!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ! ! BIO namelist : MEDUSA biological model option and parameter input ! ------------- ! !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' ! natbio Shared parameters for dynamics/advection/thermo !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ! !! Primary production and chl related quantities !! xxi : conversion factor from gC to mmolN !! xaln : Chl-a specific initial slope of P-I curve for non-diatoms !! xald : Chl-a specific initial slope of P-I curve for diatoms !! jphy : phytoplankton T-dependent growth switch !! xvpn : maximum growth rate for non-diatoms !! xvpd : maximum growth rate for diatoms !! xthetam : maximum Chl to C ratio for non-diatoms !! xthetamd : maximum Chl to C ratio for diatoms !! !! Diatom silicon parameters !! xsin0 : minimum diatom Si:N ratio !! xnsi0 : minimum diatom N:Si ratio !! xuif : hypothetical growth ratio at infinite Si:N ratio !! !! Nutrient limitation !! jliebig : Liebig nutrient uptake switch !! xnln : half-sat constant for DIN uptake by non-diatoms !! xnld : half-sat constant for DIN uptake by diatoms !! xsl : half-sat constant for Si uptake by diatoms !! xfld : half-sat constant for Fe uptake by diatoms !! xfln : half-sat constant for Fe uptake by non-datoms !! !! Grazing !! xgmi : microzoo maximum growth rate !! xgme : mesozoo maximum growth rate !! xkmi : microzoo grazing half-sat parameter !! xkme : mesozoo grazing half-sat parameter !! xphi : micro/mesozoo grazing inefficiency !! xbetan : micro/mesozoo N assimilation efficiency !! xbetac : micro/mesozoo C assimilation efficiency !! xkc : micro/mesozoo net C growth efficiency !! xpmipn : grazing preference of microzoo for non-diatoms !! xpmid : grazing preference of microzoo for diatoms !! xpmepn : grazing preference of mesozoo for non-diatoms !! xpmepd : grazing preference of mesozoo for diatoms !! xpmezmi : grazing preference of mesozoo for microzoo !! xpmed : grazing preference of mesozoo for detritus !! !! Metabolic losses !! xmetapn : non-diatom metabolic loss rate !! xmetapd : diatom metabolic loss rate !! xmetazmi : microzoo metabolic loss rate !! xmetazme : mesozoo metabolic loss rate !! !! Mortality losses !! jmpn : non-diatom mortality functional form !! xmpn : non-diatom mortality rate !! xkphn : non-diatom mortality half-sat constant !! jmpd : diatom mortality functional form !! xmpd : diatom mortality rate !! xkphd : diatom mortality half-sat constant !! jmzmi : microzoo mortality functional form !! xmzmi : microzoo mortality rate !! xkzmi : microzoo mortality half-sat constant !! jmzme : mesozoo mortality functional form !! xmzme : mesozoo mortality rate !! xkzme : mesozoo mortality half-sat constant !! !! Remineralisation !! jmd : detritus T-dependent remineralisation switch !! jsfd : accelerate seafloor detritus remin. switch !! xmd : detrital nitrogen remineralisation rate !! xmdc : detrital carbon remineralisation rate !! !! Stochiometric ratios !! xthetapn : non-diatom C:N ratio !! xthetapd : diatom C:N ratio !! xthetazmi : microzoo C:N ratio !! xthetazme : mesozoo C:N ratio !! xthetad : detritus C:N ratio (FOR IMPLICIT DTC ONLY) !! xrfn : phytoplankton Fe:N ratio !! xrsn : phytoplankton Si:N ratio (LEGACY; NOT USED) !! !! Iron parameters !! jiron : iron scavenging submodel switch !! xfe_mass : iron atomic mass !! xfe_sol : aeolian iron solubility !! xfe_sed : sediment iron input !! xLgT : total ligand concentration (umol/m3) !! xk_FeL : dissociation constant for (Fe + L) !! xk_sc_Fe : scavenging rate of "free" iron !! !! Fast-sinking detritus parameters !! jmartin : fast detritus remineralisation switch !! jfdfate : fate of fast detritus at seafloor switch !! jrratio : rain ratio switch !! jocalccd : CCD switch !! xridg_r0 : Ridgwell rain ratio coefficient !! xfdfrac1 : fast-sinking fraction of diatom nat. mort. losses !! xfdfrac2 : fast-sinking fraction of mesozooplankton mort. losses !! xfdfrac3 : fast-sinking fraction of diatom silicon grazing losses !! xcaco3a : polar (high latitude) CaCO3 fraction !! xcaco3b : equatorial (low latitude) CaCO3 fraction !! xmassc : organic C mass:mole ratio, C106 H175 O40 N16 P1 !! xmassca : calcium carbonate mass:mole ratio, CaCO3 !! xmasssi : biogenic silicon mass:mole ratio, (H2SiO3)n !! xprotca : calcium carbonate protection ratio !! xprotsi : biogenic silicon protection ratio !! xfastc : organic C remineralisation length scale !! xfastca : calcium carbonate dissolution length scale !! xfastsi : biogenic silicon dissolution length scale !! !! Benthos parameters !! jorgben : does organic detritus go to the benthos? !! jinorgben : does inorganic detritus go to the benthos? !! xsedn : organic nitrogen sediment remineralisation rate !! xsedfe : organic iron sediment remineralisation rate !! xsedsi : inorganic silicon sediment dissolution rate !! xsedc : organic carbon sediment remineralisation rate !! xsedca : inorganic carbon sediment dissolution rate !! xburial : burial fraction of sediment material !! !! River parameters !! jriver_n : riverine N input? !! jriver_si : riverine Si input? !! jriver_c : riverine C input? !! jriver_alk : riverine alkalinity input? !! jriver_dep : depth of riverine input? !! !! Miscellaneous !! xsdiss : diatom frustule dissolution rate !! !! Gravitational sinking !! vsed : detritus gravitational sinking rate !! xhr : coeff for Martin's remineralisation profile !! !! Additional parameters !! jpkb : vertical layer for diagnostic of the vertical flux !! !! UKESM1 - new diagnostics !! Jpalm !! chl_out : (IF key_oasis) use surf Chl (1) or mld Chl (2) !! dmscut : (if jdms_model=1) modify Anderson et al. 2001 param !! default = 1.72 !! dmsmin : (if jdms_model=1) modify Anderson et al. 2001 dms minimum !! default = 2.29 !! dmsslp : (if jdms_model=1) modify Anderson et al. 2001 dms slope !! default = 8.24 !! jdms : include dms diagnostics !! jdms_input : use instant (0) or diel-avg (1) inputs !! jdms_model : which DMS model is passed to atmosphere !! scl_chl : (IF key_oasis) scaling the exported to UM chlorophyll field !! &natbio ! !! Primary production and chl related quantities xxi = 0.01257 !! xaln = 15.0 !! EKP (05/03/09) xald = 11.25 !! EKP (05/03/09) jphy = 1 !! 0 = T-independent; 1 = T-dependent; 2 = T-dependent-Q10 xvpn = 0.640 !! EKP (05/03/09) -- daily avg = 0.530; daily cycle = 1.060; Q10 = 0.64 xvpd = 0.600 !! EKP (05/03/09) -- daily avg = 0.500; daily cycle = 1.000; Q10 = 0.6 xthetam = 0.05 !! EKP (05/03/09) xthetamd = 0.05 !! EKP (05/03/09) jq10 = 1.50 !! Jpalm (17-06-2016) !! !! Diatom silicon parameters xsin0 = 0.2 !! Mongin et al. (2003) xnsi0 = 0.2 !! Mongin et al. (2003) xuif = 1.5 !! Mongin et al. (2003) !! !! Nutrient limitation jliebig = 0 !! 0 = multiplicative, 1 = Liebig xnln = 0.5 !! Fasham (1993) xnld = 0.75 !! EKP (05/03/09) xsld = 3.00 !! Fasham et al. (2006)-ish xfln = 0.00033 !! EKP (29/10/09); Parekh et al. (2005) xfld = 0.00067 !! EKP (29/10/09); Parekh et al. (2005); filtered through Moore et al. (2004) !! !! Grazing xgmi = 2.0 !! EKP (05/03/09) xgme = 0.5 !! AXY (21/12/09) xkmi = 0.8 !! EKP (26/02/09) xkme = 0.3 !! EKP (26/02/09) xphi = 0.20 !! Anderson & Pondaven (2003; 0.23); EKP (05/03/09; 0.20) xbetan = 0.77 !! Anderson & Pondaven (2003) xbetac = 0.64 !! Anderson & Pondaven (2003) !! xbetan = 0.69 !! compromise values inbetween those from ... !! xbetac = 0.69 !! Anderson & Pondaven (2003)for detrital carbon model xkc = 0.80 !! Anderson & Pondaven (2003) xpmipn = 0.75 !! xpmid = 0.25 !! xpmepn = 0.15 !! EKP (26/02/09) xpmepd = 0.35 !! EKP (26/02/09) xpmezmi = 0.35 !! EKP (26/02/09) xpmed = 0.15 !! EKP (26/02/09) !! !! Metabolic losses xmetapn = 0.02 !! xmetapd = 0.02 !! xmetazmi = 0.02 !! xmetazme = 0.02 !! !! !! Mortality losses jmpn = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid xmpn = 0.1 !! xkphn = 0.5 !! EKP (26/02/09): new parameter jmpd = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid xmpd = 0.1 !! xkphd = 0.5 !! EKP (26/02/09): new parameter jmzmi = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid xmzmi = 0.1 !! xkzmi = 0.5 !! jmzme = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid xmzme = 0.2 !! EKP (26/02/09) xkzme = 0.75 !! EKP (26/02/09) !! !! Remineralisation jmd = 2 !! 0 = T-independent; 1 = T-dependent; 2 = T-dependent-Q10 jsfd = 0 !! 0 = unchanged seafloor remin.; 1 = accelerated seafloor remin. xmd = 0.0190 !! T-dependent; 0.05 at 18C (Yool et al., 2010) - Q10 = 0.0190 xmdc = 0.0152 !! T-dependent; 0.04 at 18C (Yool et al., 2010) - Q10 = 0.0152 !! !! Stochiometric ratios xthetapn = 6.625 !! Redfield xthetapd = 6.625 !! Redfield xthetazmi = 5.625 !! Redfield xthetazme = 5.625 !! Redfield !! AXY (26/11/08): implicit detrital carbon change xthetad = 6.625 !! Redfield xrfn = 30.0e-6 !! Parekh et al. (2005) xrsn = 1.0 !! not used here; retained for Lobster !! !! Iron parameters jiron = 1 !! iron scavenging submodel switch xfe_mass = 55.485 !! Fe atomic mass xfe_sol = 0.00532 !! scaled to get same input as Parekh et al. (2005) xfe_sed = 0.000228 !! AXY (10/07/12): Moore-ish xLgT = 1.0 !! from Diat-HadOCC; from Parekh et al. (2005) xk_FeL = 100.0 !! from Diat-HadOCC xk_sc_Fe = 1.e-3 !! from Dutkiewicz et al. (2005) !! !! Fast-sinking detritus parameters jexport = 1 !! 1 = ballast; 2 = Martin (1987); 3 = Henson (2011) jfdfate = 0 !! 0 = instant remin.; 1 = transmogrify into slow detritus jrratio = 2 !! 0 = Dunne (2005); 1 = Ridgwell (2007) surface; 2 = Ridgwell (2007) 3D jocalccd = 1 !! 0 = default, fixed; 1 = calculated, dynamic xridg_r0 = 0.026 !! = 0.044, Ridgwell et al. (2007); scaled to 60% from preliminary sims xfdfrac1 = 0.333 !! control parameter; no "real" value (AXY; 12/03/09) xfdfrac2 = 1.00 !! control parameter; no "real" value (AXY; 12/03/09) xfdfrac3 = 0.80 !! control parameter; no "real" value (AXY; 12/03/09) xcaco3a = 0.02 !! Dunne et al. (2005); not an exact value xcaco3b = 0.10 !! Dunne et al. (2005); not an exact value !! AXY (06/01/09): after contacting Dunne, new values are used for masses ... !! xmassc = 22.1188 !! !! xmassca = 100.086 !! original values; replaced by Dunne suggestion !! xmasssi = 78.0988 !! xmassc = 12.011 !! C atomic mass xmassca = 100.086 !! CaCO3; based on atomic masses xmasssi = 60.084 !! SiO2; based on atomic masses xprotca = 0.070 !! Dunne et al. (2005) xprotsi = 0.026 !! Dunne et al. (2005) xfastc = 188.0 !! Dunne et al. (2005) xfastca = 3500.0 !! Dunne et al. (2005) xfastsi = 2000.0 !! Dunne et al. (2005) !! !! Benthos parameters jorgben = 1 !! 0 = no; 1 = yes jinorgben = 1 !! 0 = no; 1 = yes xsedn = 0.05 !! default ERSEM-ish value xsedfe = 0.05 !! default ERSEM-ish value xsedsi = 0.01 !! default ERSEM-ish value xsedc = 0.05 !! default ERSEM-ish value xsedca = 0.01 !! default ERSEM-ish value xburial = 0.0 !! set to zero !! !! River parameters jriver_n = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes jriver_si = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes jriver_c = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes jriver_alk= 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes jriver_dep= 5 !! depth to which river nutrients are added !! !! Miscellaneous xsdiss = 0.006 !! Mongin et al. (2003); 0.006 is an alternative !! !! Gravitational sinking vsed = 3.472e-5 !! EKP (05/03/09) !! !! Additional parameters jpkb = 16 !! !! !! UKESM1 - new diagnostics !! Jpalm chl_out = 1 !! (IF key_oasis) use surf Chl (1) or mld Chl (2) dmscut = 1.72 !! (if jdms_model=1) modify Anderson et al. 2001 param !! default = 1.72 dmsmin = 2.29 !! (if jdms_model=1) modify Anderson et al. 2001 dms minimum !! default = 2.29 dmsslp = 8.24 !! (if jdms_model=1) modify Anderson et al. 2001 dms slope !! default = 8.24 jdms = 1 !! include dms diagnostics jdms_input = 1 !! use instant (0) or diel-avg (1) inputs jdms_model = 3 !! choice of DMS model passed to atmosphere !! 1 = ANDR, 2 = SIMO, 3 = ARAN, 4 = HALL scl_chl = 1.0 !! (IF key_oasis) scaling the exported to UM chlorophyll field !! / !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' ! natroam !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ! !! xthetaphy : oxygen evolution/consumption by phytoplankton !! = (32 / 16) + (6.625 * (119 / 106)) = (2 + 7.4375) mol O2 / mol N !! xthetazoo : oxygen consumption by zooplankton !! = (32 / 16) + (5.625 * (119 / 106)) = (2 + 6.3149) mol O2 / mol N !! xthetanit : oxygen consumption by nitrogen remineralisation !! = (32 / 16) = 2 mol O2 / mol N !! xthetarem : oxygen consumption by carbon remineralisation !! = (119 / 106) = 1.1226 mol O2 / mol C !! xo2min : oxygen minimum concentration ! &natroam xthetaphy = 9.4375 xthetazoo = 8.3149 xthetanit = 2.0 xthetarem = 1.1226 xo2min = 4.0 / !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' ! natopt !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ! ! xkg0 : green water absorption coefficient [m-1] ! xkr0 : red water absorption coefficient [m-1] ! xkgp : pigment green absorption coefficient [m-1] ! xkrp : pigment red absorption coefficient [m-1] ! xlg : green chl exposant ! xlr : red chl exposant ! rpig : chla / (chla+phea) ratio ! &natopt xkg0 = 0.0232 xkr0 = 0.225 xkgp = 0.074 xkrp = 0.037 xlg = 0.629 xlr = 0.674 rpig = 0.7 / !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' ! natdbi used if key_trc_diabio is set !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ! ! ctrbio : array of biological trend numbers ! ctrbil : character string describing each biological trend ! ctrbiu : array of unit numbers used for trend output ! nwritebio : frequency of biological model output [timesteps] ! &natdbi 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" 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" 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" nwritebio = 10 !/ !&natopt / !================================================= ! nammeddia Passive tracers additional diagnostics !================================================= ! ! ctrc2d : 2d output field name ! ctrc2u : 2d output field unit ! ctrc2l : 2d output field long name ! ! nwriteadd: frequency of additional arrays outputs(namelist) &nammeddia / !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' &nammedsbc ! parameters for inputs deposition !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation ! land/sea mask ! ! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing ! filename ! sn_dust = 'dust.orca' , -1 , 'dust' , .true. , .true. , 'yearly' , '' , '' , '' ! cn_dir = './' ! root directory for the location of the dynamical files bdustfer = .true. ! boolean for dust input from the atmosphere /