/[MITgcm]/MITgcm_contrib/darwin2/pkg/monod/MONOD.h
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Revision 1.4 - (hide annotations) (download)
Wed Nov 9 23:34:17 2011 UTC (13 years, 8 months ago) by jahn
Branch: MAIN
CVS Tags: ctrb_darwin2_ckpt63l_20120405, ctrb_darwin2_ckpt63f_20111201, ctrb_darwin2_ckpt63i_20120124, ctrb_darwin2_ckpt63m_20120506, ctrb_darwin2_ckpt63j_20120217, ctrb_darwin2_ckpt63g_20111220, ctrb_darwin2_ckpt63h_20111230, ctrb_darwin2_ckpt63k_20120317
Changes since 1.3: +3 -3 lines
File MIME type: text/plain
add Shannon and Simpson diversity indices

1 jahn 1.4 C $Header: /u/gcmpack/MITgcm_contrib/darwin2/pkg/monod/MONOD.h,v 1.3 2011/10/21 20:56:53 stephd Exp $
2 stephd 1.2 C $Name: $
3 jahn 1.1
4     c MONOD.h
5     c description: Key parameter arrays for generalized ecosystem model
6     c Mick Follows, Scott Grant Fall/Winter 2005
7     c Stephanie Dutkiewicz Spring/Summer 2006
8     c
9     c
10     c npmax = no of "functional groups" of phytoplankton
11     c nzmax = no of "functional groups" of zooplankton
12     c
13     c
14     c NOTE: list not complete!!
15     c mu = max growth rate (s-1)
16     c ksat = half sat coeff, phyto specific for each nutrient
17     c ksatlight = half sat coeff wrt light, phyto specific
18     c graze = grazing rate, phyto specific for each zooplankton
19     c mortzoo = mortality rate for each zooplankton
20 stephd 1.3 c mortzoo2 = quadratic mortality rate for each zooplankton
21 jahn 1.1 c wsink = sinking speed, phyto specific
22     c R_XY = stoichiometric ratios of nutrients in phytoplankton
23     c specific to each functional group, relative to Phos
24     c physize = size class of phytoplankton; 0.0="small", 1.0="big"
25     c diacoc: 1.0 uses silica, 0.0 does not use silica
26     c diacoc: 2.0 uses PIC, 0.0 does not use PIC
27     c diazotrph: 1.0 fixes nitrogen, 0.0 does not fix nitrogen
28     c zoosize = size class of zooplankton; 0.0="small", 1.0="big"
29     c ExportFracZ(nzmax) = fraction of Z mortality sinking out:
30     c rest remineralizes locally
31     c Kpremin_xx = remin rate constant for particulate detritus
32     c ngroups = tracks how many different "functional groups" of phyto
33     c have been tried
34    
35    
36     COMMON/darwin_ecoparam/mu,ksatPO4,ksatNO3,ksatNO2,ksatNH4,
37     & ksatSi,ksatFeT,ksatPAR,
38     & mortzoo,wsink,R_NP,R_FeP,R_SiP,R_PC,R_PICPOC, physize,
39     & diacoc,diazotroph,zoosize,ExportFracZ,
40     & Kpremin_P, Kpremin_N, Kpremin_Fe, Kpremin_Si,
41     & sig1,sig2,sig3,
42     & phytoTempCoeff, phytoTempExp1,
43     & phytoTempExp2, phytoTempOptimum, phytoDecayPower,
44     & zooTempCoeff, zooTempExp, zooTempOptimum, kinhib,
45     & diatomgraz, coccograz, olargegraz,
46     & mortphy, ExportFracP,
47 stephd 1.3 & mortzoo2,
48 jahn 1.1 & Smallgrow, Biggrow, Smallmort, Bigmort,
49     & Smallgrowrange, Biggrowrange, Smallmortrange,
50     & Bigmortrange,
51     & Smallexport, Bigexport,
52     & smallksatpar, smallksatparstd,
53     & smallkinhib, smallkinhibstd,
54     & Bigksatpar, Bigksatparstd,
55     & Bigkinhib, Bigkinhibstd,
56     & tempcoeff1, tempcoeff2_small,
57     & tempcoeff2_big, tempcoeff3,
58     & tempmax, temprange, tempnorm, tempdecay,
59     & SmallPsat, BigPsat, ProcPsat,
60     & SmallPsatrange, BigPsatrange, ProcPsatrange,
61     & prochlPsat,
62     & UniDzPsat, UniDzPsatrange,
63     & depthdenit, o2crit, denit_np,
64     #ifdef OLD_GRAZE
65     & graze,
66     & kgrazesat,
67     & GrazeEffsmall, GrazeEffbig, GrazeFast, GrazeSlow,
68     #else
69     & grazemax, palat, asseff,
70     & kgrazesat,
71     & GrazeEfflow, GrazeEffmod, GrazeEffhi,
72     & GrazeFast, GrazeSlow,
73     & palathi, palatlo,
74     & phygrazmin,
75     & ExportFracGraz,
76     & ExGrazfracbig, ExGrazfracsmall,
77 stephd 1.2 & hollexp,
78 jahn 1.1 #endif
79     & ZoomortSmall, ZoomortBig, ZooexfacSmall, ZooexfacBig,
80 stephd 1.3 & ZoomortSmall2, ZoomortBig2,
81 jahn 1.1 & val_R_SiP_diatom, val_R_NP_diaz, val_RFeP_diaz,
82     & val_R_NP, val_RFeP, val_R_PC,
83     & val_R_PICPOC,
84     & ksatNH4fac, ksatNO2fac, val_ksatsi,
85     & ngrowfac, ilight,
86     & phymin, PAR0, diaz_growfac,
87     & phyto_esd, phyto_vol,
88     & zoo_esd, zoo_vol
89     #ifdef IRON_SED_SOURCE
90     & ,depthfesed,fesedflux,fesedflux_pcm
91     #endif
92     #ifdef PART_SCAV
93     & ,scav_rat, scav_inter, scav_exp
94     #endif
95     & ,nsource,ngroups
96    
97     _RL mu(npmax)
98     _RL ksatPO4(npmax)
99     _RL ksatNO3(npmax)
100     _RL ksatNO2(npmax)
101     _RL ksatNH4(npmax)
102     _RL ksatSi(npmax)
103     _RL ksatFeT(npmax)
104     _RL ksatPAR(npmax)
105     _RL mortzoo(nzmax)
106 stephd 1.3 _RL mortzoo2(nzmax)
107 jahn 1.1 _RL wsink(npmax)
108     _RL R_NP(npmax)
109     _RL R_FeP(npmax)
110     _RL R_SiP(npmax)
111     _RL R_PC(npmax)
112     _RL R_PICPOC(npmax)
113     _RL physize(npmax)
114     _RL diacoc(npmax)
115     _RL diazotroph(npmax)
116     _RL zoosize(nzmax)
117     _RL ExportFracZ(nzmax)
118     _RL Kpremin_P
119     _RL Kpremin_N
120     _RL Kpremin_Fe
121     _RL Kpremin_Si
122     _RL phytoTempCoeff(npmax)
123     _RL phytoTempExp1(npmax)
124     _RL phytoTempExp2(npmax)
125     _RL phytoTempOptimum(npmax)
126     _RL phytoDecayPower(npmax)
127     _RL zooTempCoeff(nzmax)
128     _RL zooTempExp(nzmax)
129     _RL zooTempOptimum(nzmax)
130     _RL diatomgraz, coccograz, olargegraz
131     _RL kinhib(npmax)
132     _RL mortphy(npmax)
133     _RL ExportFracP(npmax)
134     _RL Smallgrow, Biggrow
135     _RL Smallmort, Bigmort
136     _RL Smallgrowrange, Biggrowrange
137     _RL Smallmortrange, Bigmortrange
138     _RL Smallexport, Bigexport
139     _RL smallksatpar, smallksatparstd
140     _RL smallkinhib, smallkinhibstd
141     _RL tempcoeff1, tempcoeff2_big
142     _RL tempcoeff2_small, tempcoeff3
143     _RL tempmax, temprange, tempnorm,tempdecay
144     _RL Bigksatpar, Bigksatparstd
145     _RL Bigkinhib, Bigkinhibstd
146     _RL SmallPsat, BigPsat, ProcPsat
147     _RL SmallPsatrange, BigPsatrange, ProcPsatrange
148     _RL prochlPsat
149     _RL UniDzPsat, UniDzPsatrange
150     _RL depthdenit
151     _RL o2crit
152     _RL denit_np
153     _RL ksatNH4fac, ksatNO2fac
154     _RL sig1,sig2,sig3
155     _RL val_ksatsi
156     #ifdef OLD_GRAZE
157     _RL graze(npmax,nzmax)
158     _RL kgrazesat
159     _RL GrazeEffsmall, GrazeEffbig, GrazeFast, GrazeSlow
160     #else
161     _RL grazemax(nzmax)
162     _RL palat(npmax,nzmax)
163     _RL asseff(npmax,nzmax)
164     _RL kgrazesat
165     _RL GrazeEfflow, GrazeEffmod, GrazeEffhi
166     _RL GrazeFast, GrazeSlow
167     _RL palathi, palatlo
168     _RL phygrazmin
169     _RL ExportFracGraz(nzmax)
170     _RL ExGrazfracbig, ExGrazfracsmall
171 stephd 1.2 _RL hollexp
172 jahn 1.1 #endif
173     _RL ZoomortSmall, ZoomortBig, ZooexfacSmall, ZooexfacBig
174 stephd 1.3 _RL ZoomortSmall2, ZoomortBig2
175 jahn 1.1 _RL val_R_SiP_diatom, val_R_NP_diaz, val_RFeP_diaz,
176     & val_R_NP, val_RFeP, val_R_PC, val_R_PICPOC
177     _RL ngrowfac,ilight
178     _RL phymin
179     _RL PAR0
180     _RL phyto_esd(npmax)
181     _RL phyto_vol(npmax)
182     _RL zoo_esd(nzmax)
183     _RL zoo_vol(nzmax)
184     #ifdef IRON_SED_SOURCE
185     _RL depthfesed, fesedflux, fesedflux_pcm
186     #endif
187     #ifdef PART_SCAV
188     _RL scav_rat, scav_inter, scav_exp
189     #endif
190    
191     INTEGER nsource(npmax)
192     INTEGER ngroups
193    
194    
195     COMMON/darwin_detritus/wp_sink,wn_sink,wfe_sink,wsi_sink,
196     & Kdop,Kdon,KdoFe,SmallSink,BigSink,
197     & Knita, Knitb
198     _RL wp_sink
199     _RL wn_sink
200     _RL wfe_sink
201     _RL wsi_sink
202     _RL Kdop
203     _RL Kdon
204     _RL KdoFe
205     _RL SmallSink
206     _RL BigSink
207     _RL Knita
208     _RL Knitb
209     _RL diaz_growfac
210    
211     c k0, kc - light coefficients
212     COMMON/darwin_lightparam/ k0, kc, parfrac, parconv
213     _RL k0, kc, parfrac, parconv
214    
215     c chlpmax - chl:p max ratio
216     c chlpmin - chl:p min ratio
217     c istar - photoadaptation light limit
218     COMMON/darwin_chlparam/ chlpmax, chlpmin, istar
219     _RL chlpmax, chlpmin, istar
220    
221     COMMON/darwin_diags_param/
222     & diver_thresh0, diver_thresh1,
223     & diver_thresh2, diver_thresh3,
224 jahn 1.4 & diver_thresh4, shannon_thresh
225 jahn 1.1
226     _RL diver_thresh0, diver_thresh1
227     _RL diver_thresh2, diver_thresh3
228 jahn 1.4 _RL diver_thresh4, shannon_thresh
229 jahn 1.1
230     #ifdef GEIDER
231     c ANNA geider by mQyield instead of alpha
232     COMMON/geider_vars/
233     & pcmax, alphachl, chl2cmax, chl2cmin,
234     & mQyield,aphy_chl_ave,
235     & inhibcoef_geid, inhibcoef_geid_val,
236     #ifdef WAVEBANDS
237     & alpha_mean,
238     #endif
239     #ifdef DYNAMIC_CHL
240     & acclimtimescl,
241     #endif
242     c & Bigalphachl, Bigalphachlrange,
243     c & Smallalphachl, Smallalphachlrange,
244     & BigmQyield, BigmQyieldrange,
245     & SmallmQyield, SmallmQyieldrange,
246     & Bigchl2cmax, Bigchl2cmaxrange,
247     & Smallchl2cmax, Smallchl2cmaxrange
248     c _RL phychl(npmax)
249     _RL pcmax(npmax)
250     _RL alphachl(npmax)
251     _RL mQyield(npmax)
252     _RL chl2cmax(npmax)
253     _RL chl2cmin(npmax)
254     _RL inhibcoef_geid(npmax)
255     _RL inhibcoef_geid_val
256     #ifdef WAVEBANDS
257     _RL alpha_mean(npmax)
258     #endif
259     #ifdef DYNAMIC_CHL
260     _RL acclimtimescl
261     #endif
262    
263    
264     c _RL Bigalphachl, Bigalphachlrange,
265     c & Smallalphachl, Smallalphachlrange,
266     _RL BigmQyield, BigmQyieldrange,
267     & SmallmQyield, SmallmQyieldrange,
268     & Bigchl2cmax, Bigchl2cmaxrange,
269     & Smallchl2cmax, Smallchl2cmaxrange,
270     & aphy_chl_ave
271     #endif
272     #ifdef DAR_DIAG_CHL
273     COMMON/DAR_DIAG_CHL_VARS/
274     & Geider_alphachl, Geider_chl2cmin, Geider_chl2cmax
275     _RL Geider_alphachl(npmax)
276     _RL Geider_chl2cmin(npmax)
277     _RL Geider_chl2cmax(npmax)
278     #endif /* DAR_DIAG_CHL */
279    
280    
281     #ifdef ALLOW_CARBON
282     COMMON/darwin_carbon/ R_OP, wc_sink, wpic_sink,
283     & Kdoc, Kpremin_C, Kdissc
284     _RL R_OP
285     _RL wc_sink
286     _RL wpic_sink
287     _RL Kdoc
288     _RL Kpremin_C
289     _RL Kdissc
290     #endif
291    

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