Construction d'un nouveau modele biogeochimique bio_gsj, base sur bio_ismer,...

Construction d'un nouveau modele biogeochimique bio_gsj, base sur bio_ismer, comprenant une classe hydrocarbure et une deuxieme classe de bacteries pouvant degrader les hydrocarbures. Le traceur hydrocarbon (hcb) est calque sur le traceur nitrate auquel on a ajoute la possibilite de specifier, via la namelist bio_gsj, une vitesse vertical (settling or rising). Trois fichers namelist sont affectes par ce changement (bio, obs et bio_gsj).

nml/bio.nml

@@ -10,6 +10,7 @@
 !                  4: Fasham et al. 1990       (7 variables)
 !                  5: IOW-ERGOM MaBenE version (9 variables)
 !                  6: ISMER model              (9 variables)
+!                  7: GSJ model                (11 variables)
 !
 !  bio_eulerian    -> state variables are Eulerian (.true./.false.)
 !

nml/bio_gsj.nml

+#$Id$
+!-------------------------------------------------------------------------------
+! Fasham et al. biological model with modifications by Kuehn and Radach
+! 
+!  numc=        number of compartments for geobiochemical model
+!
+!  p1_init = initial flagellate concentration                    [mmol n/m3]
+!  p2_init = initial diatom concentration                        [mmol n/m3]
+!  z1_init = initial micro-zooplakton concentration              [mmol n/m3] 
+!  z2_init = initial meso-zooplakton concentration               [mmol n/m3] 
+!  b_init  = initial bacteria concentration                      [mmol n/m3]
+!  d_init  = initial detritus concentration                      [mmol n/m3]
+!  l_init  = initial LDON concentration                          [mmol n/m3]
+!  p0      = minimum phytoplankton concentration                 [mmol n/m3]
+!  z0      = minimum zooplakton concentration                    [mmol n/m3]
+!  b0      = minimum bacteria concentration                      [mmol n/m3]
+!  mte     = if .true. use temperature-dependent metabolic rates
+!  ca1     = temp-dependence coeff for p1
+!  ca2     = temp-dependence coeff for p2
+!  ch1     = temp-dependence coeff for z1
+!  ch2     = temp-dependence coeff for z2
+!  amratio = Mass ratio between p2 and p1
+!  hmratio = Mass ratio between z2 and z1
+!  vp1     = maximum flagellate uptake rate by flagellates       [1/day] 
+!  vp2     = maximum diatom uptake rate by diatoms               [1/day] 
+!  alpha1  = slope of the flagellate PI-curve                    [m2/(W day)] 
+!  alpha2  = slope of the diatom PI-curve                        [m2/(W day)] 
+!  inib1   = inhibition slope of the flagellate PI-curve (pos.)  [m2/(W day)]
+!  inib2   = inhibition slope of the PI-curve (pos.)             [m2/(W day)]
+!  kn1     = half sat. constant nitrate uptake by p1             [mmol n/m3]
+!  ka1     = half sat. constant ammonium uptake by p1            [mmol n/m3]
+!  kn2     = half sat. constant nitrate uptake by p2             [mmol n/m3]
+!  ka2     = half sat. constant ammonium uptake by p2            [mmol n/m3]
+!  mu11    = mortality rate for p1                               [1/day] 
+!  mu12    = mortality rate for p2                               [1/day] 
+!  k5      = half sat. constant phy. mortality                   [mmol n/m3]
+!  gamma   = exudation fraction                                  [-]
+!  w_p1    = settling velocity for p1                            [m/day]
+!  w_p2    = settling velocity for p2                            [m/day]
+!  theta   = phytoplancton buoyancy parameter                    [m3 day/(mmol N)]
+!  g1max   = maximum ingestion rate for z1                       [1/day]
+!  g2max   = maximum ingestion rate for z2                       [1/day]
+!  k3      = half saturation constant ingestion                  [mmol n/m3]
+!  beta    = grazing efficiency                                  [-]
+!  k6      = half saturation zooplankton loss (z1 & z2)          [mmol n/m3]
+!  mu21    = maximum loss rate for z1                            [1/day]
+!  mu22    = maximum loss rate for z2                            [1/day]
+!  delta   = fractional zooplankton loss to LDON (z1 & z2)       [-]
+!  epsi    = fractional zooplankton loss to ammonium (z1 & z2)   [-]
+!  r11     = z1 grazing preference on p1                         [-]
+!  r12     = z1 grazing preference on p2                         [-] 
+!  r13     = z1 grazing preference on bacteria                   [-] 
+!  r14     = z1 grazing preference on detritus                   [-] 
+!  r21     = z2 grazing preference on p1                         [-]
+!  r22     = z2 grazing preference on p2                         [-] 
+!  r23     = z2 grazing preference on detritus                   [-] 
+!  r24     = z2 grazing preference on z1                         [-] 
+!  vb      = maximum bacterial uptake rate                       [1/day]
+!  k4      = half saturation bacterial uptake                    [mmol n/m3]
+!  mu3     = bacteria excretion rate                             [1/day]  
+!  eta     = uptake ratio ammonium:LDON                          [-]  
+!  mu4     = detritus breakdown rate                             [1/day] 
+!  mu5     = nitrification rate                                  [1/day] 
+!  w_d     = detritus settling velocity                          [m/day]
+!  kc      = attenuation constant for the self shading effect    [m**2/mmol N]
+!-------------------------------------------------------------------------------
+ &bio_gsj_nml
+  numc    = 11 
+  p1_init = 0.012
+  p2_init = 0.012
+  z1_init = 0.012
+  z2_init = 0.012
+  b_init  = 0.001
+  d_init  = 0.01
+  l_init  = 0.1
+  p0      = 0.0001
+  z0      = 0.0001
+  b0      = 0.0001
+  mte     = .true.
+  ca1     = 3.61
+  ca2     = 14.58
+  ch1     = 3.265
+  ch2     = 24.923
+  amratio = 200
+  hmratio = 1000
+  vp1     = 0.02
+  vp2     = 0.8
+  alpha1  = 0.02
+  alpha2  = 0.04
+  inib1   = 0.0
+  inib2   = 0.006
+  kn1     = 1.0
+  ka1     = 0.8
+  kn2     = 1.0
+  ka2     = 0.8
+  mu11    = 0.05
+  mu12    = 0.05
+  k5      = 0.2
+  gamma   = 0.05
+  w_p1    =-0.38
+  w_p2    =-0.00
+  theta   = 0.0
+  w_p1min =-0.01
+  w_p1max =-0.10
+  w_p2min =-0.05
+  w_p2max =-0.38
+  g1max   = 1.0
+  g2max   = 1.0
+  k3      = 1.0
+  beta    = 0.625
+  mu21    = 0.3
+  mu22    = 0.3
+  k6      = 0.2
+  delta   = 0.1
+  epsi    = 0.70
+  r11     = 0.55
+  r12     = 0.30
+  r13     = 0.05
+  r14     = 0.10
+  r21     = 0.50
+  r22     = 0.30
+  r23     = 0.05
+  r24     = 0.15
+  vb      = 0.24
+  k4      = 0.5
+  k10     = 0.5
+  w_h     = 100.0
+  mu3     = 0.03
+  eta     = 0.0
+  mu4     = 0.02
+  mu5     = 0.00
+  w_d     = -5.0
+  kc      = 0.03
+ /

nml/obs.nml

@@ -63,6 +63,68 @@
   SRelaxSurf=      0.
  /
 
+!-------------------------------------------------------------------------------
+! observed or prescribed potential temperature profiles
+!
+! t_prof_method    -> method to create initial or observed temperature profiles
+!                  0: no initial values, T-equation is not solved
+!                  1: use analytically prescribed initial profile
+!                  2: read profiles at different dates from "t_prof_file"
+!                     and interpolate to GOTM timestep
+!
+! t_analyt_method  -> method to create analytically precribed inital profile
+!                  1: set profile to constant value s_1
+!                  2: set "two layer" stratification (see user's guide)
+!                  3: set profile with constant N^2 (see user's guide)
+!                     This option can only be used toghether with
+!                     s_analyt_method=1 (constant salinity).
+!
+! z_t1             -> upper layer thickness if t_analyt_method=2
+!
+! t_1              -> constant temperature     if t_analyt_method=1
+!                     upper layer temperature  if t_analyt_method=2
+!                     surface temperature      if t_analyt_method=3
+!
+! z_t2             -> depth of top of lower layer if t_analyt_method=2
+!
+! t_2              -> lower layer temperature if t_analyt_method=2
+!
+! t_obs_NN         -> constant value N^2 corresponding to temperature profile
+!                     if t_analyt_method=3
+
+! t_prof_file      -> filename of file with temperature profiles
+!                     if t_prof_method=2
+!
+! The computed profiles can be relaxed towards observed or prescribed
+! profiles with a certain relaxation time. If you do not want relaxation,
+! set the relaxation times to 1.e15 (something large). It is possible to choose
+! different relaxation times in a surface and bottom layer.
+!
+! TRelaxTauM       -> relaxation time for bulk of the flow 
+! TRelaxTauB       -> relaxation time for bottom layer 
+! TRelaxTauS       -> relaxation time for surface layer
+! TRelaxBott       -> height of bottom relaxation layer
+!                     (set to 0. if not used)
+! TRelaxSurf       -> height of surface relaxation layer
+!                     (set to 0. if not used)
+!
+!-------------------------------------------------------------------------------
+ &tprofile
+  t_prof_method=   2
+  t_analyt_method= 2
+  z_t1=            25.
+  t_1=             -1.0
+  z_t2=            35.
+  t_2=             0.0
+  t_obs_NN=        2.56e-4
+  t_prof_file=     'franklin_tprof_ctd.dat'
+  TRelaxTauM=      1209600.
+  TRelaxTauB=      1209600.
+  TRelaxTauS=      1209600.
+  TRelaxBott=      0.
+  TRelaxSurf=      0.
+ /
+
 !-------------------------------------------------------------------------------
 ! observed or prescribed nitrate profiles
 !
@@ -85,7 +147,6 @@
 !
 ! n_2              -> lower layer nitrate if n_analyt_method=2
 !
-
 ! n_prof_file      -> filename of file with nitrate profiles
 !                     if n_prof_method=2
 !
@@ -172,65 +233,57 @@
  /
 
 !-------------------------------------------------------------------------------
-! observed or prescribed potential temperature profiles
+! observed or prescribed hydrocarbon profiles
 !
-! t_prof_method    -> method to create initial or observed temperature profiles
-!                  0: no initial values, T-equation is not solved
+! hc_prof_method   -> method to create initial or observed hydroarbon profiles
+!                  0: no initial values, N-equation is not solved
 !                  1: use analytically prescribed initial profile
-!                  2: read profiles at different dates from "t_prof_file"
+!                  2: read profiles at different dates from "hc_prof_file"
 !                     and interpolate to GOTM timestep
 !
-! t_analyt_method  -> method to create analytically precribed inital profile
-!                  1: set profile to constant value s_1
+! hc_analyt_method  -> method to create analytically precribed inital profile
+!                  1: set profile to constant value hc_1
 !                  2: set "two layer" stratification (see user's guide)
-!                  3: set profile with constant N^2 (see user's guide)
-!                     This option can only be used toghether with
-!                     s_analyt_method=1 (constant salinity).
 !
-! z_t1             -> upper layer thickness if t_analyt_method=2
+! z_hc1            -> upper layer thickness if hc_analyt_method=2
 !
-! t_1              -> constant temperature     if t_analyt_method=1
-!                     upper layer temperature  if t_analyt_method=2
-!                     surface temperature      if t_analyt_method=3
+! hc_1             -> constant nitrate     if hc_analyt_method=1
+!                     upper layer nitrate  if hc_analyt_method=2
 !
-! z_t2             -> depth of top of lower layer if t_analyt_method=2
+! z_hc2            -> depth of top of lower layer if hc_analyt_method=2
 !
-! t_2              -> lower layer temperature if t_analyt_method=2
+! hc_2             -> lower layer nitrate if hc_analyt_method=2
 !
-! t_obs_NN         -> constant value N^2 corresponding to temperature profile
-!                     if t_analyt_method=3
-
-! t_prof_file      -> filename of file with temperature profiles
-!                     if t_prof_method=2
+! hc_prof_file      -> filename of file with hydrocarbon profiles
+!                     if hc_prof_method=2
 !
 ! The computed profiles can be relaxed towards observed or prescribed
 ! profiles with a certain relaxation time. If you do not want relaxation,
 ! set the relaxation times to 1.e15 (something large). It is possible to choose
 ! different relaxation times in a surface and bottom layer.
 !
-! TRelaxTauM       -> relaxation time for bulk of the flow 
-! TRelaxTauB       -> relaxation time for bottom layer 
-! TRelaxTauS       -> relaxation time for surface layer
-! TRelaxBott       -> height of bottom relaxation layer
+! HCRelaxTauM       -> relaxation time for bulk of the flow 
+! HCRelaxTauB       -> relaxation time for bottom layer 
+! HCRelaxTauS       -> relaxation time for surface layer
+! HCRelaxBott       -> height of bottom relaxation layer
 !                     (set to 0. if not used)
-! TRelaxSurf       -> height of surface relaxation layer
+! HCRelaxSurf       -> height of surface relaxation layer
 !                     (set to 0. if not used)
 !
 !-------------------------------------------------------------------------------
- &tprofile
-  t_prof_method=   2
-  t_analyt_method= 2
-  z_t1=            25.
-  t_1=             -1.0
-  z_t2=            35.
-  t_2=             0.0
-  t_obs_NN=        2.56e-4
-  t_prof_file=     'franklin_tprof_ctd.dat'
-  TRelaxTauM=      1209600.
-  TRelaxTauB=      1209600.
-  TRelaxTauS=      1209600.
-  TRelaxBott=      0.
-  TRelaxSurf=      0.
+ &hcprofile
+  hc_prof_method=   1
+  hc_analyt_method= 2
+  z_hc1=            35.
+  hc_1=             3.0
+  z_hc2=            70.
+  hc_2=             15.0
+  hc_prof_file=     'hcprof.dat'
+  HCRelaxTauM=      1.e15
+  HCRelaxTauB=      1.e15
+  HCRelaxTauS=      1.e15
+  HCRelaxBott=      0.
+  HCRelaxSurf=      0.
  /
 
 !-------------------------------------------------------------------------------

src/Makefile

-#$Id: Makefile,v 1.9 2005-08-16 14:38:37 kbk Exp $
+#Id: Makefile,v 1.9 2005-08-16 14:38:37 kbk Exp $
 #
 # Master Makefile for making the GOTM executable.
 #

src/extras/bio/Makefile

@@ -15,9 +15,11 @@ bio_iow.F90		\
 bio_sed.F90		\
 bio_fasham.F90		\
 bio_ismer.F90		\
+bio_gsj.F90             \
 bio_save.F90		\
 nitrate.F90		\
-ammonium.F90
+ammonium.F90            \
+hydrocarbon.F90
 
 OBJ   = \
 ${LIB}(bio_var.o)	\
@@ -27,11 +29,13 @@ ${LIB}(bio_npzd.o)	\
 ${LIB}(bio_iow.o)	\
 ${LIB}(bio_mab.o)	\
 ${LIB}(bio_ismer.o)	\
+${LIB}(bio_gsj.o)	\
 ${LIB}(bio_fasham.o)	\
 ${LIB}(bio_sed.o)	\
 ${LIB}(bio_save.o)	\
 ${LIB}(nitrate.o)	\
 ${LIB}(ammonium.o)	\
+${LIB}(hydrocarbon.o)	\
 ${LIB}(bio.o)
 
 all: ${OBJ}

src/extras/bio/ammonium.F90

@@ -172,6 +172,10 @@
       do i=1,nlev
          amm(i) = cc(9,i)
       end do
+   else if (bio_model.eq.7) then
+      do i=1,nlev
+         amm(i) = cc(9,i)
+      end do
    end if
 #endif
 

src/extras/bio/bio.F90

@@ -30,16 +30,19 @@
 
    use bio_fasham, only : init_bio_fasham,init_var_fasham,var_info_fasham
    use bio_fasham, only : light_fasham,do_bio_fasham
-!DD
+
    use bio_ismer, only : init_bio_ismer,init_var_ismer,var_info_ismer
    use bio_ismer, only : light_ismer,do_bio_ismer
 
-   use bio_sed, only : init_bio_sed,init_var_sed,var_info_sed
+   use bio_gsj,   only : init_bio_gsj,init_var_gsj,var_info_gsj
+   use bio_gsj,   only : light_gsj,do_bio_gsj
+
+   use bio_sed,   only : init_bio_sed,init_var_sed,var_info_sed
 
-   use bio_mab, only : init_bio_mab,init_var_mab,var_info_mab
-   use bio_mab, only : light_mab,surface_fluxes_mab,do_bio_mab
+   use bio_mab,   only : init_bio_mab,init_var_mab,var_info_mab
+   use bio_mab,   only : light_mab,surface_fluxes_mab,do_bio_mab
 
-   use output, only: out_fmt,write_results,ts
+   use output,    only: out_fmt,write_results,ts
 
    use util
 !
@@ -314,6 +317,16 @@
 
          call var_info_ismer()
 
+      case (7)  ! The GSJ model, modified from ISMER
+
+         call init_bio_gsj(namlst,'bio_gsj.nml',unit)
+
+         call allocate_memory(nlev)
+
+         call init_var_gsj(nlev)
+
+         call var_info_gsj()
+
       case default
          stop "bio: no valid biomodel specified in bio.nml !"
       end select
@@ -409,8 +422,8 @@
 ! modules
 !
 ! !INTERFACE: 
-   subroutine set_env_bio(nlev,h_,t_,s_,nit_,amm_,rho_,nuh_,rad_,wind_,I_0_, &   !CHG3-5
-                          w_,w_adv_ctr_)
+  subroutine set_env_bio(nlev,h_,t_,s_,nit_,amm_,hcb_,rho_,nuh_,rad_,wind_, &
+                          I_0_,w_,w_adv_ctr_)
 !
 ! !DESCRIPTION:
 !
@@ -423,8 +436,9 @@
    REALTYPE, intent(in)                :: nuh_(0:nlev)
    REALTYPE, intent(in)                :: t_(0:nlev)
    REALTYPE, intent(in)                :: s_(0:nlev)
-   REALTYPE, intent(in)                :: nit_(0:nlev)   !CHG3
-   REALTYPE, intent(in)                :: amm_(0:nlev)   !CHG5
+   REALTYPE, intent(in)                :: nit_(0:nlev)
+   REALTYPE, intent(in)                :: amm_(0:nlev)
+   REALTYPE, intent(in)                :: hcb_(0:nlev)
    REALTYPE, intent(in)                :: rho_(0:nlev)
    REALTYPE, intent(in)                :: rad_(0:nlev)
    REALTYPE, intent(in)                :: wind_
@@ -443,9 +457,10 @@
    h         = h_
    t         = t_
    s         = s_
-   nit       = nit_                 !CHG3
-   amm       = amm_                 !CHG5
+   nit       = nit_
+   amm       = amm_
    rho       = rho_
+   hcb       = hcb_
    nuh       = nuh_
    rad       = rad_
    wind      = wind_
@@ -565,7 +580,19 @@
       if (bio_eulerian) then
          do j=1,numcc
 
-            if      (j==1 .and. bio_model==6) then
+            if      (j==1 .and. bio_model==7) then
+               do i=1,nlev
+                  cc(j,i) = nit(i)
+               end do
+            else if (j==9 .and. bio_model==7) then
+               do i=1,nlev
+                   cc(j,i) = amm(i)
+               end do
+            else if (j==10 .and. bio_model==7) then
+               do i=1,nlev
+                   cc(j,i) = hcb(i)
+               end do
+            else if      (j==1 .and. bio_model==6) then
                do i=1,nlev
                   cc(j,i) = nit(i)
                end do
@@ -679,6 +706,9 @@
             case (6)
                call light_ismer(nlev,bioshade_feedback)
                call ode_solver(ode_method,numc,nlev,dt_eff,cc,do_bio_ismer)
+            case (7)
+               call light_gsj(nlev,bioshade_feedback)
+               call ode_solver(ode_method,numc,nlev,dt_eff,cc,do_bio_gsj)
          end select
 
       end do
@@ -772,6 +802,7 @@
    if (allocated(s))              deallocate(s)
    if (allocated(nit))            deallocate(nit)                   !CHG3
    if (allocated(amm))            deallocate(amm)                   !CHG5
+   if (allocated(hcb))            deallocate(hcb)
    if (allocated(rho))            deallocate(rho)
    if (allocated(rad))            deallocate(rad)
    if (allocated(w))              deallocate(w)
@@ -892,6 +923,12 @@
    allocate(aprof(0:nlev),stat=rc)                              !CHG5
    if (rc /= 0) stop 'init_bio(): Error allocating (aprof)'
 
+   allocate(hcb(0:nlev),stat=rc)
+   if (rc /= 0) stop 'init_bio(): Error allocating (hcb)'
+
+   allocate(hcprof(0:nlev),stat=rc)
+   if (rc /= 0) stop 'init_bio(): Error allocating (hcprof)'
+
    allocate(rho(0:nlev),stat=rc)
    if (rc /= 0) stop 'init_bio(): Error allocating (rho)'
 

src/extras/bio/bio_gsj.F90

+!$Id: bio_ismer.F90,v 1.11 2007-01-06 11:49:15 kbk Exp $
+#include"cppdefs.h"
+!-----------------------------------------------------------------------
+!BOP
+!
+! !MODULE: bio_gsj --- Modified from Fasham et al. biological model \label{sec:bio-fasham}
+!
+! !INTERFACE:
+   module bio_gsj
+!
+! !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_gsj, init_var_gsj, var_info_gsj, &
+          light_gsj, do_bio_gsj, end_bio_gsj
+!
+! !PRIVATE DATA MEMBERS:
+!
+! !REVISION HISTORY:!
+!  Original author(s): Hans Burchard & Karsten Bolding
+!
+!
+! !LOCAL VARIABLES:
+!  from a namelist
+   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
+   LOGICAL                   ::  mte     = .true.
+   REALTYPE                  ::  ca1     = 3.61
+   REALTYPE                  ::  ca2     = 14.58    
+   REALTYPE                  ::  ch1     = 3.265
+   REALTYPE                  ::  ch2     = 24.923
+   REALTYPE                  ::  amratio = 200.0
+   REALTYPE                  ::  hmratio = 1000.0
+   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                  ::  mu11    = 0.05
+   REALTYPE                  ::  mu12    = 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                  ::  mu21    = 0.3
+   REALTYPE                  ::  mu22    = 0.3
+   REALTYPE                  ::  k6      = 0.2
+   REALTYPE                  ::  delta   = 0.1
+   REALTYPE                  ::  epsi    = 0.70
+   REALTYPE                  ::  r11     = 0.55
+   REALTYPE                  ::  r12     = 0.30
+   REALTYPE                  ::  r13     = 0.05
+   REALTYPE                  ::  r14     = 0.10
+   REALTYPE                  ::  r21     = 0.50
+   REALTYPE                  ::  r22     = 0.30
+   REALTYPE                  ::  r23     = 0.05
+   REALTYPE                  ::  r24     = 0.15
+   REALTYPE                  ::  vb      = 1.2
+   REALTYPE                  ::  k4      = 0.5
+   REALTYPE                  ::  k10     = 0.5
+   REALTYPE                  ::  w_h     = 0.0
+   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
+   integer                   ::  out_unit
+   integer, parameter        ::  n=1,p1=2,p2=3,z1=4,z2=5,d=6,l=7,b1=8,a=9,hc=10,b2=11
+!EOP
+!-----------------------------------------------------------------------
+
+   contains
+
+!-----------------------------------------------------------------------
+!BOP
+!
+! !IROUTINE: Initialise the bio module
+!
+! !INTERFACE:
+   subroutine init_bio_gsj(namlst,fname,unit)
+!