1   ATTPHY (was 0.04)   PARFRAC [0.45*24/14]    R_ATTH2O (m-1)
     0.016               0.45                   0.18
2   PHOTORM  PHOTOR0   PHOTOINH   PHIM
    27.78e-4   4.03e-6   2.01e-7   0.0
3   HSNO3     HSNH4     NO3INH
     0.1       0.1       3.5
4   NQUOTA    NO3URM    NH4URM 
     0.0       0.0       0.0  
5   PHYLR1    PHYLR2
     0.0       0.0
6   GRAZRM   CIVLEV   ZOOEXCN    ZOOEXCD
     0.50      0.14      0.33      0.33
7   ZOOLR1    ZOOLR2    ZOOLF1    ZOOLF2
     0.010     0.010     0.30      0.20
8   WSNKPHY   WSNKDET  FRACRMN   FRACPHY   FRACDET   FRNH4NO3
     0.3       0.5       0.2       0.65      0.65      0.65
9   REMNNH4   REMNDET
     0.00      0.02  
10   BIOPOS   IPMOD
      1        0
11   C2N     C2CHL   CHA2CHB   CHA2CHC   CHA2PSC   CHA2PPC
     0.15     -0.01      0.25       0.0      0.55      0.09
12   CHL2C0  CHL2C1  IR0_WM2  IR1_WM2   CHLCRATE
      100.0    120.0    0.0    1000.0    0.16666667
13  (NO3) (QN3) (ZOO) (NH4) (DET) (CHL) (QN4) (NH4PR) (NO3PR) (ZGRPHY)
      1     1     1     1     1     1     1      1       1       1    
14  ABSONAM (a80): Absorption coefficients input file, if any
/dev/null
99  END of biological parameters
 
 
                               GLOSSARY
                               --------

*** Card 1:
 
ATTPHY    phytoplankton light attenuation scale (liter umole-1 m-1).
PARFRAC   fraction of shortwave radiation that is photosynthetically
          active (nondimensional).
R_ATTH2O  Regional light attenuation scale of sea water (m-1).
          Note that clear water value is atth2o=4.0e-4 cm-1 (0.04 m-1).

*** Card 2:

PHOTORM   maximum photosynthetic rate (mgC/mgChl/sec).
PHOTOR0   initial slope of photosynthesis response to light 
          ((mgC/mgChl/sec)/(umole photons/m2/sec)).
PHOTOINH  photoinhibition parameter 
          ((mgC/mgChl/sec)/(umole photons/m2/sec)).
PHIM      maximum quantum yield (mol C/mol photons).

*** Card 3:

HSNO3     half saturation constant for nitrate uptake (umoles/l).
HSNH4     half saturation constant for ammonium uptake (umoles/l).
NO3INH    strength of ammonium inhibition of nitrate uptake (l/umoles).

*** Card 4:

NQUOTA    minimum nitrogen content for growth (umolesN/ug chl).
NO3URM    maximum nitrate uptake rate (umoles N/ug chl 1/day).
NH4URM    maximum ammonia uptake rate (umoles N/ug chl 1/day).

*** Card 5:

PHYLR1    linear phytoplankton mortality rate (1/day).
PHYLR2    quadratic phytoplankton mortality rate (1/day l/umoles).

*** Card 6:

GRAZRM    maximum phytoplankton grazing rate (1/day).
CIVLEV    Ivlev constant for zooplankton grazing of phytoplankton (l/umoles).
ZOOEXCN   fraction of zooplankton grazing that is excreted as ammonium
          (nondimensional).
ZOOEXCD   fraction of zooplankton grazing that is excreted as detritus
          (nondimensional).

*** Card 7:

ZOOLR1    linear zooplankton loss rate (1/day).
ZOOLR2    quadratic zooplankton loss rate (1/day l/umoles).
ZOOLF1    fraction of linear zooplankton loss to detritus
          (nondimensional).
ZOOLF2    fraction of quadratic zooplankton loss to detritus
          (nondimensional).

*** Card 8:

WSNKPHY   sinking rate for phytoplankton (positive down)  (m/day).
WSNKDET   sinking rate for detritus (positive down)  (m/day).
FRACRMN   fraction of the sinking phytoplankton and detritus flux that
          reaches the seafloor that remineralizes in the bottom level;
          the remainder is "buried" (nondimensional).

*** Card 9:

REMNNH4   ammonium remineralization (nitrification) timescale (1/day).
REMNDET   detritus remineralization timescale (1/day).

*** Card 10:

BIOPOS    switch to enforce positive biological fields:
            [0] do not enforce,
            [1] enforce.
          use BIOPOS only for debugging purposes
IPMOD     switch for productivity model
            [0] exponential model
            [1] hyperbolic tangent model
            [2] not used (to be Kiefer and Mitchel model)
            [3] smith et al (modified hyperbole) model
            [4] bidigare et al (spectral - phi based) model     

*** Card 11:

C2N       Nitrogen:Carbon ratio of phytoplankton (mol N/mol C).
C2CHL     Chlorophyl:Carbon ratio (mg Chl/ mg C).
CHA2CHB   Chl a to Chl b conversion (b:a ratio) (mg/mg).
CHA2CHC   Chl a to Chl c conversion (c:a ratio) (mg/mg).
CHA2PSC   Chl a to PS carotenoids (psc:a ratio) (mg/mg).
CHA2PPC   Chl a to PP carotenoids (ppc:a ratio) (mg/mg).

*** Card 12:

CHL2C0    y0 of fully-adapted Carbon:Chlorophyll ratio (mgC/mgChl)
CHL2C1    y1 of fully-adapted Carbon:Chlorophyll ratio (mgC/mgChl)
IR0_WM2   x0, irradiance corresponding to y0 (Watts meters-2)
IR1_WM2   x1, irradiance corresponding to y1 (Watts meters-2)
CHLCRATE  Photoacclimation rate for chl:c ratio (day-1)

*** Card 13: biological model output field switches:

         Convention:
         [0] do not write,
         [1] write.

IBIOUT(1) nitrate concentraction (millimoles nitrogen meter-3).
IBIOUT(2) phytoplankton nitrogen (nitrate) (millimoles nitrogen meter-3).
IBIOUT(3) zooplankton (millimoles nitrogen meter-3).
IBIOUT(4) ammonium (millimoles nitrogen meter-3).
IBIOUT(5) detritus (millimoles nitrogen meter-3).
IBIOUT(6) chlorophyll (milligrams chlorophyll meter-3).
IBIOUT(7) phytoplankton nitrogen (ammonia) (millimoles nitrogen meter-3).
IBIOUT(8) recycled (NH4) production rate (millimoles nitrogen meter-3 day-1).
IBIOUT(9) new (NO3) production rate (millimoles nitrogen meter-3 day-1).
IBIOUT(10) zooplankton grazing rate (millimoles nitrogen meter-3 day-1).

          1 millimole = 10^-3 moles
