
|MacroAlgae
 
|DISSDON
 
|fraction of dissolved organic material excreted by macroalgae
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|DT
+
|LW_EXTINCTION_COLUMN
|Time step compute macroalgae biogeochemical processes
+
|
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|ENDREPC
 
|Macroalgae endogenous respiration rate
 
 
|
 
|
 
|
 
|
 +
|-
 +
| rowspan="2" |Base 1
 +
| rowspan="2" |LightExtinction
 +
| rowspan="2" |LW_EXTINCTION_TYPE
 +
| rowspan="2" |The method used in light extinction estimate
 +
|1
 +
|Constant
 +
| rowspan="2" |1
 +
| rowspan="2" |
 +
| rowspan="2" |
 +
|-
 +
|5
 +
|Ascii file
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|EROCRITSS
+
|LW_PERCENTAGE
|Critical shear stress for macroalgae dettachment to occur
 
|
 
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|EXCRCONS
 
|Macroalgae excretion rate
 
 
|
 
|
 
|
 
|
|-
+
|0.4
| Base 1
 
|MacroAlgae
 
|GRAZCONS
 
|Grazing rate over macroalgae
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|GROWMAX
+
|SW_EXTINCTION_COEF
|macroalgae maximum growth rate
+
|Short-wave extinction coeficient
|
 
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|MACROALGAE_MINCONC
 
|Minimum residual value for macroalgae abundance
 
 
|
 
|
 +
|0.05
 
|
 
|
 +
|Real
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|MIN_OXYGEN
+
|SW_EXTINCTION_COLUMN
|Minimum oxygen concentration for macroalgae growth
 
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|MORTCON
 
|Macroalgae mortality half saturation constant
 
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|MORTMAX
 
|Macroalgae natural mortality rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 1
+
| rowspan="6" |Base 1
|MacroAlgae
+
| rowspan="6" |LightExtinction
|NITROGEN
+
| rowspan="6" |SW_EXTINCTION_TYPE
|Defines if the user wishes to compute the nitrogen cycle
+
| rowspan="6" |The method used in light extinction estimate
|
+
|1
|
+
|Constant
 +
| rowspan="6" |1
 +
| rowspan="6" |
 +
| rowspan="6" |
 +
|-
 +
|2
 +
|Parsons Ocean
 +
|-
 +
|3
 +
|Portela-Tagus Estuary
 +
|-
 +
|4
 +
|Combined Parsons-Portela
 +
|-
 +
|5
 +
|Ascii file
 +
|-
 +
|6
 +
|Multiparameter
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|NSATCONS
+
|SW_KW
|nitrogen half-saturation constant for macroalgae
+
|Short wave absorption coefficient
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|PELAGIC_MODEL
+
|SW_LW_EXTINCTION_FILE
|Pelagic biogeochemical module coupled
 
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|PHOSPHORUS
 
|Defines if the user wishes to compute the phosphorus cycle
 
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|PHOTOIN
 
|macroalgae optimum radiation value
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|MacroAlgae
+
|LightExtinction
|PHOTORES
+
|SW_PERCENTAGE
|Macroalgae photorespiration rate
+
|
 
|
 
|
 
|
 
|
|-
+
|0.6
| Base 1
 
|MacroAlgae
 
|PSATCONS
 
|phosphorus half-saturation constant for macroalgae
 
 
|
 
|
 
|
 
|
 +
|}
 +
 +
=== Module MacroAlgae===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleMacroAlgae.F90 Source Code]
 +
{| class="wikitable"
 +
|-
 +
! scope="col" |Project
 +
! scope="col" |Module
 +
! scope="col" |Keyword
 +
! scope="col" |Keyword description
 +
! scope="col" |Options
 +
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|RATIONC
+
|BEACHED_MORT_RATE
|Macroalgae nitrogen/carbon ratio
+
|Beached drifting macroalgae mortality rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|RATIOPC
 
|Macroalgae phosphorus/carbon ratio
 
 
|
 
|
 
|
 
|
Line 1,242: Line 1,644:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|SALT_EFFECT
+
|DEPLIM
|Include salinity limitation on macroalgae growth
+
|Maximum SPM deposition flux allowed for macroalgae to grow
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,249: Line 1,654:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|SALTCRIT
+
|DISSDON
|Macroalgae critical salinity limit growth
+
|fraction of dissolved organic material excreted by macroalgae
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,256: Line 1,664:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|SALTMAX
+
|DT
|Macroalgae maximum salinity for growth
+
|Time step compute macroalgae biogeochemical processes
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,263: Line 1,674:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|SALTMIN
+
|ENDREPC
|Macroalgae minimum salinity for growth
+
|Macroalgae endogenous respiration rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,270: Line 1,684:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|SALTOPT
+
|EROCRITSS
|Macroalgae optimum salinity for growth
+
|Critical shear stress for macroalgae detachment to occur
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,277: Line 1,694:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|SOLEXCR
+
|EXCRCONS
|Fraction of soluble inorganic material excreted by macroalgae
+
|Macroalgae excretion rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|TCONST1
 
|Constant to control temperature response curve shape
 
 
|
 
|
 
|
 
|
Line 1,291: Line 1,704:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|TCONST2
+
|GRAZCONS
|Constant to control temperature response curve shape
+
|Grazing rate over macroalgae
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|TCONST3
 
|Constant to control temperature response curve shape
 
 
|
 
|
 
|
 
|
Line 1,305: Line 1,714:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|TCONST4
+
|GROWMAX
|Constant to control temperature response curve shape
+
|macroalgae maximum growth rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|MacroAlgae
 
|TMIN
 
|Macroalgae minimum temperature for growth
 
 
|
 
|
 
|
 
|
Line 1,319: Line 1,724:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|TOPTMAX
+
|MACROALGAE_MINCONC
|Macroalgae optimum maximum temperature for growth
+
|Minimum residual value for macroalgae abundance
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 1,326: Line 1,734:
 
| Base 1
 
| Base 1
 
|MacroAlgae
 
|MacroAlgae
|TOPTMIN
+
|MIN_OXYGEN
|Macroalgae optimum minimum temperature for growth
+
|Minimum oxygen concentration for macroalgae growth
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
|}
 
=== Module Profile===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
 
|-
 
|-
 
| Base 1
 
| Base 1
|Profile
+
|MacroAlgae
|DT_OUTPUT_TIME
+
|MORTCON
|Time step to perform profile outputs in HDF5
+
|Macroalgae mortality half saturation constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|Profile
+
|MacroAlgae
|LOCALIZATION_I
+
|MORTMAX
|Grid cell index I where to perform profile output
+
|Macroalgae natural mortality rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|Profile
+
|MacroAlgae
|LOCALIZATION_J
+
|NITROGEN
|Grid cell index J where to perform profile output
+
|Defines if the user wishes to compute the nitrogen cycle
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|Profile
+
|MacroAlgae
|NAME
+
|NSATCONS
|Name of profile output
+
|nitrogen half-saturation constant for macroalgae
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
|}
 
=== Module SedimentQuality===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|Acoef
+
|PELAGIC_MODEL
|Coeficient for labil OM decay rate
+
|Pelagic biogeochemical module coupled
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|Acoef
 
|Coeficient for labil OM decay rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|Acoef
+
|PHOSPHORUS
|Acoef for Heterotrophs decay rate
+
|Defines if the user wishes to compute the phosphorus cycle
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|Acoef
 
|Acoef for Autotrophs C specific decay (death) Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|Acoef
+
|PHOTOIN
|Acoef for the Anaerobic C specific decay (death) Rate
+
|macroalgae optimum radiation value
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|Acoef
 
|Calculates the AmmoniaToNitrate (nitrification) specific Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|Acoef
+
|PHOTORES
|A coef for
+
|Macroalgae photorespiration rate
the AmmoniaImobilization specific Rate
+
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|Acoef
 
|Acoef for for the NitrateToNgas specific Rate (denitrification)
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|Acoef
+
|PSATCONS
|Acoef for the  NitrateImobilization specific Rate
+
|phosphorus half-saturation constant for macroalgae
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|AE
 
|Activation Energy for labil organic mater carbon decay rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|AE
+
|RATIONC
|Coeficient for refractory OM decay rate
+
|Macroalgae nitrogen/carbon ratio
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|AE
 
|AE for Heterotrophs decay rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|AE
+
|RATIOPC
|AE activation energy for the Autotrophs C specific decay (death) Rate
+
|Macroalgae phosphorus/carbon ratio
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|AE
 
|AE for the Anaerobic C specific decay (death) Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|AE
+
|SALT_EFFECT
|Calculates the AmmoniaToNitrate (nitrification) specific Rate.
+
|Include salinity limitation on macroalgae growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|AE
 
|Calculates the AmmoniaImobilization specific Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|AE
+
|SALTCRIT
|Activation Energy for the NitrateToNgas specific Rate
+
|Macroalgae critical salinity limit growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|AE
 
|Activation Energy for the  NitrateImobilization specific Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|CARBON
+
|SALTMAX
|Determines if calculations of carbon related properties is performed
+
|Macroalgae maximum salinity for growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|CARBON_EFICIENCY
 
|Efifiency on the assimilation of carbon for the Hetrotrophic population. The remaining is lost as CO2
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|CARBON_EFICIENCY
+
|SALTMIN
|Carbon assimilation efficiency for Anaerobic population
+
|Macroalgae minimum salinity for growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|CN_RATIO
 
|CN ratio of Hetrotrophs biomass
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|CN_RATIO
+
|SALTOPT
|CN ratio of Autotrophs biomass
+
|Macroalgae optimum salinity for growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|CN_RATIO
 
|CN ratio of anaerobic population.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|DTSECONDS
+
|SOLEXCR
|Time step for sediment quality calculation
+
|Fraction of soluble inorganic material excreted by macroalgae
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|EXPLICIT
 
|Sistem is solved with explicit formulation
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|MINIMUM_POPULATION
+
|TCONST1
|Minimum population for death rate to occur (below value no death)
+
|Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|MINIMUM_POPULATION
 
|Minimum population for death rated to take place
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|MINIMUM_POPULATION     
+
|TCONST2
|Minimum population for death rate top occur
+
|Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|NITROGEN
 
|Option to activate or deactivate the calculation of Nitrogen related properties
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|NITROGEN_EFICIENCY
+
|TCONST3
|NITROGEN EFICIENCY for autotrophic population
+
|Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|NITROGEN_EFICIENCY
 
|Nitrogen assimilation efficiency of anaerobic population
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|POPULATION_CARBON_RATIO
+
|TCONST4
|Convertion form carbon concentration to population for Anaerobic populations
+
|Constant to control temperature response curve shape
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|POPULATION_CARBON_RATIO
+
|TMIN
|COnversion form Carbon mass of hetrotrphs to population nºs
+
|Macroalgae minimum temperature for growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|POPULATION_CARBON_RATIO
 
|Convertion form carbon biomass to nº of individual cells
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|Temperature
+
|TOPTMAX
|Temperature for Autotrophs C specific decay (death) Rate
+
|Macroalgae optimum maximum temperature for growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|Temperature
 
|Optimum temperature for the Anaerobic C specific decay (death) Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|MacroAlgae
|Temperature
+
|TOPTMIN
|Optimum temperature for the AmmoniaToNitrate (nitrification) specific Rate
+
|Macroalgae optimum minimum temperature for growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|Temperature
 
|Optimum temperature for the AmmoniaImobilization specific Rate
 
 
|
 
|
 
|
 
|
 +
|}
 +
 +
=== Module Profile===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleProfile.F90 Source Code]
 +
{| class="wikitable"
 +
|-
 +
! scope="col" |Project
 +
! scope="col" |Module
 +
! scope="col" |Keyword
 +
! scope="col" |Keyword description
 +
! scope="col" |Options
 +
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|Profile
|Temperature
+
|DT_OUTPUT_TIME
|OPtimum temperature for the NitrateToNgas specific Rate
+
|Time step to perform profile outputs in HDF5
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|SedimentQuality
 
|Temperature
 
|Optimum temperature for the  NitrateImobilization specific Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|Profile
|Temperature
+
|LOCALIZATION_I
|Optimum temperature for decay rate
+
|Grid cell index I where to perform profile output
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|Profile
|Temperature 
+
|LOCALIZATION_J
|Optimum Temperature for rate
+
|Grid cell index J where to perform profile output
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|SedimentQuality
+
|Profile
|Temperature 
+
|NAME
|Optimum Temperature for rate
+
|Name of profile output
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|}
 
|}
=== Module WaterQuality===
+
 
 +
=== Module SedimentQuality===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleSedimentQuality.F90 Source Code]
 
{| class="wikitable"
 
{| class="wikitable"
 
 
|-
 
|-
 
! scope="col" |Project
 
! scope="col" |Project
Line 1,700: Line 2,048:
 
! scope="col" |Options
 
! scope="col" |Options
 
! scope="col" |Option description
 
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|AFG
+
|Acoef
|Growth coefficient dependent of fishfood availability HalfSaturationConstant
+
|Coefficient for labile OM decay rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|AGE
+
|Acoef
|Water "Age" : Lagrangean property
+
|Acoef for Heterotrophs decay rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|ASS_EFIC
 
|Phytoplankton: Assimilation efficiency of flagellates by the zooplankton
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|ATG
+
|Acoef
|Growth coefficient dependent of temperature
+
|Acoef for Autotrophs C specific decay (death) Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|ATZ
 
|Death coefficient dependent of temperature
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|AWG
+
|Acoef
|Growth coefficient dependent of larvae weight
+
|Acoef for the Anaerobic C specific decay (death) Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|AWZ
+
|Acoef
|Death coefficient dependent of larvae weight
+
|Calculates the AmmoniaToNitrate (nitrification) specific Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BACINGCIL
+
|Acoef
|Ciliates: Proportion of bacteria in microzooplankton ingestion
+
|A coef for the AmmoniaImobilization specific Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|BACMINSUB
 
|Bacteria: Minimum substract concentration for bacteria uptake
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BACNCONS
+
|Acoef
|Bacteria: Half-saturation constant for bacteria nutrient uptake
+
|Acoef for for the NitrateToNgas specific Rate (denitrification)
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|BACTERIA
 
|Bacteria: Processes Simulation
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BACTRATIOOC
+
|Acoef
|Oxygen: Bacteria Oxygen/Carbon Ratio
+
|Acoef for the  NitrateImobilization specific Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|BARESPCO
 
|Bacteria: Excretion Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BMAXUPTA
+
|ActivationE
|Bacteria: Maximum nutrient uptake at the reference temperature
+
|Activation Energy for labil organic mater carbon decay rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|BOD
 
|BOD: Processes Simulation
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BODCOEF
+
|ActivationE
|BOD: BOD oxidation coefficient
+
|Coeficient for refractory OM decay rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BODOSSAT
+
|ActivationE
|BOD: Oxygen limitation half-saturation constant
+
|AE for Heterotrophs decay rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|BODREF
 
|BOD: BOD oxidation at the reference temperature
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BRATIONC
+
|ActivationE
|Bacteria: Nitrogen/Carbon Ratio
+
|AE activation energy for the Autotrophs C specific decay (death) Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|BTG
 
|Growth coefficient dependent of temperature
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BTZ
+
|ActivationE
|Death coefficient dependent of temperature
+
|AE for the Anaerobic C specific decay (death) Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|BWG
 
|Growth coefficient dependent of larvae weight
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|BWZ
+
|ActivationE
|Death coefficient dependent of larvae weight
+
|Calculates the AmmoniaToNitrate (nitrification) specific Rate.
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|CEXCCONS
 
|Ciliates: Excretion constant curve
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|CEXCFAC
+
|ActivationE
|Ciliates: Excretion factor
+
|Calculates the AmmoniaImobilization specific Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|CILBACASS
 
|Ciliates: Assimilation coefficient of bacteria by microzooplankton
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|CILCORATIO
+
|ActivationE
|Oxygen: Oxygen/Carbon ratio in microzooplankton respiration
+
|Activation Energy for the NitrateToNgas specific Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|CILEFFCAPBA
+
|ActivationE
|Ciliates: Capture efficiency of bacteria
+
|Activation Energy for the  NitrateImobilization specific Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|CILEFFCAPPHY
+
|CARBON
|Ciliates: Capture efficiency of phytoplankton
+
|Determines if calculations of carbon related properties is performed
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|CILIATE
 
|Ciliates: Processes Simulation
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|CILPHYASS
+
|CARBON_EFICIENCY
|Ciliates: Assimilation coefficient of flagellates by microzooplankton
+
|Efifiency on the assimilation of carbon for the Hetrotrophic population. The remaining is lost as CO2
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|CILPREYMIN
 
|Ciliates: Minimum prey concentration for grazing
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|CILRATINGZOO
+
|CARBON_EFICIENCY
|Zooplankton: Proportion of microzooplankton in mesozooplankton ingestion
+
|Carbon assimilation efficiency for Anaerobic population
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|CINGMAX
 
|Ciliates: Maximum ingestion rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|CRATIONC
+
|CN_RATIO
|Ciliates: Nitrogen/Carbon Ratio
+
|CN ratio of Hetrotrophs biomass
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|CRATIOPC
 
|Ciliates: Phosphorus/Carbon Ratio
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|CREFRESP
+
|CN_RATIO
|Ciliates: Carbon consumption rate by respiration
+
|CN ratio of Autotrophs biomass
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DENITREF
+
|CN_RATIO
|Nitrogen: Reference denitirfication rate
+
|CN ratio of anaerobic population.
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DENSATCO
+
|DTSECONDS
|Nitrogen: Denitrification half-saturation constant
+
|Time step for sediment quality calculation
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIASS_EFIC
 
|Diatoms: Assimilation efficiency of diatoms by zooplankton
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIATOMS
+
|EXPLICIT
|Diatoms: Processes Simulation
+
|Sistem is solved with explicit formulation
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIDISSDON
 
|Diatoms: Fraction of dissolved organic material in excretions
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIEXCRCONS
+
|MINIMUM_POPULATION
|Diatoms: Excretion constant
+
|Minimum population for death rate to occur (below value no death)
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIFENDREPC
 
|Diatoms: Endogenous respiration constant
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIGRAZMIN
+
|MINIMUM_POPULATION
|Zooplankton: Minimum diatoms concentration for grazing
+
|Minimum population for death rated to take place
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIGROWMAX
 
|Diatoms: Maximum gross growth rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIMORTCON
+
|MINIMUM_POPULATION     
|Diatoms: Mortality half-saturation Constant
+
|Minimum population for death rate top occur
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIMORTMAX
 
|Diatoms: Maximum Mortality Rate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DINSATCONS
+
|NITROGEN
|Diatoms: Nitrogen half-saturation constant
+
|Option to activate or deactivate the calculation of Nitrogen related properties
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIPHOTOIN
 
|Diatoms: Optimum light intensity for photosynthesis
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIPHOTORES
+
|NITROGEN_EFICIENCY
|Diatoms: Fraction of actual photosynthesis oxidized by photorespiration
+
|NITROGEN EFICIENCY for autotrophic population
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIPSATCONS
 
|Diatoms: Phosphorus half-saturation constant
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIRATINGZOO
+
|NITROGEN_EFICIENCY
|Zooplankton: Proportion of diatoms in mesozooplankton ingestion
+
|Nitrogen assimilation efficiency of anaerobic population
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIRATIONC
 
|Diatoms: Nitrogen/Carbon Ratio
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIRATIOPC
+
|POPULATION_CARBON_RATIO
|Diatoms: Phosphorus/Carbon Ratio
+
|Convertion form carbon concentration to population for Anaerobic populations
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DIRATIOSIC
 
|Diatoms: Silica/Carbon Ratio
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DISISATCONS
+
|POPULATION_CARBON_RATIO
|Diatoms: Silicate half-saturation constant
+
|COnversion form Carbon mass of hetrotrphs to population nºs
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DISOLEXCR
+
|POPULATION_CARBON_RATIO
|Diatoms: Fraction of soluble inorganic material in excretions
+
|Convertion form carbon biomass to nº of individual cells
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DITCONST1
+
|Temperature
|Diatoms: Constant to control temperature response curve shape
+
|Temperature for Autotrophs C specific decay (death) Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DITCONST2
 
|Diatoms: Constant to control temperature response curve shape
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DITCONST3
+
|Temperature
|Diatoms: Constant to control temperature response curve shape
+
|Optimum temperature for the Anaerobic C specific decay (death) Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DITCONST4
 
|Diatoms: Constant to control temperature response curve shape
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DITMAX
+
|Temperature
|Diatoms: Maximum temperature tolerable for growth
+
|Optimum temperature for the AmmoniaToNitrate (nitrification) specific Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DITMIN
 
|Diatoms: Minimum tolerable temperature for growth
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DITOPTMAX
+
|Temperature
|Diatoms: Maximum temperature of the optimal interval for photosynthesis
+
|Optimum temperature for the AmmoniaImobilization specific Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DITOPTMIN
 
|Diatoms:  Minimum temperature of the optimal interval for photosynthesis
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIZOASS
+
|Temperature
|Zooplankton: Assimilation coefficient of diatoms by mesozooplankton
+
|OPtimum temperature for the NitrateToNgas specific Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|DIZOOEFFCAP
+
|Temperature
|Zooplankton: Capture efficiency of diatoms
+
|Optimum temperature for the  NitrateImobilization specific Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|DTSECONDS
 
|Time step for water quality processes calculation
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|EXCRCONS
+
|Temperature
|Phytoplankton: Excretion constant
+
|Optimum temperature for decay rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|EXPLICIT
 
|Explicit Method
 
 
|
 
|
 
|
 
|
 
|-
 
|-
 
| Base 1
 
| Base 1
|WaterQuality
+
|SedimentQuality
|FDISSDON
+
|Temperature 
|Phytoplankton: Fraction of dissolved organic material in excretions
+
|Optimum Temperature for rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|FENDREPC
 
|Phytoplankton: Endogenous respiration constant
 
 
|
 
|
 
|
 
|
 +
|}
 +
 +
=== Module WaterQuality===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase1/ModuleWaterQuality.F90 Source Code]
 +
{| class="wikitable"
 +
|-
 +
! scope="col" |Project
 +
! scope="col" |Module
 +
! scope="col" |Keyword
 +
! scope="col" |Keyword description
 +
! scope="col" |Options
 +
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|FINAL_AGE
+
|AFG
|Larvae Final Age
+
|Growth coefficient dependent of fishfood availability HalfSaturationConstant
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|FINAL_LENGTH
 
|Larvae Final Length
 
 
|
 
|
 
|
 
|
Line 2,228: Line 2,499:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|FISHFOOD_REF
+
|AGE
|Reference food availability
+
|Water "Age" : Lagrangean property
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,235: Line 2,509:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|FMORTCON
+
|ASS_EFIC
|Phytoplankton: Mortality half saturation rate
+
|Phytoplankton: Assimilation efficiency of flagellates by the zooplankton
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,242: Line 2,519:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|FMORTMAX
+
|ATG
|Phytoplankton: Maximum mortality
+
|Growth coefficient dependent of temperature
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,249: Line 2,529:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|FRATIONC
+
|ATZ
|Phytoplankton: Nitrogen/Carbon Ratio
+
|Death coefficient dependent of temperature
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,256: Line 2,539:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|FRATIOPC
+
|AWG
|Phytoplankton: Phosphorus/Carbon ratio
+
|Growth coefficient dependent of larvae weight
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,263: Line 2,549:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|FREGSATC
+
|AWZ
|Nutrients: Nutrient regeneration half-saturation rate
+
|Death coefficient dependent of larvae weight
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,270: Line 2,559:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|FSOLEXCR
+
|BACINGCIL
|Phytoplankton: Fraction of soluble inorganic in excretions
+
|Ciliates: Proportion of bacteria in microzooplankton ingestion
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,277: Line 2,569:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|GRAZBACMIN
+
|BACMINSUB
|Ciliates: Minimum flagellates concentration for grazing
+
|Bacteria: Minimum substract concentration for bacteria uptake
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,284: Line 2,579:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|GRAZCILMIN
+
|BACNCONS
|Zooplankton: Minimum microzooplankton concentration for grazing
+
|Bacteria: Half-saturation constant for bacteria nutrient uptake
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,291: Line 2,589:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|GRAZFITOMIN
+
|BACTERIA
|Zooplankton: Minimum fagellates concentration for grazing
+
|Bacteria: Processes Simulation
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,298: Line 2,599:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|GROWMAXF
+
|BACTRATIOOC
|Phytoplankton: Maximum growth rate
+
|Oxygen: Bacteria Oxygen/Carbon Ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,305: Line 2,609:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|GROWMAXZ
+
|BARESPCO
|Zooplankton: Maximum zooplankton growth rate
+
|Bacteria: Excretion Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,312: Line 2,619:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|IMPLICIT
+
|BMAXUPTA
|Implicit Method Calculation
+
|Bacteria: Maximum nutrient uptake at the reference temperature
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,319: Line 2,629:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|INGCONSC
+
|BOD
|Ciliates: Half-saturation constant for grazing
+
|BOD: Processes Simulation
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,326: Line 2,639:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|INGCONSZ
+
|BODCOEF
|Zooplankton: Half-saturation constant for predation
+
|BOD: BOD oxidation coefficient
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|INIT_AGE
 
|Larvae Inital Age
 
 
|
 
|
 
|
 
|
Line 2,340: Line 2,649:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|INIT_LENGTH
+
|BODOSSAT
|Larvae Inital Length
+
|BOD: Oxygen limitation half-saturation constant
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|INTER_AGE
 
|Larvae Intermediate Age
 
 
|
 
|
 
|
 
|
Line 2,354: Line 2,659:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|INTER_LENGTH
+
|BODREF
|Larvae Intermediate Length
+
|BOD: BOD oxidation at the reference temperature
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|IVLEVCON
 
|Zooplankton: Ivlev grazing constant
 
 
|
 
|
 
|
 
|
Line 2,368: Line 2,669:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|LARVAE
+
|BRATIONC
|Larvae Processes Simulation
+
|Bacteria: Nitrogen/Carbon Ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,375: Line 2,679:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|LDENSITY
+
|BTG
|Larvae density factor
+
|Growth coefficient dependent of temperature
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,382: Line 2,689:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|LSHAPE
+
|BTZ
|Larvae shape factor
+
|Death coefficient dependent of temperature
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,389: Line 2,699:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|MAXMORTCI
+
|BWG
|Ciliates: Maximum Mortality Rate
+
|Growth coefficient dependent of larvae weight
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,396: Line 2,709:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|MAXMORTZ
+
|BWZ
|Zooplankton: Maximum mortality rate
+
|Death coefficient dependent of larvae weight
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,403: Line 2,719:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|MINMORTCI
+
|CEXCCONS
|Ciliates: Minimum Mortality rate
+
|Ciliates: Excretion constant curve
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,410: Line 2,729:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|MINMORTZ
+
|CEXCFAC
|Zooplankton: Minimum mortality rate
+
|Ciliates: Excretion factor
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,417: Line 2,739:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|MINOXYGEN
+
|CILBACASS
|Oxygen: Minimum oxygen concentration allowed
+
|Ciliates: Assimilation coefficient of bacteria by microzooplankton
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,424: Line 2,749:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|MORTCICOEF
+
|CILCORATIO
|Ciliates: Mortality coefficient
+
|Oxygen: Oxygen/Carbon ratio in microzooplankton respiration
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,431: Line 2,759:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|MORTZCOEF
+
|CILEFFCAPBA
|Zooplankton: Shape factor for the mortality curve of zooplankton
+
|Ciliates: Capture efficiency of bacteria
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,438: Line 2,769:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|NATMORB
+
|CILEFFCAPPHY
|Bacteria: Natural mortality rate
+
|Ciliates: Capture efficiency of phytoplankton
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,445: Line 2,779:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|NITONRAT
+
|CILIATE
|Oxygen: Oxygen/Carbon in Nitrate
+
|Ciliates: Processes Simulation
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,452: Line 2,789:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|NITRIREF
+
|CILPHYASS
|Nitrogen: Reference nitrification rate
+
|Ciliates: Assimilation coefficient of flagellates by microzooplankton
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,459: Line 2,799:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|NITROGEN
+
|CILPREYMIN
|Nitrogen: Biogeochemical Processes Simulation
+
|Ciliates: Minimum prey concentration for grazing
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,466: Line 2,809:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|NITSATCO
+
|CILRATINGZOO
|Nitrogen: Nitrification half-saturation constant
+
|Zooplankton: Proportion of microzooplankton in mesozooplankton ingestion
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|NMINENR
 
|Nitrogen: Reference mineralization rate for dissolved organic nitrogen non refractory (DONnr)
 
 
|
 
|
 
|
 
|
Line 2,480: Line 2,819:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|NMINR
+
|CINGMAX
|Nitrogen: Reference mineralization rate for Dissolved Organic Nitrogen refractory (DONr)
+
|Ciliates: Maximum ingestion rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|NOPCOEF
 
|Nitrogen: PON decomposition temperature coefficient
 
 
|
 
|
 
|
 
|
Line 2,494: Line 2,829:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|NOPREF
+
|CRATIONC
|Nitrogen: Reference Mineralization Rate for Particulate Organic Nitrogen (PON)
+
|Ciliates: Nitrogen/Carbon Ratio
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|NPHASES
 
|Number of larvae phases (valid values are 1 and 2)
 
 
|
 
|
 
|
 
|
Line 2,508: Line 2,839:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|NSATCONS
+
|CRATIOPC
|Phytoplankton: Nitrogen half-saturation constant
+
|Ciliates: Phosphorus/Carbon Ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,515: Line 2,849:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|OCRATIO
+
|CREFRESP
|Oxygen: Oxygen/Carbon in CO2
+
|Ciliates: Carbon consumption rate by respiration
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,522: Line 2,859:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|OMRATIONC
+
|DENITREF
|Oxygen: Organic Matter Nitrogen/Carbon Ratio
+
|Nitrogen: Reference denitirfication rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,529: Line 2,869:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|OMRATIOPC
+
|DENSATCO
|Oxygen: Organic Matter Phosphorus/Carbon Ratio
+
|Nitrogen: Denitrification half-saturation constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,536: Line 2,879:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHDECOMP
+
|DIASS_EFIC
|Nitrogen: Fraction of PON available for mineralization
+
|Diatoms: Assimilation efficiency of diatoms by zooplankton
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,543: Line 2,889:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHOSOPRAT
+
|DIATOMS
|Oxygen: Oxygen/Carbon in Phosphate
+
|Diatoms: Processes Simulation
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,550: Line 2,899:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHOSPHOR
+
|DIDISSDON
|Phosphorus: Biogeochemical Processes Simulation
+
|Diatoms: Fraction of dissolved organic material in excretions
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,557: Line 2,909:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHOTOIN
+
|DIEXCRCONS
|Phytoplankton: Optimum light intensity for photosyntesis
+
|Diatoms: Excretion constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,564: Line 2,919:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHOTORES
+
|DIFENDREPC
|Phytoplankton: Faction of actual photosynthesis oxidised by photorespiration
+
|Diatoms: Endogenous respiration constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,571: Line 2,929:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHOTOSOC
+
|DIGRAZMIN
|Oxygen: Photosynthesis Oxygen/Carbon ratio
+
|Zooplankton: Minimum diatoms concentration for grazing
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,578: Line 2,939:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHYINGCIL
+
|DIGROWMAX
|Ciliates: Proportion of flagellates in microzooplankton ingestion
+
|Diatoms: Maximum gross growth rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,585: Line 2,949:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHYRATING
+
|DIMORTCON
|Zooplankton: proportion of phytoplankton in mesozooplankton ingestion
+
|Diatoms: Mortality half-saturation Constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,592: Line 2,959:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PHYTO
+
|DIMORTMAX
|Phytoplankton: Processes Simulation
+
|Diatoms: Maximum Mortality Rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,599: Line 2,969:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PLANK_OC_RAT
+
|DINSATCONS
|Oxygen: Oxygen/Carbon ratio in plankton respiration
+
|Diatoms: Nitrogen half-saturation constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,606: Line 2,979:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PMINNR
+
|DIPHOTOIN
|Phosphorus: DOPnr mineralization rate at reference temperature
+
|Diatoms: Optimum light intensity for photosynthesis
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|PMINNRCOEF
 
|Phosphorus: DOPnr mineralization temperature coefficient
 
 
|
 
|
 
|
 
|
Line 2,620: Line 2,989:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PMINR
+
|DIPHOTORES
|Phosphorus: DOPre mineralization rate at reference tempearture
+
|Diatoms: Fraction of actual photosynthesis oxidized by photorespiration
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|PMINRCOEF
 
|Phosphorus: DOPre mineralization temperature coefficient
 
 
|
 
|
 
|
 
|
Line 2,634: Line 2,999:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|PPARTMIN
+
|DIPSATCONS
|Phosphorus: POP decomposition rate at reference temperature
+
|Diatoms: Phosphorus half-saturation constant
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|PSATCONS
 
|Phytoplankton: Phosphorus half-saturation constant
 
 
|
 
|
 
|
 
|
Line 2,648: Line 3,009:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|SEMIIMP
+
|DIRATINGZOO
|Semi-implicit Method Calculation
+
|Zooplankton: Proportion of diatoms in mesozooplankton ingestion
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,655: Line 3,019:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|SIDISSTCOEF
+
|DIRATIONC
|Silica: Biogenic silica dissolution temperature coefficient
+
|Diatoms: Nitrogen/Carbon Ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,662: Line 3,029:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|SIKDISS
+
|DIRATIOPC
|Silica: Biogenic silica dissolution rate in the water column at the reference temperature
+
|Diatoms: Phosphorus/Carbon Ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,669: Line 3,039:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|SILICA
+
|DIRATIOSIC
|Silica: Processes Simulation
+
|Diatoms: Silica/Carbon Ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,676: Line 3,049:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TBCONST1
+
|DISISATCONS
|Bacteria: Constant to control temperature response curve shape
+
|Diatoms: Silicate half-saturation constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,683: Line 3,059:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TBCONST2
+
|DISOLEXCR
|Bacteria: Constant to control temperature response curve shape
+
|Diatoms: Fraction of soluble inorganic material in excretions
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,690: Line 3,069:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TBCONST3
+
|DITCONST1
|Bacteria: Constant to control temperature response curve shape
+
|Diatoms: Constant to control temperature response curve shape
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,697: Line 3,079:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TBCONST4
+
|DITCONST2
|Bacteria: Constant to control temperature response curve shape
+
|Diatoms: Constant to control temperature response curve shape
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,704: Line 3,089:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TBMAX
+
|DITCONST3
|Bacteria: Maximum temperature tolerable temperature for growth
+
|Diatoms: Constant to control temperature response curve shape
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,711: Line 3,099:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TBMIN
+
|DITCONST4
|Bacteria: Minimum temperature tolerable for growth
+
|Diatoms: Constant to control temperature response curve shape
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,718: Line 3,109:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TDENCOEF
+
|DITMAX
|Nitrogen: Denitrification Temperature Coefficient
+
|Diatoms: Maximum temperature tolerable for growth
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,725: Line 3,119:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TEMPERATURE_REF
+
|DITMIN
|Larvae Reference temperature
+
|Diatoms: Minimum tolerable temperature for growth
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,732: Line 3,129:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TFCONST1
+
|DITOPTMAX
|Phytoplankton: Constant to control temperature response curve shape
+
|Diatoms: Maximum temperature of the optimal interval for photosynthesis
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,739: Line 3,139:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TFCONST2
+
|DITOPTMIN
|Phytoplankton: Constant to control temperature response curve shape
+
|Diatoms: Minimum temperature of the optimal interval for photosynthesis
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,746: Line 3,149:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TFCONST3
+
|DIZOASS
|Phytoplankton: Constant to control temperature response curve shape
+
|Zooplankton: Assimilation coefficient of diatoms by mesozooplankton
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|TFCONST4
 
|Phytoplankton: Constant to control temperature response curve shape
 
 
|
 
|
 
|
 
|
Line 2,760: Line 3,159:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TFMAX
+
|DIZOOEFFCAP
|Phytoplankton: Maximum temperature tolerable for growth
+
|Zooplankton: Capture efficiency of diatoms
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|TFMIN
 
|Phytoplankton: Minimum  temperature tolerable for growth
 
 
|
 
|
 
|
 
|
Line 2,774: Line 3,169:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TMINNR
+
|DTSECONDS
|Nitrogen: DONnr mineralization temperature coefficient
+
|Time step for water quality processes calculation
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|TMINR
 
|Nitrogen: DONr mineralization temperature coefficient
 
 
|
 
|
 
|
 
|
Line 2,788: Line 3,179:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TNITCOEF
+
|EXCRCONS
|Nitrogen: Nitrification temperature coefficient
+
|Phytoplankton: Excretion constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,795: Line 3,189:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TOPTBMAX
+
|EXPLICIT
|Bacteria: Maximum temperature of the optimal interval for growth
+
|Explicit Method
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,802: Line 3,199:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TOPTBMIN
+
|FDISSDON
|Bacteria: Minimum temperature of the optimal interval for growth
+
|Phytoplankton: Fraction of dissolved organic material in excretions
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,809: Line 3,209:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TOPTFMAX
+
|FENDREPC
|Phytoplankton: Maximum temperature of the optimal interval for photosyntesis
+
|Phytoplankton: Endogenous respiration constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,816: Line 3,219:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TOPTFMIN
+
|FINAL_AGE
|Phytoplankton: Minimum temperature of the optimal interval forphotosyntesis
+
|Larvae Final Age
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,823: Line 3,229:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TOPTZMAX
+
|FINAL_LENGTH
|Zooplankton: Maximum temperature of the optimal interval for the zooplankton growth
+
|Larvae Final Length
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,830: Line 3,239:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TOPTZMIN
+
|FISHFOOD_REF
|Zooplankton: Minimum temperature of the optimal interval for the zooplankton growth
+
|Reference food availability
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,837: Line 3,249:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TPPARTMINCOEF
+
|FMORTCON
|Phosphorus: POP decomposition temperature coefficient
+
|Phytoplankton: Mortality half saturation rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,844: Line 3,259:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TZCONST1
+
|FMORTMAX
|Zooplankton: Constant to control temperature response curve shape
+
|Phytoplankton: Maximum mortality
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,851: Line 3,269:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TZCONST2
+
|FRATIONC
|Zooplankton: Constant to control temperature response curve shape
+
|Phytoplankton: Nitrogen/Carbon Ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,858: Line 3,279:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TZCONST3
+
|FRATIOPC
|Zooplankton: Constant to control temperature response curve shape
+
|Phytoplankton: Phosphorus/Carbon ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,865: Line 3,289:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TZCONST4
+
|FREGSATC
|Zooplankton: Constant to control temperature response curve shape
+
|Nutrients: Nutrient regeneration half-saturation rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,872: Line 3,299:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TZMAX
+
|FSOLEXCR
|Zooplankton: Maximum temperature tolerable for growth
+
|Phytoplankton: Fraction of soluble inorganic in excretions
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,879: Line 3,309:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|TZMIN
+
|GRAZBACMIN
|Zooplankton: Minimum temperature tolerable for growth
+
|Ciliates: Minimum flagellates concentration for grazing
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,886: Line 3,319:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZDISSDON
+
|GRAZCILMIN
|Zooplankton: Dissolved organic fraction in excretions
+
|Zooplankton: Minimum microzooplankton concentration for grazing
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|ZEXCCONS
 
|Zooplankton: Excretion constant for zooplankton
 
 
|
 
|
 
|
 
|
Line 2,900: Line 3,329:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZEXCFAC
+
|GRAZFITOMIN
|Zooplankton: Excretion Factor
+
|Zooplankton: Minimum fagellates concentration for grazing
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|ZINGMAX
 
|Zooplankton: Maximun ingestion rate
 
 
|
 
|
 
|
 
|
Line 2,914: Line 3,339:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZOCILASS
+
|GROWMAXF
|Zooplankton: Assimilation coefficient of microzooplankton by mesozooplankton
+
|Phytoplankton: Maximum growth rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 1
 
|WaterQuality
 
|ZOCRATIO
 
|Oxygen: Oxygen/Carbon ratio in mesozooplankton respiration
 
 
|
 
|
 
|
 
|
Line 2,928: Line 3,349:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZOO
+
|GROWMAXZ
|Zooplankton: Processes Simulation
+
|Zooplankton: Maximum zooplankton growth rate
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,935: Line 3,359:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZOOEFFCAPCIL
+
|IMPLICIT
|Zooplankton: Capture efficiency of microzoolankton
+
|Implicit Method Calculation
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,942: Line 3,369:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZOOEFFCAPHY
+
|INGCONSC
|Zooplankton: Capture efficiency of phytoplankton
+
|Ciliates: Half-saturation constant for grazing
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,949: Line 3,379:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZOOPREYMIN
+
|INGCONSZ
|Zooplankton: Minimum prey concentration for grazing
+
|Zooplankton: Half-saturation constant for predation
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,956: Line 3,389:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZOPHYASS
+
|INIT_AGE
|Zooplankton: Assimilation coefficient of flagellates by mesozooplankton
+
|Larvae Inital Age
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,963: Line 3,399:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZPREDMOR
+
|INIT_LENGTH
|Zooplankton:  Predatory mortality rate (predation by higher trophic levels)
+
|Larvae Inital Length
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,970: Line 3,409:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZRATIONC
+
|INTER_AGE
|Zooplankton: Nitrogen/Carbon Ratio
+
|Larvae Intermediate Age
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,977: Line 3,419:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZRATIOPC
+
|INTER_LENGTH
|Zooplankton: Phosphorus/Carbon ratio
+
|Larvae Intermediate Length
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,984: Line 3,429:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZREFRESP
+
|IVLEVCON
|Zooplankton: Carbon consumption rate by respiration
+
|Zooplankton: Ivlev grazing constant
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
Line 2,991: Line 3,439:
 
| Base 1
 
| Base 1
 
|WaterQuality
 
|WaterQuality
|ZSOLEXCR
+
|LARVAE
|Zooplankton: Soluble inorganic fraction in excretions
+
|Larvae Processes Simulation
 +
|
 
|
 
|
 
|
 
|
|}
 
 
==MOHID Base 2==
 
=== Module Atmosphere===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
|-
 
| Base 2
 
|Atmosphere
 
|BOX_TIME_SERIE
 
|Output of property values in time series files, integrated in boxes.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Atmosphere
+
|WaterQuality
|DATA_COLUMN
+
|LDENSITY
|Number of column in the time serie file.
+
|Larvae density factor
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Atmosphere
 
|FILENAME
 
|Path to the file with the time serie.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Atmosphere
+
|WaterQuality
|IRRIGATION
+
|LSHAPE
|Property added by irrigation
+
|Larvae shape factor
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Atmosphere
 
|NO_INTERPOLATION
 
|NoInterpolation of Value In Time (instead of interpolation calculates the exact amount of property in a time period). This requires VariableDT.
 
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Atmosphere
+
|WaterQuality
|OUTPUT_HDF
+
|MAXMORTCI
|Output of property values in HDF files.
+
|Ciliates: Maximum Mortality Rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Atmosphere
 
|OUTPUT_TIME
 
|Output instants of HDF5 file.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Atmosphere
+
|WaterQuality
|RADIATION_METHOD
+
|MAXMORTZ
|Method to compute solar radiation
+
|Zooplankton: Maximum mortality rate
|1
+
|
|Climatologic solar radiation algorithm
 
|-
 
| Base 2
 
|Atmosphere
 
|RADIATION_METHOD
 
|Method to compute solar radiation
 
|2
 
|CEQUALW2 solar radiation algorithm
 
|-
 
| Base 2
 
|Atmosphere
 
|RANDOM_COMPONENT
 
|Random component of property.
 
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Atmosphere
 
|STATISTICS
 
|Choose to compute the statistics of this property
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Atmosphere
+
|WaterQuality
|STATISTICS_FILE
+
|MINMORTCI
|Path to the file with the statistics definition for this property.
+
|Ciliates: Minimum Mortality rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Atmosphere
 
|TIME_SERIE
 
|Output of property values in time series files.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Atmosphere
+
|WaterQuality
|TIME_SERIE_LOCATION
+
|MINMORTZ
|Path to the file that has the time series location characteristics.
+
|Zooplankton: Minimum mortality rate
 +
|
 
|
 
|
 
|
 
|
|}
 
=== Module BasinGeometry===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
|-
 
| Base 2
 
|BasinGeometry
 
|DELINEATE_BASIN
 
|Option to delineate basin
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|DELINEATION_FILE
+
|MINOXYGEN
|Output deliniation file location
+
|Oxygen: Minimum oxygen concentration allowed
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BasinGeometry
 
|DRAINAGE_DIRECTION
 
|Option to write drainage direction output asci grid file
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|DRAINAGE_DIRECTION_FILE
+
|MORTCICOEF
|Output file location
+
|Ciliates: Mortality coefficient
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BasinGeometry
 
|DRAINED_AREA
 
|Option to write Drained area asci grid data
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|DRAINED_AREA_FILE
+
|MORTZCOEF
|Drained area output file location
+
|Zooplankton: Shape factor for the mortality curve of zooplankton
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BasinGeometry
 
|NEW_TOPOGRAPHY_FILE
 
|Path to new file that will be created once depretions are removed.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|OUTLET_I
+
|NATMORB
|Outlet cell location (I-Coordinate)
+
|Bacteria: Natural mortality rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BasinGeometry
 
|OUTLET_J
 
|Outlet cell location (J- Coordinate)
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|OUTPUT_HDF5
+
|NITONRAT
|Output to HDF file
+
|Oxygen: Oxygen/Carbon in Nitrate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BasinGeometry
 
|REACHES_FILE
 
|Output file location
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|REMOVE_DEPRESSIONS
+
|NITRIREF
|If this option is active basin delimiter removes depretions in the terrain so that evry cell can drain to one of its 8 neighbours
+
|Nitrogen: Reference nitrification rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BasinGeometry
 
|RESERVOIRS
 
|Consider reservoir in the terrain
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|RESERVOIRS_FILE
+
|NITROGEN
|Reservoir file location
+
|Nitrogen: Biogeochemical Processes Simulation
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BasinGeometry
 
|SLOPE_DEPRESSIONS
 
|Minimum Slope in Depressions
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|TRESHOLD_AREA
+
|NITSATCO
|Minimum area that a cell must drain to be marked as river point
+
|Nitrogen: Nitrification half-saturation constant
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BasinGeometry
 
|WRITE_DELINEATION
 
|Option to write output basin deliniation file
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BasinGeometry
+
|WaterQuality
|WRITE_REACHES
+
|NMINENR
|Write output drainage network reach file
+
|Nitrogen: Reference mineralization rate for dissolved organic nitrogen non refractory (DONnr)
 +
|
 
|
 
|
 
|
 
|
|}
 
=== Module BoxDif===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
|-
 
| Base 2
 
|BoxDif
 
|OUTPUT_FILE
 
|Output file location
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|BoxDif
+
|WaterQuality
|TYPE
+
|NMINR
|Coordinate Type
+
|Nitrogen: Reference mineralization rate for Dissolved Organic Nitrogen refractory (DONr)
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|BoxDif
 
|WRITE_BOXES
 
|Option to write boxes output file
 
 
|
 
|
 
|
 
|
|}
 
=== Module FillMatrix===
 
{| class="wikitable"
 
 
 
|-
 
|-
! scope="col" |Project
+
| Base 1
! scope="col" |Module
+
|WaterQuality
! scope="col" |Keyword
+
|NOPCOEF
! scope="col" |Keyword description
+
|Nitrogen: PON decomposition temperature coefficient
! scope="col" |Options
+
|
! scope="col" |Option description
 
|-
 
| Base 2
 
|FillMatrix
 
|BOXES_VALUES                       
 
|Sequence of values for each box starting from box 1.
 
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|FillMatrix
 
|CoefA
 
|Coeficient to compute analitical profile.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|CoefB
+
|NOPREF
|Coeficient to compute analitical profile
+
|Nitrogen: Reference Mineralization Rate for Particulate Organic Nitrogen (PON)
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|FillMatrix
 
|DATA_COLUMN
 
|DATA_COLUMN is the number of the relevant column in the time serie file.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|DEFAULTVALUE
+
|NPHASES
|Default value when INITIALIZATION_METHOD is used.
+
|Number of larvae phases (valid values are 1 and 2)
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|FillMatrix
 
|DEPTH_PROFILE
 
|Sequence of depth values. Used with PROFILE option.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|FILE_IN_TIME
+
|NSATCONS
|Defines the kind of reading operation performed in time to modify the field
+
|Phytoplankton: Nitrogen half-saturation constant
|PROFILE_TIME_SERIE
+
|
|Read solution from various profiles in time
 
|-
 
| Base 2
 
|FillMatrix
 
|FILE_IN_TIME
 
|Defines the kind of reading operation performed in time to modify the field
 
|TIMESERIE
 
|The data is given at a certain location with a time serie. See time series to know about time series file format. File path is given in FILEME. The number of the column containing needed data of the timeserie file must be indicated in DATA_COLUMN.
 
|-
 
| Base 2
 
|FillMatrix
 
|FILE_IN_TIME
 
|Defines the kind of reading operation performed in time to modify the field
 
|NONE
 
|Matrix is not modified from reading values from file
 
|-
 
| Base 2
 
|FillMatrix
 
|FILE_IN_TIME
 
|Defines the kind of reading operation performed in time to modify the field
 
|HDF
 
|Reads data from an HDF5 file. There are restrictions regarding file format:
 
1) The fields stored in the file must correspond to the modeled domain, that is, they must correspond to the same horizontal and vertical grid.
 
2) In the Grid folder it is required to have the data sets: "Bathimetry", "ConnectionX", "ConnectionY", "Latitude", "Longitude" and "WaterPoints".
 
3) The name of the fields must be recognised by Mohid (see list of supported names)
 
4) Time data set must contain as many instants as the field data sets
 
5) Time data set must also contain dates for a period of the same or greater duration of the simulation.
 
 
 
|-
 
| Base 2
 
|FillMatrix
 
|FILENAME
 
|Path to the file containing imposed data
 
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|FillMatrix
 
|FILENAME_DEFAULT
 
|Path to the file containing data for initialization of default value.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|HDF_FIELD_NAME
+
|OCRATIO
|HDF5 group name
+
|Oxygen: Oxygen/Carbon in CO2
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|FillMatrix
 
|INITIALIZATION_DEFAULT
 
|Initial condition for default value, usable with INITIALIZATION_METHOD options not valid for all domain.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|INITIALIZATION_METHOD
+
|OMRATIONC
|Initial condition data input method.
+
|Oxygen: Organic Matter Nitrogen/Carbon Ratio
|PROFILE_TIMESERIE
+
|
|Read initial field from various profiles.
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|INITIALIZATION_METHOD
+
|OMRATIOPC
|Initial condition data input method.
+
|Oxygen: Organic Matter Phosphorus/Carbon Ratio
|BOXES
+
|
|Initialization by boxes (polygonal sub-domains) for which a constant value is specified. Boxes are specified in separate file (path given by FILEME keyword) blocks that have specific format.
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|INITIALIZATION_METHOD
+
|PHDECOMP
|Initial condition data input method.
+
|Nitrogen: Fraction of PON available for mineralization
|LAYERS
+
|
|Initialization by horizontal layers. alues are specified with LAYERS_VALUES keyword.
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|INITIALIZATION_METHOD
+
|PHOSOPRAT
|Initial condition data input method.
+
|Oxygen: Oxygen/Carbon in Phosphate
|TIMESERIE
+
|
|Reads initial values from a time serie file. If necessary the initial value is interpolated in time.
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|INITIALIZATION_METHOD
+
|PHOSPHOR
|Initial condition data input method.
+
|Phosphorus: Biogeochemical Processes Simulation
|CONSTANT
+
|
|Constant value for all domain.
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|INITIALIZATION_METHOD
+
|PHOTOIN
|Initial condition data input method.
+
|Phytoplankton: Optimum light intensity for photosyntesis
|HDF
+
|
|Reads initial field from a HDF file. Field is interpolated in time if necessary.
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|INITIALIZATION_METHOD
+
|PHOTORES
|Initial condition data input method.
+
|Phytoplankton: Faction of actual photosynthesis oxidised by photorespiration
|PROFILE
+
|
|Initialization made by vertical profile. Horizontal distribution is considered uniform. Profile must be specified with NDEPTH, DEPTH_PROFILE and PROFILE_VALUES keywords. Layers must no correspond to vertical discretization. The program interpolates the data on the vertical as needed.
+
|
|-
+
|
| Base 2
 
|FillMatrix
 
|INITIALIZATION_METHOD
 
|Initial condition data input method.
 
|ALYTIC PROFILE
 
|Initialization made by an analitical vertical profile.
 
|-
 
| Base 2
 
|FillMatrix
 
|INITIALIZATION_METHOD
 
|Initial condition data input method.
 
|ASCII_FILE
 
|Initialization with text file. File path given at FILEME. File format is a griddata file (2D or 3D). In points of the domain where no values are given the DEFAULTVALUE is assumed.
 
If griddata file is 2D and the domain is 3D, a unique value is assumed for the whole water column.
 
|-
 
| Base 2
 
|FillMatrix
 
|LAYERS_VALUES
 
|Sequence of values for each layer starting from the bottom layer.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|MULTIPLYING_FACTOR
+
|PHOTOSOC
|Data field multiplying factor. HDF5 only.
+
|Oxygen: Photosynthesis Oxygen/Carbon ratio
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|FillMatrix
 
|NDEPTHS
 
|Number of values that the define the profile.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|FillMatrix
+
|WaterQuality
|PROFILE_TYPE
+
|PHYINGCIL
|Type of analitical profile
+
|Ciliates: Proportion of flagellates in microzooplankton ingestion
|LINEAR
+
|
|Profile has a linear format, given by the following expression:  
+
|
Value = DefaultValue + CoefA * CellDepth / CoefB
+
|
|-
 
| Base 2
 
|FillMatrix
 
|PROFILE_TYPE
 
|Type of analitical profile
 
|EXPONENTIAL
 
|Profile has an exponential format, given by the following expression Value = DefaultValue - CoefA * exp(- CellDepth / CoefB)
 
|-
 
| Base 2
 
|FillMatrix
 
|PROFILE_VALUES
 
|Sequence of values that constitute the profile.
 
 
|
 
|
 
|
 
|
|}
 
=== Module Geometry===
 
{| class="wikitable"
 
 
 
|-
 
|-
! scope="col" |Project
+
| Base 1
! scope="col" |Module
+
|WaterQuality
! scope="col" |Keyword
+
|PHYRATING
! scope="col" |Keyword description
+
|Zooplankton: proportion of phytoplankton in mesozooplankton ingestion
! scope="col" |Options
+
|
! scope="col" |Option description
 
|-
 
| Base 2
 
|Geometry
 
|DISPLACEMENT_LIMIT
 
|the maximum displacement that the model allow cell faces to move vertically in meters
 
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Geometry
 
|DOMAINDEPTH
 
|The depth of the domain lower limit. User must give a value to this keyword or else the model do not run.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|EMPTY_TOP_LAYERS
+
|PHYTO
|Number of empty layers counting from top
+
|Phytoplankton: Processes Simulation
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Geometry
 
|EQUIDISTANT
 
|Thickness of layers admitting that all the layers have the same thickness
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|FACES_OPTION
+
|PLANK_OC_RAT
|Methodology to compute areas between cells
+
|Oxygen: Oxygen/Carbon ratio in plankton respiration
|2
+
|
|Average thickness of the adjacent water columns (advised option)
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|FACES_OPTION
+
|PMINNR
|Methodology to compute areas between cells
+
|Phosphorus: DOPnr mineralization rate at reference temperature
|3
+
|
|Minimum thickness of the adjacent water columns (advanced user option)
+
|
|-
 
| Base 2
 
|Geometry
 
|GRIDMOVEMENTDUMP
 
 
|
 
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|ID
+
|PMINNRCOEF
|Domain ID
+
|Phosphorus: DOPnr mineralization temperature coefficient
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Geometry
 
|IMPER_COEF_U
 
|U Coefficient to compute faces areas in U points
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|IMPER_COEF_V
+
|PMINR
|V Coefficient to compute faces areas in V points
+
|Phosphorus: DOPre mineralization rate at reference tempearture
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Geometry
 
|IMPER_COEFX_U
 
|X_U Coefficient to compute faces areas in U points
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|IMPER_COEFX_V
+
|PMINRCOEF
|X_V Coefficient to compute faces areas in V points
+
|Phosphorus: DOPre mineralization temperature coefficient
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Geometry
 
|IMPERMEABILITY
 
|Consider impermeable cell faces
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|INITIALIZATION_METHOD
+
|PPARTMIN
|Type of initialization used in the case of a lagrangian coordinate. This is also the reference coordinate in relation to which the lagrangian coordinate suffers distortion function of the vertical velocity
+
|Phosphorus: POP decomposition rate at reference temperature
|CARTESIAN
+
|
|Cartesian type coordinates
+
|
|-
+
|
| Base 2
 
|Geometry
 
|INITIALIZATION_METHOD
 
|Type of initialization used in the case of a lagrangian coordinate. This is also the reference coordinate in relation to which the lagrangian coordinate suffers distortion function of the vertical velocity
 
|SIGMA
 
|Sigma type coordinates
 
|-
 
| Base 2
 
|Geometry
 
|LAYERS
 
|Number of layers
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|LAYERTHICKNESS
+
|PSATCONS
|If not equidistant specifies layers thicknesses, starting from bottom layers.  The number of values must be equal to the number of layers
+
|Phytoplankton: Phosphorus half-saturation constant
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Geometry
 
|MIN_TOP_THICKNESS
 
|minimum thickness of colapsing cells of the Harmonic domain
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|MINEVOLVELAYERTHICKNESS
+
|SEMIIMP
|coeficient which indicates how much a Lagrangian layer
+
|Semi-implicit Method Calculation
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Geometry
 
|MINIMUMDEPTH
 
|water column thickness below which the cell is considered uncovered
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|MININITIALLAYERTHICKNESS
+
|SIDISSTCOEF
|minimal thickness of the bottom cells
+
|Silica: Biogenic silica dissolution temperature coefficient
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Geometry
 
|TOLERANCEDEPTH
 
|Thickness of layer below which the bathymetry is corrected. Valid only for the sigma and lagrangian (sigma initializaton) coordinate
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|TOTALTHICKNESS
+
|SIKDISS
|Total domain thickness. Valid only for the FixSpacing and FixSediment coordinates
+
|Silica: Biogenic silica dissolution rate in the water column at the reference temperature
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|TYPE
+
|SILICA
|Type of vertical coordinate of the domain
+
|Silica: Processes Simulation
|CARTESIANTOP
+
|
|A Cartesian Coordinate which is calculated downwards from the Digital Terrain (MOHID Land only)
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|TYPE
+
|TBCONST1
|Type of vertical coordinate of the domain
+
|Bacteria: Constant to control temperature response curve shape
|LAGRANGIAN
+
|
|Lagrangian coordinates - moves the upper and
+
|
lower faces with the vertical flow velocity.
+
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|TYPE
+
|TBCONST2
|Type of vertical coordinate of the domain
+
|Bacteria: Constant to control temperature response curve shape
|FIXSEDIMENT
+
|
|Fixed Sediment coordinates
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|Geometry
+
|WaterQuality
|TYPE
+
|TBCONST3
|Type of vertical coordinate of the domain
+
|Bacteria: Constant to control temperature response curve shape
|FIXSPACING
+
|
|Fixed Spacing coordinates - used to study flows close to the bottom
 
|-
 
| Base 2
 
|Geometry
 
|TYPE
 
|Type of vertical coordinate of the domain
 
|SIGMA
 
|Sigma coordinates
 
|-
 
| Base 2
 
|Geometry
 
|TYPE
 
|Type of vertical coordinate of the domain
 
|SIGMATOP
 
|A Sigma Coordinate which is calculated downwards from the Digital Terrain (MOHID Land only). Needs Normal Sigma Below
 
|-
 
| Base 2
 
|Geometry
 
|TYPE
 
|Type of vertical coordinate of the domain
 
|HARMONIC
 
|Harmonic coordinates - the horizontal faces close to the surface
 
expand and collapse depending on the variation of the surface elevation. This
 
coordinate was implemented in the geometry module to simulate reservoirs.
 
|-
 
| Base 2
 
|Geometry
 
|TYPE
 
|Type of vertical coordinate of the domain
 
|CARTESIAN
 
|Cartesian coordinates
 
|}
 
 
 
=== Module GridData===
 
{| class="wikitable"
 
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
|-
 
| Base 2
 
|GridData
 
|EVOLUTION
 
|Gets if the bathymetry can change in time
 
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|GridData
 
|EVOLUTION_FILE
 
|Path tyo file that describes the time evolution.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|GridData
+
|WaterQuality
|FILL_VALUE
+
|TBCONST4
|Default value for points with no data
+
|Bacteria: Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|GridData
 
|PROPERTY_NAME
 
|Name of the property that will change in time
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|GridData
+
|WaterQuality
|TYPE_ZUV
+
|TBMAX
|Matrix Types (Centered in Z, U or V)
+
|Bacteria: Maximum temperature tolerable temperature for growth
 +
|
 
|
 
|
 
|
 
|
|}
 
=== Module HorizontalGrid===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
|-
 
| Base 2
 
|HorizontalGrid
 
|CONSTANT_SPACING_X
 
|Check if the spacing in X is constant
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|HorizontalGrid
+
|WaterQuality
|CONSTANT_SPACING_Y
+
|TBMIN
|Check if constant Spacing in y is used
+
|Bacteria: Minimum temperature tolerable for growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|HorizontalGrid
 
|COORD_TIP
 
|Coordinate type of grid
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|HorizontalGrid
+
|WaterQuality
|DX
+
|TDENCOEF
|Grid spacing dx
+
|Nitrogen: Denitrification Temperature Coefficient
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|HorizontalGrid
 
|DY
 
|Gets DY spacing
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|HorizontalGrid
+
|WaterQuality
|GRID_ANGLE
+
|TEMPERATURE_REF
|Grid angle with north
+
|Larvae Reference temperature
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|HorizontalGrid
 
|ILB_IUB
 
|minimum and maximum i in grid
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|HorizontalGrid
+
|WaterQuality
|JLB_JUB
+
|TFCONST1
|minimum and maximum J in grid
+
|Phytoplankton: Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|HorizontalGrid
 
|LATITUDE
 
|Latitude of grid
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|HorizontalGrid
+
|WaterQuality
|LONGITUDE
+
|TFCONST2
|Longitude of grid
+
|Phytoplankton: Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|HorizontalGrid
 
|ORIGIN
 
|X and Y origin of grid
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|HorizontalGrid
+
|WaterQuality
|ZONE
+
|TFCONST3
|UTM zone of coordinate
+
|Phytoplankton: Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|}
 
=== Module Interpolation===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
|-
 
| Base 2
 
|Interpolation
 
|EXTRAPOLATE_2D
 
|? Paulo?
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|EXTRAPOLATE_PROFILE
+
|TFCONST4
|Chek if the user wants to extrapolate in the vertical
+
|Phytoplankton: Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Interpolation
 
|IWD_N
 
|Coefficent use in the inverse weight interpolation
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|KERNEL_TYPE
+
|TFMAX
|Type of kernel used in the convolution interpolations
+
|Phytoplankton: Maximum temperature tolerable for growth
|Exponential
+
|
 +
|
 +
|
 +
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|KERNEL_TYPE
+
|TFMIN
|Type of kernel used in the convolution interpolations
+
|Phytoplankton: Minimum  temperature tolerable for growth
|Gaussian
+
|
 +
|
 +
|
 +
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|MAX_DISTANCE
+
|TMINNR
|Max distance for points to be consider in the inverse weight interpolation
+
|Nitrogen: DONnr mineralization temperature coefficient
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|MAX_ITERATIONS
+
|TMINR
|Maximum number of iterations allowed in the logistic regression in the data-oriented convolution.
+
|Nitrogen: DONr mineralization temperature coefficient
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|METHODOLOGY
+
|TNITCOEF
|The methodology used in the interpolation process
+
|Nitrogen: Nitrification temperature coefficient
|1
+
|
|Conservative convolution
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|METHODOLOGY
+
|TOPTBMAX
|The methodology used in the interpolation process
+
|Bacteria: Maximum temperature of the optimal interval for growth
|2
+
|
|NonConservative convolution
 
|-
 
| Base 2
 
|Interpolation
 
|METHODOLOGY
 
|The methodology used in the interpolation process
 
|3
 
|Triangulation
 
|-
 
| Base 2
 
|Interpolation
 
|METHODOLOGY
 
|The methodology used in the interpolation process
 
|4
 
|Bilinear
 
|-
 
| Base 2
 
|Interpolation
 
|METHODOLOGY
 
|The methodology used in the interpolation process
 
|5
 
|Spline 2D
 
|-
 
| Base 2
 
|Interpolation
 
|METHODOLOGY
 
|The methodology used in the interpolation process
 
|6
 
|Inverse weight
 
|-
 
| Base 2
 
|Interpolation
 
|N_DIM
 
|The number of dimensions of the field to interpolate
 
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Interpolation
 
|N_GROUPS
 
|Number of groups generated for each dimension in the data-oriented convolution.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|NC_TYPE
+
|TOPTBMIN
|Cheks what class of NonConservative convolution process to use
+
|Bacteria: Minimum temperature of the optimal interval for growth
|1
+
|
|User defined kernel for the NonConservative convolution
 
|-
 
| Base 2
 
|Interpolation
 
|NC_TYPE
 
|Cheks what class of NonConservative convolution process to use
 
|2
 
|Smoothes the field using the PHI value
 
|-
 
| Base 2
 
|Interpolation
 
|NC_TYPE
 
|Cheks what class of NonConservative convolution process to use
 
|3
 
|Data
 
|-
 
| Base 2
 
|Interpolation
 
|PHI
 
|Smoothing parameter. Gives the degree of smoothing in the interpolated field. Its range is ]0,1].
 
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Interpolation
 
|POLI_DEGREE_VERT
 
|The order of the polinomial use to interpolate in the vertical
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Interpolation
+
|WaterQuality
|SAMPLE_SIZE
+
|TOPTFMAX
|Number of observations needed for the logistic regression in the data-oriented convolution.
+
|Phytoplankton: Maximum temperature of the optimal interval for photosyntesis
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Interpolation
 
|TYPE_ZUV
 
|Where points are defined in the cell (Z - center; U - Face U; V : Face V)
 
 
|
 
|
 
|
 
|
|}
 
 
=== Module Statistic===
 
{| class="wikitable"
 
 
 
|-
 
|-
! scope="col" |Project
+
| Base 1
! scope="col" |Module
+
|WaterQuality
! scope="col" |Keyword
+
|TOPTFMIN
! scope="col" |Keyword description
+
|Phytoplankton: Minimum temperature of the optimal interval forphotosyntesis
! scope="col" |Options
+
|
! scope="col" |Option description
 
|-
 
| Base 2
 
|Statistic
 
|DAILY_STATISTIC
 
|Performs dayly integration of statistic values
 
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Statistic
 
|GEOMETRIC_MEAN
 
|Performs geometric mean calculation for non negative parameters
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Statistic
+
|WaterQuality
|GLOBAL_STATISTIC
+
|TOPTZMAX
|Performs statistic calculation os every timestep
+
|Zooplankton: Maximum temperature of the optimal interval for the zooplankton growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Statistic
 
|LAYER_DEFINITION
 
|Layer defenition
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Statistic
+
|WaterQuality
|MAX_DEPTH
+
|TOPTZMIN
|Max depth of layer
+
|Zooplankton: Minimum temperature of the optimal interval for the zooplankton growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Statistic
 
|MAX_LAYER
 
|Max layer k index
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Statistic
+
|WaterQuality
|METHOD_STATISTIC
+
|TPPARTMINCOEF
|Way to perform the statistcis (full matrix, layers, etc)
+
|Phosphorus: POP decomposition temperature coefficient
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Statistic
+
|WaterQuality
|MIN_DEPTH
+
|TZCONST1
|Minumum depth of layer
+
|Zooplankton: Constant to control temperature response curve shape
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Statistic
+
|WaterQuality
|MIN_LAYER
+
|TZCONST2
|Layer lower index start
+
|Zooplankton: Constant to control temperature response curve shape
 +
|
 
|
 
|
 
|
 
|
|-
 
| Base 2
 
|Statistic
 
|MONTHLY_STATISTIC
 
|Performs montly integration of statistic values
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Base 2
+
| Base 1
|Statistic
+
|WaterQuality
|PERCENTILE
+
|TZCONST3
 +
|Zooplankton: Constant to control temperature response curve shape
 
|
 
|
 
|
 
|
 
|
 
|
|}
 
 
==MOHID Land==
 
=== Module Runoff===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
 
 
|-
 
| Land
 
|Runoff
 
|MIN_SLOPE
 
|Slope between overland waterlevel and channel waterlevel from which fluxes between overland flow and channel flow are calculted
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Land
+
| Base 1
|Runoff
+
|WaterQuality
|ROUTING
+
|TZCONST4
|The overland flow routing method.
+
|Zooplankton: Constant to control temperature response curve shape
|1
+
|
|Manning Equation
 
|-
 
| Land
 
|Runoff
 
|ROUTING
 
|The overland flow routing method.
 
|2
 
|Chezy Equation
 
|}
 
 
 
==MOHID Water==
 
=== Module Assimilation===
 
{| class="wikitable"
 
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
 
 
 
 
|-
 
| Water
 
|Assimilation
 
|COLD_RELAX_PERIOD
 
|Period of time along which relaxation has a linear increase
 
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Assimilation
 
|DESCRIPTION
 
|Short description about the assimilation property
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Assimilation
+
|WaterQuality
|DIMENSION
+
|TZMAX
|Number of dimensions of the assimilation field
+
|Zooplankton: Maximum temperature tolerable for growth
|2
+
|
|Two-Dimensional property
 
|-
 
| Water
 
|Assimilation
 
|DIMENSION
 
|Number of dimensions of the assimilation field
 
|3
 
|Three-Dimensional property
 
|-
 
| Water
 
|Assimilation
 
|NAME
 
|Name of the assimilation property
 
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Assimilation
 
|OUTPUT_HDF
 
|Output HDF results for assimilation property
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Assimilation
+
|WaterQuality
|OUTPUT_TIME
+
|TZMIN
|Vector with instants (starting from 0) when to perform outputs. The last number in the vector is the time step to perform the remaining outputs.
+
|Zooplankton: Minimum temperature tolerable for growth
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Assimilation
 
|TIME_SERIE
 
|Output time series for assimilation property
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Assimilation
+
|WaterQuality
|TIME_SERIE_LOCATION
+
|ZDISSDON
|Path to time serie locations file
+
|Zooplankton: Dissolved organic fraction in excretions
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Assimilation
 
|TYPE_ZUV
 
|Reference of the field to the grid.
 
|U
 
|Variable is referenced to the XX faces of the control volume
 
|-
 
| Water
 
|Assimilation
 
|TYPE_ZUV
 
|Reference of the field to the grid.
 
|Z
 
|Variable is defined in the center of the control volume
 
|-
 
| Water
 
|Assimilation
 
|TYPE_ZUV
 
|Reference of the field to the grid.
 
|V
 
|Variable is referenced to the YY faces of the control volume
 
|-
 
| Water
 
|Assimilation
 
|TYPE_ZUV
 
|Reference of the field to the grid.
 
|V
 
|Variable is referenced to the YY faces of the control volume
 
|-
 
| Water
 
|Assimilation
 
|TYPE_ZUV
 
|Reference of the field to the grid.
 
|U
 
|Variable is referenced to the XX faces of the control volume
 
|-
 
| Water
 
|Assimilation
 
|TYPE_ZUV
 
|Reference of the field to the grid.
 
|Z
 
|Variable is defined in the center of the control volume
 
 
 
|-
 
| Water
 
|Assimilation
 
|UNITS
 
|Assimilation property units
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Assimilation
+
|WaterQuality
|VGROUP_PATH
+
|ZEXCCONS
 +
|Zooplankton: Excretion constant for zooplankton
 
|
 
|
 
|
 
|
 
|
 
|
|}
 
 
=== Module Consolidation===
 
{| class="wikitable"
 
 
|-
 
! scope="col" |Project
 
! scope="col" |Module
 
! scope="col" |Keyword
 
! scope="col" |Keyword description
 
! scope="col" |Options
 
! scope="col" |Option description
 
|-
 
| Water
 
|Consolidation
 
|BOXFLUXES
 
|Path to boxes file. If specified in input data file, computes box integration based on the defined file.
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Consolidation
+
|WaterQuality
|COMPUTE_SHEAR_STRESS
+
|ZEXCFAC
|Compute shear stress or read from file
+
|Zooplankton: Excretion Factor
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Consolidation
 
|CONSOLIDATION
 
|Specifies if consolidation is to be computed
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Consolidation
+
|WaterQuality
|CONSOLIDATION_DT
+
|ZINGMAX
|Time step for consolidation
+
|Zooplankton: Maximun ingestion rate
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Consolidation
 
|CONTINUOUS
 
|Speficies if initialization is based in previous run
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Consolidation
+
|WaterQuality
|CSE_COEF
+
|ZOCILASS
|Coeficient to compute exponential increase of critical shear stress for erosion with depth
+
|Zooplankton: Assimilation coefficient of microzooplankton by mesozooplankton
|
 
 
|
 
|
|-
 
| Water
 
|Consolidation
 
|DECAYMENT
 
|Computes porosity decayment (compaction) inside the sediment compartment
 
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Consolidation
 
|DECAYTIME
 
|Decay factor for consolidation
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Consolidation
+
|WaterQuality
|INFINITE_CSE
+
|ZOCRATIO
|Maximum critical shear stress for erosion
+
|Oxygen: Oxygen/Carbon ratio in mesozooplankton respiration
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Consolidation
 
|MAX_THICKNESS
 
|Maximum layer thickness allowed for a sediment layer
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Consolidation
+
|WaterQuality
|MIN_THICKNESS
+
|ZOO
|Minimum thickness allowed for a sediment layer
+
|Zooplankton: Processes Simulation
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Consolidation
 
|OUTPUT_HDF
 
|Output HDF results
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Consolidation
+
|WaterQuality
|OUTPUT_TIME
+
|ZOOEFFCAPCIL
|Vector with instants (starting from 0) when to perform outputs. The last number in the vector is the time step to perform the remaining outputs.
+
|Zooplankton: Capture efficiency of microzoolankton
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Consolidation
 
|SURFACE_CSE
 
|Critical shear stress for erosion for the top layer
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|Consolidation
+
|WaterQuality
|TIME_SERIE
+
|ZOOEFFCAPHY
|Output time series
+
|Zooplankton: Capture efficiency of phytoplankton
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Consolidation
 
|TIME_SERIE_LOCATION
 
|Path to time serie locations file
 
 
|
 
|
 
|
 
|
|}
 
=== Module FreeVerticalMovement===
 
{| class="wikitable"
 
 
 
|-
 
|-
! scope="col" |Project
+
| Base 1
! scope="col" |Module
+
|WaterQuality
! scope="col" |Keyword
+
|ZOOPREYMIN
! scope="col" |Keyword description
+
|Zooplankton: Minimum prey concentration for grazing
! scope="col" |Options
+
|
! scope="col" |Option description
 
|-
 
| Water
 
|FreeVerticalMovement
 
|CHS
 
|Hindered settling concentration threshold
 
 
|
 
|
 
|
 
|
|-
 
| Water
 
|FreeVerticalMovement
 
|DEPOSITION
 
|Compute deposition for particulate property
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|FreeVerticalMovement
+
|WaterQuality
|FREEVERT_IMPEXP_ADV
+
|ZOPHYASS
|Coeficient to compute vertical movement through implicit or explicit methods
+
|Zooplankton: Assimilation coefficient of flagellates by mesozooplankton
|0.0
+
|
|Implicit
 
|-
 
| Water
 
|FreeVerticalMovement
 
|FREEVERT_IMPEXP_ADV
 
|Coeficient to compute vertical movement through implicit or explicit methods
 
|1.0
 
|Explicit
 
|-
 
| Water
 
|FreeVerticalMovement
 
|KL
 
|Parameter to compute settling velocity based on cohesive sediment concentration
 
 
|
 
|
 
|
 
|
|-
 
| Water
 
|FreeVerticalMovement
 
|KL1
 
|Parameter to compute settling velocity based on cohesive sediment concentration
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|FreeVerticalMovement
+
|WaterQuality
|M
+
|ZPREDMOR
|Parameter to compute settling velocity based on cohesive sediment concentration
+
|Zooplankton:  Predatory mortality rate (predation by higher trophic levels)
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|FreeVerticalMovement
 
|ML
 
|Parameter to compute settling velocity based on cohesive sediment concentration
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|FreeVerticalMovement
+
|WaterQuality
|SALTINT
+
|ZRATIONC
|Definition of free vertical movement being function of salinity
+
|Zooplankton: Nitrogen/Carbon Ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|FreeVerticalMovement
+
|WaterQuality
|SALTINTVALUE
+
|ZRATIOPC
|Salinity limit. For salinity values smaller the settling velocity is zero. For salinity values greater then this limit the settling velocity is computed/prescribed.
+
|Zooplankton: Phosphorus/Carbon ratio
 +
|
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 1
|FreeVerticalMovement
+
|WaterQuality
|WS_TYPE
+
|ZREFRESP
|Method to compute settling velocity
+
|Zooplankton: Carbon consumption rate by respiration
|1
+
|
|Prescribe a constant settling velocity for particulate property
+
|
 +
|
 +
|
 +
|
 
|-
 
|-
| Water
+
| Base 1
|FreeVerticalMovement
+
|WaterQuality
|WS_TYPE
+
|ZSOLEXCR
|Method to compute settling velocity
+
|Zooplankton: Soluble inorganic fraction in excretions
|2
 
|Compute settling velocity as function of cohesive sediment concentration
 
|-
 
| Water
 
|FreeVerticalMovement
 
|ws_value
 
 
|
 
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|FreeVerticalMovement
 
|WS_VALUE
 
|Prescribed constant settling velocity
 
 
|
 
|
 
|
 
|
 
|}
 
|}
  
=== Module Hydrodynamic===
+
==MOHID Base 2==
 +
 
 +
=== Module Atmosphere===
 +
[https://github.com/Mohid-Water-Modelling-System/Mohid/blob/master/Software/MOHIDBase2/ModuleAtmosphere.F90 Source Code]
 
{| class="wikitable"
 
{| class="wikitable"
 
 
|-
 
|-
 
! scope="col" |Project
 
! scope="col" |Project
Line 4,542: Line 4,350:
 
! scope="col" |Options
 
! scope="col" |Options
 
! scope="col" |Option description
 
! scope="col" |Option description
 +
! scope="col" |Default Value
 +
! scope="col" |Units
 +
! scope="col" |Type
 
|-
 
|-
| Water
+
| Base 2
|Hydrodynamic
+
|Atmosphere
|ADV_METHOD_H
+
|BOX_TIME_SERIE
|!!! Defines the horizontal numerical method of advection.
+
|Output of property values in time series files, integrated in boxes.
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Hydrodynamic
 
|ADV_METHOD_V
 
 
|
 
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 2
|Hydrodynamic
+
|Atmosphere
|ATM_PRESSURE
+
|DATA_COLUMN
|Checks if the user wants to consider the effect of the Atmospheric Pressure
+
|Number of column in the time series file.
 +
|
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Hydrodynamic
 
|ATM_PRESSURE_TYPE
 
|0 - no atmospheric reference field
 
1 - use "atmospheric pressure" from Module Atmosphere
 
2 - use "mslp" (aka Mean Sea Level Pressure) from Module Atmosphere
 
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 2
|Hydrodynamic
+
|Atmosphere
|BAROCLINIC
+
|FILENAME
|Checks if the user pretends to compute the baroclinic pressure
+
|Path to the file with the time series.
 
|
 
|
 
|
 
|
|-
 
| Water
 
|Hydrodynamic
 
|BAROCLINIC_METHOD
 
 
|
 
|
 
|
 
|
 
|
 
|
 
|-
 
|-
| Water
+
| Base 2
|Hydrodynamic
+
|Atmosphere
|BAROCLINIC_OBC_DISCRET
+
|IRRIGATION
 +
|Property added by irrigation
 +
|
 +
|
 
|
 
|
 
|
 
|
 
|
 
|
 
|