1   ATTPHY (was 0.04)   PARFRAC [0.45*24/14]
     0.0                 0.77
2   PHOTORM(3.1e-4*1.1*12/24)   PHOTOR0   PHOTOINH   PHIM
    1.70e-4                     4.4e-6       0.0      0.0
3   HSNO3     HSNH4     NO3INH
     0.5       0.05      1.5
4   NQUOTA    NO3URM    NH4URM 
     0.0       0.0        0.0  
5   PHYLR1    PHYLR2
     0.063     0.0 
6   GRAZRM   CIVLEV   ZOOEXCN    ZOOEXCD
     0.69       1.0       0.25      0.04 
7   ZOOLR1    ZOOLR2    ZOOLF1    ZOOLF2
     0.11       0.52       0.75      0.5
8   WSNKPHY   WSNKDET   FRACRMN
     0.0       1.5      1.0
9   REMNNH4   REMNDET
     0.1       0.015
10   BIOPOS   IPMOD
      0         0
11   C2N     C2CHL   CHA2CHB   CHA2CHC   CHA2PSC   CHA2PPC
     0.15    0.025     0.25       0.0     0.55       0.09
12   CDZMIN   CDZMAX   CDKZ   CDKP   CDTMIN   CDTMAX   CDKT   CDSPD   CDWMAX
       5.0     600.0   0.01    5e4    -0.5     10.0   2.5e4   100.0    0.1
13  (NO3) (QN3) (ZOO) (NH4) (DET) (CHL) (QN4) (COD) (NH4PR) (NO3PR)  (1:10)
      1     1     1     1     1     1     1     1      1       1    
14  (ZGRPHY) ( )  ( )  ( )  ( )  ( )  ( )   ( )    ( )    ( )        (11:20)
       1      0    0    0    0    0    0     0      0      0    
15  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).

*** 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     Chlorophyll: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:  (Cod parameters)

CDZMIN   Cod minimum preferred depth                  (m)
CDZMAX   Cod maximum preferred depth                  (m)
CDKZ     Cod response to depth coefficient
         (unlimited response CPP option "codunlim")   (1/s)
         (limited response CPP option "codlim")       (1/cm)
CDKP     Cod response to prey coefficient
         (unlimited response CPP option "codunlim")   [(cm^2 l)/(s umole N)]
         (limited response CPP option "codlim")       [(cm l)/(umole N)]
CDTMIN   Cod minimum preferred temperature            (deg C)
CDTMAX   Cod maximum preferred temperature            (deg C)
CDKT     Cod response to temperature coefficient
         (unlimited response CPP option "codunlim")   {cm^2/[s (deg C)^2]}
         (limited response CPP option "codlim")       [cm/(deg C)^2]
CDSPD    Cod maximum cruising speed                   (cm/s)
         (only active for limited response,
          CPP option "codlim")
CDWMAX   Cod maximum vertical swimming speed          (cm/s)
            (set large to resist all upwelling)

*** Cards 13-14: biological model output field switches:

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

IBIOUT(1)     nitrate concentration (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)     cod concentration (millimoles nitrogen meter-3).
IBIOUT(9)     recycled (NH4) production rate (millimoles nitrogen meter-3 day-1)
IBIOUT(10)    new (NO3) production rate (millimoles nitrogen meter-3 day-1).
IBIOUT(11)    zooplankton grazing rate (millimoles nitrogen meter-3 day-1).
IBIOUT(12-20) not used

          1 millimole = 10^-3 moles

