!
!  EcoSim Biological Model Parameters.
!
!svn $Id: ecosim.in 294 2009-01-09 21:37:26Z arango $
!========================================================= Hernan G. Arango ===
!  Copyright (c) 2002-2009 The ROMS/TOMS Group              W. Paul Bissett   !
!    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.              !
!                                                                             !
!=============================================================================!
!
! Switch to control the computation of EcoSim within nested and/or multiple
! connected grids.

      Lbiology == T

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

       BioIter == 1

! Logical switch (T/F) to calculate CDOC UV photolysis.

    RtUVR_flag == T

! Logical switch (T/F) to calculate temperature based nitrogen fixation.

     NFIX_flag == F

! Logical switch (T/F) to calculate fecal matter regeneration.

    Regen_flag == T

!-----------------------------------------------------------------------------
! Phytoplankton group parameters.
!-----------------------------------------------------------------------------
!
! Half-saturation for phytoplankton NO3 uptake (micromole_NO3/liter),
! [Nphy,Ngrids] values are expected.

         HsNO3 == 8.2400d-01  4.1200d-01  8.2400d-01  1.6700d-01

! Half-saturation for phytoplankton NH4 uptake (micromole_NH4/liter),
! [Nphy,Ngrids] values are expected.

         HsNH4 == 4.1400d-01  2.0800d-01  4.1400d-01  8.3000d-02

! Half-saturation for phytoplankton SiO uptake (micromole_SiO/liter),
! [Nphy,Ngrids] values are expected. A value of 1.0d+30 denotes no SiO
! uptake being calculated for that phytoplankton group. 

         HsSiO == 1.8240d+00  1.4120d+00  1.0000d+30  1.0000d+30

! Half-saturation for phytoplankton PO4 uptake (micromole_PO4/liter),
! [Nphy,Ngrids] values are expected.

         HsPO4 == 5.1500d-02  2.5750d-02  5.1500d-02  1.0438d-02

! Half-saturation for phytoplankton Fe uptake (micromole_Fe/liter),
! [Nphy,Ngrids] values are expected. A value of 1.0d+30 denotes no Fe
! uptake being calculated for that phytoplankton group. 

          HsFe == 1.0000d+30  1.0000d+30  1.0000d+30  1.0000d+30

! Maximum phytoplankton 24 hour growth rate (1/d),
! [Nphy,Ngrids] values are expected.

     GtALG_max == 3.7000d+00  3.7000d+00  2.0000d+00  2.0000d+00

! Phytoplankton temperature base for exponential response to temperature
! (Celsius), [Nphy,Ngrids] values are expected.

      PhyTbase == 4*27.0d0

! Phytoplankton exponential temperature factor (1/Celsius),
! [Nphy,Ngrids] values are expected.

       PhyTfac == 4*0.0633d0

! Nitrate uptake inhibition for NH4 (l/micromole),
! [Nphy,Ngrids] values are expected.

          BET_ == 1.2800d+00  2.6000d+00  1.2800d+00  6.5000d+00

! Maximum phytoplankton C:N ratio (micromole_C/micromole_N),
! [Nphy,Ngrids] values are expected.

     maxC2nALG == 1.4000d+01  1.7750d+01  1.7000d+01  6.6250d+00

! Balanced phytoplankton C:N ratio (micromole_C/micromole_N),
! [Nphy,Ngrids] values are expected.

     minC2nALG == 6.6250d+00  6.6250d+00  6.6250d+00  6.6250d+00

! Absolute minimum phytoplankton C:N ratio (micromole_C/micromole_N),
! [Nphy,Ngrids] values are expected.

  C2nALGminABS == 5.5000d+00  5.5000d+00  5.5000d+00  5.5000d+00

! Maximum phytoplankton C:Si ratio (micromole_C/micromole_Si),
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no silica used.

    maxC2SiALG == 5.5210d+00  5.5210d+00  0.0000d+00  0.0000d+00

! Balanced phytoplankton C:Si ratio (micromole_C/micromole_Si),
! [Nphy,Ngrids] values are expected. A value of 1.0 denotes no silica used.

    minC2SiALG == 5.5210d+00  5.5210d+00  1.0000d+00  1.0000d+00

! Absolute minimum phytoplankton C:Si ratio (micromole_C/micromole_Si)
! [Nphy,Ngrids] values are expected. A value of 1.0 denotes no silica used.

 C2SiALGminABS == 4.5831d+00  4.5831d+00  1.0000d+00  1.0000d+00

! Maximum phytoplankton C:P ratio (micromole_C/micromole_P),
! [Nphy,Ngrids] values are expected. A value of 1.0 denotes no silica used.

     maxC2pALG == 1.0600d+02  1.0600d+02  1.3000d+02  1.0600d+02

! Balanced phytoplankton C:P ratio (micromole_C/micromole_P),
! [Nphy,Ngrids] values are expected.

     minC2pALG == 1.0600d+02  1.0600d+02  1.0600d+02  1.0600d+02

! Absolute minimum phytoplankton C:P ratio (micromole_C/micromole_P),
! [Nphy,Ngrids] values are expected.

  C2pALGminABS == 8.800d+01   8.800d+01   8.800d+01   8.800d+01

! Maximum phytoplankton C:Fe ratio (micromole_C/micromole_Fe),
! [Nphy,Ngrids] values are expected. A value of 1.0d+30 denotes no Fe
! uptake being calculated. 

    maxC2FeALG == 1.0000d+30  1.0000d+30  1.0000d+30  1.0000d+30

! Balanced phytoplankton C:Fe ratio (micromole_C/micromole_Fe),
! [Nphy,Ngrids] values are expected. A value of 1.0d+30 denotes no Fe
! uptake being calculated.

    minC2FeALG == 1.0000d+30  1.0000d+30  1.0000d+30  1.0000d+30

! Absolute minimum phytoplankton C:Fe ratio (micromole_C/micromole_Fe),
! [Nphy,Ngrids] values are expected. A value of 1.0d+30 denotes no Fe
! uptake being calculated. 

 C2FeALGminABS == 1.0000d+30  1.0000d+30  1.0000d+30  1.0000d+30

! Maximum quantum yield (micromole_C/micromole_quanta),
! [Nphy,Ngrids] values are expected.

        qu_yld == 8.3300d-02  8.3300d-02  8.3300d-02  8.3300d-02

! Compensation light level (micromole_quanta),
! [Nphy,Ngrids] values are expected.

       E0_comp == 1.0000d+01  1.0000d+01  1.0000d+01  6.0000d+00

! Light level for onset of photoinhibition (micromole_quanta),
! [Nphy,Ngrids] values are expected.

      E0_inhib == 1.0000d+04  1.0000d+04  1.0500d+02  1.0000d+04

! Exponential decay factor for light limited growth (1/micromole_quanta),
! [Nphy,Ngrids] values are expected.

     inhib_fac == 0.0000d+00  0.0000d+00  1.0000d-03  0.0000d+00

! Maximum lighted limited (nutrient replete) C:Chl ratio
! (microgram_C/microgram_Chl), [Nphy,Ngrids] values are expected.

     C2CHL_max == 6.0000d+01  4.2000d+01  1.2400d+02  1.6000d+02

! Rate of change in light limited C:Chl ratio
! (microgram_C/microgram_Chl/micromole_quanta),
! [Nphy,Ngrids] values are expected.

        mxC2Cl == 1.2000d-01  1.1440d-01  4.7790d-01  1.0000d-01

! Minimum lighted limited (nutrient replete) C:Chl ratio
! (microgram_C/microgram_Chl), [Nphy,Ngrids] values are expected.

        b_C2Cl == 2.5000d+01  1.4800d+01  4.7530d+01  3.0000d+01

! Rate of change in nutient limited C:Chl ratio
! [(microgram_C/microgram_Chl)/(micromole_C/micromole_N)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in C:Chl with nutrient status.

        mxC2Cn == 1.2200d+01  6.8315d+00  1.0350d+01  0.0000d+00

! Minimum nutrient limited C:Chl ratio (microgram_C/microgram_Chl),
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in C:Chl with nutrient status.

        b_C2Cn == 6.0000d+01  4.2000d+01  1.2400d+02  0.0000d+00

! Rate of change in package effect [1/(microgram_C/microgram_Chl)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in package effect.

      mxPacEff == 1.4290d-02  1.8380d-02  0.0000d+00  0.0000d+00

! Maximum package effect [1/(microgram_C/microgram_Chl)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in package effect.

      b_PacEff == 5.0000d-01  5.0000d-01  0.0000d+00  0.0000d+00

! Rate of change in the Chl_b:Chl_a ratio
! [(microgram_Chl_b/microgram_Chl_a)/[microgram_C/microgram_Chl_ a)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotea no change
! in Chl_b:Chl_a ratio.

        mxChlB == 0.0000d+00  0.0000d+00  0.0000d+00  0.0000d+00

! Maximum Chl_b:Chl_a ratio (microgram_Chl_b/microgram_Chl_a),
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no Chl_b.

        b_ChlB == 0.0000d+00  0.0000d+00  0.0000d+00  0.0000d+00

! Rate of change in the Chl_c:Chl_a ratio.
! [(microgram_Chl_c/microgram_Chl_a)/(microgram_C/microgram_Chl_a)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in Chl_c:Chl_a ratio.

        mxChlC == -1.3600d-03 -1.2000d-03 0.0000d+00  0.0000d+00

! Maximum Chl_c:Chl_a ratio (microgram_Chl_c/microgram_Chl_a),
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no Chl_c.

        b_ChlC == 3.4000d-01  3.4000d-01  5.6000d-02  0.0000d+00

! Rate of change in the PSC:Chl_a ratio
! [(microgram_PSC/microgram_Chl_a)/microgram_C/microgram_Chl_a)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in PSC:Chl_a ratio.

         mxPSC == -1.2000d-02 -1.0400d-02 0.0000d+00  0.0000d+00

! Maximum PSC:Chl_a ratio (microgram_PSC/microgram_Chl_a),
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no
! Photosynthetic Caroteniods.

         b_PSC == 2.0000d+00  2.0000d+00  1.1060d+00  0.0000d+00

! Rate of change in the PPC:Chl_a ratio
! [(microgram_PPC/microgram_Chl_a)/(microgram_C/microgram_Chl_ a)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in PPC:Chl_a ratio.

         mxPPC == 0.0000d+00  0.0000d+00  1.8000d-03  9.0000d-03

! Maximum PPC:Chl_a ratio (microgram_Chl_c/microgram_Chl_a),
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no
! Photoprotective Caroteniods.

         b_PPC == 1.0000d-01  1.0000d-01  1.6000d-01  3.0000d-01

! Rate of change in the LPUb:Chl_a ratio
! [(microgram_LPUb/microgram_Chl_a)/(microgram_C/microgram_Chl_a)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in LPUb:Chl_a ratio.

        mxLPUb == 0.0000d+00  0.0000d+00  0.0000d+00  0.0000d+00

! Maximum LPUb:Chl_a ratio (migrogram_HPUb/microgram_Chl_a),
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no LPUb.

        b_LPUb == 0.0000d+00  0.0000d+00  0.0000d+00  0.0000d+00

! Rate of change in the HPUb:Chl_a ratio
! [(microgram_HPUb/microgram_Chl_a)/(microgram_C/microgram_Chl_a)],
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no change
! in HPUb:Chl_a ratio.

        mxHPUb == 0.0000d+00  0.0000d+00  0.0000d+00 -1.3000d-01

! Maximum HPUb:Chl_a ratio (microgram_HPUb/microgram_Chl_a),
! [Nphy,Ngrids] values are expected. A value of 0.0 denotes no HPUb.

        b_HPUb == 0.0000d+00  0.0000d+00  0.0000d+00  2.0000d+01

! Proportion of grazing stress that is apportioned to DOM
! (nondimensional), [Nphy,Ngrids] values are expected.

        FecDOC == 3.3330d-01  3.3330d-01  3.3330d-01  4.1670d-01

! Proportion of grazing stress that is apportioned to fecal
! (nondimensional), [Nphy,Nfec,Ngrids] values are expected.

        FecPEL == 3*1.6670d-01  8.3350d-02  3*1.6670d-01  8.3350d-02

! Proportion of grazing stress that is recycled (nondimensional),
! [Nphy,Ngrids] values are expected.

        FecCYC == 3.3330d-01  3.3330d-01  3.3330d-01  4.1660d-01

! Proportion of daily production that is lost to excretion
! (nondimensional), [Nphy,Ngrids] values are expected.

         ExALG == 5.0000d-03  5.0000d-03  5.0000d-03  5.0000d-03

! Phytoplankton sinking speed (meters/day),
! [Nphy,Ngrids] values are expected.

            WS == 0.0000d+00  0.0000d+00  0.0000d+00  0.0000d+00

! Phytoplankton grazing parameter (nondimensional).
! [Nphy,Ngrids] values are expected.

         HsGRZ == 0.0100d+00  0.0100d+00  0.0100d+00  0.0100d+00

! Refuge Phytoplankton population (micromole_C/liter),
! [Nphy,Ngrids] values are expected.

     MinRefuge == 2.0000d-02  2.0000d-02  2.0000d-02  2.0000d-02

! Maximum Refuge Phytoplankton depth (meters),
! [Nphy,Ngrids] values are expected.

     RefugeDep == 4.0000d+01  4.0000d+01  4.0000d+01  4.0000d+01

! Normalized Volume factor (nondimensional),
! [Nphy,Ngrids] values are expected. (1 micron diameter cell = 1).

      Norm_Vol == 7.2398d+01  7.2398d+01  7.2398d+01  4.6370d+00

! Normalized Surface Area factor (nondimensional),
! [Nphy,Ngrids] values are expected. (1 micron diameter cell = 1).

     Norm_Surf == 1.7361d+01  1.7361d+01  1.7361d+01  2.7781d+00

! Half Saturation Constant for DOP uptake (micromole_DOP/liter),
! [Nphy,Ngrids] values are expected.

         HsDOP == 1.0000d-05  1.0000d-05  2.0000d+00  1.0000d-05

! C:P ratio where DOP uptake begins (micromole_C/micromole_P),
! [Nphy,Ngrids] values are expected. Values above maxC2pALG denote
! no DOP uptake.

    C2pALKPHOS == 5.0000d+02  5.0000d+02  1.1000d+02  5.0000d+02

! Half Saturation constant for DON uptake (micromole_DON/liter),
! [Nphy,Ngrids] values are expected.

         HsDON == 1.0000d-05  1.0000d-05  2.0000d+00  1.0000d-05

! C:N ratio where DON uptake begins (micromole_C/micromole_N),
! [Nphy,Ngrids] values are expected. Values above maxC2nALG denote
! no DOP uptake.

     C2nNupDON == 5.0000d+02  5.0000d+02  1.4000d+01  5.0000d+02

!-----------------------------------------------------------------------------
! Bacteria group parameters.
!-----------------------------------------------------------------------------
!
! Half saturation constant for bacteria DOC uptake (micromole_DOC/liter),
! [Nbac,Ngrids] values are expected.

      HsDOC_ba == 130.0d+00

! Maximum 24 hour bacterial growth rate (1/day),
! [Nbac,Ngrids] values are expected.

     GtBAC_max == 2.0d+00

! Bacteria temperature base for exponential response to temperature
! (Celsius), [Nbac,Ngrids] values are expected.

      BacTbase == 27.0d+0

! Bacteria exponential temperature factor (1/Celsius),
! [Nbac,Ngrids] values are expected.

       BacTfac == 0.092d+00

! Carbon to Nitrogen ratio of Bacteria (micromole_C/micromole_N),
! [Ngrids] values are expected.

        C2nBAC == 5.0d+00

! Carbon to Phosphorus ratio of Bacteria (micromole_C/micromole_P)
! [Ngrids] values are expected.

        C2pBAC == 60.0d+00

! Carbon to Iron ratio of Bacteria (micromole_C/micromole_Fe),
! [Ngrids] values are expected.

       C2FeBAC == 1000.0d+00

! Proportion of bacteria grazing stress that is apportioned to DOM
! (nondimensional), [Ngrids] values are expected.

        BacDOC == 4.583d-01

! Proportion of bacteria grazing stress that is apportioned to fecal
! (nondimensional), [Ngrids] values are expected.

        BacPEL == 8.340d-02

! Proportion of bacteria grazing stress that is recycled
! (nondimensional), [Ngrids] values are expected.

        BacCYC == 4.583d-01

! Bacterial recalcitrant carbon excretion as a proportion of uptake
! (nondimensional), [Ngrids] values are expected.

       ExBAC_c == 4.0d-02

! Bacterial recalcitrant excretion carbon to nitrogen ratio
! (micromole_C/micromole_N), [Ngrids] values are expected.

      ExBacC2N == 15.0d0

! Bacterial gross growth carbon efficiency (nondimensional),
! [Ngrids] values are expected.

      Bac_Ceff == 0.3d0

! Maximum nitrification rate (1/day),
! [Ngrids] values are expected.

         RtNIT == 0.4d0

! Half-saturation constant for bacterial nitrification (micromole_NH4/liter),
! [Ngrids] values are expected.

         HsNIT == 0.1d0

!-----------------------------------------------------------------------------
! DOM group parameters.
!-----------------------------------------------------------------------------
!
! Colored fraction of DOC from phytoplankton and bacterial losses
! (nondimensional), [Ndom,Ngrids] values are expected

    cDOCfrac_c == 0.0323d0  0.0930d0

! UV degradation of DOC into DIC
! (micromole/meter/liter/hour at 410 nm),
! [Ngrids] values are expected.

     RtUVR_DIC == 0.0193d0

! UV degradation of DOC to colorless labile DOC
! (micromole/meter/liter/hour at 410 nm),
! [Ngrids] values are expected.
 
     RtUVR_DOC == 0.0034d0

!-----------------------------------------------------------------------------
! Fecal and detritus group parameters.
!-----------------------------------------------------------------------------
!
! Fecal sinking flux (meters/day),
! [Nfec,Ngrids] values are expected.

            WF == 0.0d0   100.0d0

! Fecal regeneration temp base for exponential response to tempemperaute
! (Celsius), [Nfec,Ngrids] values are expected.

      RegTbase == 2*27.0d0

! Fecal regeneration exponential temperature factor,
! (1/Celsius), [Nfec,Ngrids] values are expected.

       RegTfac == 2*0.092d0

! Fecal carbon regeneration rate (1/day),
! [Nfec,Ngrids] values are expected.

         RegCR == 0.10d0  0.0d0

! Fecal nitrogen regeneration rate (1/day),
! [Nfec,Ngrids] values are expected.

         RegNR == 0.10d0  0.0d0

! Fecal silica regeneration rate (1/day),
! [Nfec,Ngrids] values are expected.

         RegSR == 0.13d0  0.0d0

! Fecal phosphorus regeneration rate (1/day),
! [Nfec,Ngrids] values are expected.

         RegPR == 0.10d0  0.0d0

! Fecal iron regeneration rate (1/day),
! [Nfec,Ngrids] values are expected.

         RegFR == 0.10d0  0.0d0

!-----------------------------------------------------------------------------
! Physical and output parameters 
!-----------------------------------------------------------------------------

! Lateral, constant, harmonic/biharmonic horizontal diffusion of biological
! tracer, [NBT,Ngrids] values are expected.

          TNU2 == 63*0.0d0                       ! m2/s

! Lateral, constant, harmonic/biharmonic horizontal diffusion of biological
!! tracer, [NBT,Ngrids] values are expected.

          TNU4 == 63*0.0d0                       ! m4/s

! Vertical mixing coefficients for biological tracers,
! [NBT,Ngrids] values are expected.

       AKT_BAK == 63*1.0d-6                      ! m2/s

! Nudging/relaxation time scales, inverse scales will be computed internally, 
! [NBT,Ngrids] values are expected.

         TNUDG == 63*0.0d0                       ! days

! Logical switches (T/F)  to write biological tracers into output NetCDF
! files, [NBT,Ngrids] values are expected.

  Hout(idTvar) == 63*T                           ! biological tracer
  Hout(idTsur) == 63*F                           ! surface tracer flux

!
!  GLOSSARY:
!  =========
!
!==============================================================================
! EcoSim Biological Model Parameters.
!==============================================================================
!
! EcoSim equations and representative parameters may be found in:
!
!    Bissett, W.P., J.J. Walsh, D.A. Dieterle, K.L. Carder, 1999:
!      Carbon cycling in the upper waters of the Sargasso Sea: I.
!      Numerical  simulation of  differential carbon and nitrogen
!      fluxes,  Deep-Sea Res., 46, 205-269.
!
!    Bissett, W.P., K.L. Carder, J.J. Walsh, D.A. Dieterle, 1999:
!      Carbon cycling in the upper waters of the Sargasso Sea: II.
!      Numerical  simulation  of  apparent  and  inherent optical
!      properties, Deep-Sea Res., 46, 271-317.
!
!    Bissett, W., Arnone, R., DeBra, S., Dieterle, D., Dye, D.,
!      Kirkpatrick, G., Schofield, O. and Vargo, G., 2003.
!      Predicting the optical properties of the West Florida Shelf:
!      Resolving the potential impacts of a terrestrial boundary
!      condition on the distribution of colored dissolved and
!      particulate matter. Marine Chemistry, submitted.
!      (For a PDF preprint, see: www.flenvironmental.org/Publications)
!
!------------------------------------------------------------------------------
! Model switches and flags.
!------------------------------------------------------------------------------
!  
!  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.
!
!  BioIter        Maximum number of iterations to achieve convergence of
!                   the nonlinear solution.
!
!  RtUVR_flag     Logical switch (T/F) to calculate CDOC UV photolysis.
!
!  NFIX_flag      Logical switch (T/F) to calculate temperature based nitrogen
!                   fixation. (Not tested at this time; No nitrogen fixation 
!                   being calculated).
!
!  Regen_flag     Logical switch (T/F) to calculate fecal matter regeneration.
!
!------------------------------------------------------------------------------
! Phytoplankton Parameters. Unless specified, [Nphy,Ngrids] values are
! expected. This file is configured for Nphy=1 and Ngrids=1. The order
! of phytoplankton are:
!                          [1] larger diatoms
!                          [2] small diatoms
!                          [3] dinoflagellates
!                          [4] synechococcus
!------------------------------------------------------------------------------
!
!  HsNO3          Half-saturation for phytoplankton NO3 uptake,
!                   (micromole_NO3/liter).
!
!  HsNH4          Half-saturation for phytoplankton NH4 uptake,
!                   (micromole_NH4/liter).
!
!  HsSiO          Half-saturation for phytoplankton SiO uptake,
!                   (micromole_SiO/liter).
!                   << 1.0d+30 denotes no SiO uptake being calculated >>
!
!  HsPO4          Half-saturation for phytoplankton PO4 uptake,
!                   (micromole_PO4/liter).
!
!  HsFe           Half-saturation for phytoplankton Fe uptake,
!                  (micromole_Fe/liter).
!                  << 1.0d+30 denotes no Fe uptake being calculated >>
!
!  GtALG_max      Maximum 24 hour growth rate,
!                   (1/day).
!
!  PhyTbase       Phytoplankton temperature base for exponential response
!                   to temperature, (Celsius).
!
!  PhyTfac        Phytoplankton exponential temperature factor,
!                   (1/Celsius).
!
!  BET_           Nitrate uptake inhibition for NH4,
!                   (l/micromole).
!
!  maxC2nALG      Maximum phytoplankton C:N ratio,
!                   (micromole_C/micromole_N).
!
!  minC2nALG      Balanced phytoplankton C:N ratio,
!                   (micromole_C/micromole_N).
!
!  C2nALGminABS   Absolute minimum phytoplankton C:N ratio,
!                   (micromole_C/micromole_N).
!
!  maxC2SiALG     Maximum phytoplankton C:Si ratio,
!                   (micromole_C/micromole_Si).
!                   (0.0 denotes no silica used)
!
!  minC2SiALG     Balanced phytoplankton C:Si ratio,
!                   (micromole_C/micromole_Si).
!                   << 1.0 denotes no silica used >>
!
!  C2SiALGminABS  Absolute minimum phytoplankton C:Si ratio, 
!                  (micromole_C/micromole_Si).
!                  (1.0 denotes no silica used)
!
!  maxC2pALG      Maximum phytoplankton C:P ratio,
!                   (micromole_C/micromole_P).
!
!  minC2pALG      Balanced phytoplankton C:P ratio,
!                   (micromole_C/micromole_P).
!
!  C2pALGminABS   Absolute minimum phytoplankton C:P ratio,
!                   (micromole_C/micromole_P).
!
!  maxC2FeALG     Maximum phytoplankton C:Fe ratio,
!                   (micromole_C/micromole_Fe).
!                   << 1.0d+30 denotes no Fe uptake being calculated >>
!
!  minC2FeALG     Balanced phytoplankton C:Fe ratio,
!                   (micromole_C/micromole_Fe).
!                   << 1.0d+30 denotes no Fe uptake being calculated >>
!
!  C2FeALGminABS  Absolute minimum phytoplankton C:Fe ratio,
!                   (micromole_C/micromole_Fe).
!                   << 1.0d+30 denotes no Fe uptake being calculated >>
!
!  qu_yld         Maximum quantum yield,
!                   (micromole_C/micromole_quanta).
!
!  E0_comp        Compensation light level,
!                   (micromole_quanta).
!
!  E0_inhib       Light level for onset of photoinhibition,
!                   (micromole_quanta).
!
!  inhib_fac      Exponential decay factor for light limited growth,
!                   (1/micromole_quanta).
!
!  C2Chl_max      Maximum lighted limited (nutrient replete) C:Chl ratio,
!                   (microgram_C/microgram_Chl).
!
!  mxC2Cl         Rate of change in the lighted limited C:Chl ratio,
!                   (microgram_C/microgram_Chl/micromole_quanta).
!
!  b_C2Cl         Minimum lighted limited (nutrient replete) C:Chl ratio,
!                   (microgram_C/microgram_Chl).
!
!  mxC2Cn         Rate of change in the nutrient limited C:Chl ratio,
!                   [(microgram_C/microgram_Chl)/(micromole_C/micromole_N)].
!                   << Zeros denote no change in C:Chl with nutrient status >>
!
!  b_C2Cn         Minimum nutrient limited C:Chl ratio,
!                   (microgram_C/microgram_Chl).
!                   << Zeros denote no change in C:Chl with nutrient status >>
!
!  mxPacEff       Rate of change in package effect,
!                   [1/(microgram_C/microgram_Chl)].
!                   << Zeros denote no change in Package Effect >>
!
!  b_PacEff       Maximum package effect,
!                   [1/(microgram_C/microgram_Chl)].
!                   << Zeros denote no package effect >>
!
!  mxChlB         Rate of change in the Chl_b:Chl_a ratio,
!                   [(microgram_Chl_b/microgram_Chl_a)/
!                    (microgram_C/microgram_Chl_a)].
!                   << Zeros denote no change in Chl_b:Chl_a ratio >>
!
!  b_ChlB         Maximum Chl_b:Chl_a ratio,
!                   (microgram_Chl_b/microgram_Chl_a).
!                   (Zeros denote no Chl_b)
!
!  mxChlC         Rate of change in the Chl_c:Chl_a ratio.
!                   [(microgram_Chl_c/microgram_Chl_a)/
!                    (microgram_C/microgram_Chl_a)].
!                   << Zeros denote no change in Chl_c:Chl_a ratio >>
!
!  b_ChlC         Maximum Chl_c:Chl_a ratio,
!                   (microgram_Chl_c/microgram_Chl_a).
!                   << Zeros denote no Chl_c >>
!
!  mxPSC          Rate of change in the PSC:Chl_a ratio,
!                   [(microgram_PSC/microgram_Chl_a)/
!                    (microgram_C/microgram_Chl_a)].
!                   << Zeros denote no change in PSC:Chla ratio >>
!
!  b_PSC          Maximum PSC:Chl_a ratio,
!                  (microgram_Chl_c/microgram_Chl_a).
!                  << Zeros denote no Photosynthetic Caroteniods >>
!
!  mxPPC          Rate of change in the PPC:Chl_a ratio,
!                   [(microgram_PPC/microgram_Chl_a)/
!                    (microgram_C/microgram_Chl_a)].
!                   << Zeros denote no change in PPC:Chl_a ratio >>
!
!  b_PPC          Maximum PPC:Chl_a ratio,
!                  (microgram_Chl_c/microgram_Chl_a).
!                  << Zeros denote no Photoprotective Caroteniods >>
!
!  mxLPUb         Rate of change in the LPUb:Chl_a ratio,
!                   [(microgram_LPUb/microgram_Chl_a)/
!                    (microgram_C/microgram_Chl_a)].
!                   << Zeros denote no change in LPUb:Chl_a ratio >>
!
!  b_LPUb         Maximum LPUb:Chl_a ratio,
!                   (microgram_HPUb/microgram_Chl_a).
!                   << Zeros denote no LPUb >>
!
!  mxHPUb         Rate of change in the HPUb:Chl_a ratio,
!                   [(microgram_HPUb/microgram_Chl_a)/
!                    (microgram_C/microgram_Chl_a)].
!                   << Zeros denote no change in HPUb:Chl_a ratio >>
!
!  b_HPUb         Maximum HPUb:Chl_a ratio,
!                   (microgram_HPUb/microgram_Chl_a).
!                   << Zeros denote no HPUb >>
!
!  FecDOC         Proportion of grazing stress which is apportioned to DOM,
!                   (nondimensional).
!
!  FecPEL         Proportion of grazing stress which is apportioned to fecal 
!                   pellets, (nondimesional).
!                   [Nphy,Nfec,Ngrids] values are expected.
!
!  FecCYC         Proportion of grazing stress which is apportioned to direct
!                   remineralization, (nondimensional).
!
!  ExALG          Proportion of daily production that is lost to excretion,
!                   (nondimensional).
!
!  WS             Phytoplankton sinking speed,
!                   (meters/day).
!
!  HsGRZ          Phytoplankton grazing parameter,
!                   (nondimensional).
!
!  MinRefuge      Refuge Phytoplankton population,
!                   (micromole_C/liter).
!
!  RefugeDep      Maximum Refuge Phytoplankton depth,
!                   (meters).
!
!  Norm_Vol       Normalized Volume factor,
!                   (nondimensional).
!                   << 1 micron diameter cell = 1 >>
!
!  Norm_Surf      Normalized surface area factor,
!                   (nondimensional).
!                   << 1 micron diameter cell = 1 >>
!
!  HsDOP          Half Saturation Constant for DOP uptake,
!                   (micromole_DOP/liter).
!
!  C2pALKPHOS     C:P ratio where DOP uptake begins,
!                   (micromole_C/micromole_P).
!                   << Values above maxC2pALG denote no DOP uptake >>
!
!  HsDON          Half Saturation Constant for DON uptake,
!                   (micromole_DON/liter).
!
!  C2nNupDON      C:N ratio where DON uptake begins,
!                   (micromole_C/micromole_N).
!                   << Values above maxC2nALG denote no DOP uptake >>
!
!------------------------------------------------------------------------------
! Bacteria Parameters. Unless specified, [Ngrids] values are expected. This
! file is configured for Nbac=1 and Ngrids=1.
!------------------------------------------------------------------------------
!
!  HsDOC_ba       Half saturation constant for bacteria DOC uptake,
!                   (micromole_DOC/liter).
!                   [Nbac,Ngrids] values are expected.
!
!  GtBAC_max      Maximum 24 hour bacterial growth rate,
!                   (1/day).
!                   [Nbac,Ngrids] values are expected.
!
!  BacTbase       Phytoplankton temperature base for exponential response to 
!                   temperature, (Celsius).
!                   [Nbac,Ngrids] values are expected.
!
!  BacTfac        Phytoplankton exponential temperature factor,
!                   (1/Celsius).
!                   [Nbac,Ngrids] values are expected.
!
!  C2nBAC         Carbon to Nitrogen ratio of Bacteria,
!                   (micromole_C/micromole_N).
!
!  C2pBAC         Carbon to Phosphorus ratio of Bacteria,
!                   (micromole_C/micromole_P).
!
!  C2FeBAC        Carbon to Iron ratio of Bacteria,
!                   (micromole_C/micromole_Fe).
!
!  BacDOC         Proportion of bacterial grazing stress which is apportioned
!                   to DOM, (nondimensional).
!
!  BacPEL         Proportion of bacterial grazing stress which is apportioned
!                   to fecal pellets, (nondimensional).
!
!  BacCYC         Proportion of bacterial grazing stress which is apportioned
!                   to direct remineralization, (nondimensional).
!
!  ExBAC_c        Bacterial recalcitrant carbon excretion as a proportion
!                   of uptake, (nondimensional)
!
!  ExBacC2N       Bacterial recalcitrant excretion carbon to nitrogen ratio,
!                   (micromole_C/micromole_N).
!
!  Bac_Ceff       Bacterial gross growth carbon efficiency,
!                   (nondimensional).
!
!  RtNIT          Maximum nitrification rate,
!                   (1/day).
!
!  HsNIT          Half-saturation constant for bacterial nitrification,  
!                   (micromole_NH4/liter).
!
!------------------------------------------------------------------------------
! DOM Parameters. Unless specified, [Ngrids] values are expected. This
! file is configured for Ndom=2 and Ngrids=1.
!------------------------------------------------------------------------------
!
!  cDOCfrac_c     Colored fraction of DOC production from phytoplankton and
!                   bacterial losses, (nondimensional).
!                   [Ndom,Ngrids] values are expected.
!
!  RtUVR_DIC      UV degradation of DOC into DIC,
!                   (micromole/meter/liter/hour at 410 nanometer). 
!
!  RtUVR_DOC      UV degradation of DOC into colorless labile DOC,  
!                   (micromole/meter/liter/hour at 410 nanometer). 
!
!------------------------------------------------------------------------------
! Fecal and detritus Parameters. Unless specified, [Nfec,Ngrids] values are
! expected. This file is configured for Nfec=2 and Ngrids=1.
!------------------------------------------------------------------------------
!
!  WF             Fecal sinking flux,
!                   (meters/day)
!
!  RegTbase       Fecal regeneration temperature base for exponential response
!                   to temperature, (Celsius).
!
!  RegTfac        Fecal regeneration exponential temperature factor,
!                   (1/Celsius).
!
!  RegCR          Fecal carbon regeneration rate,
!                   (1/day).
!
!  RegNR          Fecal nitrogen regeneration rate,
!                   (1/day).
!
!  RegSR          Fecal silica regeneration rate,
!                   (1/day).
!
!  RegPR          Fecal phosphorus regeneration rate,
!                   (1/day).
!
!  RegFR          Fecal iron regeneration rate,
!                   (1/day)
!
!------------------------------------------------------------------------------
! Physical and output parameters. This file is configured for NBT=63.
!------------------------------------------------------------------------------
!
!  TNU2           Lateral, Laplacian, 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 to write out biological tracers into
!                    output NetCDF files, [1:NBT,1:Ngrids] values are
!                    expected.
!
!                    Hout(idTvar)     biological tracers
!                    Hout(idTsur)     biological tracers surface flux
!
