Commit 18bfc708ded2007b0beeebba8cffbba85e1b0872

Authored by dumoda01
1 parent aee6c9dc
Exists in master and in 1 other branch snow

Les changements de la revision precedente, qui permettent d'uniformiser le trait…

…ement de la lumiere entre les modules physique et biologique, ont ete appliques a tous les modeles biologiques et leurs namelists respectives.
nml/bio.nml
... ... @@ -44,7 +44,7 @@
44 44 !-------------------------------------------------------------------------------
45 45 &bio_nml
46 46 bio_calc= .true.
47   - bio_model= 4
  47 + bio_model= 2
48 48 bio_eulerian= .true.
49 49 cnpar= 1.0
50 50 w_adv_discr= 6
... ... @@ -52,5 +52,5 @@
52 52 split_factor= 1
53 53 bioshade_feedback= .true.
54 54 bio_lagrange_mean= .false.
55   - bio_npar= 1000
  55 + bio_npar= 100000
56 56 /
... ...
nml/bio_fasham.nml
... ... @@ -86,6 +86,4 @@
86 86 mu4= 0.02
87 87 w_d= -5.0
88 88 kc= 0.03
89   - aa= 0.70
90   - g2= 14.0
91 89 /
... ...
nml/bio_iow.nml 0 → 100644
... ... @@ -0,0 +1,138 @@
  1 +#$Id$
  2 +!-------------------------------------------------------------------------------
  3 +! IOW biological model according to Neumann et al. 2002 and Burchard et al. 2005
  4 +!
  5 +! numc -> number of compartments for geobiochemical model
  6 +! p1_initial -> initial diatoms concentration [mmol n/m3]
  7 +! p2_initial -> initial flagellates concentration [mmol n/m3]
  8 +! p3_initial -> initial cyanobacterias concentration [mmol n/m3]
  9 +! zo_initial -> initial zooplankton concentration [mmol n/m3]
  10 +! de_initial -> initial detritus concentration [mmol n/m3]
  11 +! am_initial -> initial ammonium concentration [mmol n/m3]
  12 +! ni_initial -> initial nitrate concentration [mmol n/m3]
  13 +! po_initial -> initial phosphate concentration [mmol p/m3]
  14 +! o2_initial -> initial oxygen concentration [mmol n/m3]
  15 +! sfl_po -> constant surface phosphate flux [mmol n/m2/d]
  16 +! sfl_am -> constant surface ammonium flux [mmol n/m2/d]
  17 +! sfl_ni -> constant surface nitrate flux [mmol n/m2/d]
  18 +! surface_flux_method -> 0: constant; 2: from file 'bio_fluxes.dat'
  19 +! fluff -> .true.: caluclate fluff layer
  20 +! fl_initial -> initial fluff concentration [mmol n/m2]
  21 +! p10= -> minimum diatoms concentration [mmol n/m3]
  22 +! p20= -> minimum flagellates concentration [mmol n/m3]
  23 +! p30= -> minimum cyanobacterias concentration [mmol n/m3]
  24 +! zo0= -> minimum zooplankton concentration [mmol n/m3]
  25 +! w_p1= -> sinking speed diatom [m/d]
  26 +! w_p2= -> sinking speed flagellates [m/d]
  27 +! w_p3= -> sinking speed cyanobacteria [m/d]
  28 +! w_de= -> sinking speed detritus [m/d]
  29 +! kc= -> attenuation constant for the self shading effect [m2/mmol N]
  30 +! i_min= -> minimum photosynthetically active radiation (PAR) [W/m2]
  31 +! r1max= -> maximum growth rate diatoms [1/d]
  32 +! r2max= -> maximum growth rate flagellates [1/d]
  33 +! r3max= -> maximum growth rate cyanobacteria [1/d]
  34 +! alpha1= -> half saturation diatoms [mmol n/m3]
  35 +! alpha2= -> half saturation flagellates [mmol n/m3]
  36 +! alpha3= -> half saturation cyanobacteria [mmol n/m3]
  37 +! lpa= -> p --> a rate (p respiration) [1/d]
  38 +! lpd= -> p --> d rate (p mortality) [1/d]
  39 +! tf= -> temperature control flagellates [deg C]
  40 +! tbg= -> temperature control cyanos [deg C]
  41 +! beta_bg= -> temperature control cyanos [1/deg C]
  42 +! g1max= -> maximum grazing rate on diatoms [1/d]
  43 +! g2max= -> maximum grazing rate on flagellates [1/d]
  44 +! g3max= -> maximum grazing rate on cyanos [1/d]
  45 +! lza= -> z --> a rate (z exkudation) [m3/d/mmol n]
  46 +! lzd= -> z --> d rate (z mortality) [m3/d/mmol n]
  47 +! iv= -> Ivlev constant [1/(mmol n/m3)3]
  48 +! topt= -> optimum temperature [deg C]
  49 +!
  50 +! lan= -> nitrification constant [1/d]
  51 +! oan= -> oxygen parameter [ - ]
  52 +! beta_an= -> temperature control [1/deg C]
  53 +!
  54 +! lda= -> detritus mineralisation constant [1/d]
  55 +! tda= -> temperature control [deg C]
  56 +! lds= -> rate of detritus sinking into sediment [m/d]
  57 +! lsa= -> rate of sediment mineralisation [1/d]
  58 +! bsa= -> temperature control of sediment mineralisation [1/deg C]
  59 +! ph1= -> release of phosphate [ - ]
  60 +! ph2= -> release of phosphate [ - ]
  61 +! pvel= -> piston velocity [m/d]
  62 +!
  63 +! sr= -> redfield ratio(p/n) [ - ]
  64 +! s1= -> reduced nitrate/oxidized detritus [ - ]
  65 +! s2= -> oxygen produktion/recycled nitrogen [ - ]
  66 +! s3= -> oyxgen produktion related to n [ - ]
  67 +! s4= -> nitrification [ - ]
  68 +!
  69 +! a0= -> osat Parameter [mmol/m**3]
  70 +! a1= -> osat Parameter [ - ]
  71 +! a2= -> osat Parameter [1/ deg C]
  72 +!-------------------------------------------------------------------------------
  73 + &bio_iow_nml
  74 + numc= 9
  75 + p1_initial= 0.1
  76 + p2_initial= 0.1
  77 + p3_initial= 0.1
  78 + zo_initial= 0.1
  79 + de_initial= 5.0
  80 + am_initial= 0.1
  81 + ni_initial= 5.0
  82 + po_initial= 0.6
  83 + o2_initial= 85.0
  84 + sfl_po= -0.055
  85 + sfl_am= -0.36
  86 + sfl_ni= -0.45
  87 + surface_flux_method= 0
  88 + fluff= .true.
  89 + fl_initial= 0.0
  90 + p10= 0.0045
  91 + p20= 0.0045
  92 + p30= 0.0045
  93 + zo0= 0.0045
  94 + w_p1= -0.5
  95 + w_p2= 0.
  96 + w_p3= 0.1
  97 + w_de= -3.
  98 + kc= 0.03
  99 + i_min= 25.
  100 + r1max= 2.0
  101 + r2max= 0.7
  102 + r3max= 0.5
  103 + alpha1= 1.35
  104 + alpha2= 0.675
  105 + alpha3= 0.5
  106 + lpa= 0.01
  107 + lpd= 0.02
  108 + tf= 10.
  109 + tbg= 14.
  110 + beta_bg= 1.
  111 + g1max= 0.5
  112 + g2max= 0.5
  113 + g3max= 0.25
  114 + lza= 0.0666666666
  115 + lzd= 0.1333333333
  116 + iv= 0.24444444
  117 + topt= 20.
  118 + lan= 0.1
  119 + oan= 0.01
  120 + beta_an= 0.11
  121 + lda= 0.003
  122 + tda= 13.
  123 + beta_da= 20.
  124 + lds= 3.5
  125 + lsa= 0.001
  126 + bsa= 0.15
  127 + ph1= 0.15
  128 + ph2= 0.1
  129 + pvel= 5.
  130 + sr= 0.0625
  131 + s1= 5.3
  132 + s2= 6.625
  133 + s3= 8.125
  134 + s4= 0.6666666666666
  135 + a0= 31.25
  136 + a1= 14.603
  137 + a2= 0.4025
  138 + /
... ...
nml/bio_npzd.nml
... ... @@ -22,8 +22,6 @@
22 22 ! rpdu= p --> d rate (p mortality), in euphotic zone [1/d]
23 23 ! rpdl= p --> d rate (p mortality), below euphotic zone [1/d]
24 24 ! rzd= z --> d rate (z mortality) [1/d]
25   -! aa= used by light_npzd
26   -! g2= used by light_npzd
27 25 !-------------------------------------------------------------------------------
28 26 &bio_npzd_nml
29 27 numc= 4
... ... @@ -49,6 +47,4 @@
49 47 rpdu= 0.02
50 48 rpdl= 0.1
51 49 rzd= 0.02
52   - aa= 0.62
53   - g2= 20.0
54 50 /
... ...
src/extras/bio/bio_fasham.F90
... ... @@ -145,8 +145,6 @@
145 145 REALTYPE :: mu4 = 0.02
146 146 REALTYPE :: w_d = -2.0
147 147 REALTYPE, public :: kc = 0.03
148   -! REALTYPE :: aa = 0.70
149   -! REALTYPE :: g2 = 14.0
150 148 integer :: out_unit
151 149 integer, parameter :: p=1,z=2,b=3,d=4,n=5,a=6,l=7
152 150 !EOP
... ... @@ -221,10 +219,6 @@
221 219 write(10,901) w_pmin
222 220 write(*,900) ' w_pmax = ',w_pmax
223 221 write(10,901) w_pmax
224   - write(*,900) ' A = ',A
225   - write(10,901) A
226   - write(*,900) ' g2 = ',g2
227   - write(10,901) g2
228 222  
229 223 900 format (a,f8.5)
230 224 901 format (f8.5)
... ...
src/extras/bio/bio_iow.F90
... ... @@ -58,6 +58,7 @@
58 58 ! !USES:
59 59 ! default: all is private.
60 60 use bio_var
  61 + use observations, only : aa,g2
61 62 private
62 63 !
63 64 ! !PUBLIC MEMBER FUNCTIONS:
... ... @@ -212,8 +213,6 @@
212 213 REALTYPE :: a0=31.25
213 214 REALTYPE :: a1=14.603
214 215 REALTYPE :: a2=0.4025
215   - REALTYPE :: aa=0.62
216   - REALTYPE :: g2=20.0
217 216 integer :: out_unit
218 217 integer, parameter :: p1=1,p2=2,p3=3,zo=4,de=5, &
219 218 am=6,ni=7,po=8,o2=9,fl=10
... ... @@ -257,7 +256,7 @@
257 256 alpha3,lpa,lpd,tf,tbg,beta_bg,g1max,g2max, &
258 257 g3max,lza,lzd,iv,topt,lan,oan,beta_an,lda, &
259 258 tda,beta_da,lds,lsa,bsa,ph1,ph2,pvel,sr, &
260   - s1,s2,s3,s4,a0,a1,a2,aa,g2
  259 + s1,s2,s3,s4,a0,a1,a2
261 260 !EOP
262 261 !-----------------------------------------------------------------------
263 262 !BOC
... ...
src/extras/bio/bio_mab.F90
... ... @@ -15,6 +15,7 @@
15 15 ! !USES:
16 16 ! default: all is private.
17 17 use bio_var
  18 + use observations, only : aa,g2
18 19 private
19 20 !
20 21 ! !PUBLIC MEMBER FUNCTIONS:
... ... @@ -92,8 +93,6 @@
92 93 REALTYPE :: a0=31.25
93 94 REALTYPE :: a1=14.603
94 95 REALTYPE :: a2=0.4025
95   - REALTYPE :: aa=0.62
96   - REALTYPE :: g2=20.0
97 96 integer :: out_unit
98 97 integer, parameter :: p1=1,p2=2,p3=3,zo=4,de=5, &
99 98 am=6,ni=7,po=8,o2=9,se=10,fl=11
... ... @@ -138,7 +137,7 @@
138 137 alpha3,lpa,lpd,tf,tbg,beta_bg,g1max,g2max, &
139 138 g3max,lza,lzd,iv,topt,lan,oan,beta_an,lda, &
140 139 tda,beta_da,lds,lsa,bsa,ph1,ph2,pvel,sr, &
141   - s1,s2,s3,s4,a0,a1,a2,aa,g2
  140 + s1,s2,s3,s4,a0,a1,a2
142 141 !EOP
143 142 !-----------------------------------------------------------------------
144 143 !BOC
... ...
src/extras/bio/bio_npzd.F90
... ... @@ -27,6 +27,7 @@
27 27 ! default: all is private.
28 28 use bio_var
29 29 use output
  30 + use observations, only : aa,g2
30 31 private
31 32 !
32 33 ! !PUBLIC MEMBER FUNCTIONS:
... ... @@ -109,8 +110,6 @@
109 110 REALTYPE :: rpdl=1.157407e-06
110 111 REALTYPE :: rpd
111 112 REALTYPE :: rzd=2.314814e-07
112   - REALTYPE :: aa=0.62
113   - REALTYPE :: g2=20.0
114 113 integer :: out_unit
115 114 integer, parameter :: n=1,p=2,z=3,d=4
116 115 !EOP
... ... @@ -176,10 +175,6 @@
176 175 write(11,901) inib
177 176 write(*,900) ' k1 = ',k1
178 177 write(11,901) k1
179   - write(*,900) ' aa = ',aa
180   - write(11,901) aa
181   - write(*,900) ' g2 = ',g2
182   - write(11,901) g2
183 178  
184 179 900 format (a,f8.5)
185 180 901 format (f8.5)
... ...