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Commit 18bfc708 authored by dumoda01's avatar dumoda01
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Les changements de la revision precedente, qui permettent d'uniformiser le... 

Les changements de la revision precedente, qui permettent d'uniformiser le traitement de la lumiere entre les modules physique et biologique, ont ete appliques a tous les modeles biologiques et leurs namelists respectives.
parent aee6c9dc
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Showing with 145 additions and 26 deletions
nml/bio.nml
View file @ 18bfc708
......@@ -44,7 +44,7 @@
!-------------------------------------------------------------------------------
&bio_nml
bio_calc= .true.
bio_model= 4
bio_model= 2
bio_eulerian= .true.
cnpar= 1.0
w_adv_discr= 6
......@@ -52,5 +52,5 @@
split_factor= 1
bioshade_feedback= .true.
bio_lagrange_mean= .false.
bio_npar= 1000
bio_npar= 100000
/
nml/bio_fasham.nml
View file @ 18bfc708
......@@ -86,6 +86,4 @@
mu4= 0.02
w_d= -5.0
kc= 0.03
aa= 0.70
g2= 14.0
/
nml/bio_iow.nml 0 → 100644
View file @ 18bfc708
#$Id$
!-------------------------------------------------------------------------------
! IOW biological model according to Neumann et al. 2002 and Burchard et al. 2005
!
! numc -> number of compartments for geobiochemical model
! p1_initial -> initial diatoms concentration [mmol n/m3]
! p2_initial -> initial flagellates concentration [mmol n/m3]
! p3_initial -> initial cyanobacterias concentration [mmol n/m3]
! zo_initial -> initial zooplankton concentration [mmol n/m3]
! de_initial -> initial detritus concentration [mmol n/m3]
! am_initial -> initial ammonium concentration [mmol n/m3]
! ni_initial -> initial nitrate concentration [mmol n/m3]
! po_initial -> initial phosphate concentration [mmol p/m3]
! o2_initial -> initial oxygen concentration [mmol n/m3]
! sfl_po -> constant surface phosphate flux [mmol n/m2/d]
! sfl_am -> constant surface ammonium flux [mmol n/m2/d]
! sfl_ni -> constant surface nitrate flux [mmol n/m2/d]
! surface_flux_method -> 0: constant; 2: from file 'bio_fluxes.dat'
! fluff -> .true.: caluclate fluff layer
! fl_initial -> initial fluff concentration [mmol n/m2]
! p10= -> minimum diatoms concentration [mmol n/m3]
! p20= -> minimum flagellates concentration [mmol n/m3]
! p30= -> minimum cyanobacterias concentration [mmol n/m3]
! zo0= -> minimum zooplankton concentration [mmol n/m3]
! w_p1= -> sinking speed diatom [m/d]
! w_p2= -> sinking speed flagellates [m/d]
! w_p3= -> sinking speed cyanobacteria [m/d]
! w_de= -> sinking speed detritus [m/d]
! kc= -> attenuation constant for the self shading effect [m2/mmol N]
! i_min= -> minimum photosynthetically active radiation (PAR) [W/m2]
! r1max= -> maximum growth rate diatoms [1/d]
! r2max= -> maximum growth rate flagellates [1/d]
! r3max= -> maximum growth rate cyanobacteria [1/d]
! alpha1= -> half saturation diatoms [mmol n/m3]
! alpha2= -> half saturation flagellates [mmol n/m3]
! alpha3= -> half saturation cyanobacteria [mmol n/m3]
! lpa= -> p --> a rate (p respiration) [1/d]
! lpd= -> p --> d rate (p mortality) [1/d]
! tf= -> temperature control flagellates [deg C]
! tbg= -> temperature control cyanos [deg C]
! beta_bg= -> temperature control cyanos [1/deg C]
! g1max= -> maximum grazing rate on diatoms [1/d]
! g2max= -> maximum grazing rate on flagellates [1/d]
! g3max= -> maximum grazing rate on cyanos [1/d]
! lza= -> z --> a rate (z exkudation) [m3/d/mmol n]
! lzd= -> z --> d rate (z mortality) [m3/d/mmol n]
! iv= -> Ivlev constant [1/(mmol n/m3)3]
! topt= -> optimum temperature [deg C]
!
! lan= -> nitrification constant [1/d]
! oan= -> oxygen parameter [ - ]
! beta_an= -> temperature control [1/deg C]
!
! lda= -> detritus mineralisation constant [1/d]
! tda= -> temperature control [deg C]
! lds= -> rate of detritus sinking into sediment [m/d]
! lsa= -> rate of sediment mineralisation [1/d]
! bsa= -> temperature control of sediment mineralisation [1/deg C]
! ph1= -> release of phosphate [ - ]
! ph2= -> release of phosphate [ - ]
! pvel= -> piston velocity [m/d]
!
! sr= -> redfield ratio(p/n) [ - ]
! s1= -> reduced nitrate/oxidized detritus [ - ]
! s2= -> oxygen produktion/recycled nitrogen [ - ]
! s3= -> oyxgen produktion related to n [ - ]
! s4= -> nitrification [ - ]
!
! a0= -> osat Parameter [mmol/m**3]
! a1= -> osat Parameter [ - ]
! a2= -> osat Parameter [1/ deg C]
!-------------------------------------------------------------------------------
&bio_iow_nml
numc= 9
p1_initial= 0.1
p2_initial= 0.1
p3_initial= 0.1
zo_initial= 0.1
de_initial= 5.0
am_initial= 0.1
ni_initial= 5.0
po_initial= 0.6
o2_initial= 85.0
sfl_po= -0.055
sfl_am= -0.36
sfl_ni= -0.45
surface_flux_method= 0
fluff= .true.
fl_initial= 0.0
p10= 0.0045
p20= 0.0045
p30= 0.0045
zo0= 0.0045
w_p1= -0.5
w_p2= 0.
w_p3= 0.1
w_de= -3.
kc= 0.03
i_min= 25.
r1max= 2.0
r2max= 0.7
r3max= 0.5
alpha1= 1.35
alpha2= 0.675
alpha3= 0.5
lpa= 0.01
lpd= 0.02
tf= 10.
tbg= 14.
beta_bg= 1.
g1max= 0.5
g2max= 0.5
g3max= 0.25
lza= 0.0666666666
lzd= 0.1333333333
iv= 0.24444444
topt= 20.
lan= 0.1
oan= 0.01
beta_an= 0.11
lda= 0.003
tda= 13.
beta_da= 20.
lds= 3.5
lsa= 0.001
bsa= 0.15
ph1= 0.15
ph2= 0.1
pvel= 5.
sr= 0.0625
s1= 5.3
s2= 6.625
s3= 8.125
s4= 0.6666666666666
a0= 31.25
a1= 14.603
a2= 0.4025
/
nml/bio_npzd.nml
View file @ 18bfc708
......@@ -22,8 +22,6 @@
! rpdu= p --> d rate (p mortality), in euphotic zone [1/d]
! rpdl= p --> d rate (p mortality), below euphotic zone [1/d]
! rzd= z --> d rate (z mortality) [1/d]
! aa= used by light_npzd
! g2= used by light_npzd
!-------------------------------------------------------------------------------
&bio_npzd_nml
numc= 4
......@@ -49,6 +47,4 @@
rpdu= 0.02
rpdl= 0.1
rzd= 0.02
aa= 0.62
g2= 20.0
/
src/extras/bio/bio_fasham.F90
View file @ 18bfc708
......@@ -145,8 +145,6 @@
REALTYPE :: mu4 = 0.02
REALTYPE :: w_d = -2.0
REALTYPE, public :: kc = 0.03
! REALTYPE :: aa = 0.70
! REALTYPE :: g2 = 14.0
integer :: out_unit
integer, parameter :: p=1,z=2,b=3,d=4,n=5,a=6,l=7
!EOP
......@@ -221,10 +219,6 @@
write(10,901) w_pmin
write(*,900) ' w_pmax = ',w_pmax
write(10,901) w_pmax
write(*,900) ' A = ',A
write(10,901) A
write(*,900) ' g2 = ',g2
write(10,901) g2
900 format (a,f8.5)
901 format (f8.5)
......
src/extras/bio/bio_iow.F90
View file @ 18bfc708
......@@ -58,6 +58,7 @@
! !USES:
! default: all is private.
use bio_var
use observations, only : aa,g2
private
!
! !PUBLIC MEMBER FUNCTIONS:
......@@ -212,8 +213,6 @@
REALTYPE :: a0=31.25
REALTYPE :: a1=14.603
REALTYPE :: a2=0.4025
REALTYPE :: aa=0.62
REALTYPE :: g2=20.0
integer :: out_unit
integer, parameter :: p1=1,p2=2,p3=3,zo=4,de=5, &
am=6,ni=7,po=8,o2=9,fl=10
......@@ -257,7 +256,7 @@
alpha3,lpa,lpd,tf,tbg,beta_bg,g1max,g2max, &
g3max,lza,lzd,iv,topt,lan,oan,beta_an,lda, &
tda,beta_da,lds,lsa,bsa,ph1,ph2,pvel,sr, &
s1,s2,s3,s4,a0,a1,a2,aa,g2
s1,s2,s3,s4,a0,a1,a2
!EOP
!-----------------------------------------------------------------------
!BOC
......
src/extras/bio/bio_mab.F90
View file @ 18bfc708
......@@ -15,6 +15,7 @@
! !USES:
! default: all is private.
use bio_var
use observations, only : aa,g2
private
!
! !PUBLIC MEMBER FUNCTIONS:
......@@ -92,8 +93,6 @@
REALTYPE :: a0=31.25
REALTYPE :: a1=14.603
REALTYPE :: a2=0.4025
REALTYPE :: aa=0.62
REALTYPE :: g2=20.0
integer :: out_unit
integer, parameter :: p1=1,p2=2,p3=3,zo=4,de=5, &
am=6,ni=7,po=8,o2=9,se=10,fl=11
......@@ -138,7 +137,7 @@
alpha3,lpa,lpd,tf,tbg,beta_bg,g1max,g2max, &
g3max,lza,lzd,iv,topt,lan,oan,beta_an,lda, &
tda,beta_da,lds,lsa,bsa,ph1,ph2,pvel,sr, &
s1,s2,s3,s4,a0,a1,a2,aa,g2
s1,s2,s3,s4,a0,a1,a2
!EOP
!-----------------------------------------------------------------------
!BOC
......
src/extras/bio/bio_npzd.F90
View file @ 18bfc708
......@@ -27,6 +27,7 @@
! default: all is private.
use bio_var
use output
use observations, only : aa,g2
private
!
! !PUBLIC MEMBER FUNCTIONS:
......@@ -109,8 +110,6 @@
REALTYPE :: rpdl=1.157407e-06
REALTYPE :: rpd
REALTYPE :: rzd=2.314814e-07
REALTYPE :: aa=0.62
REALTYPE :: g2=20.0
integer :: out_unit
integer, parameter :: n=1,p=2,z=3,d=4
!EOP
......@@ -176,10 +175,6 @@
write(11,901) inib
write(*,900) ' k1 = ',k1
write(11,901) k1
write(*,900) ' aa = ',aa
write(11,901) aa
write(*,900) ' g2 = ',g2
write(11,901) g2
900 format (a,f8.5)
901 format (f8.5)
......
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