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namelist_medusa_ref in branches/NERC/dev_r5518_GO6_MEDUSA_DMS_TUNING/NEMOGCM/CONFIG/SHARED – NEMO

source: branches/NERC/dev_r5518_GO6_MEDUSA_DMS_TUNING/NEMOGCM/CONFIG/SHARED/namelist_medusa_ref @ 9246

Last change on this file since 9246 was 9246, checked in by jpalmier, 6 years ago

JPALM -- correct namelist_*_ref errors introduced in the last commit

File size: 18.8 KB
Line 
1!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2!
3! BIO namelist :  MEDUSA biological model option and parameter input
4! -------------
5!
6!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
7!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
8!       natbio   Shared parameters for dynamics/advection/thermo
9!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
10!
11!! Primary production and chl related quantities
12!!       xxi         :  conversion factor from gC to mmolN
13!!       xaln        :  Chl-a specific initial slope of P-I curve for non-diatoms
14!!       xald        :  Chl-a specific initial slope of P-I curve for diatoms
15!!       jphy        :  phytoplankton T-dependent growth switch
16!!       xvpn        :  maximum growth rate for non-diatoms
17!!       xvpd        :  maximum growth rate for diatoms
18!!       xthetam     :  maximum Chl to C ratio for non-diatoms     
19!!       xthetamd    :  maximum Chl to C ratio for diatoms
20!!
21!! Diatom silicon parameters
22!!       xsin0       :  minimum diatom Si:N ratio
23!!       xnsi0       :  minimum diatom N:Si ratio
24!!       xuif        :  hypothetical growth ratio at infinite Si:N ratio
25!!
26!! Nutrient limitation
27!!       jliebig     :  Liebig nutrient uptake switch
28!!       xnln        :  half-sat constant for DIN uptake by non-diatoms
29!!       xnld        :  half-sat constant for DIN uptake by diatoms
30!!       xsl         :  half-sat constant for Si uptake by diatoms
31!!       xfld        :  half-sat constant for Fe uptake by diatoms 
32!!       xfln        :  half-sat constant for Fe uptake by non-datoms
33!!
34!! Grazing
35!!       xgmi        :  microzoo maximum growth rate
36!!       xgme        :  mesozoo maximum growth rate
37!!       xkmi        :  microzoo grazing half-sat parameter
38!!       xkme        :  mesozoo grazing half-sat parameter
39!!       xphi        :  micro/mesozoo grazing inefficiency
40!!       xbetan      :  micro/mesozoo N assimilation efficiency
41!!       xbetac      :  micro/mesozoo C assimilation efficiency
42!!       xkc         :  micro/mesozoo net C growth efficiency
43!!       xpmipn      :  grazing preference of microzoo for non-diatoms
44!!       xpmid       :  grazing preference of microzoo for diatoms
45!!       xpmepn      :  grazing preference of mesozoo for non-diatoms
46!!       xpmepd      :  grazing preference of mesozoo for diatoms
47!!       xpmezmi     :  grazing preference of mesozoo for microzoo
48!!       xpmed       :  grazing preference of mesozoo for detritus
49!!
50!! Metabolic losses
51!!       xmetapn     :  non-diatom metabolic loss rate
52!!       xmetapd     :  diatom     metabolic loss rate
53!!       xmetazmi    :  microzoo   metabolic loss rate
54!!       xmetazme    :  mesozoo    metabolic loss rate
55!!
56!! Mortality losses
57!!       jmpn        :  non-diatom mortality functional form
58!!       xmpn        :  non-diatom mortality rate
59!!       xkphn       :  non-diatom mortality half-sat constant
60!!       jmpd        :  diatom     mortality functional form
61!!       xmpd        :  diatom     mortality rate
62!!       xkphd       :  diatom     mortality half-sat constant
63!!       jmzmi       :  microzoo   mortality functional form
64!!       xmzmi       :  microzoo   mortality rate
65!!       xkzmi       :  microzoo   mortality half-sat constant
66!!       jmzme       :  mesozoo    mortality functional form
67!!       xmzme       :  mesozoo    mortality rate
68!!       xkzme       :  mesozoo    mortality half-sat constant
69!!
70!! Remineralisation
71!!       jmd         :  detritus T-dependent remineralisation switch
72!!       jsfd        :  accelerate seafloor detritus remin. switch
73!!       xmd         :  detrital nitrogen remineralisation rate
74!!       xmdc        :  detrital carbon   remineralisation rate
75!!
76!! Stochiometric ratios
77!!       xthetapn    :  non-diatom C:N ratio
78!!       xthetapd    :  diatom C:N ratio
79!!       xthetazmi   :  microzoo C:N ratio
80!!       xthetazme   :  mesozoo C:N ratio
81!!       xthetad     :  detritus C:N ratio (FOR IMPLICIT DTC ONLY)
82!!       xrfn        :  phytoplankton Fe:N ratio
83!!  xrsn        :  phytoplankton Si:N ratio (LEGACY; NOT USED)
84!!
85!! Iron parameters
86!!       jiron       :  iron scavenging submodel switch
87!!       xfe_mass    :  iron atomic mass
88!!  xfe_sol     :  aeolian iron solubility
89!!  xfe_sed     :  sediment iron input
90!!  xLgT      :  total ligand concentration (umol/m3)
91!!  xk_FeL       :  dissociation constant for (Fe + L)
92!!  xk_sc_Fe    :  scavenging rate of "free" iron
93!! 
94!! Fast-sinking detritus parameters
95!!       jmartin     :  fast detritus remineralisation switch
96!!       jfdfate     :  fate of fast detritus at seafloor switch
97!!       jrratio     :  rain ratio switch
98!!  jocalccd    :  CCD switch
99!!  xridg_r0    :  Ridgwell rain ratio coefficient
100!!       xfdfrac1    :  fast-sinking fraction of diatom nat. mort. losses
101!!       xfdfrac2    :  fast-sinking fraction of mesozooplankton mort. losses
102!!       xfdfrac3    :  fast-sinking fraction of diatom silicon grazing losses
103!!       xcaco3a     :  polar (high latitude) CaCO3 fraction
104!!       xcaco3b     :  equatorial (low latitude) CaCO3 fraction
105!!       xmassc      :  organic C mass:mole ratio, C106 H175 O40 N16 P1
106!!       xmassca     :  calcium carbonate mass:mole ratio, CaCO3
107!!       xmasssi     :  biogenic silicon mass:mole ratio, (H2SiO3)n
108!!       xprotca     :  calcium carbonate protection ratio
109!!       xprotsi     :  biogenic silicon protection ratio
110!!       xfastc      :  organic C remineralisation length scale
111!!       xfastca     :  calcium carbonate dissolution length scale
112!!       xfastsi     :  biogenic silicon dissolution length scale
113!!
114!! Benthos parameters
115!!       jorgben     :  does   organic detritus go to the benthos?
116!!       jinorgben   :  does inorganic detritus go to the benthos?
117!!       xsedn       :  organic   nitrogen sediment remineralisation rate
118!!       xsedfe      :  organic   iron     sediment remineralisation rate
119!!       xsedsi      :  inorganic silicon  sediment dissolution      rate
120!!       xsedc       :  organic   carbon   sediment remineralisation rate
121!!       xsedca      :  inorganic carbon   sediment dissolution      rate
122!!       xburial     :  burial fraction of sediment material
123!!
124!! River parameters
125!!       jriver_n    :  riverine N          input?
126!!       jriver_si   :  riverine Si         input?
127!!       jriver_c    :  riverine C          input?
128!!       jriver_alk  :  riverine alkalinity input?
129!!       jriver_dep  :  depth of riverine   input?
130!!
131!! Miscellaneous
132!!       xsdiss      :  diatom frustule dissolution rate
133!!
134!! Gravitational sinking     
135!!       vsed        :  detritus gravitational sinking rate
136!!       xhr         :  coeff for Martin's remineralisation profile
137!!
138!! Additional parameters
139!!       jpkb        :  vertical layer for diagnostic of the vertical flux
140!!
141!! UKESM1 - new diagnostics  !! Jpalm
142!!       chl_out     : (IF key_oasis) use surf Chl (1) or mld Chl (2)
143!!       dmscut      : (if jdms_model=1) modify Anderson et al. 2001 param
144!!                     default = 1.72
145!!       dmsmin      : (if jdms_model=1) modify Anderson et al. 2001 dms minimum
146!!                     default = 2.29
147!!       dmsslp      : (if jdms_model=1) modify Anderson et al. 2001 dms slope
148!!                     default = 8.24
149!!       jdms        :  include dms diagnostics
150!!       jdms_input  :  use instant (0) or diel-avg (1) inputs
151!!       jdms_model  :  which DMS model is passed to atmosphere
152!!       scl_chl     : (IF key_oasis) scaling the exported to UM chlorophyll field
153!!       
154&natbio
155!
156!! Primary production and chl related quantities
157      xxi       = 0.01257   !!
158      xaln      = 15.0      !! EKP (05/03/09)
159      xald      = 11.25     !! EKP (05/03/09)
160      jphy      = 1         !! 0 = T-independent; 1 = T-dependent; 2 = T-dependent-Q10
161      xvpn      = 0.640     !! EKP (05/03/09) -- daily avg = 0.530; daily cycle = 1.060; Q10 = 0.64
162      xvpd      = 0.600     !! EKP (05/03/09) -- daily avg = 0.500; daily cycle = 1.000; Q10 = 0.6
163      xthetam   = 0.05      !! EKP (05/03/09)
164      xthetamd  = 0.05      !! EKP (05/03/09)
165      jq10      = 1.50      !! Jpalm (17-06-2016)
166!!
167!! Diatom silicon parameters
168      xsin0     = 0.2       !! Mongin et al. (2003)
169      xnsi0     = 0.2       !! Mongin et al. (2003)
170      xuif      = 1.5       !! Mongin et al. (2003)
171!!
172!! Nutrient limitation
173      jliebig   = 0         !! 0 = multiplicative, 1 = Liebig
174      xnln      = 0.5       !! Fasham (1993)
175      xnld      = 0.75      !! EKP (05/03/09)
176      xsld      = 3.00      !! Fasham et al. (2006)-ish
177      xfln      = 0.00033   !! EKP (29/10/09); Parekh et al. (2005)
178      xfld      = 0.00067   !! EKP (29/10/09); Parekh et al. (2005); filtered through Moore et al. (2004)
179!!
180!! Grazing
181      xgmi      = 2.0       !! EKP (05/03/09)
182      xgme      = 0.5       !! AXY (21/12/09)
183      xkmi      = 0.8       !! EKP (26/02/09)
184      xkme      = 0.3       !! EKP (26/02/09)
185      xphi      = 0.20      !! Anderson & Pondaven (2003; 0.23); EKP (05/03/09; 0.20)
186      xbetan    = 0.77      !! Anderson & Pondaven (2003)
187      xbetac    = 0.64      !! Anderson & Pondaven (2003)
188!!    xbetan    = 0.69      !! compromise values inbetween those from ...
189!!    xbetac    = 0.69      !! Anderson & Pondaven (2003)for detrital carbon model
190      xkc       = 0.80      !! Anderson & Pondaven (2003)
191      xpmipn    = 0.75      !!
192      xpmid     = 0.25      !!
193      xpmepn    = 0.15      !! EKP (26/02/09)
194      xpmepd    = 0.35      !! EKP (26/02/09)
195      xpmezmi   = 0.35      !! EKP (26/02/09)
196      xpmed     = 0.15      !! EKP (26/02/09)
197!!
198!! Metabolic losses
199      xmetapn   = 0.02      !!
200      xmetapd   = 0.02      !!
201      xmetazmi  = 0.02      !!
202      xmetazme  = 0.02      !!
203!!
204!! Mortality losses
205      jmpn      = 3         !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid
206      xmpn      = 0.1       !!
207      xkphn     = 0.5       !! EKP (26/02/09): new parameter
208      jmpd      = 3         !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid
209      xmpd      = 0.1       !!
210      xkphd     = 0.5       !! EKP (26/02/09): new parameter
211      jmzmi     = 3         !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid
212      xmzmi     = 0.1       !!
213      xkzmi     = 0.5       !!
214      jmzme     = 3         !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid
215      xmzme     = 0.2       !! EKP (26/02/09)
216      xkzme     = 0.75      !! EKP (26/02/09)
217!!
218!! Remineralisation
219      jmd       = 2         !! 0 = T-independent; 1 = T-dependent; 2 = T-dependent-Q10
220      jsfd      = 0         !! 0 = unchanged seafloor remin.; 1 = accelerated seafloor remin.
221      xmd       = 0.0190    !! T-dependent; 0.05 at 18C (Yool et al., 2010) - Q10 = 0.0190
222      xmdc      = 0.0152    !! T-dependent; 0.04 at 18C (Yool et al., 2010) - Q10 = 0.0152
223!!
224!! Stochiometric ratios
225      xthetapn  = 6.625     !! Redfield
226      xthetapd  = 6.625     !! Redfield
227      xthetazmi = 5.625     !! Redfield
228      xthetazme = 5.625     !! Redfield
229!! AXY (26/11/08): implicit detrital carbon change
230      xthetad   = 6.625     !! Redfield
231      xrfn      = 30.0e-6   !! Parekh et al. (2005)
232      xrsn      = 1.0       !! not used here; retained for Lobster
233!!
234!! Iron parameters
235      jiron     = 1         !! iron scavenging submodel switch
236      xfe_mass  = 55.485    !! Fe atomic mass
237      xfe_sol   = 0.00532   !! scaled to get same input as Parekh et al. (2005)
238      xfe_sed   = 0.000228  !! AXY (10/07/12): Moore-ish
239      xLgT      = 1.0       !! from Diat-HadOCC; from Parekh et al. (2005)
240      xk_FeL   = 100.0     !! from Diat-HadOCC
241      xk_sc_Fe  = 1.e-3     !! from Dutkiewicz et al. (2005)
242!!
243!! Fast-sinking detritus parameters
244      jexport   = 1         !! 1 = ballast; 2 = Martin (1987); 3 = Henson (2011)
245      jfdfate   = 0         !! 0 = instant remin.; 1 = transmogrify into slow detritus
246      jrratio   = 2         !! 0 = Dunne (2005); 1 = Ridgwell (2007) surface; 2 = Ridgwell (2007) 3D
247      jocalccd  = 1         !! 0 = default, fixed; 1 = calculated, dynamic
248      xridg_r0  = 0.026     !! = 0.044, Ridgwell et al. (2007); scaled to 60% from preliminary sims
249      xfdfrac1  = 0.333     !! control parameter; no "real" value (AXY; 12/03/09)
250      xfdfrac2  = 1.00      !! control parameter; no "real" value (AXY; 12/03/09)
251      xfdfrac3  = 0.80      !! control parameter; no "real" value (AXY; 12/03/09)
252      xcaco3a   = 0.02      !! Dunne et al. (2005); not an exact value
253      xcaco3b   = 0.10      !! Dunne et al. (2005); not an exact value
254!! AXY (06/01/09): after contacting Dunne, new values are used for masses ...
255!!    xmassc    = 22.1188   !!
256!!    xmassca   = 100.086   !! original values; replaced by Dunne suggestion
257!!    xmasssi   = 78.0988   !!
258      xmassc    = 12.011    !! C atomic mass
259      xmassca   = 100.086   !! CaCO3; based on atomic masses
260      xmasssi   = 60.084    !! SiO2; based on atomic masses
261      xprotca   = 0.070     !! Dunne et al. (2005)
262      xprotsi   = 0.026     !! Dunne et al. (2005)
263      xfastc    = 188.0     !! Dunne et al. (2005)
264      xfastca   = 3500.0    !! Dunne et al. (2005)
265      xfastsi   = 2000.0    !! Dunne et al. (2005)
266!!
267!! Benthos parameters
268      jorgben   = 1         !! 0 = no; 1 = yes
269      jinorgben = 1         !! 0 = no; 1 = yes
270      xsedn     = 0.05      !! default ERSEM-ish value
271      xsedfe    = 0.05      !! default ERSEM-ish value
272      xsedsi    = 0.01      !! default ERSEM-ish value
273      xsedc     = 0.05      !! default ERSEM-ish value
274      xsedca    = 0.01      !! default ERSEM-ish value
275      xburial   = 0.0       !! set to zero
276!!
277!! River parameters
278      jriver_n  = 0         !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes
279      jriver_si = 0         !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes
280      jriver_c  = 0         !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes
281      jriver_alk= 0         !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes
282      jriver_dep= 5         !! depth to which river nutrients are added
283!!
284!! Miscellaneous
285      xsdiss    = 0.006     !! Mongin et al. (2003); 0.006 is an alternative
286!!
287!! Gravitational sinking
288      vsed      = 3.472e-5  !! EKP (05/03/09)
289!!
290!! Additional parameters
291      jpkb      = 16        !!
292!!
293!! UKESM1 - new diagnostics !! Jpalm
294      chl_out    = 1        !! (IF key_oasis) use surf Chl (1) or mld Chl (2)
295      dmscut     = 1.72     !! (if jdms_model=1) modify Anderson et al. 2001 param
296!!                             default = 1.72
297      dmsmin     = 2.29     !! (if jdms_model=1) modify Anderson et al. 2001 dms minimum
298!!                             default = 2.29
299      dmsslp     = 8.24     !! (if jdms_model=1) modify Anderson et al. 2001 dms slope
300!!                             default = 8.24
301      jdms       = 1        !! include dms diagnostics
302      jdms_input = 1        !! use instant (0) or diel-avg (1) inputs
303      jdms_model = 3        !! choice of DMS model passed to atmosphere
304!!                             1 = ANDR, 2 = SIMO, 3 = ARAN, 4 = HALL
305      scl_chl    = 1.0      !! (IF key_oasis) scaling the exported to UM chlorophyll field
306!!
307/
308!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
309!       natroam
310!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
311!
312!!       xthetaphy :  oxygen evolution/consumption by phytoplankton
313!!                    = (32 / 16) + (6.625 * (119 / 106)) = (2 + 7.4375) mol O2 / mol N
314!!       xthetazoo :  oxygen consumption by zooplankton
315!!                    = (32 / 16) + (5.625 * (119 / 106)) = (2 + 6.3149) mol O2 / mol N
316!!       xthetanit :  oxygen consumption by nitrogen remineralisation
317!!                    = (32 / 16) = 2 mol O2 / mol N
318!!       xthetarem :  oxygen consumption by carbon remineralisation
319!!                    = (119 / 106) = 1.1226 mol O2 / mol C
320!!       xo2min    :  oxygen minimum concentration
321!
322&natroam
323   xthetaphy = 9.4375
324   xthetazoo = 8.3149
325   xthetanit = 2.0
326   xthetarem = 1.1226
327   xo2min    = 4.0
328/
329!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
330!       natopt
331!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
332!
333!   xkg0 : green water absorption coefficient   [m-1]
334!   xkr0 : red water absorption coefficient     [m-1]
335!  xkgp  : pigment green absorption coefficient [m-1]
336!  xkrp  : pigment red absorption coefficient   [m-1]
337!  xlg   : green chl exposant
338!  xlr   : red chl exposant
339!  rpig  : chla / (chla+phea) ratio
340!
341&natopt
342   xkg0 = 0.0232
343   xkr0 = 0.225
344   xkgp = 0.074
345   xkrp = 0.037
346   xlg  = 0.629
347   xlr  = 0.674
348   rpig = 0.7
349/
350!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
351!       natdbi used if key_trc_diabio is set
352!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
353!
354!  ctrbio    : array of biological trend numbers
355!  ctrbil    : character string describing each biological trend
356!  ctrbiu    : array of unit numbers used for trend output
357!  nwritebio : frequency of biological model output [timesteps]
358!
359&natdbi
360   ctrbio    = "BIO_01", "BIO_02", "BIO_03", "BIO_04", "BIO_05", "BIO_06", "BIO_07", "BIO_08", "BIO_09", "BIO_10", "BIO_11", "BIO_12", "BIO_13", "BIO_14", "BIO_15", "BIO_16", "BIO_17", "BIO_18", "BIO_19", "BIO_20", "BIO_21", "BIO_22", "BIO_23", "BIO_24", "BIO_25", "BIO_26", "BIO_27", "BIO_28", "BIO_29", "BIO_30", "BIO_31", "BIO_32", "BIO_33", "BIO_34"
361   ctrbil    = "BIO_01", "BIO_02", "BIO_03", "BIO_04", "BIO_05", "BIO_06", "BIO_07", "BIO_08", "BIO_09", "BIO_10", "BIO_11", "BIO_12", "BIO_13", "BIO_14", "BIO_15", "BIO_16", "BIO_17", "BIO_18", "BIO_19", "BIO_20", "BIO_21", "BIO_22", "BIO_23", "BIO_24", "BIO_25", "BIO_26", "BIO_27", "BIO_28", "BIO_29", "BIO_30", "BIO_31", "BIO_32", "BIO_33", "BIO_34"
362   ctrbiu    = "m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m","m"
363   nwritebio = 10
364!/
365!&natopt
366/
367!=================================================
368! nammeddia    Passive tracers additional diagnostics
369!=================================================
370!
371!      ctrc2d  : 2d output field name
372!      ctrc2u  : 2d output field unit
373!      ctrc2l  : 2d output field long name
374!
375!      nwriteadd: frequency of additional arrays outputs(namelist)
376&nammeddia
377/
378!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
379&nammedsbc     !   parameters for inputs deposition
380!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
381!              !  file name        ! frequency (hours) ! variable      ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
382!              !                   !  (if <0  months)  !   name        !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
383   sn_dust     = 'dust.orca'       ,     -1            , 'dust'        ,  .true.      , .true. , 'yearly'  , ''       , ''    , ''
384!
385   cn_dir      = './'      !  root directory for the location of the dynamical files
386   bdustfer    =  .true.   ! boolean for dust input from the atmosphere
387/
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