Blame view

src/extras/bio/bio_fasham.F90 20 KB
33b83817   dumoda01   Depot du modele /...
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
!$Id: bio_fasham.F90,v 1.11 2007-01-06 11:49:15 kbk Exp $
#include"cppdefs.h"
!-----------------------------------------------------------------------
!BOP
!
! !MODULE: bio_fasham --- Fasham et al. biological model \label{sec:bio-fasham}
!
! !INTERFACE:
   module bio_fasham
!
! !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
eb3930d2   dumoda01   Ecriture dun fich...
41
   use output
aee6c9dc   dumoda01   Le code a ete mod...
42
   use observations, only : aa,g2
33b83817   dumoda01   Depot du modele /...
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
   private
!
! !PUBLIC MEMBER FUNCTIONS:
   public init_bio_fasham, init_var_fasham, var_info_fasham, &
          light_fasham, do_bio_fasham, end_bio_fasham
!
! !PRIVATE DATA MEMBERS:
!
! !REVISION HISTORY:!
!  Original author(s): Hans Burchard & Karsten Bolding
!
!  $Log: bio_fasham.F90,v $
!  Revision 1.11  2007-01-06 11:49:15  kbk
!  namelist file extension changed .inp --> .nml
!
!  Revision 1.10  2006-10-26 13:12:46  kbk
!  updated bio models to new ode_solver
!
!  Revision 1.9  2005-12-02 20:57:27  hb
!  Documentation updated and some bugs fixed
!
!  Revision 1.8  2005-11-17 09:58:18  hb
!  explicit argument for positive definite variables in diff_center()
!
!  Revision 1.7  2005/09/12 14:48:33  kbk
!  merged generic biological module support
!
!  Revision 1.6.2.1  2005/07/05 20:25:35  hb
!  added control over par calculation
!
!  Revision 1.6  2004/08/09 11:53:39  hb
!  bioshading now without detritus
!
!  Revision 1.5  2004/08/02 08:34:36  hb
!  updated init routines to reflect new internal bio interface
!
!  Revision 1.4  2004/08/01 15:52:57  hb
!  alpha now devided by seconds per day
!
!  Revision 1.3  2004/07/30 09:22:20  hb
!  use bio_var in specific bio models - simpliefied internal interface
!
!  Revision 1.2  2004/07/28 11:34:29  hb
!  Bioshade feedback may now be switched on or off, depending on bioshade_feedback set to .true. or .false. in bio.nml
!
!  Revision 1.1  2004/06/29 08:03:16  hb
!  Fasham et al. 1990 model implemented
!
!  Revision 1.2  2003/10/16 15:42:16  kbk
!  simple mussesl model implemented - filter only
!
!  Revision 1.1  2003/07/23 12:27:31  hb
!  more generic support for different bio models
!
!  Revision 1.3  2003/04/05 07:01:41  kbk
!  moved bioshade variable to meanflow - to compile properly
!
!  Revision 1.2  2003/04/04 14:25:52  hb
!  First iteration of four-compartment geobiochemical model implemented
!
!  Revision 1.1  2003/04/01 17:01:00  hb
!  Added infrastructure for geobiochemical model
!
! !LOCAL VARIABLES:
!  from a namelist
   REALTYPE                  ::  p_initial= 0.056666666
   REALTYPE                  ::  z_initial= 0.05
   REALTYPE                  ::  b_initial= 0.001
   REALTYPE                  ::  d_initial= 0.416666666
524b0746   dumoda01   Les parametres n_...
112
113
114
!  Nitrate and ammonium are initialized within the GOTM observation module
!   REALTYPE                  ::  n_initial= 8.3
!   REALTYPE                  ::  a_initial= 0.22
33b83817   dumoda01   Depot du modele /...
115
116
117
118
119
120
   REALTYPE                  ::  l_initial= 0.14
   REALTYPE                  ::  p0       = 0.0
   REALTYPE                  ::  z0       = 0.0
   REALTYPE                  ::  b0       = 0.0
   REALTYPE                  ::  vp       = 1.5
   REALTYPE                  ::  alpha    = 0.065
1025a7c4   dumoda01   Ajout de diagnost...
121
   REALTYPE                  ::  I_opt    = 10.0
1025a7c4   dumoda01   Ajout de diagnost...
122
   REALTYPE                  ::  inib     = 0.05
1025a7c4   dumoda01   Ajout de diagnost...
123
   REALTYPE                  ::  theta    = 0.0
3e5d6e6b   dumoda01   Ajout de la varia...
124
125
   REALTYPE                  ::  w_pmin   = -0.06
   REALTYPE                  ::  w_pmax   = -0.38
33b83817   dumoda01   Depot du modele /...
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
   REALTYPE                  ::  k1       = 0.2
   REALTYPE                  ::  k2       = 0.8
   REALTYPE                  ::  mu1      = 0.05
   REALTYPE                  ::  k5       = 0.2
   REALTYPE                  ::  gamma    = 0.05
   REALTYPE                  ::  w_p      = -0.5
   REALTYPE                  ::  gmax     = 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                  ::  r1       = 0.55
   REALTYPE                  ::  r2       = 0.4
   REALTYPE                  ::  r3       = 0.05
   REALTYPE                  ::  vb       = 1.2
   REALTYPE                  ::  k4       = 0.5
   REALTYPE                  ::  mu3      = 0.15
   REALTYPE                  ::  eta      = 0.0
   REALTYPE                  ::  mu4      = 0.02
   REALTYPE                  ::  w_d      = -2.0
3e5d6e6b   dumoda01   Ajout de la varia...
148
   REALTYPE, public          ::  kc       = 0.03
33b83817   dumoda01   Depot du modele /...
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
   integer                   ::  out_unit
   integer, parameter        ::  p=1,z=2,b=3,d=4,n=5,a=6,l=7
!EOP
!-----------------------------------------------------------------------

   contains

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Initialise the bio module
!
! !INTERFACE:
   subroutine init_bio_fasham(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
eb3930d2   dumoda01   Ecriture dun fich...
175
   character(len=20)              :: pfile
33b83817   dumoda01   Depot du modele /...
176
177
178
179
180
181
182
   integer,          intent(in)   :: unit
!
! !REVISION HISTORY:
!  Original author(s): Hans Burchard & Karsten Bolding
!
! !LOCAL VARIABLES:
   namelist /bio_fasham_nml/ numc, &
524b0746   dumoda01   Les parametres n_...
183
184
                        p_initial,z_initial,b_initial,d_initial,           &
                        l_initial,p0,z0,b0,vp,alpha,k1,k2,mu1,k5,          &
33b83817   dumoda01   Depot du modele /...
185
                        gamma,w_p,gmax,k3,beta,mu2,k6,delta,epsi,r1,r2,r3, &
aee6c9dc   dumoda01   Le code a ete mod...
186
                        vb,k4,mu3,eta,mu4,w_d,kc,                          &
33b83817   dumoda01   Depot du modele /...
187
                        I_opt,inib,                                        &    !CHG1
3e5d6e6b   dumoda01   Ajout de la varia...
188
                        theta,w_pmax,w_pmin                                     !CHG2
33b83817   dumoda01   Depot du modele /...
189
190
191
192
193
194
195
196
197
198
199
!EOP
!-----------------------------------------------------------------------
!BOC
   LEVEL2 'init_bio_fasham'

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

   numcc=numc

1faa4fe1   dumoda01   Printout de param...
200
! Print some parameter values in standard output
eb3930d2   dumoda01   Ecriture dun fich...
201
202
203
204
! and save them in a separate file [out_fn]_fasham.par
   pfile = trim(out_fn) // '_fasham.par'
   open(10,status='unknown',action='write',file=pfile)
   LEVEL3 'FASHAM parameters saved in ', pfile
1faa4fe1   dumoda01   Printout de param...
205
   write(*,900) '                vp     = ',vp
eb3930d2   dumoda01   Ecriture dun fich...
206
   write(10,901) vp
1faa4fe1   dumoda01   Printout de param...
207
   write(*,900) '                alpha  = ',alpha
eb3930d2   dumoda01   Ecriture dun fich...
208
   write(10,901) alpha
1faa4fe1   dumoda01   Printout de param...
209
   write(*,900) '                inib   = ',inib
eb3930d2   dumoda01   Ecriture dun fich...
210
   write(10,901) inib
1faa4fe1   dumoda01   Printout de param...
211
   write(*,900) '                k1     = ',k1
eb3930d2   dumoda01   Ecriture dun fich...
212
   write(10,901) k1
1faa4fe1   dumoda01   Printout de param...
213
   write(*,900) '                k2     = ',k2
eb3930d2   dumoda01   Ecriture dun fich...
214
   write(10,901) k2
1faa4fe1   dumoda01   Printout de param...
215
   write(*,900) '                w_p    = ',w_p
eb3930d2   dumoda01   Ecriture dun fich...
216
   write(10,901) w_p
1faa4fe1   dumoda01   Printout de param...
217
   write(*,900) '                theta  = ',theta
eb3930d2   dumoda01   Ecriture dun fich...
218
   write(10,901) theta
1faa4fe1   dumoda01   Printout de param...
219
   write(*,900) '                w_pmin = ',w_pmin
eb3930d2   dumoda01   Ecriture dun fich...
220
   write(10,901) w_pmin
1faa4fe1   dumoda01   Printout de param...
221
   write(*,900) '                w_pmax = ',w_pmax
eb3930d2   dumoda01   Ecriture dun fich...
222
   write(10,901) w_pmax
1faa4fe1   dumoda01   Printout de param...
223

eb3930d2   dumoda01   Ecriture dun fich...
224
225
900 format (a,f8.5)
901 format (f8.5)
1faa4fe1   dumoda01   Printout de param...
226

33b83817   dumoda01   Depot du modele /...
227
228
229
230
231
232
233
234
235
!  Conversion from day to second
   vp   = vp   /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
   gmax = gmax /secs_pr_day
   w_p  = w_p  /secs_pr_day
9538a482   dumoda01   Fonction de flott...
236
237
238
   w_pmin = w_pmin /secs_pr_day   !DD
   w_pmax = w_pmax /secs_pr_day   !DD
   theta  = theta  /secs_pr_day   !DD
33b83817   dumoda01   Depot du modele /...
239
240
   w_d  = w_d  /secs_pr_day
   alpha= alpha/secs_pr_day
9538a482   dumoda01   Fonction de flott...
241
   inib = inib /secs_pr_day       !CHG1
33b83817   dumoda01   Depot du modele /...
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294

   out_unit=unit

   LEVEL3 'FASHAM bio module initialised ...'

   return

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

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Initialise the concentration variables
!
! !INTERFACE:
   subroutine init_var_fasham(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                   !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(p,i)=p_initial
      cc(z,i)=z_initial
      cc(b,i)=b_initial
      cc(d,i)=d_initial
33b83817   dumoda01   Depot du modele /...
295
      cc(n,i)=nprof(i)                                  !CHG3
c91f14d2   dumoda01   Bogue mineur
296
      cc(a,i)=aprof(i)                                  !CHG5
33b83817   dumoda01   Depot du modele /...
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
      cc(l,i)=l_initial
   end do

   do i=0,nlev
      ws(z,i) = _ZERO_
      ws(b,i) = _ZERO_
      ws(n,i) = _ZERO_
      ws(a,i) = _ZERO_
      ws(l,i) = _ZERO_
      ws(p,i) = w_p
      ws(d,i) = w_d
   end do

   posconc(p) = 1
   posconc(z) = 1
   posconc(b) = 1
   posconc(d) = 1
   posconc(n) = 1
   posconc(a) = 1
   posconc(l) = 1

#if 0
   mussels_inhale(p) = .true.
   mussels_inhale(z) = .true.
   mussels_inhale(b) = .false.
   mussels_inhale(d) = .true.
   mussels_inhale(n) = .false.
   mussels_inhale(a) = .false.
   mussels_inhale(l) = .true.
#endif

   LEVEL3 'FASHAM variables initialised ...'

   return

   end subroutine init_var_fasham
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Providing info on variables
!
! !INTERFACE:
   subroutine var_info_fasham()
!
! !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) = 'phy'
   var_units(1) = 'mmol/m**3'
   var_long(1)  = 'phytoplankton'

   var_names(2) = 'zoo'
   var_units(2) = 'mmol/m**3'
   var_long(2)  = 'zooplankton'

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

   var_names(4) = 'det'
   var_units(4) = 'mmol/m**3'
   var_long(4)  = 'detritus'

   var_names(5) = 'nit'
   var_units(5) = 'mmol/m**3'
   var_long(5)  = 'nitrate'

   var_names(6) = 'amm'
   var_units(6) = 'mmol/m**3'
   var_long(6)  = 'ammonium'

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

   return
   end subroutine var_info_fasham
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Light properties for the Fasham model
!
! !INTERFACE:
   subroutine light_fasham(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(p,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(p,i)+p0)
      zz=zz+0.5*h(i)
      if (bioshade_feedback) bioshade_(i)=exp(-kc*add)
   end do


   return
   end subroutine light_fasham
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Right hand sides of geobiochemical model \label{sec:bio-fasham-rhs}
!
! !INTERFACE:
   subroutine do_bio_fasham(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:
1025a7c4   dumoda01   Ajout de diagnost...
543
   REALTYPE                   :: ff,fac,fac2,min67,q1,q2
33b83817   dumoda01   Depot du modele /...
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
   REALTYPE                   :: Ps                           !CHG1
   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
      Ps= vp/((alpha/(alpha+inib))*(alpha/(alpha+inib))**(inib/alpha))
3e5d6e6b   dumoda01   Ajout de la varia...
570
      ff= Ps*(1.-exp(-1.*alpha*par(ci)/Ps))*exp(-1.*inib*par(ci)/Ps)
33b83817   dumoda01   Depot du modele /...
571
572
! --------------------------------------------------------------------

1025a7c4   dumoda01   Ajout de diagnost...
573
574
575

      q1=(cc(n,ci)/k1)/(1.+cc(n,ci)/k1+cc(a,ci)/k2)
      q2=(cc(a,ci)/k2)/(1.+cc(n,ci)/k1+cc(a,ci)/k2)
33b83817   dumoda01   Depot du modele /...
576
577
578
579
      fac=(cc(z,ci)+z0)/(k3*(r1*cc(p,ci)+r2*cc(b,ci)+r3*cc(d,ci))+  &
                      r1*cc(p,ci)**2+r2*cc(b,ci)**2+r3*cc(d,ci)**2)
      min67=min(cc(a,ci),eta*cc(l,ci))

1025a7c4   dumoda01   Ajout de diagnost...
580
581
582
583
584
      ! Light and nutrient limitation factors
      lumlim(ci)=ff
      nitlim(ci)=q1
      ammlim(ci)=q2
      
33b83817   dumoda01   Depot du modele /...
585
586
      dd(p,d,ci)=mu1*(cc(p,ci)+p0)/(k5+cc(p,ci)+p0)*cc(p,ci)  &
                 +(1.-beta)*gmax*r1*cc(p,ci)**2*fac
1025a7c4   dumoda01   Ajout de diagnost...
587
      dd(p,l,ci)=gamma*ff*(q1+q2)*cc(p,ci)
33b83817   dumoda01   Depot du modele /...
588
589
590
591
592
593
594
595
596
      dd(b,d,ci)=(1.-beta)*gmax*r2*cc(b,ci)**2*fac
      dd(p,z,ci)=beta*gmax*r1*cc(p,ci)**2*fac
      dd(b,z,ci)=beta*gmax*r2*cc(b,ci)**2*fac
      dd(d,z,ci)=beta*gmax*r3*cc(d,ci)**2*fac
      dd(b,a,ci)=mu3*cc(b,ci)
      dd(d,l,ci)=mu4*cc(d,ci)
      dd(z,d,ci)=(1.-epsi-delta)*mu2*(cc(z,ci)+z0)/(k6+cc(z,ci)+z0)*cc(z,ci)
      dd(z,a,ci)=epsi*mu2*(cc(z,ci)+z0)/(k6+cc(z,ci)+z0)*cc(z,ci)
      dd(z,l,ci)=delta*mu2*(cc(z,ci)+z0)/(k6+cc(z,ci)+z0)*cc(z,ci)
1025a7c4   dumoda01   Ajout de diagnost...
597
598
      dd(n,p,ci)=ff*q1*(cc(p,ci)+p0)
      dd(a,p,ci)=ff*q2*(cc(p,ci)+p0)
33b83817   dumoda01   Depot du modele /...
599
600
601
      dd(a,b,ci)=vb*min67/(k4+min67+cc(l,ci))*(cc(b,ci)+b0)
      dd(l,b,ci)=vb*cc(l,ci)/(k4+min67+cc(l,ci))*(cc(b,ci)+b0)

3e5d6e6b   dumoda01   Ajout de la varia...
602
! Taux de chute du phytoplancton en fonction de la croissance
9538a482   dumoda01   Fonction de flott...
603
604
!      ws(p,ci)=w_pmin+(w_pmax-w_pmin)*exp(-ff/theta)
!      ws(p,ci)=w_pmax-(w_pmax-w_pmin)*(ff/theta/(1.+ff/theta))
3e5d6e6b   dumoda01   Ajout de la varia...
605
      ws(p,ci)=w_p
33b83817   dumoda01   Depot du modele /...
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649

      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_fasham
!EOC

!-----------------------------------------------------------------------
!BOP
!
! !IROUTINE: Finish the bio calculations
!
! !INTERFACE:
   subroutine end_bio_fasham
!
! !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_fasham
!EOC

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

   end module bio_fasham

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