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src/extras/bio/bio_ismer.F90 20.5 KB
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!$Id: bio_ismer.F90,v 1.11 2007-01-06 11:49:15 kbk Exp $
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#include"cppdefs.h"
!-----------------------------------------------------------------------
!BOP
!
! !MODULE: bio_ismer --- Modified from Fasham et al. biological model \label{sec:bio-fasham}
!
! !INTERFACE:
   module bio_ismer
!
! !DESCRIPTION:
!  The model developed by \cite{Fashametal1990} 
!  uses nitrogen as 'currency' according to the evidence that in
!  most cases nitrogen is the limiting macronutrient. It consists of
!  seven state variables: phytoplankton, zooplankton, bacteria,
!  particulate organic matter (detritus), dissolved organic matter
!  and the nutrients nitrate and ammonium.
!  The structure of the \cite{Fashametal1990} biogeochemical model
!  is given in figure \ref{fig_fasham}.
! \begin{figure}
! \begin{center}
! \scalebox{0.5}{\includegraphics{figures/fasham_structure.eps}}
! \caption{Structure of the \cite{Fashametal1990} model with bacteria (bac),
! phytoplankton (phy), detritus (det), zooplankton (zoo), labile dissolved
! organic nitrogen (don), ammonium (amm) and nitrate (nit) as the seven
! state variables.
! The concentrations are in mmol N\,m$^{-3}$,
! all fluxes (green arrows) are conservative.
! }\label{fig_fasham}
! \end{center}
! \end{figure}
!  A detailed mathematical description of all
!  processes is given in section \ref{sec:bio-fasham-rhs}.
!  The version of the \cite{Fashametal1990} model which is implemented includes
!  slight modifications by \cite{KuehnRadach1997} and has been 
!  included into GOTM by \cite{Burchardetal05}. 

! !USES:
!  default: all is private.
   use bio_var
   use output
   use observations, only : aa,g2
   private
!
! !PUBLIC MEMBER FUNCTIONS:
   public init_bio_ismer, init_var_ismer, var_info_ismer, &
          light_ismer, do_bio_ismer, end_bio_ismer
!
! !PRIVATE DATA MEMBERS:
!
! !REVISION HISTORY:!
!  Original author(s): Hans Burchard & Karsten Bolding
!
!
! !LOCAL VARIABLES:
!  from a namelist
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   REALTYPE                  ::  p1_init = 0.05
   REALTYPE                  ::  p2_init = 0.05
   REALTYPE                  ::  z1_init = 0.05
   REALTYPE                  ::  z2_init = 0.05
   REALTYPE                  ::  b_init  = 0.001
   REALTYPE                  ::  d_init  = 0.4
   REALTYPE                  ::  l_init  = 0.14
   REALTYPE                  ::  p0      = 0.0
   REALTYPE                  ::  z0      = 0.0
   REALTYPE                  ::  b0      = 0.0
   REALTYPE                  ::  vp1     = 1.5
   REALTYPE                  ::  alpha1  = 0.065
   REALTYPE                  ::  inib1   = 0.05
   REALTYPE                  ::  vp2     = 1.5
   REALTYPE                  ::  alpha2  = 0.065
   REALTYPE                  ::  inib2   = 0.05
   REALTYPE                  ::  theta   = 0.0
   REALTYPE                  ::  w_p1min = -0.06
   REALTYPE                  ::  w_p1max = -0.38
   REALTYPE                  ::  w_p2min = -0.06
   REALTYPE                  ::  w_p2max = -0.38
   REALTYPE                  ::  kn1     = 0.2
   REALTYPE                  ::  ka1     = 0.8
   REALTYPE                  ::  kn2     = 0.2
   REALTYPE                  ::  ka2     = 0.8
   REALTYPE                  ::  mu1     = 0.05
   REALTYPE                  ::  k5      = 0.2
   REALTYPE                  ::  gamma   = 0.05
   REALTYPE                  ::  w_p1    = -0.5
   REALTYPE                  ::  w_p2    = -0.5
   REALTYPE                  ::  g1max   = 1.0
   REALTYPE                  ::  g2max   = 1.0
   REALTYPE                  ::  k3      = 1.0
   REALTYPE                  ::  beta    = 0.625
   REALTYPE                  ::  mu2     = 0.3
   REALTYPE                  ::  k6      = 0.2
   REALTYPE                  ::  delta   = 0.1
   REALTYPE                  ::  epsi    = 0.70
   REALTYPE                  ::  r11     = 0.55
   REALTYPE                  ::  r12     = 0.4
   REALTYPE                  ::  r13     = 0.05
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   REALTYPE                  ::  r21     = 0.50
   REALTYPE                  ::  r22     = 0.30
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   REALTYPE                  ::  r23     = 0.05
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   REALTYPE                  ::  r24     = 0.15
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   REALTYPE                  ::  vb      = 1.2
   REALTYPE                  ::  k4      = 0.5
   REALTYPE                  ::  mu3     = 0.15
   REALTYPE                  ::  eta     = 0.0
   REALTYPE                  ::  mu4     = 0.02
   REALTYPE                  ::  mu5     = 0.00
   REALTYPE                  ::  w_d     = -2.0
   REALTYPE, public          ::  kc      = 0.03
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   integer                   ::  out_unit
   integer, parameter        ::  n=1,p1=2,p2=3,z1=4,z2=5,d=6,l=7,b=8,a=9
!EOP
!-----------------------------------------------------------------------

   contains

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Initialise the bio module
!
! !INTERFACE:
   subroutine init_bio_ismer(namlst,fname,unit)
!
! !DESCRIPTION:
!  Here, the bio namelist {\tt bio\_fasham.nml} is read and
!  various variables (rates and settling velocities)
!  are transformed into SI units.
!
! !USES:
   IMPLICIT NONE
!
! !INPUT PARAMETERS:
   integer,          intent(in)   :: namlst
   character(len=*), intent(in)   :: fname
   character(len=20)              :: pfile
   integer,          intent(in)   :: unit
!
! !REVISION HISTORY:
!  Original author(s): Hans Burchard & Karsten Bolding
!
! !LOCAL VARIABLES:
   namelist /bio_ismer_nml/ numc, &
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                        p1_init,p2_init,z1_init,z2_init,                 &
                        b_init,d_init,l_init,                            &
                        p0,z0,b0,vp1,alpha1,inib1,vp2,alpha2,inib2,      &
                        kn1,ka1,kn2,ka2,mu1,k5,gamma,w_p1,w_p2,          &
                        g1max,g2max,k3,beta,mu2,k6,delta,epsi,           &
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                        r11,r12,r13,r21,r22,r23,r24,                     &
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                        vb,k4,mu3,eta,mu4,w_d,kc,mu5,                    &
                        theta,w_p1max,w_p1min,w_p2min,w_p2max
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!EOP
!-----------------------------------------------------------------------
!BOC
   LEVEL2 'init_bio_ismer'

   open(namlst,file=fname,action='read',status='old',err=98)
   read(namlst,nml=bio_ismer_nml,err=99)
   close(namlst)

   numcc=numc

! Print some parameter values in standard output
! and save them in a separate file [out_fn]_ismer.par
   pfile = trim(out_fn) // '_ismer.par'
   open(10,status='unknown',action='write',file=pfile)
   LEVEL3 'ISMER parameters saved in ', pfile
!   write(*,900) '                vp     = ',vp
!   write(10,901) vp
!   write(*,900) '                alpha  = ',alpha
!   write(10,901) alpha
!   write(*,900) '                inib   = ',inib
!   write(10,901) inib

900 format (a,f8.5)
901 format (f8.5)

!  Conversion from day to second
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   vp1     = vp1     /secs_pr_day
   vp2     = vp2     /secs_pr_day
   vb      = vb      /secs_pr_day
   mu1     = mu1     /secs_pr_day
   mu2     = mu2     /secs_pr_day
   mu3     = mu3     /secs_pr_day
   mu4     = mu4     /secs_pr_day
   mu5     = mu5     /secs_pr_day
   g1max   = g1max   /secs_pr_day
   g2max   = g2max   /secs_pr_day
   w_p1    = w_p1    /secs_pr_day
   w_p2    = w_p2    /secs_pr_day
   w_p1min = w_p1min /secs_pr_day
   w_p1max = w_p1max /secs_pr_day
   w_p2min = w_p2min /secs_pr_day
   w_p2max = w_p2max /secs_pr_day
   theta   = theta   /secs_pr_day
   w_d     = w_d     /secs_pr_day
   alpha1  = alpha1  /secs_pr_day
   inib1   = inib1   /secs_pr_day
   alpha2  = alpha2  /secs_pr_day
   inib2   = inib2   /secs_pr_day
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   out_unit=unit

   LEVEL3 'ISMER bio module initialised ...'

   return

98 LEVEL2 'I could not open bio_ismer.nml'
   LEVEL2 'If thats not what you want you have to supply bio_ismer.nml'
   LEVEL2 'See the bio example on www.gotm.net for a working bio_ismer.nml'
   return
99 FATAL 'I could not read bio_ismer.nml'
   stop 'init_bio_ismer'
   end subroutine init_bio_ismer
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Initialise the concentration variables
!
! !INTERFACE:
   subroutine init_var_ismer(nlev)
!
! !DESCRIPTION:
!  Here, the the initial conditions are set and the settling velocities are
!  transferred to all vertical levels. All concentrations are declared
!  as non-negative variables, and it is defined which variables would be
!  taken up by benthic filter feeders.
!
! !USES:
   use observations,    only: nprof,aprof               !CHG3-5
   use meanflow,        only: nit,amm,T,S               !CHG3-5

   IMPLICIT NONE

!
! !INPUT PARAMETERS:
   integer, intent(in)                 :: nlev
!
! !REVISION HISTORY:
!  Original author(s): Hans Burchard & Karsten Bolding

! !LOCAL VARIABLES:
  integer                    :: i
!EOP
!-----------------------------------------------------------------------
!BOC
   do i=1,nlev
      cc(n,i) = nprof(i)                                  !CHG3
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      cc(p1,i)= p1_init
      cc(p2,i)= p2_init
      cc(z1,i)= z1_init
      cc(z2,i)= z2_init
      cc(d,i) = d_init
      cc(l,i) = l_init
      cc(b,i) = b_init
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      cc(a,i) = aprof(i)                                  !CHG5
   end do

   do i=0,nlev
      ws(n,i)  = _ZERO_
      ws(p1,i) = w_p1
      ws(p2,i) = w_p2
      ws(z1,i) = _ZERO_
      ws(z2,i) = _ZERO_
      ws(d,i)  = w_d
      ws(l,i)  = _ZERO_
      ws(b,i)  = _ZERO_
      ws(a,i)  = _ZERO_
   end do

   posconc(n)  = 1
   posconc(p1) = 1
   posconc(p2) = 1
   posconc(z1) = 1
   posconc(z2) = 1
   posconc(d)  = 1
   posconc(l)  = 1
   posconc(b)  = 1
   posconc(a)  = 1

   LEVEL3 'ISMER variables initialised ...'

   return

   end subroutine init_var_ismer
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Providing info on variables
!
! !INTERFACE:
   subroutine var_info_ismer()
!
! !DESCRIPTION:
!  This subroutine provides information about the variable names as they
!  will be used when storing data in NetCDF files.
!
! !USES:
   IMPLICIT NONE
!
! !REVISION HISTORY:
!  Original author(s): Hans Burchard & Karsten Bolding
!
! !LOCAL VARIABLES:
!EOP
!-----------------------------------------------------------------------
!BOC
   var_names(1) = 'nit'
   var_units(1) = 'mmol/m**3'
   var_long(1)  = 'nitrate'

   var_names(2) = 'fla'
   var_units(2) = 'mmol/m**3'
   var_long(2)  = 'flagellates'

   var_names(3) = 'dia'
   var_units(3) = 'mmol/m**3'
   var_long(3)  = 'diatoms'

   var_names(4) = 'mcz'
   var_units(4) = 'mmol/m**3'
   var_long(4)  = 'micro-zooplankton'

   var_names(5) = 'msz'
   var_units(5) = 'mmol/m**3'
   var_long(5)  = 'meso-zooplankton'

   var_names(6) = 'det'
   var_units(6) = 'mmol/m**3'
   var_long(6)  = 'detritus'

   var_names(7) = 'ldn'
   var_units(7) = 'mmol/m**3'
   var_long(7)  = 'labile_dissolved_organic_nitrogen'

   var_names(8) = 'bac'
   var_units(8) = 'mmol/m**3'
   var_long(8)  = 'bacteria'

   var_names(9) = 'amm'
   var_units(9) = 'mmol/m**3'
   var_long(9)  = 'ammonium'

   return
   end subroutine var_info_ismer
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Light properties for the ISMER model
!
! !INTERFACE:
   subroutine light_ismer(nlev,bioshade_feedback)
!
! !DESCRIPTION:
! Here, the photosynthetically available radiation is calculated
! by simply assuming that the short wave part of the total
! radiation is available for photosynthesis. 
! The photosynthetically
! available radiation, $I_{PAR}$, follows from (\ref{light}).
! The user should make
! sure that this is consistent with the light class given in the
! {\tt extinct} namelist of the {\tt obs.nml} file.
! The self-shading effect is also calculated in this subroutine,
! which may be used to consider the effect of bio-turbidity also
! in the temperature equation (if {\tt bioshade\_feedback} is set
! to true in {\tt bio.nml}).
! For details, see section \ref{sec:do-bio}.
!
! !USES:
   IMPLICIT NONE
!
! !INPUT PARAMETERS:
  integer, intent(in)                  :: nlev
  logical, intent(in)                  :: bioshade_feedback
!
! !REVISION HISTORY:
!  Original author(s): Hans Burchard, Karsten Bolding
!
! !LOCAL VARIABLES:
   integer                   :: i
   REALTYPE                  :: zz,add
!EOP
!-----------------------------------------------------------------------
!BOC
   zz = _ZERO_
   add = _ZERO_
   do i=nlev,1,-1
      add=add+0.5*h(i)*(cc(p1,i)+cc(p2,i)+p0)
      zz=zz+0.5*h(i)
      par(i)=rad(nlev)*(1.-aa)*exp(-zz/g2)*exp(-kc*add)
      add=add+0.5*h(i)*(cc(p1,i)+cc(p2,i)+p0)
      zz=zz+0.5*h(i)
      if (bioshade_feedback) bioshade_(i)=exp(-kc*add)
   end do


   return
   end subroutine light_ismer
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Right hand sides of geobiochemical model \label{sec:bio-fasham-rhs}
!
! !INTERFACE:
   subroutine do_bio_ismer(first,numc,nlev,cc,pp,dd)
!
! !DESCRIPTION:
! 
! The \cite{Fashametal1990} model consisting of the $I=7$
! state variables phytoplankton, bacteria, detritus, zooplankton, 
! nitrate, ammonium and dissolved organic nitrogen is described here
! in detail.
! 
! Phytoplankton mortality and zooplankton grazing loss of phytoplankton:
! \begin{equation}\label{d13}
! d_{1,3} = \mu_1 \frac{c_1+c_{1}^{\min}}{K_5+c_1+c_{1}^{\min}}c_1+
! (1-\beta)\frac{g\rho_1 c_1^2}{K_3 \sum_{j=1}^3 \rho_jc_j
! + \sum_{j=1}^3 \rho_jc_j^2} (c_4+c_{4}^{\min}).
! \end{equation}
! Phytoplankton loss to LDON (labile dissolved organic nitrogen):
! \begin{equation}\label{d17}
! d_{1,7} = \gamma
! F(I_{PAR})\frac{\frac{c_5}{K_1}
! +\frac{c_6}{K_2}}{1+\frac{c_5}{K_1}+\frac{c_6}{K_2}}c_1,
! \end{equation}
! with
! \begin{equation}\label{FI}
!  F(I_{PAR}) = \frac{V_p\alpha I_{PAR}(z)}{\left(V_p^2+\alpha^2(I_{PAR}(z))^2 
! \right)^{1/2}}.
! \end{equation}
! With $I_{PAR}$ from (\ref{light}). 
! 
! Zooplankton grazing loss:
! \begin{equation}\label{di3}
! d_{2,3} = (1-\beta)\frac{g\rho_2 c_2^2}{K_3 \sum_{j=1}^3 \rho_jc_j 
! + \sum_{j=1}^3 \rho_jc_j^2} (c_4+c_{4}^{\min}).
! \end{equation}
! Zooplankton grazing:
! \begin{equation}\label{di4}
! d_{i,4} = \beta\frac{g\rho_i c_i^2}{K_3 \sum_{j=1}^3 \rho_jc_j 
! + \sum_{j=1}^3 \rho_jc_j^2} (c_4+c_{4}^{\min}), \quad i=1,\dots,3.
! \end{equation}
! Bacteria excretion rate:
! \begin{equation}\label{d26}
! d_{2,6} = \mu_3 c_2.
! \end{equation}
! Detritus breakdown rate:
! \begin{equation}\label{d37}
! d_{3,7} = \mu_4 c_3.
! \end{equation}
! Zooplankton losses to detritus, ammonium and LDON:
! \begin{equation}\label{d43}
! d_{4,3} = (1-\epsilon-\delta)\mu_2 
! \frac{c_4+c_{4}^{\min}}{K_6+c_4+c_{4}^{\min}}c_4.
! \end{equation}
! \begin{equation}\label{d46}
! d_{4,6} = \epsilon\mu_2 \frac{c_4+c_{4}^{\min}}{K_6+c_4+c_{4}^{\min}}c_4.
! \end{equation}
! \begin{equation}\label{d47}
! d_{4,7} = \delta\mu_2 \frac{c_4+c_{4}^{\min}}{K_6+c_4+c_{4}^{\min}}c_4.
! \end{equation}
! Nitrate uptake by phytoplankton:
! \begin{equation}\label{d51}
! d_{5,1} = F(I_{PAR})\frac{\frac{c_5}{K_1}}{1+\frac{c_5}{K_1}
! +\frac{c_6}{K_2}}(c_1+c_{1}^{\min}).
! \end{equation}
! Ammonium uptake by phytoplankton:
! \begin{equation}\label{d61}
! d_{6,1} = F(I_{PAR})\frac{\frac{c_6}{K_2}}{1+\frac{c_5}{K_1}
! +\frac{c_6}{K_2}}(c_1+c_{1}^{\min}).
! \end{equation}
! Ammonium uptake by bacteria:
! \begin{equation}\label{d62}
! d_{6,2} = V_b \frac{\min(c_6,\eta c_7)}{K_4+\min(c_6,\eta c_7)+c_7} 
! (c_2+c_{2}^{\min}).
! \end{equation}
! LDON uptake by bacteria:
! \begin{equation}\label{d72}
! d_{7,2} = V_b \frac{c_7}{K_4+\min(c_6,\eta c_7)+c_7} (c_2+c_{2}^{\min}).
! \end{equation}
!
! !USES:
   IMPLICIT NONE
!
! !INPUT PARAMETERS:
   logical, intent(in)                 :: first
   integer, intent(in)                 :: numc,nlev
   REALTYPE, intent(in)                :: cc(1:numc,0:nlev)
!
! !OUTPUT PARAMETERS:
   REALTYPE, intent(out)               :: pp(1:numc,1:numc,0:nlev)
   REALTYPE, intent(out)               :: dd(1:numc,1:numc,0:nlev)
!
! !REVISION HISTORY:
!  Original author(s): Hans Burchard, Karsten Bolding
!
! !LOCAL VARIABLES:
   REALTYPE                   :: fac1,fac2,fac3,minal,qn1,qa1,qn2,qa2
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   REALTYPE                   :: ps1,ps2,ff1,ff2                    !CHG1
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   integer                    :: i,j,ci
!EOP
!-----------------------------------------------------------------------
!BOC
!KBK - is it necessary to initialise every time - expensive in a 3D model
   pp = _ZERO_
   dd = _ZERO_

   do ci=1,nlev

!CHG1
! Smith (1936) - saturation (default)
!      ff= vp*alpha*par(ci)/sqrt(vp**2+alpha**2*par(ci)**2)
! Blackman (1919)
!      if (par(ci) .lt. vp/alpha) then
!          ff=alpha*par(ci)
!      else
!          ff=vp
!      endif       
! Steele (1962) - inhibition
!      ff= vp*((par(ci)/I_opt)*exp(1-(par(ci)/I_opt)))
! Parker (1974) - inhibition
!      ff= vp*((par(ci)/I_opt)*exp(1-(par(ci)/I_opt)))**2
! Platt et al. (1980) - inhibition
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      ! Light limitation factor (PI curve)
      ps1= vp1/((alpha1/(alpha1+inib1))*(alpha1/(alpha1+inib1))**(inib1/alpha1))
      ff1= ps1*(1.-exp(-1.*alpha1*par(ci)/ps1))*exp(-1.*inib1*par(ci)/ps1)
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      ps2= vp2/((alpha2/(alpha2+inib2))*(alpha2/(alpha2+inib2))**(inib2/alpha2))
      ff2= ps2*(1.-exp(-1.*alpha2*par(ci)/ps2))*exp(-1.*inib2*par(ci)/ps2)

      ! Nutrient limitation factors
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      qn1=(cc(n,ci)/kn1)/(1.+cc(n,ci)/kn1+cc(a,ci)/ka1)
      qa1=(cc(a,ci)/ka1)/(1.+cc(n,ci)/kn1+cc(a,ci)/ka1)

      qn2=(cc(n,ci)/kn2)/(1.+cc(n,ci)/kn2+cc(a,ci)/ka2)
      qa2=(cc(a,ci)/ka2)/(1.+cc(n,ci)/kn2+cc(a,ci)/ka2)

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      ! Grazing preference normalization factors
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      fac1=(cc(z1,ci)+z0)/(k3*(r11*cc(p1,ci)+r12*cc(b,ci)+r13*cc(d,ci))+  &
                      r11*cc(p1,ci)**2+r12*cc(b,ci)**2+r13*cc(d,ci)**2)

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      fac2=(cc(z2,ci)+z0)/(k3*(r21*cc(p1,ci)+r22*cc(p2,ci)                &
                     +r23*cc(d,ci)+r24*cc(z1,ci))                         &
                     +r21*cc(p1,ci)**2+r22*cc(p2,ci)**2                   &
                     +r23*cc(d,ci)**2+r24*cc(z1,ci)**2)
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      minal=min(cc(a,ci),eta*cc(l,ci))
      
      ! Temperature-dependent function for zooplankton grazing (for test purposes)
      ! This function should come from thermodynamical arguments
      !fac3 = max(0.0,tanh(0.5*(T(ci)+1.9)))
      fac3 = 1.0

      ! Light and nutrient limitation factors
      lumlim(ci) =ff1
      nitlim(ci) =qn1
      ammlim(ci) =qa1
      
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      ! Nutrient uptake by flagellates and diatoms 
      dd(n,p1,ci) =ff1*qn1*(cc(p1,ci)+p0)
      dd(a,p1,ci) =ff1*qa1*(cc(p1,ci)+p0)
      dd(n,p2,ci) =ff2*qn2*(cc(p2,ci)+p0)
      dd(a,p2,ci) =ff2*qa2*(cc(p2,ci)+p0)

      dd(p1,l,ci) =gamma*ff1*(qn1+qa1)*cc(p1,ci)
      dd(p2,l,ci) =gamma*ff2*(qn2+qa2)*cc(p2,ci)
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      dd(p1,d,ci) =mu1*(cc(p1,ci)+p0)/(k5+cc(p1,ci)+p0)*cc(p1,ci)  &
                   +fac3*(1.-beta)*cc(p1,ci)**2*(g1max*r11*fac1+g2max*r21*fac2)
      dd(p2,d,ci) =mu1*(cc(p2,ci)+p0)/(k5+cc(p2,ci)+p0)*cc(p2,ci)  &
                   +fac3*(1.-beta)*g2max*r21*cc(p2,ci)**2*fac2
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      dd(b,d,ci)  =fac3*(1.-beta)*g1max*r12*cc(b,ci)**2*fac1
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      dd(p1,z1,ci)=fac3*beta*g1max*r11*cc(p1,ci)**2*fac1
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      dd(b,z1,ci) =fac3*beta*g1max*r12*cc(b,ci)**2*fac1
      dd(d,z1,ci) =fac3*beta*g1max*r13*cc(d,ci)**2*fac1
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      dd(p1,z2,ci)=fac3*beta*g2max*r21*cc(p1,ci)**2*fac2
      dd(p2,z2,ci)=fac3*beta*g2max*r22*cc(p2,ci)**2*fac2
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      dd(d,z2,ci) =fac3*beta*g2max*r23*cc(d,ci)**2*fac2
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      dd(z1,z2,ci)=fac3*beta*g2max*r24*cc(z1,ci)**2*fac2
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      dd(b,a,ci)  =mu3*cc(b,ci)
      dd(d,l,ci)  =mu4*cc(d,ci)
      dd(a,n,ci)  =mu5*cc(a,ci)
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      dd(z1,d,ci) =(1.-epsi-delta)*mu2*(cc(z1,ci)+z0)/(k6+cc(z1,ci)+z0)*cc(z1,ci)
      dd(z1,a,ci) =epsi*mu2*(cc(z1,ci)+z0)/(k6+cc(z1,ci)+z0)*cc(z1,ci)
      dd(z1,l,ci) =delta*mu2*(cc(z1,ci)+z0)/(k6+cc(z1,ci)+z0)*cc(z1,ci)
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      dd(z2,d,ci) =(1.-epsi-delta)*mu2*(cc(z2,ci)+z0)/(k6+cc(z2,ci)+z0)*cc(z2,ci)
      dd(z2,a,ci) =epsi*mu2*(cc(z2,ci)+z0)/(k6+cc(z2,ci)+z0)*cc(z2,ci)
      dd(z2,l,ci) =delta*mu2*(cc(z2,ci)+z0)/(k6+cc(z2,ci)+z0)*cc(z2,ci)
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      dd(a,b,ci)  =vb*minal/(k4+minal+cc(l,ci))*(cc(b,ci)+b0)
      dd(l,b,ci)  =vb*cc(l,ci)/(k4+minal+cc(l,ci))*(cc(b,ci)+b0)
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      do i=1,numc
         do j=1,numc
            pp(i,j,ci)=dd(j,i,ci)
         end do
      end do
   end do

   return
   end subroutine do_bio_ismer
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Finish the bio calculations
!
! !INTERFACE:
   subroutine end_bio_ismer
!
! !DESCRIPTION:
!  Nothing done yet --- supplied for completeness.
!
! !USES:
   IMPLICIT NONE
!
! !REVISION HISTORY:
!  Original author(s): Hans Burchard & Karsten Bolding
!
!EOP
!-----------------------------------------------------------------------
!BOC

   return
   end subroutine end_bio_ismer
!EOC

!-----------------------------------------------------------------------

   end module bio_ismer

!-----------------------------------------------------------------------
! Copyright by the GOTM-team under the GNU Public License - www.gnu.org
!-----------------------------------------------------------------------