- Timestamp:
- 2021-01-07T23:09:56+01:00 (4 years ago)
- Location:
- NEMO/branches/2019/dev_r11708_aumont_PISCES_QUOTA/cfgs/SHARED
- Files:
-
- 3 edited
-
field_def_nemo-pisces.xml (modified) (6 diffs)
-
namelist_pisces_ref (modified) (17 diffs)
-
namelist_sediment_ref (modified) (7 diffs)
Legend:
- Unmodified
- Added
- Removed
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NEMO/branches/2019/dev_r11708_aumont_PISCES_QUOTA/cfgs/SHARED/field_def_nemo-pisces.xml
r11536 r14276 112 112 <field id="DOM_e3t" long_name="DOM * e3t" unit="mmol-N/m2" > DOM * e3t </field > 113 113 114 114 115 </field_group> 115 116 … … 136 137 <field id="SedpH" long_name="PH" unit="1" /> 137 138 <field id="SedCO3por" long_name="Bicarbonates" unit="mol/m3" /> 139 <field id="Sedligand" long_name="Ligands Concentration" unit="mol/m3" /> 138 140 </field_group> 139 141 … … 150 152 <field id="FlxSO4" long_name="SO4 sediment flux" unit="mol/cm2/s" /> 151 153 <field id="FlxFe2" long_name="Fe2+ sediment flux" unit="mol/cm2/s" /> 152 <field id="Flxtot" long_name="Sediment net burial rate" unit="cm/s" />153 154 <field id="dzdep" long_name="Sedimentation rate" unit="cm/s" /> 154 155 <field id="sflxclay" long_name="Clay sedimentation rate" unit="g/m2/s" /> … … 157 158 <field id="sflxpoc" long_name="POC Sedimentation rate" unit="mol/m2/s" /> 158 159 <field id="sflxfeo" long_name="Fe(OH)3 Sedimentation rate" unit="mol/m2/s" /> 160 <field id="FlxBSi" long_name="BSi burial flux" unit="g/cm2/s" /> 161 <field id="FlxClay" long_name="Clay burial flux" unit="g/cm2/s" /> 162 <field id="FlxPOC" long_name="POC burial flux" unit="g/cm2/s" /> 163 <field id="FlxCaCO3" long_name="Calcite burial flux" unit="g/cm2/s" /> 164 <field id="FlxPOS" long_name="POS burial flux" unit="g/cm2/s" /> 165 <field id="FlxPOR" long_name="POR burial flux" unit="g/cm2/s" /> 166 <field id="FlxFeO" long_name="FeO burial flux" unit="g/cm2/s" /> 167 <field id="FlxFeS" long_name="FeS burial flux" unit="g/cm2/s" /> 159 168 </field_group> 160 169 … … 206 215 <field id="SIZEP" long_name="Mean relative size of picophyto." unit="-" grid_ref="grid_T_3D" /> 207 216 <field id="SIZED" long_name="Mean relative size of diatoms" unit="-" grid_ref="grid_T_3D" /> 217 <field id="RASSD" long_name="Mean relative size of diatoms" unit="-" grid_ref="grid_T_3D" /> 218 <field id="RASSN" long_name="Mean relative size of diatoms" unit="-" grid_ref="grid_T_3D" /> 219 <field id="RASSP" long_name="Mean relative size of diatoms" unit="-" grid_ref="grid_T_3D" /> 208 220 <field id="Fe3" long_name="Iron III concentration" unit="nmol/m3" grid_ref="grid_T_3D" /> 209 221 <field id="FeL1" long_name="Complexed Iron concentration with L1" unit="nmol/m3" grid_ref="grid_T_3D" /> … … 240 252 <field id="BACT" long_name="Bacterial Biomass" unit="mmol/m3" grid_ref="grid_T_3D" /> 241 253 <field id="FEBACT" long_name="Bacterial uptake of Fe" unit="molFe/m3/s" grid_ref="grid_T_3D" /> 254 <field id="FEPREC" long_name="precipitation of Fe" unit="molFe/m3/s" grid_ref="grid_T_3D" /> 242 255 <field id="LPRODR" long_name="OM remineralisation ligand production rate" unit="nmol-L/m3/s" grid_ref="grid_T_3D" /> 243 256 <field id="LPRODP" long_name="phytoplankton ligand production rate" unit="nmol-L/m3/s" grid_ref="grid_T_3D" /> -
NEMO/branches/2019/dev_r11708_aumont_PISCES_QUOTA/cfgs/SHARED/namelist_pisces_ref
r13234 r14276 14 14 !----------------------------------------------------------------------- 15 15 ln_p2z = .false. ! LOBSTER model used 16 ln_p4z = . true.! PISCES model used17 ln_p5z = . false.! PISCES QUOTA model used16 ln_p4z = .false. ! PISCES model used 17 ln_p5z = .true. ! PISCES QUOTA model used 18 18 ln_ligand = .false. ! Enable organic ligands 19 19 ln_sediment = .false. ! Enable sediment module … … 44 44 &nampisbio ! biological parameters 45 45 !----------------------------------------------------------------------- 46 nrdttrc = 1 ! time step frequency for biology 47 wsbio = 2. ! POC sinking speed 48 xkmort = 2.E-7 ! half saturation constant for mortality 49 ferat3 = 10.E-6 ! Fe/C in zooplankton 50 wsbio2 = 50. ! Big particles sinking speed 51 wsbio2max = 50. ! Big particles maximum sinking speed 52 wsbio2scale = 5000. ! Big particles length scale of sinking 46 nrdttrc = 1 ! time step frequency for biology 47 wsbio = 2. ! POC sinking speed 48 xkmort = 2.E-7 ! half saturation constant for mortality 49 feratz = 10.E-6 ! Fe/C in zooplankton 50 feratm = 15.E-6 ! Fe/C in mesozooplankton 51 wsbio2 = 50. ! Big particles sinking speed 52 wsbio2max = 50. ! Big particles maximum sinking speed 53 wsbio2scale = 5000. ! Big particles length scale of sinking 53 54 ! ! ln_ligand enabled 54 ldocp = 1.E-4! Phyto ligand production per unit doc55 ldocz = 1.E-4! Zoo ligand production per unit doc56 lthet = 1.0! Proportional loss of ligands due to Fe uptake55 ldocp = 1.E-4 ! Phyto ligand production per unit doc 56 ldocz = 1.E-4 ! Zoo ligand production per unit doc 57 lthet = 1.0 ! Proportional loss of ligands due to Fe uptake 57 58 ! ! ln_p5z enabled 58 no3rat3 = 0.151! N/C ratio in zooplankton59 po4rat3 = 0.00943! P/C ratio in zooplankton59 no3rat3 = 0.151 ! N/C ratio in zooplankton 60 po4rat3 = 0.00944 ! P/C ratio in zooplankton 60 61 / 61 62 !----------------------------------------------------------------------- … … 64 65 concnno3 = 1.e-6 ! Nitrate half saturation of nanophytoplankton 65 66 concdno3 = 3.E-6 ! Nitrate half saturation for diatoms 66 concnnh4 = 1.E- 7! NH4 half saturation for phyto67 concdnh4 = 3.E- 7! NH4 half saturation for diatoms68 concnfer = 1.E-9 ! Iron half saturation for phyto69 concdfer = 3.E-9 ! Iron half saturation for diatoms70 concbfe = 1.E-11 ! Iron half-saturation for DOC remin.71 concbnh4 = 6.E-8! NH4 half saturation for DOC remin.72 concbno3 = 2.E-7 ! Nitrate half saturation for DOC remin.67 concnnh4 = 1.E-6 ! NH4 half saturation for phyto 68 concdnh4 = 3.E-6 ! NH4 half saturation for diatoms 69 concnfer = 3.E-9 ! Iron half saturation for phyto 70 concdfer = 9.E-9 ! Iron half saturation for diatoms 71 concbfe = 3.E-11 ! Iron half-saturation for DOC remin. 72 concbnh4 = 3.E-7 ! NH4 half saturation for DOC remin. 73 concbno3 = 3.E-7 ! Nitrate half saturation for DOC remin. 73 74 xsizedia = 1.E-6 ! Minimum size criteria for diatoms 74 75 xsizephy = 1.E-6 ! Minimum size criteria for phyto … … 78 79 xksi2 = 20E-6 ! half saturation constant for Si/C 79 80 xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization 80 qnfelim = 7.E-6! Optimal quota of phyto81 qdfelim = 7.E-6! Optimal quota of diatoms82 caco3r = 0. 3! mean rain ratio81 qnfelim = 10.E-6 ! Optimal quota of phyto 82 qdfelim = 10.E-6 ! Optimal quota of diatoms 83 caco3r = 0.28 ! mean rain ratio 83 84 oxymin = 1.E-6 ! Half-saturation constant for anoxia 84 85 / … … 86 87 &namp5zlim ! parameters for nutrient limitations PISCES QUOTA - ln_p5z 87 88 !----------------------------------------------------------------------- 88 concnno3 = 3e-6 ! Nitrate half saturation of nanophytoplankton89 concpno3 = 8e-7 ! Nitrate half saturation of picophytoplankton90 concdno3 = 5E-6 ! Phosphate half saturation for diatoms91 concnnh4 = 1E-6 ! NH4 half saturation for phyto92 concpnh4 = 2.3E-7! NH4 half saturation for picophytoplankton93 concdnh4 = 1.7E-6! NH4 half saturation for diatoms94 concnpo4 = 3E-6 ! PO4 half saturation for phyto95 concppo4 = 8E-7 ! PO4 half saturation for picophytoplankton96 concdpo4 = 5E-6 ! PO4 half saturation for diatoms97 concnfer = 3E-9 ! Iron half saturation for phyto98 concpfer = 8E-10! Iron half saturation for picophytoplankton99 concdfer = 5E-9 ! Iron half saturation for diatoms100 concbfe = 1.E-11! Half-saturation for Fe limitation of Bacteria101 concbnh4 = 1.E-7 ! NH4 half saturation for phyto102 concbno3 = 5.E-7 ! Phosphate half saturation for diatoms103 concbpo4 = 1E-7! Phosphate half saturation for bacteria89 concnno3 = 2e-6 ! Nitrate half saturation of nanophytoplankton 90 concpno3 = 7e-7 ! Nitrate half saturation of picophytoplankton 91 concdno3 = 3E-6 ! Phosphate half saturation for diatoms 92 concnnh4 = 2E-6 ! NH4 half saturation for phyto 93 concpnh4 = 7E-7 ! NH4 half saturation for picophytoplankton 94 concdnh4 = 3E-6 ! NH4 half saturation for diatoms 95 concnpo4 = 2E-6 ! PO4 half saturation for phyto 96 concppo4 = 7E-7 ! PO4 half saturation for picophytoplankton 97 concdpo4 = 3E-6 ! PO4 half saturation for diatoms 98 concnfer = 6E-9 ! Iron half saturation for phyto 99 concpfer = 2E-9 ! Iron half saturation for picophytoplankton 100 concdfer = 9E-9 ! Iron half saturation for diatoms 101 concbfe = 3E-11 ! Half-saturation for Fe limitation of Bacteria 102 concbnh4 = 4.E-7 ! NH4 half saturation for phyto 103 concbno3 = 4.E-7 ! Phosphate half saturation for diatoms 104 concbpo4 = 4.E-7 ! Phosphate half saturation for bacteria 104 105 xsizedia = 1.E-6 ! Minimum size criteria for diatoms 105 106 xsizephy = 1.E-6 ! Minimum size criteria for phyto … … 117 118 &namp5zquota ! parameters for nutrient limitations PISCES quota - ln_p5z 118 119 !----------------------------------------------------------------------- 119 qfnopt = 7.E-6! Optimal Fe quota of nanophyto120 qfpopt = 7.E-6! Optimal Fe quota of picophyto121 qfdopt = 7.E-6! Optimal quota of diatoms120 qfnopt = 10.E-6 ! Optimal Fe quota of nanophyto 121 qfpopt = 10.E-6 ! Optimal Fe quota of picophyto 122 qfdopt = 10.E-6 ! Optimal quota of diatoms 122 123 qnnmin = 0.61 ! Minimal N quota for nano 123 124 qnnmax = 1.25 ! Maximal N quota for nano 124 125 qpnmin = 0.24 ! Minimal P quota for nano 125 126 qpnmax = 1.35 ! Maximal P quota for nano 126 qnpmin = 1.0 4! Minimal N quota for pico127 qnpmax = 1. 525! Maximal N quota for pico127 qnpmin = 1.02 ! Minimal N quota for pico 128 qnpmax = 1.39 ! Maximal N quota for pico 128 129 qppmin = 0.19 ! Minimal P quota for pico 129 130 qppmax = 1.15 ! Maximal P quota for pico 130 qndmin = 0.5 3! Minimal N quota for diatoms131 qndmin = 0.51 ! Minimal N quota for diatoms 131 132 qndmax = 1.25 ! Maximal N quota for diatoms 132 133 qpdmin = 0.24 ! Minimal P quota for diatoms 133 134 qpdmax = 1.525 ! Maximal P quota for diatoms 134 qfnmax = 80E-6 ! Maximal Fe quota for nano135 qfpmax = 80E-6 ! Maximal Fe quota for pico136 qfdmax = 80E-6 ! Maximal Fe quota for diatoms135 qfnmax = 60E-6 ! Maximal Fe quota for nano 136 qfpmax = 60E-6 ! Maximal Fe quota for pico 137 qfdmax = 60E-6 ! Maximal Fe quota for diatoms 137 138 / 138 139 !----------------------------------------------------------------------- … … 149 150 &namp4zprod ! parameters for phytoplankton growth for PISCES std - ln_p4z 150 151 !----------------------------------------------------------------------- 151 pislopen = 2. 152 pisloped = 2. 152 pislopen = 2.5 ! P-I slope 153 pisloped = 2.5 ! P-I slope for diatoms 153 154 xadap = 0. ! Adaptation factor to low light 154 155 excretn = 0.05 ! excretion ratio of phytoplankton … … 157 158 chlcnm = 0.033 ! Maximum Chl/C in nanophytoplankton 158 159 chlcdm = 0.05 ! Maximum Chl/C in diatoms 159 chlcmin = 0.00 4! Minimum Chl/c in phytoplankton160 fecnm = 40E-6 ! Maximum Fe/C in nanophytoplankton161 fecdm = 40E-6 ! Maximum Fe/C in diatoms162 grosip = 0.1 1! mean Si/C ratio160 chlcmin = 0.003 ! Minimum Chl/c in phytoplankton 161 fecnm = 60E-6 ! Maximum Fe/C in nanophytoplankton 162 fecdm = 60E-6 ! Maximum Fe/C in diatoms 163 grosip = 0.13 ! mean Si/C ratio 163 164 / 164 165 !----------------------------------------------------------------------- 165 166 &namp5zprod ! parameters for phytoplankton growth for PISCES quota- ln_p5z 166 167 !----------------------------------------------------------------------- 167 pislopen = 4.! P-I slope of nanophytoplankton168 pislopep = 4.! P-I slope for picophytoplankton169 pisloped = 4.! P-I slope for diatoms168 pislopen = 5 ! P-I slope of nanophytoplankton 169 pislopep = 5 ! P-I slope for picophytoplankton 170 pisloped = 5 ! P-I slope for diatoms 170 171 excretn = 0.05 ! excretion ratio of phytoplankton 171 172 excretp = 0.05 ! excretion ratio of picophytoplankton … … 176 177 thetanpm = 0.3 ! Maximum Chl/N in picophytoplankton 177 178 thetandm = 0.4 ! Maximum Chl/N in diatoms 178 chlcmin = 0.00 4! Minimum Chl/c in phytoplankton179 grosip = 0.1 1! mean Si/C ratio179 chlcmin = 0.003 ! Minimum Chl/c in phytoplankton 180 grosip = 0.12 ! mean Si/C ratio 180 181 / 181 182 !----------------------------------------------------------------------- … … 183 184 !----------------------------------------------------------------------- 184 185 wchln = 0.01 ! quadratic mortality of phytoplankton 185 wchld = 0.01 ! maximum quadratic mortality of diatoms 186 wchldm = 0.03 ! maximum quadratic mortality of diatoms 186 wchld = 0.03 ! maximum quadratic mortality of diatoms 187 187 mpratn = 0.01 ! phytoplankton mortality rate 188 188 mpratd = 0.01 ! Diatoms mortality rate … … 193 193 wchln = 0.01 ! quadratic mortality of nanophytoplankton 194 194 wchlp = 0.01 ! quadratic mortality of picophytoplankton 195 wchld = 0.01 ! maximum quadratic mortality of diatoms 196 wchldm = 0.03 ! maximum quadratic mortality of diatoms 195 wchld = 0.03 ! maximum quadratic mortality of diatoms 197 196 mpratn = 0.01 ! nanophytoplankton mortality rate 198 197 mpratp = 0.01 ! picophytoplankton mortality rate … … 205 204 grazrat2 = 0.5 ! maximal mesozoo grazing rate 206 205 resrat2 = 0.005 ! exsudation rate of mesozooplankton 207 mzrat2 = 0.0 2! mesozooplankton mortality rate206 mzrat2 = 0.01 ! mesozooplankton mortality rate 208 207 xpref2d = 1. ! mesozoo preference for diatoms 209 208 xpref2n = 0.3 ! mesozoo preference for nanophyto. 210 209 xpref2z = 1. ! mesozoo preference for microzoo. 211 210 xpref2c = 0.3 ! mesozoo preference for poc 212 xthresh2zoo = 1E-8! zoo feeding threshold for mesozooplankton213 xthresh2dia = 1E-8! diatoms feeding threshold for mesozooplankton214 xthresh2phy = 1E-8! nanophyto feeding threshold for mesozooplankton215 xthresh2poc = 1E-8! poc feeding threshold for mesozooplankton211 xthresh2zoo = 1E-8 ! zoo feeding threshold for mesozooplankton 212 xthresh2dia = 1E-8 ! diatoms feeding threshold for mesozooplankton 213 xthresh2phy = 1E-8 ! nanophyto feeding threshold for mesozooplankton 214 xthresh2poc = 1E-8 ! poc feeding threshold for mesozooplankton 216 215 xthresh2 = 3E-7 ! Food threshold for grazing 217 216 xkgraz2 = 20.E-6 ! half saturation constant for meso grazing 218 epsher2 = 0. 35! Efficicency of Mesozoo growth219 epsher2min = 0. 35! Minimum efficiency of mesozoo growth217 epsher2 = 0.4 ! Efficicency of Mesozoo growth 218 epsher2min = 0.4 ! Minimum efficiency of mesozoo growth 220 219 sigma2 = 0.6 ! Fraction of mesozoo excretion as DOM 221 220 unass2 = 0.3 ! non assimilated fraction of P by mesozoo 222 grazflux = 3.e3 ! flux-feeding rate 223 ln_dvm_meso = .false. ! Activates DVM for mesozooplankton 224 xfracmig = 0.3 ! Fraction of mesozooplankton performing DVM 221 grazflux = 2.e3 ! flux-feeding rate 222 xsigma2 = 0.5 ! Predation window size 223 xsigma2del = 1.0 ! Predation window size scaling 224 ln_dvm_meso = .false. ! Activates DVM for mesozooplankton 225 xfracmig = 0.3 ! Fraction of mesozooplankton performing DVM 225 226 / 226 227 !----------------------------------------------------------------------- 227 228 &namp5zmes ! parameters for mesozooplankton 228 229 !----------------------------------------------------------------------- 229 part2 = 0.75 ! part of calcite not dissolved in mesozoo guts 230 grazrat2 = 0.75 ! maximal mesozoo grazing rate 231 bmetexc2 = .true. ! Metabolic use of excess carbon 232 resrat2 = 0.005 ! exsudation rate of mesozooplankton 233 mzrat2 = 0.03 ! mesozooplankton mortality rate 234 xpref2d = 1. ! meso preference for diatoms 235 xpref2n = 0.3 ! meso preference for nano 236 xpref2z = 1. ! meso preference for zoo 237 xpref2m = 0.1 ! meso preference for zoo 238 xpref2c = 0.3 ! meso preference for poc 239 xthresh2zoo = 1E-8 ! zoo feeding threshold for mesozooplankton 240 xthresh2dia = 1E-8 ! diatoms feeding threshold for mesozooplankton 241 xthresh2phy = 1E-8 ! nanophyto feeding threshold for mesozooplankton 242 xthresh2mes = 1E-8 ! meso feeding threshold for mesozooplankton 243 xthresh2poc = 1E-8 ! poc feeding threshold for mesozooplankton 244 xthresh2 = 3E-7 ! Food threshold for grazing 245 xkgraz2 = 20.E-6 ! half sturation constant for meso grazing 246 epsher2 = 0.5 ! Efficicency of Mesozoo growth 247 epsher2min = 0.5 ! Minimum efficiency of mesozoo growth 248 ssigma2 = 0.5 ! Fraction excreted as semi-labile DOM 249 srespir2 = 0.2 ! Active respiration 250 unass2c = 0.3 ! non assimilated fraction of C by mesozoo 251 unass2n = 0.3 ! non assimilated fraction of N by mesozoo 252 unass2p = 0.3 ! non assimilated fraction of P by mesozoo 253 grazflux = 3.e3 ! flux-feeding rate 230 part2 = 0.75 ! part of calcite not dissolved in mesozoo guts 231 grazrat2 = 0.5 ! maximal mesozoo grazing rate 232 bmetexc2 = .true. ! Metabolic use of excess carbon 233 resrat2 = 0.005 ! exsudation rate of mesozooplankton 234 mzrat2 = 0.01 ! mesozooplankton mortality rate 235 xpref2d = 1. ! meso preference for diatoms 236 xpref2n = 0.3 ! meso preference for nano 237 xpref2z = 1. ! meso preference for zoo 238 xpref2m = 0. ! meso preference for zoo 239 xpref2c = 0.3 ! meso preference for poc 240 xthresh2zoo = 1E-8 ! zoo feeding threshold for mesozooplankton 241 xthresh2dia = 1E-8 ! diatoms feeding threshold for mesozooplankton 242 xthresh2phy = 1E-8 ! nanophyto feeding threshold for mesozooplankton 243 xthresh2mes = 1E-8 ! meso feeding threshold for mesozooplankton 244 xthresh2poc = 1E-8 ! poc feeding threshold for mesozooplankton 245 xthresh2 = 3E-7 ! Food threshold for grazing 246 xkgraz2 = 20.E-6 ! half sturation constant for meso grazing 247 epsher2 = 0.5 ! Efficicency of Mesozoo growth 248 epsher2min = 0.5 ! Minimum efficiency of mesozoo growth 249 ssigma2 = 0.5 ! Fraction excreted as semi-labile DOM 250 srespir2 = 0.2 ! Active respiration 251 unass2c = 0.3 ! non assimilated fraction of C by mesozoo 252 unass2n = 0.3 ! non assimilated fraction of N by mesozoo 253 unass2p = 0.3 ! non assimilated fraction of P by mesozoo 254 xsigma2 = 0.5 ! Predation window size 255 xsigma2del = 1.0 ! Predation window size scaling 256 grazflux = 2.e3 ! flux-feeding rate 257 ln_dvm_meso = .false. ! Activates DVM for mesozooplankton 258 xfracmig = 0.25 ! Fraction of mesozooplankton performing DVM 254 259 / 255 260 !----------------------------------------------------------------------- 256 261 &namp4zzoo ! parameters for microzooplankton for PISCES std - ln_p4z 257 262 !----------------------------------------------------------------------- 258 part = 0. 5! part of calcite not dissolved in microzoo guts263 part = 0.75 ! part of calcite not dissolved in microzoo guts 259 264 grazrat = 2.0 ! maximal zoo grazing rate 260 resrat = 0.0 3! Linear mortality rate of zooplankton265 resrat = 0.02 ! Linear mortality rate of zooplankton 261 266 mzrat = 0.005 ! zooplankton mortality rate 262 267 xprefc = 0.1 ! Microzoo preference for POM … … 268 273 xthresh = 3.E-7 ! Food threshold for feeding 269 274 xkgraz = 20.E-6 ! half sturation constant for grazing 270 epsher = 0. 35! Efficiency of microzoo growth271 epshermin = 0. 35! Minimum efficiency of microzoo growth275 epsher = 0.4 ! Efficiency of microzoo growth 276 epshermin = 0.4 ! Minimum efficiency of microzoo growth 272 277 sigma1 = 0.6 ! Fraction of microzoo excretion as DOM 273 278 unass = 0.3 ! non assimilated fraction of phyto by zoo 279 xsigma = 0.5 ! Predation window size 280 xsigmadel = 1.0 ! Predation window size scaling 274 281 / 275 282 !----------------------------------------------------------------------- 276 283 &namp5zzoo ! parameters for microzooplankton 277 284 !----------------------------------------------------------------------- 278 part = 0. 5! part of calcite not dissolved in microzoo gutsa279 grazrat = 3.0 ! maximal zoo grazing rate285 part = 0.75 ! part of calcite not dissolved in microzoo gutsa 286 grazrat = 2.0 ! maximal zoo grazing rate 280 287 bmetexc = .true. ! Metabolic use of excess carbon 281 resrat = 0.0 3! exsudation rate of zooplankton282 mzrat = 0.00 4! zooplankton mortality rate288 resrat = 0.02 ! exsudation rate of zooplankton 289 mzrat = 0.005 ! zooplankton mortality rate 283 290 xprefc = 0.1 ! Microzoo preference for POM 284 291 xprefn = 1.0 ! Microzoo preference for Nanophyto 285 292 xprefp = 1.0 ! Microzoo preference for picophyto 286 293 xprefd = 0.8 ! Microzoo preference for Diatoms 287 xprefz = 0. 1! Microzoo preference for microzooplankton294 xprefz = 0. ! Microzoo preference for microzooplankton 288 295 xthreshdia = 1.E-8 ! Diatoms feeding threshold for microzooplankton 289 296 xthreshphy = 1.E-8 ! Nanophyto feeding threshold for microzooplankton … … 300 307 unassn = 0.3 ! non assimilated fraction of N by zoo 301 308 unassp = 0.3 ! non assimilated fraction of P by zoo 309 xsigma = 0.5 ! Predation window size 310 xsigmadel = 1.0 ! Predation window size scaling 302 311 / 303 312 !----------------------------------------------------------------------- … … 305 314 !----------------------------------------------------------------------- 306 315 ln_ligvar = .false. ! variable ligand concentration 307 xlam1 = 0.0 05 ! scavenging rate of Iron by biogenic particles316 xlam1 = 0.05 ! scavenging rate of Iron by biogenic particles 308 317 xlamdust = 150.0 ! Scavenging rate of Iron by dust 309 ligand = 7E-10! Ligands concentration318 ligand = 1E-9 ! Ligands concentration 310 319 kfep = 0.01 ! Nanoparticle formation rate constant 320 scaveff = 1.0 ! Fraction of scavenged Fe that goes to POFe 311 321 / 312 322 !----------------------------------------------------------------------- 313 323 &nampisrem ! parameters for remineralization 314 324 !----------------------------------------------------------------------- 315 xremik = 0.3 ! remineralization rate of DOC316 325 nitrif = 0.05 ! NH4 nitrification rate 317 326 xsirem = 0.003 ! remineralization rate of Si 318 327 xsiremlab = 0.03 ! fast remineralization rate of Si 319 328 xsilab = 0.5 ! Fraction of labile biogenic silica 320 feratb = 10.E-6 ! Fe/C quota in bacteria329 feratb = 30.E-6 ! Fe/C quota in bacteria 321 330 xkferb = 3E-10 ! Half-saturation constant for bacteria Fe/C 322 331 ! ! ln_p5z 323 xremikc = 0.25 ! remineralization rate of DOC 324 xremikn = 0.3 ! remineralization rate of DON 325 xremikp = 0.4 ! remineralization rate of DOP 326 ! feratb = 20E-6 ! Bacterial Fe/C ratio 327 ! xkferb = 3E-10 ! Half-saturation constant for bact. Fe/C 332 xremikc = 0.4 ! remineralization rate of DOC 333 xremikn = 0.4 ! remineralization rate of DON 334 xremikp = 0.5 ! remineralization rate of DOP 328 335 / 329 336 !----------------------------------------------------------------------- 330 337 &nampispoc ! parameters for organic particles 331 338 !----------------------------------------------------------------------- 332 xremip = 0.03 339 xremip = 0.035 ! remineralisation rate of POC 333 340 jcpoc = 15 ! Number of lability classes 334 341 rshape = 1.0 ! Shape of the gamma function … … 341 348 &nampiscal ! parameters for Calcite chemistry 342 349 !----------------------------------------------------------------------- 343 kdca = 6. ! calcite dissolution rate constant (1/time)344 nca = 1. ! order of dissolution reaction (dimensionless)350 kdca = 3. ! calcite dissolution rate constant (1/time) 351 nca = 2. ! order of dissolution reaction (dimensionless) 345 352 / 346 353 !----------------------------------------------------------------------- … … 377 384 icefeinput = 15.e-9 ! Iron concentration in sea ice 378 385 nitrfix = 1.e-7 ! Nitrogen fixation rate 379 diazolight = 50. ! Diazotrophs sensitivity to light (W/m2)386 diazolight = 30. ! Diazotrophs sensitivity to light (W/m2) 380 387 concfediaz = 1.e-10 ! Diazotrophs half-saturation Cste for Iron 381 388 hratio = 1.e+7 ! Fe to 3He ratio assumed for vent iron supply -
NEMO/branches/2019/dev_r11708_aumont_PISCES_QUOTA/cfgs/SHARED/namelist_sediment_ref
r12361 r14276 18 18 &nam_geom ! Characteristics of the sediment columns 19 19 !----------------------------------------------------------------------- 20 jpksed = 11! Number of vertical layers21 sedzmin = 0. 3! Minimum vertical spacing22 sedhmax = 1 0.0 ! Maximum depth of the sediment23 sedkth = 7.0 ! Default parameters20 jpksed = 18 ! Number of vertical layers 21 sedzmin = 0.1 ! Minimum vertical spacing 22 sedhmax = 15.0 ! Maximum depth of the sediment 23 sedkth = 9.0 ! Default parameters 24 24 sedacr = 2.0 ! Default parameters 25 porsurf = 0.9! Sediment porosity at the surface26 porinf = 0.75! Sediment porosity at infinite depth27 rhox = 0.33! Length scale of porosity variation (cm)25 porsurf = 0.9 ! Sediment porosity at the surface 26 porinf = 0.75 ! Sediment porosity at infinite depth 27 rhox = 0.33 ! Length scale of porosity variation (cm) 28 28 / 29 29 !----------------------------------------------------------------------- … … 57 57 ! 58 58 seddiag3d(1) = 'SedpH ' , 'pH ', '- ' 59 seddiag3d(2) = 'SedCO3por ' , 'Dissolved CO3 cocnentration ', 'mol/L' 59 seddiag3d(2) = 'SedCO3por ' , 'Dissolved CO3 concentration ', 'mol/L' 60 seddiag3d(3) = 'Sedligand' , 'ligand concentration ', 'mol/L' 60 61 seddiag2d(1) = 'FlxSi ' , 'Silicate flux ', 'mol/cm2/s' 61 62 seddiag2d(2) = 'FlxO2 ' , 'Dissolved Oxygen Flux ', 'mol/L' … … 67 68 seddiag2d(8) = 'FlxH2S ' , 'Total H2S flux ', 'mol/cm2/s' 68 69 seddiag2d(9) = 'FlxSO4 ' , 'Total SO4 flux ', 'mol/cm2/s' 69 seddiag2d(10) = 'FlxFe2 ' , 'Total Fe2+ flux ', 'mol/cm2/s' 70 seddiag2d(11) = 'Flxtot ' , 'Total net sediment burial rate ', 'cm/s' 71 seddiag2d(12) = 'dzdep ' , 'Sedimentation rate ', 'cm/s' 70 seddiag2d(10) = 'FlxFe2 ' , 'Total Fe2+ flux ', 'mol/cm2/s' 71 seddiag2d(11) = 'FlxBSi ' , 'Total net BSi burial rate ', 'g/cm2/s' 72 seddiag2d(12) = 'FlxClay ' , 'Total net CLay burial rate ', 'g/cm2/s' 73 seddiag2d(13) = 'FlxPOC ' , 'Total net POC burial rate ', 'g/cm2/s' 74 seddiag2d(14) = 'FlxCaCO3 ' , 'Total net CaCO3 burial rate ', 'g/cm2/s' 75 seddiag2d(15) = 'FlxPOS ' , 'Total net POS burial rate ', 'g/cm2/s' 76 seddiag2d(16) = 'FlxPOR ' , 'Total net POR burial rate ', 'g/cm2/s' 77 seddiag2d(17) = 'FlxFeO ' , 'Total net FeO burial rate ', 'g/cm2/s' 78 seddiag2d(18) = 'FlxFeS ' , 'Total net FeS burial rate ', 'g/cm2/s' 79 seddiag2d(19) = 'Flxtot ' , 'Total burial flux ', 'mol/cm2/s' 80 seddiag2d(20) = 'dzdep ' , 'Sedimentation rate ', 'cm/s' 72 81 / 73 82 !----------------------------------------------------------------------- … … 76 85 rcopal = 0.1 ! Reactivity for clay [l.mol-1.an-1] 77 86 dcoef = 8.0E-6 ! Diffusion coefficient in sediments (in cm**2/s) 78 rccal = 0.014! Dissolution rate of calcite [in yr-1]87 rccal = 1.4 ! Dissolution rate of calcite [in yr-1] 79 88 rcligc = 0.1 ! Degradation rate of ligands [in yr-1] 80 89 ratligc = 1.E-4 ! L/C ratio in POC … … 92 101 rcorgr = 1.E-4 ! Reactivity for refractory POC [an-1] 93 102 rcnh4 = 1E7 ! Reactivity for O2/NH4 [l.mol-1.an-1] 94 rch2s = 1 E5! Reactivity for O2/H2S [l.mol-1.an-1]103 rch2s = 1.6E5 ! Reactivity for O2/H2S [l.mol-1.an-1] 95 104 rcfe2 = 1E8 ! Reactivity for O2/Fe2+ [l.mol-1.an-1] 96 rcfeh2s = 1E4! Reactivity for FEOH/H2S [l.mol-1.an-1]97 rcfes = 1E 5! Reactivity for FE2+/H2S [l.mol-1.an-1]105 rcfeh2s = 8E3 ! Reactivity for FEOH/H2S [l.mol-1.an-1] 106 rcfes = 1E6 ! Reactivity for FE2+/H2S [l.mol-1.an-1] 98 107 rcfeso = 3E5 ! Reactivity for FES/O2 [l.mol-1.an-1] 99 108 xksedo2 = 1.E-6 ! Half-saturation constant for oxic remin [mol/l] … … 105 114 &nam_btb ! parameters for bioturbation and bioirrigation 106 115 !----------------------------------------------------------------------- 107 dbiot = 5.! Bioturbation coefficient (in cm2/yr)108 ln_btbz = . false.! Depth varying bioturbation109 dbtbzsc = 10.0! coefficient for btb attenuation. If no variation, depth of the mixed layer116 dbiot = 10. ! Bioturbation coefficient (in cm2/yr) 117 ln_btbz = .true. ! Depth varying bioturbation 118 dbtbzsc = 6.0 ! coefficient for btb attenuation. If no variation, depth of the mixed layer 110 119 adsnh4 = 1.3 ! Adsorption coefficient of NH4 111 ln_irrig = .true. ! Bioirrigation in sediment120 ln_irrig = .true. ! Bioirrigation in sediment 112 121 xirrzsc = 1.5 ! Vertical scale of the attentuation of bioirrigation [cm] 113 122 / … … 115 124 &nam_rst ! parameters for restarting the sediment module 116 125 !----------------------------------------------------------------------- 117 ln_rst_sed = .false. ! restart flag126 ln_rst_sed = .false. ! restart flag 118 127 cn_sedrst_in = "restart_sed" ! name of the input restart file name of the sediment module 119 128 cn_sedrst_indir = "." ! directory from which to read input sediment restarts
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