| 1 | !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 2 | ! |
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| 3 | ! BIO namelist : MEDUSA biological model option and parameter input |
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| 4 | ! ------------- |
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| 5 | ! |
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| 6 | !>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> |
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| 7 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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| 8 | ! natbio Shared parameters for dynamics/advection/thermo |
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| 9 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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| 10 | ! |
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| 11 | !! Primary production and chl related quantities |
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| 12 | !! xxi : conversion factor from gC to mmolN |
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| 13 | !! xaln : Chl-a specific initial slope of P-I curve for non-diatoms |
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| 14 | !! xald : Chl-a specific initial slope of P-I curve for diatoms |
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| 15 | !! jphy : phytoplankton T-dependent growth switch |
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| 16 | !! xvpn : maximum growth rate for non-diatoms |
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| 17 | !! xvpd : maximum growth rate for diatoms |
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| 18 | !! xthetam : maximum Chl to C ratio for non-diatoms |
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| 19 | !! xthetamd : maximum Chl to C ratio for diatoms |
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| 20 | !! |
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| 21 | !! Diatom silicon parameters |
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| 22 | !! xsin0 : minimum diatom Si:N ratio |
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| 23 | !! xnsi0 : minimum diatom N:Si ratio |
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| 24 | !! xuif : hypothetical growth ratio at infinite Si:N ratio |
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| 25 | !! |
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| 26 | !! Nutrient limitation |
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| 27 | !! jliebig : Liebig nutrient uptake switch |
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| 28 | !! xnln : half-sat constant for DIN uptake by non-diatoms |
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| 29 | !! xnld : half-sat constant for DIN uptake by diatoms |
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| 30 | !! xsl : half-sat constant for Si uptake by diatoms |
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| 31 | !! xfld : half-sat constant for Fe uptake by diatoms |
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| 32 | !! xfln : half-sat constant for Fe uptake by non-datoms |
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| 33 | !! |
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| 34 | !! Grazing |
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| 35 | !! xgmi : microzoo maximum growth rate |
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| 36 | !! xgme : mesozoo maximum growth rate |
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| 37 | !! xkmi : microzoo grazing half-sat parameter |
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| 38 | !! xkme : mesozoo grazing half-sat parameter |
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| 39 | !! xphi : micro/mesozoo grazing inefficiency |
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| 40 | !! xbetan : micro/mesozoo N assimilation efficiency |
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| 41 | !! xbetac : micro/mesozoo C assimilation efficiency |
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| 42 | !! xkc : micro/mesozoo net C growth efficiency |
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| 43 | !! xpmipn : grazing preference of microzoo for non-diatoms |
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| 44 | !! xpmid : grazing preference of microzoo for diatoms |
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| 45 | !! xpmepn : grazing preference of mesozoo for non-diatoms |
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| 46 | !! xpmepd : grazing preference of mesozoo for diatoms |
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| 47 | !! xpmezmi : grazing preference of mesozoo for microzoo |
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| 48 | !! xpmed : grazing preference of mesozoo for detritus |
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| 49 | !! |
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| 50 | !! Metabolic losses |
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| 51 | !! xmetapn : non-diatom metabolic loss rate |
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| 52 | !! xmetapd : diatom metabolic loss rate |
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| 53 | !! xmetazmi : microzoo metabolic loss rate |
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| 54 | !! xmetazme : mesozoo metabolic loss rate |
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| 55 | !! |
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| 56 | !! Metabolic losses |
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| 57 | !! xmetapn : non-diatom metabolic loss rate |
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| 58 | !! xmetapd : diatom metabolic loss rate |
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| 59 | !! xmetazmi : microzoo metabolic loss rate |
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| 60 | !! xmetazme : mesozoo metabolic loss rate |
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| 61 | !! |
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| 62 | !! Mortality losses |
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| 63 | !! jmpn : non-diatom mortality functional form |
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| 64 | !! xmpn : non-diatom mortality rate |
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| 65 | !! xkphn : non-diatom mortality half-sat constant |
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| 66 | !! jmpd : diatom mortality functional form |
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| 67 | !! xmpd : diatom mortality rate |
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| 68 | !! xkphd : diatom mortality half-sat constant |
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| 69 | !! jmzmi : microzoo mortality functional form |
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| 70 | !! xmzmi : microzoo mortality rate |
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| 71 | !! xkzmi : microzoo mortality half-sat constant |
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| 72 | !! jmzme : mesozoo mortality functional form |
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| 73 | !! xmzme : mesozoo mortality rate |
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| 74 | !! xkzme : mesozoo mortality half-sat constant |
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| 75 | !! |
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| 76 | !! Remineralisation |
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| 77 | !! jmd : detritus T-dependent remineralisation switch |
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| 78 | !! jsfd : accelerate seafloor detritus remin. switch |
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| 79 | !! xmd : detrital nitrogen remineralisation rate |
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| 80 | !! xmdc : detrital carbon remineralisation rate |
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| 81 | !! |
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| 82 | !! Stochiometric ratios |
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| 83 | !! xthetapn : non-diatom C:N ratio |
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| 84 | !! xthetapd : diatom C:N ratio |
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| 85 | !! xthetazmi : microzoo C:N ratio |
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| 86 | !! xthetazme : mesozoo C:N ratio |
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| 87 | !! xthetad : detritus C:N ratio (FOR IMPLICIT DTC ONLY) |
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| 88 | !! xrfn : phytoplankton Fe:N ratio |
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| 89 | !! xrsn : phytoplankton Si:N ratio (LEGACY; NOT USED) |
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| 90 | !! |
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| 91 | !! Iron parameters |
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| 92 | !! jiron : iron scavenging submodel switch |
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| 93 | !! xfe_mass : iron atomic mass |
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| 94 | !! xfe_sol : aeolian iron solubility |
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| 95 | !! xfe_sed : sediment iron input |
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| 96 | !! xLgT : total ligand concentration (umol/m3) |
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| 97 | !! xk_FeL : dissociation constant for (Fe + L) |
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| 98 | !! xk_sc_Fe : scavenging rate of "free" iron |
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| 99 | !! |
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| 100 | !! Fast-sinking detritus parameters |
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| 101 | !! jmartin : fast detritus remineralisation switch |
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| 102 | !! jfdfate : fate of fast detritus at seafloor switch |
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| 103 | !! jrratio : rain ratio switch |
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| 104 | !! jocalccd : CCD switch |
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| 105 | !! xridg_r0 : Ridgwell rain ratio coefficient |
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| 106 | !! xfdfrac1 : fast-sinking fraction of diatom nat. mort. losses |
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| 107 | !! xfdfrac2 : fast-sinking fraction of mesozooplankton mort. losses |
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| 108 | !! xfdfrac3 : fast-sinking fraction of diatom silicon grazing losses |
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| 109 | !! xcaco3a : polar (high latitude) CaCO3 fraction |
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| 110 | !! xcaco3b : equatorial (low latitude) CaCO3 fraction |
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| 111 | !! xmassc : organic C mass:mole ratio, C106 H175 O40 N16 P1 |
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| 112 | !! xmassca : calcium carbonate mass:mole ratio, CaCO3 |
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| 113 | !! xmasssi : biogenic silicon mass:mole ratio, (H2SiO3)n |
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| 114 | !! xprotca : calcium carbonate protection ratio |
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| 115 | !! xprotsi : biogenic silicon protection ratio |
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| 116 | !! xfastc : organic C remineralisation length scale |
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| 117 | !! xfastca : calcium carbonate dissolution length scale |
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| 118 | !! xfastsi : biogenic silicon dissolution length scale |
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| 119 | !! |
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| 120 | !! Benthos parameters |
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| 121 | !! jorgben : does organic detritus go to the benthos? |
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| 122 | !! jinorgben : does inorganic detritus go to the benthos? |
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| 123 | !! xsedn : organic nitrogen sediment remineralisation rate |
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| 124 | !! xsedfe : organic iron sediment remineralisation rate |
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| 125 | !! xsedsi : inorganic silicon sediment dissolution rate |
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| 126 | !! xsedc : organic carbon sediment remineralisation rate |
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| 127 | !! xsedca : inorganic carbon sediment dissolution rate |
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| 128 | !! xburial : burial fraction of sediment material |
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| 129 | !! |
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| 130 | !! River parameters |
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| 131 | !! jriver_n : riverine N input? |
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| 132 | !! jriver_si : riverine Si input? |
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| 133 | !! jriver_c : riverine C input? |
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| 134 | !! jriver_alk : riverine alkalinity input? |
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| 135 | !! jriver_dep : depth of riverine input? |
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| 136 | !! |
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| 137 | !! Miscellaneous |
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| 138 | !! xsdiss : diatom frustule dissolution rate |
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| 139 | !! |
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| 140 | !! Gravitational sinking |
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| 141 | !! vsed : detritus gravitational sinking rate |
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| 142 | !! xhr : coeff for Martin's remineralisation profile |
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| 143 | !! |
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| 144 | !! Additional parameters |
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| 145 | !! jpkb : vertical layer for diagnostic of the vertical flux |
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| 146 | !! |
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| 147 | !! UKESM1 - new diagnostics !! Jpalm |
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| 148 | !! jdms : include dms diagnostics |
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| 149 | !! |
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| 150 | !! |
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| 151 | &natbio |
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| 152 | ! |
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| 153 | !! Primary production and chl related quantities |
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| 154 | xxi = 0.01257 !! |
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| 155 | xaln = 15.0 !! EKP (05/03/09) |
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| 156 | xald = 11.25 !! EKP (05/03/09) |
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| 157 | jphy = 1 !! 0 = T-independent; 1 = T-dependent |
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| 158 | xvpn = 1.060 !! EKP (05/03/09) |
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| 159 | xvpd = 1.000 !! EKP (05/03/09) |
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| 160 | xthetam = 0.05 !! EKP (05/03/09) |
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| 161 | xthetamd = 0.05 !! EKP (05/03/09) |
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| 162 | !! |
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| 163 | !! Diatom silicon parameters |
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| 164 | xsin0 = 0.2 !! Mongin et al. (2003) |
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| 165 | xnsi0 = 0.2 !! Mongin et al. (2003) |
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| 166 | xuif = 1.5 !! Mongin et al. (2003) |
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| 167 | !! |
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| 168 | !! Nutrient limitation |
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| 169 | jliebig = 0 !! 0 = multiplicative, 1 = Liebig |
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| 170 | xnln = 0.5 !! Fasham (1993) |
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| 171 | xnld = 0.75 !! EKP (05/03/09) |
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| 172 | xsld = 3.00 !! Fasham et al. (2006)-ish |
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| 173 | xfln = 0.00033 !! EKP (29/10/09); Parekh et al. (2005) |
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| 174 | xfld = 0.00067 !! EKP (29/10/09); Parekh et al. (2005); filtered through Moore et al. (2004) |
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| 175 | !! |
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| 176 | !! Grazing |
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| 177 | xgmi = 2.0 !! EKP (05/03/09) |
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| 178 | xgme = 0.5 !! AXY (21/12/09) |
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| 179 | xkmi = 0.8 !! EKP (26/02/09) |
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| 180 | xkme = 0.3 !! EKP (26/02/09) |
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| 181 | xphi = 0.20 !! Anderson & Pondaven (2003; 0.23); EKP (05/03/09; 0.20) |
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| 182 | xbetan = 0.77 !! Anderson & Pondaven (2003) |
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| 183 | xbetac = 0.64 !! Anderson & Pondaven (2003) |
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| 184 | !! xbetan = 0.69 !! compromise values inbetween those from ... |
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| 185 | !! xbetac = 0.69 !! Anderson & Pondaven (2003)for detrital carbon model |
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| 186 | xkc = 0.80 !! Anderson & Pondaven (2003) |
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| 187 | xpmipn = 0.75 !! |
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| 188 | xpmid = 0.25 !! |
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| 189 | xpmepn = 0.15 !! EKP (26/02/09) |
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| 190 | xpmepd = 0.35 !! EKP (26/02/09) |
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| 191 | xpmezmi = 0.35 !! EKP (26/02/09) |
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| 192 | xpmed = 0.15 !! EKP (26/02/09) |
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| 193 | !! |
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| 194 | !! Metabolic losses |
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| 195 | xmetapn = 0.02 !! |
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| 196 | xmetapd = 0.02 !! |
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| 197 | xmetazmi = 0.02 !! |
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| 198 | xmetazme = 0.02 !! |
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| 199 | !! |
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| 200 | !! Mortality losses |
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| 201 | jmpn = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid |
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| 202 | xmpn = 0.1 !! |
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| 203 | xkphn = 0.5 !! EKP (26/02/09): new parameter |
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| 204 | jmpd = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid |
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| 205 | xmpd = 0.1 !! |
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| 206 | xkphd = 0.5 !! EKP (26/02/09): new parameter |
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| 207 | jmzmi = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid |
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| 208 | xmzmi = 0.1 !! |
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| 209 | xkzmi = 0.5 !! |
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| 210 | jmzme = 3 !! 1=linear; 2=quadratic; 3=hyperbolic; 4=sigmoid |
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| 211 | xmzme = 0.2 !! EKP (26/02/09) |
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| 212 | xkzme = 0.75 !! EKP (26/02/09) |
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| 213 | !! |
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| 214 | !! Remineralisation |
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| 215 | jmd = 1 !! 0 = T-independent; 1 = T-dependent |
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| 216 | jsfd = 0 !! 0 = unchanged seafloor remin.; 1 = accelerated seafloor remin. |
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| 217 | xmd = 0.0158 !! T-dependent; 0.05 at 18C (Yool et al., 2010) |
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| 218 | xmdc = 0.0127 !! T-dependent; 0.04 at 18C (Yool et al., 2010) |
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| 219 | !! |
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| 220 | !! Stochiometric ratios |
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| 221 | xthetapn = 6.625 !! Redfield |
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| 222 | xthetapd = 6.625 !! Redfield |
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| 223 | xthetazmi = 5.625 !! Redfield |
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| 224 | xthetazme = 5.625 !! Redfield |
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| 225 | !! AXY (26/11/08): implicit detrital carbon change |
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| 226 | xthetad = 6.625 !! Redfield |
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| 227 | xrfn = 30.0e-6 !! Parekh et al. (2005) |
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| 228 | xrsn = 1.0 !! not used here; retained for Lobster |
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| 229 | !! |
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| 230 | !! Iron parameters |
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| 231 | jiron = 1 !! iron scavenging submodel switch |
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| 232 | xfe_mass = 55.485 !! Fe atomic mass |
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| 233 | xfe_sol = 0.00532 !! scaled to get same input as Parekh et al. (2005) |
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| 234 | xfe_sed = 0.000228 !! AXY (10/07/12): Moore-ish |
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| 235 | xLgT = 1.0 !! from Diat-HadOCC; from Parekh et al. (2005) |
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| 236 | xk_FeL = 100.0 !! from Diat-HadOCC |
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| 237 | xk_sc_Fe = 1.e-3 !! from Dutkiewicz et al. (2005) |
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| 238 | !! |
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| 239 | !! Fast-sinking detritus parameters |
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| 240 | jexport = 1 !! 1 = ballast; 2 = Martin (1987); 3 = Henson (2011) |
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| 241 | jfdfate = 0 !! 0 = instant remin.; 1 = transmogrify into slow detritus |
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| 242 | jrratio = 2 !! 0 = Dunne (2005); 1 = Ridgwell (2007) surface; 2 = Ridgwell (2007) 3D |
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| 243 | jocalccd = 1 !! 0 = default, fixed; 1 = calculated, dynamic |
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| 244 | xridg_r0 = 0.026 !! = 0.044, Ridgwell et al. (2007); scaled to 60% from preliminary sims |
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| 245 | xfdfrac1 = 0.333 !! control parameter; no "real" value (AXY; 12/03/09) |
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| 246 | xfdfrac2 = 1.00 !! control parameter; no "real" value (AXY; 12/03/09) |
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| 247 | xfdfrac3 = 0.80 !! control parameter; no "real" value (AXY; 12/03/09) |
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| 248 | xcaco3a = 0.02 !! Dunne et al. (2005); not an exact value |
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| 249 | xcaco3b = 0.10 !! Dunne et al. (2005); not an exact value |
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| 250 | !! AXY (06/01/09): after contacting Dunne, new values are used for masses ... |
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| 251 | !! xmassc = 22.1188 !! |
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| 252 | !! xmassca = 100.086 !! original values; replaced by Dunne suggestion |
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| 253 | !! xmasssi = 78.0988 !! |
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| 254 | xmassc = 12.011 !! C atomic mass |
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| 255 | xmassca = 100.086 !! CaCO3; based on atomic masses |
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| 256 | xmasssi = 60.084 !! SiO2; based on atomic masses |
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| 257 | xprotca = 0.070 !! Dunne et al. (2005) |
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| 258 | xprotsi = 0.026 !! Dunne et al. (2005) |
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| 259 | xfastc = 188.0 !! Dunne et al. (2005) |
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| 260 | xfastca = 3500.0 !! Dunne et al. (2005) |
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| 261 | xfastsi = 2000.0 !! Dunne et al. (2005) |
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| 262 | !! |
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| 263 | !! Benthos parameters |
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| 264 | jorgben = 1 !! 0 = no; 1 = yes |
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| 265 | jinorgben = 1 !! 0 = no; 1 = yes |
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| 266 | xsedn = 0.05 !! default ERSEM-ish value |
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| 267 | xsedfe = 0.05 !! default ERSEM-ish value |
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| 268 | xsedsi = 0.01 !! default ERSEM-ish value |
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| 269 | xsedc = 0.05 !! default ERSEM-ish value |
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| 270 | xsedca = 0.01 !! default ERSEM-ish value |
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| 271 | xburial = 0.0 !! set to zero |
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| 272 | !! |
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| 273 | !! River parameters |
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| 274 | jriver_n = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes |
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| 275 | jriver_si = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes |
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| 276 | jriver_c = 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes |
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| 277 | jriver_alk= 0 !! 0 = no; 1 = runoff-dependent fluxes; 2= fixed fluxes |
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| 278 | jriver_dep= 5 !! depth to which river nutrients are added |
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| 279 | !! |
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| 280 | !! Miscellaneous |
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| 281 | xsdiss = 0.006 !! Mongin et al. (2003); 0.006 is an alternative |
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| 282 | !! |
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| 283 | !! Gravitational sinking |
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| 284 | vsed = 3.472e-5 !! EKP (05/03/09) |
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| 285 | !! |
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| 286 | !! Additional parameters |
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| 287 | jpkb = 16 !! |
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| 288 | !! |
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| 289 | / |
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| 290 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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| 291 | ! natroam |
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| 292 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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| 293 | ! |
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| 294 | !! xthetaphy : oxygen evolution/consumption by phytoplankton |
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| 295 | !! = (32 / 16) + (6.625 * (119 / 106)) = (2 + 7.4375) mol O2 / mol N |
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| 296 | !! xthetazoo : oxygen consumption by zooplankton |
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| 297 | !! = (32 / 16) + (5.625 * (119 / 106)) = (2 + 6.3149) mol O2 / mol N |
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| 298 | !! xthetanit : oxygen consumption by nitrogen remineralisation |
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| 299 | !! = (32 / 16) = 2 mol O2 / mol N |
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| 300 | !! xthetarem : oxygen consumption by carbon remineralisation |
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| 301 | !! = (119 / 106) = 1.1226 mol O2 / mol C |
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| 302 | !! xo2min : oxygen minimum concentration |
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| 303 | ! |
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| 304 | &natroam |
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| 305 | xthetaphy = 9.4375 |
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| 306 | xthetazoo = 8.3149 |
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| 307 | xthetanit = 2.0 |
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| 308 | xthetarem = 1.1226 |
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| 309 | xo2min = 4.0 |
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| 310 | / |
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| 311 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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| 312 | ! natopt |
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| 313 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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| 314 | ! |
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| 315 | ! xkg0 : green water absorption coefficient [m-1] |
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| 316 | ! xkr0 : red water absorption coefficient [m-1] |
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| 317 | ! xkgp : pigment green absorption coefficient [m-1] |
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| 318 | ! xkrp : pigment red absorption coefficient [m-1] |
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| 319 | ! xlg : green chl exposant |
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| 320 | ! xlr : red chl exposant |
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| 321 | ! rpig : chla / (chla+phea) ratio |
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| 322 | ! |
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| 323 | &natopt |
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| 324 | xkg0 = 0.0232 |
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| 325 | xkr0 = 0.225 |
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| 326 | xkgp = 0.074 |
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| 327 | xkrp = 0.037 |
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| 328 | xlg = 0.629 |
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| 329 | xlr = 0.674 |
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| 330 | rpig = 0.7 |
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| 331 | / |
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| 332 | !''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' |
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| 333 | ! natdbi used if key_trc_diabio is set |
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| 334 | !,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, |
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| 335 | ! |
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| 336 | ! ctrbio : array of biological trend numbers |
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| 337 | ! ctrbil : character string describing each biological trend |
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| 338 | ! ctrbiu : array of unit numbers used for trend output |
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| 339 | ! nwritebio : frequency of biological model output [timesteps] |
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| 340 | ! |
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| 341 | &natdbi |
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| 342 | 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" |
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| 343 | 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" |
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| 344 | 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" |
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| 345 | nwritebio = 10 |
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| 346 | !/ |
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| 347 | !&natopt |
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| 348 | / |
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| 349 | !================================================= |
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| 350 | ! nammeddia Passive tracers additional diagnostics |
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| 351 | !================================================= |
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| 352 | ! |
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| 353 | ! ctrc2d : 2d output field name |
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| 354 | ! ctrc2u : 2d output field unit |
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| 355 | ! ctrc2l : 2d output field long name |
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| 356 | ! |
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| 357 | ! nwriteadd: frequency of additional arrays outputs(namelist) |
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| 358 | &nammeddia |
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| 359 | / |
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