!  NEMURO Ecosystem Model Parameters.
!
!svn $Id: nemuro.in 294 2009-01-09 21:37:26Z arango $
!========================================================= Hernan G. Arango ===
!  Copyright (c) 2002-2009 The ROMS/TOMS Group                                !
!    Licensed under a MIT/X style license                                     !
!    See License_ROMS.txt                                                     !
!==============================================================================
!                                                                             !
! Input parameters can be entered in ANY order, provided that the parameter   !
! KEYWORD (usually, upper case) is typed correctly followed by "="  or "=="   !
! symbols. Any comment lines are allowed and must begin with an exclamation   !
! mark (!) in column one.  Comments may  appear to the right of a parameter   !
! specification to improve documentation.  Comments will be ignored  during   !
! reading.  Blank lines are also allowed and ignored. Continuation lines in   !
! a parameter specification are allowed and must be preceded by a backslash   !
! (\).  In some instances, more than one value is required for a parameter.   !
! If fewer values are provided, the  last value  is assigned for the entire   !
! parameter array.  The multiplication symbol (*),  without blank spaces in   !
! between, is allowed for a parameter specification.  For example, in a two   !
! grids nested application:                                                   !
!                                                                             !
!    AKT_BAK == 2*1.0d-6  2*5.0d-6              ! m2/s                        !
!                                                                             !
! indicates that the first two entries of array AKT_BAK,  in fortran column-  !
! major order, will have the same value of "1.0d-6" for grid 1,  whereas the  !
! next two entries will have the same value of "5.0d-6" for grid 2.           !
!                                                                             !
! In multiple levels of nesting and/or multiple connected domains  step-ups,  !
! "Ngrids" entries are expected for some of these parameters.  In such case,  !
! the order of the entries for a parameter is extremely important.  It  must  !
! follow the same order (1:Ngrids) as in the state variable declaration. The  !
! USER may follow the above guidelines for specifying his/her values.  These  !
! parameters are marked by "==" plural symbol after the KEYWORD.              !
!                                                                             !
!==============================================================================
!
! NOTICE: Input parameter units are specified within brackets and default 
! ******  values are specified within braces.
!
! Switch to control the computation of biology within nested and/or multiple
! connected grids.

    Lbiology == T

! Maximum number of iterations to achieve convergence of the nonlinear
! solution.

     BioIter == 1

! Light attenuation due to seawater [1/m].

       AttSW == 0.04d0

! Light attenuation due to phytoplankton, self-shading coefficient,
! [m2/millimole_N].

       AttPS == 0.04d0                     ! small biomass
       AttPL == 0.04d0                     ! large biomass

! Fraction of shortwave radiation that is photosynthetically active,
! [nondimensional].

     PARfrac == 0.43d0

! Phytoplankton photochemical reaction coefficient, initial slope of
! the P-I curve [1/(W/m2) 1/day].

     AlphaPS == 0.01d0                     ! small biomass
     AlphaPL == 0.01d0                     ! large biomass

! Phytoplankton photoinhibition coefficient, [1/(W/m2) 1/day].

      BetaPS == 4.5d-4                     ! small biomass
      BetaPL == 4.5d-4                     ! large biomass

! Phytoplankton maximum photosynthetic rate at 0 Celsius [1/day].

       VmaxS == 0.4d0                      ! small biomass
       VmaxL == 0.8d0                      ! large biomass

! Phytoplankton half saturation constant for Nitrate [millimole_N/m3].
  
       KNO3S == 1.0d0                      ! small biomass
       KNO3L == 3.0d0                      ! large biomass

! Phytoplankton half saturation constant for Ammonium [millimole_N/m3].

       KNH4S == 0.1d0                      ! small biomass
       KNH4L == 0.3d0                      ! large biomass

! Phytoplankton half saturation constant for Silicate [millimole_Si/m3].

        KSiL == 6.0d0                      ! large biomass

! Phytoplankton Ammonium inhibition coefficient [m3/millimole_N].

      PusaiS == 1.5d0                      ! small biomass
      PusaiL == 1.5d0                      ! large biomass

! Phytoplankton temperature coefficient for photosynthetic rate [1/Celsius].

       KGppS == 6.93d-2                    ! small biomass
       KGppL == 6.93d-2                    ! large biomass

! Phytoplankton respiration rate at 0 Celsius [1/day].

      ResPS0 == 0.03d0                     ! small biomass
      ResPL0 == 0.03d0                     ! large biomass

! Phytoplankton temperature coefficient for respiration [1/Celsius].

      KResPS == 0.0519d0                   ! small biomass
      KResPL == 0.0519d0                   ! large biomass

! Phytoplankton ratio of extracellular excretion to photosynthesis
! [nondimensional].

      GammaS == 0.135d0                    ! small biomass
      GammaL == 0.135d0                    ! large biomass

! Phytoplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].

      MorPS0 == 58.5d-3                    ! small biomass
      MorPL0 == 29.0d-3                    ! large biomass

! Phytoplankton temperature coefficient for mortality [1/Celsius].

      KMorPS == 6.93d-2                    ! small biomass
      KMorPL == 6.93d-2                    ! large biomass

! Zooplankton maximum grazing rate at 0 Celsius [1/day].

    GRmaxSps == 0.40d0                     ! small Zoo on small phy
    GRmaxLps == 0.10d0                     ! large Zoo on small Phy
    GRmaxLpl == 0.40d0                     ! large Zoo on large Phy
    GRmaxLzs == 0.40d0                     ! large Zoo on small Zoo 
    GRmaxPpl == 0.20d0                     ! predator Zoo on large Phy
    GRmaxPzs == 0.20d0                     ! predator Zoo on small Zoo 
    GRmaxPzl == 0.20d0                     ! predator Zoo on large Zoo

! Zooplankton temperature coefficient for grazing [1/Celsius].

       KGraS == 6.93d-2                    ! small biomass
       KGraL == 6.93d-2                    ! large biomass
       KGraP == 6.93d-2                    ! predator biomass

! Zooplankton Ivlev constant [m3/millimole_N].

        LamS == 1.4d0                      ! small biomass
        LamL == 1.4d0                      ! large biomass
        LamP == 1.4d0                      ! predator biomass

! Zooplankton half-saturation coefficient (squared) for ingestion used
! only when the Holling-type grazing formulation is activated
! [millimole_N/m3]^2.

      KPS2ZS == 0.16d0                     ! small Zoo on small Phy
      KPS2ZL == 0.16d0                     ! large Zoo on small Phy
      KPL2ZL == 0.16d0                     ! large Zoo on large Phy
      KZS2ZL == 0.16d0                     ! large Zoo on small Zoo
      KPL2ZP == 0.16d0                     ! predator Zoo on large Phy
      KZS2ZP == 0.16d0                     ! predator Zoo on small Zoo
      KZL2ZP == 0.16d0                     ! predator Zoo on large Zoo

! Zooplankton threshold value for grazing [millimole_N/m3].

   PS2ZSstar == 4.3d-2                     ! small Zoo on small Phy
   PS2ZLstar == 4.0d-2                     ! large Zoo on small Phy
   PL2ZLstar == 4.0d-2                     ! large Zoo on large Phy
   ZS2ZLstar == 4.0d-2                     ! large Zoo on small Zoo
   PL2ZPstar == 4.0d-2                     ! predator Zoo on large Phy
   ZS2ZPstar == 4.0d-2                     ! predator Zoo on small Zoo
   ZL2ZPstar == 4.0d-2                     ! predator Zoo on large Zoo

! Zooplankton grazing inhibition coefficient [m3/millimole_N].

     PusaiPL == 4.605d0                    ! predator Zoo on large Phy    
     PusaiZS == 3.010d0                    ! predator Zoo on small Zoo    

! Zooplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].

      MorZS0 == 58.5d-3                    ! small biomass
      MorZL0 == 58.5d-3                    ! large biomass
      MorZP0 == 58.5d-3                    ! predator biomass

! Zooplankton temperature coefficient for mortality [1/Celsius].

      KMorZS == 0.0693d0                   ! small biomass
      KMorZL == 0.0693d0                   ! large biomass
      KMorZP == 0.0693d0                   ! predator biomass

! Zooplankton assimilation efficiency [nondimemsional].

     AlphaZS == 0.70d0                     ! small biomass
     AlphaZL == 0.70d0                     ! large biomass
     AlphaZP == 0.70d0                     ! predator biomass

! Zooplankton growth efficiency [nondimensional].

      BetaZS == 0.30d0                     ! small biomass
      BetaZL == 0.30d0                     ! large biomass
      BetaZP == 0.30d0                     ! predator biomass

! Decomposition rates at 0 Celsius [1/day].

        Nit0 == 0.03d0                     ! NH4 nitrification
       VP2N0 == 0.10d0                     ! PON to NH4
       VP2D0 == 0.10d0                     ! PON to DON
       VD2N0 == 0.20d0                     ! DON to NH4
       VO2S0 == 0.10d0                     ! Opal to Silicate

! Temperature coefficients for decomposition [1/Celsius]

        KNit == 6.93d-2                    ! NH4 nitrification   
        KP2D == 6.93d-2                    ! PON to DON
        KP2N == 6.93d-2                    ! PON to NH4
        KD2N == 6.93d-2                    ! DON to NH4
        KO2S == 6.93d-2                    ! Opal to Silicate

! Si:N ratio [millimole_Si/millimole_N].

        RSiN == 2.0d0          

! Settling (sinking) velocities [m/day].

      setVPON == 40.0d0                    ! PON
     setVOpal == 40.0d0                    ! Opal

! Lateral, constant, harmonic/biharmonic horizontal diffusion of biological
! tracer: [1:NBT,Ngrids].

        TNU2 == 11*0.0d0                   ! m2/s
        TNU4 == 11*0.0d0                   ! m4/s

! Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids].

     AKT_BAK == 11*1.0d-6                  ! m2/s

! Nudging/relaxation time scales, inverse scales will be computed
! internally: [1:NBT,Ngrids].

       TNUDG == 11*0.0d0                   ! days

! Logical switches (TRUE/FALSE) to activate writing of biological tracers
! into HISTORY output file: [1:NBT,Ngrids].

Hout(idTvar) == 11*T                       ! biological tracers
Hout(idTsur) == 11*F                       ! surface tracer flux

!
!  GLOSSARY:
!  =========
!
!------------------------------------------------------------------------------
! NEMURO Ecosystem Model Parameters, [1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
!  Lbiology  Switch to control the computation of a particular module within
!              nested and/or multiple connected grids. By default this switch
!              is set to TRUE in "mod_scalars" for all grids.  Ngrids values
!              are expected. The USER has the option, for example, to compute
!              the biology in just one of the nested grids. If so, this switch
!              needs to be consistent with the dimension parameter NBT in
!              "mod_param".  In order to make the model more efficient in
!              memory usage, NBT(:) should be zero in such grids.
!
!  BioIter   Maximum number of iterations to achieve convergence of
!              the nonlinear solution.
!
!------------------------------------------------------------------------------
! Light Parameters, [1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
!  AttSW       Light attenuation due to seawater [1/m].
!
!  AttPS       Light attenuation due to Small Phytoplankton, self-shading
!                coefficient, [m2/millimole_N].
!
!  AttPL       Light attenuation due to Large Phytoplankton, self-shading
!                coefficient, [m2/millimole_N].
!
!  PARfrac     Fraction of shortwave radiation that is photosynthetically
!                active, [nondimensional].
!
!  AlphaPS     Small Phytoplankton photochemical reaction coefficient: initial
!                slope (low light) of the P-I curve (Platt et al, 1980),
!                [1/(W/m2) 1/day].
!
!  AlphaPL     Large Phytoplankton photochemical reaction coefficient: initial
!                slope (low light) of the P-I curve (Platt et al., 1980),
!                [1/(W/m2) 1/day].
!
!  BetaPS      Small Phytoplankton photoinhibition coefficient (Platt et al.,
!                1980), [1/(W/m2) 1/day].  Set it to zero for no inhibition.
!
!  BetaPL      Large Phytoplankton photoinhibition coefficient (Platt et al.,
!                1980), [1/(W/m2) 1/day].  Set it to zero for no inhibition.
!
!------------------------------------------------------------------------------
! Phytoplankton Parameters,  [1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
!  VmaxS       Maximum Small Phytoplankton photosynthetic rate [1/day] in the
!                absence of photoinhibition under optimal light.
!
!  VmaxL       Maximum Large Phytoplankton photosynthetic rate [1/day] in the
!                absence of photoinhibition under optimal light.
!
!  KNO3S       Small Phytoplankton half saturation constant for Nitrate,
!                [millimole_N/m3].
!
!  KNO3L       Large Phytoplankton half saturation constant for Nitrate,
!                [millimole_N/m3].
!
!  KNH4S       Small Phytoplankton half saturation constant for Ammonium,
!                [millimole_N/m3].
!
!  KNH4L       Large Phytoplankton half saturation constant for Ammonium,
!                [millimole_N/m3].
!
!  KSiL        Large Phytoplankton half saturation constant for Silicate,
!                [millimole_Si/m3].
!
!  PusaiS      Small Phytoplankton Ammonium inhibition coefficient,
!                [m3/millimole_N].
!
!  PusaiL      Large Phytoplankton Ammonium inhibition coefficient,
!                [m3/millimole_N].
!
!  KGppS       Small Phytoplankton temperature coefficient for photosynthetic
!                rate, [1/Celsius].
!
!  KGppL       Large Phytoplankton temperature coefficient for photosynthetic
!                rate, [1/Celsius].
!
!  ResPS0      Small Phytoplankton respiration rate at 0 Celsius, [1/day].
!
!  ResPL0      Large Phytoplankton respiration rate at 0 Celsius, [1/day].
!
!  KResPS      Small Phytoplankton temperature coefficient for respiration,
!                [1/Celsius].
!
!  KResPL      Large Phytoplankton temperature coefficient for respiration,
!                [1/Celsius].
!
!  GammaS      Small Phytoplankton ratio of extracellular excretion to
!                photosynthesis [nondimensional].
!
!  GammaL      Large Phytoplankton ratio of extracellular excretion to
!                photosynthesis [nondimensional].
!
!  MorPS0      Small Phytoplankton mortality rate at 0 Celsius,
!                [m3/millimole_N 1/day].
!
!  MorPL0      Large Phytoplankton mortality rate at 0 Celsius,
!                [m3/millimole_N 1/day].
!
!  KMorPS      Small Phytoplankton temperature coefficient for mortality,
!                [1/Celsius].
!
!  KMorPL      Large Phytoplankton temperature coefficient for mortality,
!                [1/Celsius].
!
!------------------------------------------------------------------------------
! Zooplankton parameters, [1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
!  GRmaxSps    Small Zooplankton maximum grazing rate on Small Phytoplankton
!                at 0 Celsius, [1/day].
!
!  GRmaxLps    Large Zooplankton maximum grazing rate on Small Phytoplankton
!                at 0 Celsius, [1/day].
!
!  GRmaxLpl    Large Zooplankton maximum grazing rate on Large Phytoplankton
!                at 0 Celsius, [1/day].
!
!  GRmaxLzs    Small Zooplankton maximum grazing rate on Small Zooplankton
!                at 0 Celsius, [1/day].
!
!  GRmaxPpl    Predator Zooplankton maximum grazing rate on Large Phytoplankton
!                at 0 Celsius, [1/day].
!
!  GRmaxPzs    Predator Zooplankton maximum grazing rate on Small Zooplankton
!                at 0 Celsius, [1/day].
!
!  GRmaxPzl    Predator Zooplankton maximum grazing rate on Large Phytoplankton
!                at 0 Celsius, [1/day].
!
!  KGraS       Small Zooplankton temperature coefficient for grazing,
!                [1/Celsius].
!
!  KGraL       Large Zooplankton temperature coefficient for grazing,
!                [1/Celsius].
!
!  KGraP       Predator Zooplankton temperature coefficient for grazing,
!                [1/Celsius].
!
!  LamS        Small Zooplankton Ivlev constant, [m3/millimole_N].
!
!  LamL        Large Zooplankton Ivlev constant, [m3/millimole_N].
!
!  LamP        Predator Zooplankton Ivlev constant, [m3/millimole_N].
!
!  KPS2ZS      Small Zooplankton half-saturation, squared coefficient for
!                ingestion on Small Phytoplankton [millimole_N/m3]^2.
!
!  KPS2ZL      Large Zooplankton half-saturation, squared coefficient for
!                ingestion on Small Phytoplankton [millimole_N/m3]^2.
!
!  KPL2ZL      Large Zooplankton half-saturation, squared coefficient for
!                ingestion on Large Phytoplankton [millimole_N/m3]^2.
!
!  KZS2ZL      Large Zooplankton half-saturation, squared coefficient for
!                ingestion on Small Phytoplankton [millimole_N/m3]^2.
!
!  KPL2ZP      Predator Zooplankton half-saturation, squared coefficient for
!                ingestion on Large Phytoplankton [millimole_N/m3]^2.
!
!  KZS2ZP      Predator Zooplankton half-saturation, squared coefficient for
!                ingestion on Small Zooplankton [millimole_N/m3]^2.
!
!  KZL2ZP      Predator Zooplankton half-saturation, squared coefficient for
!                ingestion on Large Zooplankton [millimole_N/m3]^2.
!
!  PS2ZSstar   Small Zooplankton threshold value for grazing on
!                Small Phytoplankton, [millimole_N/m3].
!
!  PS2ZLstar   Large Zooplankton threshold value for grazing on
!                Small Phytoplankton, [millimole_N/m3].
!
!  PL2ZLstar   Large Zooplankton threshold value for grazing on
!                Large Phytoplankton, [millimole_N/m3].
!
!  ZS2ZLstar   Large Zooplankton threshold value for grazing on
!                Small Zooplankton, [millimole_N/m3].
!
!  PL2ZPstar   Predator Zooplankton threshold value for grazing on
!                Large Phytoplankton, [millimole_N/m3].
!
!  ZS2ZPstar   Predator Zooplankton threshold value for grazing on
!                Small Zooplankton, [millimole_N/m3].
!
!  ZL2ZPstar   Small Zooplankton threshold value for grazing on
!                Small Phytoplankton, [millimole_N/m3].
!
!  PusaiPL     Predator Zooplankton grazing on Large Phytoplankton
!                inhibition coefficient, [m3/millimole_N].
!
!  PusaiZS     Predator Zooplankton grazing on Small Zooplankton
!                inhibition coefficient, [m3/millimole_N].
!
!  MorZS0      Small Zooplankton mortality rate at 0 Celsius,
!                [m3/millimole_N 1/day].
!
!  MorZL0      Large Zooplankton mortality rate at 0 Celsius,
!                [m3/millimole_N 1/day].
!
!  MorZP0      Predator Zooplankton mortality rate at 0 Celsius,
!                [m3/millimole_N 1/day].
!
!  KMorZS      Small Zooplankton temperature coefficient for mortality,
!                [1/Celsius].
!
!  KMorZL      Large Zooplankton temperature coefficient for mortality,
!                [1/Celsius].
!
!  KMorZP      Predator Zooplankton temperature coefficient for mortality,
!                [1/Celsius].
!
!  AlphaZS     Small Zooplankton assimilation efficiency [nondimemsional].
!
!  AlphaZL     Large Zooplankton assimilation efficiency [nondimemsional].
!
!  AlphaZP     Predator Zooplankton assimilation efficiency [nondimemsional].
!
!  BetaZS      Small Zooplankton growth efficiency [nondimensional].
!
!  BetaZL      Large Zooplankton growth efficiency [nondimensional].
!
!  BetaZP      Predator Zooplankton growth efficiency [nondimensional].
!
!------------------------------------------------------------------------------
! Nutrient parameters.
!------------------------------------------------------------------------------
!
!  Nit0        Nitrification (NH4 to NO3) rate at 0 Celsius, [1/day].
!
!  VP2N0       PON to NH4 decomposition rate at 0 Celsius, [1/day].
!
!  VP2D0       PON to DON decomposition rate at 0 Celsius, [1/day].
!
!  VD2N0       DON to NH4 decomposition rate at 0 Celsius, [1/day].
!
!  VO2S0       Opal to Silicate decomposition rate at 0 Celsius, [1/day].
!
!  KNit        Temperature coefficient for nitrification (NH4 -> NO3)
!                decomposition, [1/Celsius].
!
!  KP2D        Temperature coefficient for PON to DON decomposition,
!                [1/Celsius].
!
!  KP2N        Temperature coefficient for PON to NH4 decomposition,
!                [1/Celsius].
!
!  KD2N        Temperature coefficient for DON to NH4 decomposition,
!                [1/Celsius].
!
!  KO2S        Temperature coefficient for Opal to Silicate decomposition,
!                [1/Celsius].
!
!  RSiN        Si:N ratio [millimole_Si/millimole_N].
!
!  setVPON     PON Settling (sinking) velocity [m/day].
!
!  setVOpal    Opal Settling (sinking) velocity [m/day].
!
!------------------------------------------------------------------------------
! Other Parameters, [1:NBT,1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
!  TNU2        Lateral, harmonic, constant, mixing coefficient (m2/s) for
!                biological tracer variables; [1:NBT,1:Ngrids] values are
!                expected.  If variable horizontal diffusion is activated,
!                TNU2 is the mixing coefficient for the largest grid-cell
!                in the domain.
!
!  TNU4        Lateral, biharmonic, constant, mixing coefficient (m4/s) for
!                biological tracer variables; [1:NBT,1:Ngrids] values are
!                expected.  If variable horizontal diffusion is activated,
!                TNU4 is the mixing coefficient for the largest grid-cell
!                in the domain.
!
!  AKT_BAK     Background vertical mixing coefficient (m2/s) for biological
!                tracer variables, [1:NBT,1:Ngrids] values are expected.
!
!  TNUDG       Nudging time scale (days), [1:NBT,1:Ngrids].  Inverse scale will
!                be computed internally.
!
!  Hout        Logical switches (T/F) to write out biological data into output
!                History/Average NetCDF files. Currently, NEMURO has NBT=11
!                ecosystem compartments.
!
!                Hout(idTvar)           biological tracers
!                Hout(idTsur)           biological tracers surface flux
!
!                  idTvar( 1)=iPhyL     Large Phytoplankton biomass
!                  idTvar( 2)=iPhyS     Small Phytoplankton biomass
!                  idTvar( 3)=iZooL     Large Zooplankton biomass
!                  idTvar( 4)=iZooS     Small Zooplankton biomass
!                  idTvar( 5)=iZooP     Predator Zooplankton biomass
!                  idTvar( 6)=iNO3_     Nitrate concentration
!                  idTvar( 7)=iNH4_     Ammonium concentration
!                  idTvar( 8)=iPON_     Particulate Organic Nitrogen
!                  idTvar( 9)=iDON_     Dissolved Organic Nitrogen
!                  idTvar(10)=iSiOH     Silicate concentration
!                  idTvar(11)=iopal     Particulate organic silica
!
