/[MITgcm]/MITgcm_contrib/darwin2/pkg/monod/monod_init_fixed.F
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revision 1.2 by stephd, Wed Oct 5 20:37:23 2011 UTC revision 1.8 by stephd, Thu Jul 26 18:05:34 2012 UTC
# Line 106  c depth for denitrification to start Line 106  c depth for denitrification to start
106    
107  c critical oxygen for O2/NO3 remineralization  c critical oxygen for O2/NO3 remineralization
108        O2crit = 6.0 _d 0    !(Lipschultz et al 1990, DSR 37, 1513-1541)        O2crit = 6.0 _d 0    !(Lipschultz et al 1990, DSR 37, 1513-1541)
109  c ratio of no3 to p in denitrification process  c ratio of n to p in denitrification process
110        denit_np = 120.0 _d 0        denit_np = 120.0 _d 0
111    c ratio no3 used relative to all n in denitrification process
112          denit_no3 = 104.0 _d 0
113    c critical nitrate below which no denit (or remin) happens
114          no3crit = 1. _d -2
115  c  c
116  c oxidation rates for ammonium and nitrite  c oxidation rates for ammonium and nitrite
117  c i.e. Knita ...    NH4 -> NO2  c i.e. Knita ...    NH4 -> NO2
# Line 218  c ammonia and nitrite inhibition Line 221  c ammonia and nitrite inhibition
221  c set si half sat  c set si half sat
222         val_ksatsi=1. _d 0         val_ksatsi=1. _d 0
223  c set nutrient ratios for phyto  c set nutrient ratios for phyto
224    #ifdef ONLY_P_CYCLE
225           val_R_SiP_diatom=0.0 _d 0
226           val_R_NP=0.0 _d 0
227           val_RFeP=0.0 _d -3
228           val_R_NP_diaz=0.0 _d  0
229           val_RFeP_diaz=0.0 _d 0 * val_RFeP
230           val_R_PC=0.0 _d 0
231           val_R_PICPOC=0.0 _d 0
232    #else
233         val_R_SiP_diatom=16.0 _d 0  ! 32 for Fanny's runs         val_R_SiP_diatom=16.0 _d 0  ! 32 for Fanny's runs
234         val_R_NP=16.0 _d 0         val_R_NP=16.0 _d 0
235         val_RFeP=1.0 _d -3         val_RFeP=1.0 _d -3
# Line 225  c set nutrient ratios for phyto Line 237  c set nutrient ratios for phyto
237         val_RFeP_diaz=30.0 _d 0 * val_RFeP         val_RFeP_diaz=30.0 _d 0 * val_RFeP
238         val_R_PC=120.0 _d 0         val_R_PC=120.0 _d 0
239         val_R_PICPOC=0.8 _d 0         val_R_PICPOC=0.8 _d 0
240    #endif
241    c
242  #ifdef OLD_GRAZE  #ifdef OLD_GRAZE
243  c grazing hlaf saturation  c grazing hlaf saturation
244         kgrazesat = 0.1 _d 0         kgrazesat = 0.1 _d 0
# Line 269  c grazing exponential 1= holling 2, 2=ho Line 283  c grazing exponential 1= holling 2, 2=ho
283  c set zoo mortality  c set zoo mortality
284         ZoomortSmall = 1.0 _d 0/(30.0 _d 0*pday)         ZoomortSmall = 1.0 _d 0/(30.0 _d 0*pday)
285         ZoomortBig = 1.0 _d 0/(30.0 _d 0*pday)         ZoomortBig = 1.0 _d 0/(30.0 _d 0*pday)
286           ZoomortSmall2 = 0. _d 0
287           ZoomortBig2 = 0. _d 0
288  c set zoo exportfrac  c set zoo exportfrac
289         ZooexfacSmall = 0.2 _d 0         ZooexfacSmall = 0.2 _d 0
290         ZooexfacBig = 0.7 _d 0         ZooexfacBig = 0.7 _d 0
# Line 305  c sinking rate for particulate matter (m Line 321  c sinking rate for particulate matter (m
321           Pa2Atm      = 1.01325 _d 5           Pa2Atm      = 1.01325 _d 5
322  #endif  #endif
323    
324    #ifdef ALLOW_CDOM
325             fraccdom=2. _d 0 / 100. _d 0
326             cdomdegrd= 1. _d 0 / (200 _d 0 *pday)
327             cdombleach = 1. _d 0 / (15 _d 0 *pday)
328             PARcdom  = 20. _d 0
329             rnp_cdom = 16. _d 0
330             rfep_cdom = 1. _d -3
331             rcp_cdom  = 120. _d 0
332             cdomcoeff = .1 _d -1  / 1.d -4
333    #endif
334    
335  C make sure we have reserved enough space in Ptracers  C make sure we have reserved enough space in Ptracers
336        IF ( nCompZooMax .LT. 4 ) THEN        IF ( nCompZooMax .LT. 4 ) THEN
337          WRITE(msgBuf,'(A,A,I3)')          WRITE(msgBuf,'(A,A,I3)')
# Line 315  C make sure we have reserved enough spac Line 342  C make sure we have reserved enough spac
342        ENDIF        ENDIF
343        DO nz = 1,nzmax        DO nz = 1,nzmax
344          iZooP (nz)  = iZoo +                   (nz-1)*strideTypeZoo          iZooP (nz)  = iZoo +                   (nz-1)*strideTypeZoo
345    #ifdef ONLY_P_CYCLE
346            iZooN (nz)  = nptot
347            iZooFe(nz)  = nptot
348            iZooSi(nz)  = nptot
349    #else
350          iZooN (nz)  = iZoo + 1*strideCompZoo + (nz-1)*strideTypeZoo          iZooN (nz)  = iZoo + 1*strideCompZoo + (nz-1)*strideTypeZoo
351          iZooFe(nz)  = iZoo + 2*strideCompZoo + (nz-1)*strideTypeZoo          iZooFe(nz)  = iZoo + 2*strideCompZoo + (nz-1)*strideTypeZoo
352          iZooSi(nz)  = iZoo + 3*strideCompZoo + (nz-1)*strideTypeZoo          iZooSi(nz)  = iZoo + 3*strideCompZoo + (nz-1)*strideTypeZoo
353    #endif
354        ENDDO        ENDDO
355  #ifdef ALLOW_CARBON  #ifdef ALLOW_CARBON
356         DO nz = 1,nzmax         DO nz = 1,nzmax
# Line 336  c diver3 - fraction of biomass to count Line 369  c diver3 - fraction of biomass to count
369          diver_thresh3=.999 _d 0          diver_thresh3=.999 _d 0
370  c diver4 - fraction of maximum species  c diver4 - fraction of maximum species
371          diver_thresh4=1 _d -5          diver_thresh4=1 _d -5
372    c threshold on total biomass for contributing to Shannon and Simpson ind
373    c (these become large at very small biomass)
374            shannon_thresh = 1 _d -8   ! mmol P m-3
375  #endif  #endif
376    
377  c set up diagnostics  c set up diagnostics
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