From ea76aba9da368a769ce351c65459230535c82d87 Mon Sep 17 00:00:00 2001 From: Robinson Hordoir Date: Thu, 28 May 2026 14:37:19 +0200 Subject: [PATCH] Add PISCES namelists --- cfgs/SPITZ12/RUNDIR/namelist_pisces_cfg | 136 ++++++ cfgs/SPITZ12/RUNDIR/namelist_pisces_ref | 524 ++++++++++++++++++++++++ cfgs/SPITZ12/RUNDIR/namelist_top_cfg | 169 ++++++++ cfgs/SPITZ12/RUNDIR/namelist_top_ref | 185 +++++++++ 4 files changed, 1014 insertions(+) create mode 100755 cfgs/SPITZ12/RUNDIR/namelist_pisces_cfg create mode 100755 cfgs/SPITZ12/RUNDIR/namelist_pisces_ref create mode 100755 cfgs/SPITZ12/RUNDIR/namelist_top_cfg create mode 100755 cfgs/SPITZ12/RUNDIR/namelist_top_ref diff --git a/cfgs/SPITZ12/RUNDIR/namelist_pisces_cfg b/cfgs/SPITZ12/RUNDIR/namelist_pisces_cfg new file mode 100755 index 0000000..2cba622 --- /dev/null +++ b/cfgs/SPITZ12/RUNDIR/namelist_pisces_cfg @@ -0,0 +1,136 @@ +!----------------------------------------------------------------------- +&nampismod ! Model used +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisext ! air-sea exchange +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisatm ! Atmospheric prrssure +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisbio ! biological parameters +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp4zlim ! parameters for nutrient limitations for PISCES std - ln_p4z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp5zlim ! parameters for nutrient limitations PISCES QUOTA - ln_p5z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp5zquota ! parameters for nutrient limitations PISCES quota - ln_p5z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisopt ! parameters for optics +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp4zprod ! parameters for phytoplankton growth for PISCES std - ln_p4z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp5zprod ! parameters for phytoplankton growth for PISCES quota- ln_p5z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp4zmort ! parameters for phytoplankton sinks for PISCES std - ln_p4z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp5zmort ! parameters for phytoplankton sinks for PISCES quota - ln_p5z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp4zmes ! parameters for mesozooplankton for PISCES std - ln_p4z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp5zmes ! parameters for mesozooplankton +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp4zzoo ! parameters for microzooplankton for PISCES std - ln_p4z +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namp5zzoo ! parameters for microzooplankton +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisfer ! parameters for iron chemistry +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisrem ! parameters for remineralization +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampispoc ! parameters for organic particles +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampiscal ! parameters for Calcite chemistry +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisbc ! parameters for inputs deposition +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampissed ! parameters for sediments mobilization +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampislig ! Namelist parameters for ligands, nampislig +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisice ! Prescribed sea ice tracers +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampisdmp ! Damping +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&nampismass ! Mass conservation +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namlobphy ! biological parameters for phytoplankton +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namlobnut ! biological parameters for nutrients +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namlobzoo ! biological parameters for zooplankton +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namlobdet ! biological parameters for detritus +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namlobdom ! biological parameters for DOM +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namlobsed ! parameters from aphotic layers to sediment +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namlobrat ! general coefficients +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namlobopt ! optical parameters +!----------------------------------------------------------------------- +/ diff --git a/cfgs/SPITZ12/RUNDIR/namelist_pisces_ref b/cfgs/SPITZ12/RUNDIR/namelist_pisces_ref new file mode 100755 index 0000000..cdcd3f0 --- /dev/null +++ b/cfgs/SPITZ12/RUNDIR/namelist_pisces_ref @@ -0,0 +1,524 @@ +!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!! PISCES reference namelist +!! 1 - air-sea exchange (nampisext) +!! 2 - biological parameters (nampisbio) +!! 3 - parameters for nutrient limitations (nampislim) +!! 4 - parameters for phytoplankton (nampisprod,nampismort) +!! 5 - parameters for zooplankton (nampismes,nampiszoo) +!! 6 - parameters for remineralization (nampisrem) +!! 7 - parameters for calcite chemistry (nampiscal) +!! 8 - parameters for inputs deposition (nampissed) +!! 11 - Damping (nampisdmp) +!----------------------------------------------------------------------- +&nampismod ! Model used +!----------------------------------------------------------------------- + ln_p2z = .false. ! LOBSTER model used + ln_p4z = .true. ! PISCES model used + ln_p5z = .false. ! PISCES QUOTA model used + ln_ligand = .false. ! Enable organic ligands + ln_sediment = .false. ! Enable sediment module +/ +!----------------------------------------------------------------------- +&nampisext ! air-sea exchange +!----------------------------------------------------------------------- + ln_co2int = .false. ! read atm pco2 from a file (T) or constant (F) + atcco2 = 280. ! Constant value atmospheric pCO2 - ln_co2int = F + clname = 'atcco2.txt' ! Name of atm pCO2 file - ln_co2int = T + nn_offset = 0 ! Offset model-data start year - ln_co2int = T +! ! If your model year is iyy, nn_offset=(years(1)-iyy) +! ! then the first atmospheric CO2 record read is at years(1) +/ +!----------------------------------------------------------------------- +&nampisatm ! Atmospheric prrssure +!----------------------------------------------------------------------- +! ! 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_patm = 'presatm.orca2' , 24. , 'presatm' , .true. , .true. , 'yearly' , '' , '' , '' + sn_atmco2 = 'presatmco2' , -1. , 'xco2' , .true. , .true. , 'yearly' , '' , '' , '' + cn_dir = './' ! root directory for the location of the dynamical files +! + ln_presatm = .false. ! constant atmopsheric pressure (F) or from a file (T) + ln_presatmco2 = .false. ! Read spatialized atm co2 files [ppm] if TRUE +/ +!----------------------------------------------------------------------- +&nampisbio ! biological parameters +!----------------------------------------------------------------------- + nrdttrc = 1 ! time step frequency for biology + wsbio = 2. ! POC sinking speed + xkmort = 1.E-7 ! half saturation constant for mortality + feratz = 10.E-6 ! Fe/C in zooplankton + feratm = 15.E-6 ! Fe/C in mesozooplankton + wsbio2 = 50. ! Big particles sinking speed + wsbio2max = 50. ! Big particles maximum sinking speed + wsbio2scale = 5000. ! Big particles length scale of sinking +! ! ln_ligand enabled + ldocp = 1.E-4 ! Phyto ligand production per unit doc + ldocz = 1.E-4 ! Zoo ligand production per unit doc + lthet = 1.0 ! Proportional loss of ligands due to Fe uptake +! ! ln_p5z enabled + no3rat3 = 0.151 ! N/C ratio in zooplankton + po4rat3 = 0.00943 ! P/C ratio in zooplankton +/ +!----------------------------------------------------------------------- +&namp4zlim ! parameters for nutrient limitations for PISCES std - ln_p4z +!----------------------------------------------------------------------- + concnno3 = 1.e-6 ! Nitrate half saturation of nanophytoplankton + concdno3 = 3.E-6 ! Nitrate half saturation for diatoms + concnnh4 = 1.E-6 ! NH4 half saturation for phyto + concdnh4 = 3.E-6 ! NH4 half saturation for diatoms + concnfer = 1.7E-9 ! Iron half saturation for phyto + concdfer = 5.E-9 ! Iron half saturation for diatoms + concbfe = 3.E-11 ! Iron half-saturation for DOC remin. + concbnh4 = 3.E-7 ! NH4 half saturation for DOC remin. + concbno3 = 3.E-7 ! Nitrate half saturation for DOC remin. + xsizedia = 1.E-6 ! Minimum size criteria for diatoms + xsizephy = 1.E-6 ! Minimum size criteria for phyto + xsizern = 3.0 ! Size ratio for nanophytoplankton + xsizerd = 4.0 ! Size ratio for diatoms + xksi1 = 8.E-6 ! half saturation constant for Si uptake + xksi2 = 20E-6 ! half saturation constant for Si/C + xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization + qnfelim = 10.E-6 ! Optimal quota of phyto + qdfelim = 10.E-6 ! Optimal quota of diatoms + caco3r = 0.2 ! mean rain ratio + oxymin = 1.E-6 ! Half-saturation constant for anoxia +/ +!----------------------------------------------------------------------- +&namp5zlim ! parameters for nutrient limitations PISCES QUOTA - ln_p5z +!----------------------------------------------------------------------- + concnno3 = 2e-6 ! Nitrate half saturation of nanophytoplankton + concpno3 = 7e-7 ! Nitrate half saturation of picophytoplankton + concdno3 = 3E-6 ! Phosphate half saturation for diatoms + concnnh4 = 2E-6 ! NH4 half saturation for phyto + concpnh4 = 7E-7 ! NH4 half saturation for picophytoplankton + concdnh4 = 3E-6 ! NH4 half saturation for diatoms + concnpo4 = 2E-6 ! PO4 half saturation for phyto + concppo4 = 7E-7 ! PO4 half saturation for picophytoplankton + concdpo4 = 3E-6 ! PO4 half saturation for diatoms + concnfer = 3E-9 ! Iron half saturation for phyto + concpfer = 1E-9 ! Iron half saturation for picophytoplankton + concdfer = 4.5E-9 ! Iron half saturation for diatoms + concbfe = 3E-11 ! Half-saturation for Fe limitation of Bacteria + concbnh4 = 4.E-7 ! NH4 half saturation for phyto + concbno3 = 4.E-7 ! Phosphate half saturation for diatoms + concbpo4 = 4.E-7 ! Phosphate half saturation for bacteria + xsizedia = 1.E-6 ! Minimum size criteria for diatoms + xsizephy = 1.E-6 ! Minimum size criteria for phyto + xsizepic = 5.E-7 ! Minimum size criteria for picophyto + xsizern = 3.0 ! Size ratio for nanophytoplankton + xsizerp = 2.0 ! Size ratio for picophytoplankton + xsizerd = 4.0 ! Size ratio for diatoms + xksi1 = 8.E-6 ! half saturation constant for Si uptake + xksi2 = 20E-6 ! half saturation constant for Si/C + xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization + caco3r = 0.3 ! mean rain ratio + oxymin = 1.E-6 ! Half-saturation constant for anoxia +/ +!----------------------------------------------------------------------- +&namp5zquota ! parameters for nutrient limitations PISCES quota - ln_p5z +!----------------------------------------------------------------------- + qfnopt = 12.E-6 ! Optimal Fe quota of nanophyto + qfpopt = 12.E-6 ! Optimal Fe quota of picophyto + qfdopt = 12.E-6 ! Optimal quota of diatoms + qnnmin = 0.61 ! Minimal N quota for nano + qnnmax = 1.25 ! Maximal N quota for nano + qpnmin = 0.24 ! Minimal P quota for nano + qpnmax = 1.35 ! Maximal P quota for nano + qnpmin = 1.02 ! Minimal N quota for pico + qnpmax = 1.39 ! Maximal N quota for pico + qppmin = 0.19 ! Minimal P quota for pico + qppmax = 1.15 ! Maximal P quota for pico + qndmin = 0.51 ! Minimal N quota for diatoms + qndmax = 1.25 ! Maximal N quota for diatoms + qpdmin = 0.24 ! Minimal P quota for diatoms + qpdmax = 1.525 ! Maximal P quota for diatoms + qfnmax = 60E-6 ! Maximal Fe quota for nano + qfpmax = 60E-6 ! Maximal Fe quota for pico + qfdmax = 60E-6 ! Maximal Fe quota for diatoms +/ +!----------------------------------------------------------------------- +&nampisopt ! parameters for optics +!----------------------------------------------------------------------- +! ! 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_par = 'par.orca' , 24. , 'fr_par' , .true. , .true. , 'yearly' , '' , '' , '' + cn_dir = './' ! root directory for the location of the dynamical files + ln_varpar = .false. ! boolean for PAR variable + parlux = 0.43 ! Fraction of shortwave as PAR + ln_p4z_dcyc = .false. ! Diurnal cycle in PISCES +/ +!----------------------------------------------------------------------- +&namp4zprod ! parameters for phytoplankton growth for PISCES std - ln_p4z +!----------------------------------------------------------------------- + pislopen = 2. ! P-I slope + pisloped = 2. ! P-I slope for diatoms + excretn = 0.05 ! excretion ratio of phytoplankton + excretd = 0.05 ! excretion ratio of diatoms + bresp = 0.033 ! Basal respiration rate + chlcnm = 0.033 ! Maximum Chl/C in nanophytoplankton + chlcdm = 0.05 ! Maximum Chl/C in diatoms + chlcmin = 0.003 ! Minimum Chl/c in phytoplankton + fecnm = 60E-6 ! Maximum Fe/C in nanophytoplankton + fecdm = 60E-6 ! Maximum Fe/C in diatoms + grosip = 0.13 ! mean Si/C ratio +/ +!----------------------------------------------------------------------- +&namp5zprod ! parameters for phytoplankton growth for PISCES quota- ln_p5z +!----------------------------------------------------------------------- + pislopen = 5 ! P-I slope of nanophytoplankton + pislopep = 5 ! P-I slope for picophytoplankton + pisloped = 5 ! P-I slope for diatoms + excretn = 0.05 ! excretion ratio of phytoplankton + excretp = 0.05 ! excretion ratio of picophytoplankton + excretd = 0.05 ! excretion ratio of diatoms + bresp = 0.02 ! Basal respiration rate + thetannm = 0.3 ! Maximum Chl/N in nanophytoplankton + thetanpm = 0.3 ! Maximum Chl/N in picophytoplankton + thetandm = 0.4 ! Maximum Chl/N in diatoms + chlcmin = 0.003 ! Minimum Chl/c in phytoplankton + grosip = 0.12 ! mean Si/C ratio +/ +!----------------------------------------------------------------------- +&namp4zmort ! parameters for phytoplankton sinks for PISCES std - ln_p4z +!----------------------------------------------------------------------- + wchln = 0.01 ! quadratic mortality of phytoplankton + wchld = 0.03 ! maximum quadratic mortality of diatoms + mpratn = 0.01 ! phytoplankton mortality rate + mpratd = 0.01 ! Diatoms mortality rate +/ +!----------------------------------------------------------------------- +&namp5zmort ! parameters for phytoplankton sinks for PISCES quota - ln_p5z +!----------------------------------------------------------------------- + wchln = 0.01 ! quadratic mortality of nanophytoplankton + wchlp = 0.01 ! quadratic mortality of picophytoplankton + wchld = 0.03 ! maximum quadratic mortality of diatoms + mpratn = 0.01 ! nanophytoplankton mortality rate + mpratp = 0.01 ! picophytoplankton mortality rate + mpratd = 0.01 ! Diatoms mortality rate +/ +!----------------------------------------------------------------------- +&namp4zmes ! parameters for mesozooplankton for PISCES std - ln_p4z +!----------------------------------------------------------------------- + part2 = 0.75 ! part of calcite not dissolved in mesozoo guts + grazrat2 = 0.5 ! maximal mesozoo grazing rate + resrat2 = 0.005 ! exsudation rate of mesozooplankton + mzrat2 = 0.01 ! mesozooplankton mortality rate + xpref2d = 1. ! mesozoo preference for diatoms + xpref2n = 0.3 ! mesozoo preference for nanophyto. + xpref2z = 1. ! mesozoo preference for microzoo. + xpref2c = 0.3 ! mesozoo preference for poc + xthresh2zoo = 1E-8 ! zoo feeding threshold for mesozooplankton + xthresh2dia = 1E-8 ! diatoms feeding threshold for mesozooplankton + xthresh2phy = 1E-8 ! nanophyto feeding threshold for mesozooplankton + xthresh2poc = 1E-8 ! poc feeding threshold for mesozooplankton + xthresh2 = 3E-7 ! Food threshold for grazing + xkgraz2 = 20.E-6 ! half saturation constant for meso grazing + epsher2 = 0.4 ! Efficicency of Mesozoo growth + epsher2min = 0.4 ! Minimum efficiency of mesozoo growth + sigma2 = 0.6 ! Fraction of mesozoo excretion as DOM + unass2 = 0.3 ! non assimilated fraction of P by mesozoo + grazflux = 3.e3 ! flux-feeding rate + xsigma2 = 0.5 ! Predation window size + xsigma2del = 1.0 ! Predation window size scaling + ln_dvm_meso = .false. ! Activates DVM for mesozooplankton + xfracmig = 0.3 ! Fraction of mesozooplankton performing DVM +/ +!----------------------------------------------------------------------- +&namp5zmes ! parameters for mesozooplankton +!----------------------------------------------------------------------- + part2 = 0.75 ! part of calcite not dissolved in mesozoo guts + grazrat2 = 0.5 ! maximal mesozoo grazing rate + bmetexc2 = .true. ! Metabolic use of excess carbon + resrat2 = 0.005 ! exsudation rate of mesozooplankton + mzrat2 = 0.01 ! mesozooplankton mortality rate + xpref2d = 1. ! meso preference for diatoms + xpref2n = 0.3 ! meso preference for nano + xpref2z = 1. ! meso preference for zoo + xpref2m = 0. ! meso preference for zoo + xpref2c = 0.3 ! meso preference for poc + xthresh2zoo = 1E-8 ! zoo feeding threshold for mesozooplankton + xthresh2dia = 1E-8 ! diatoms feeding threshold for mesozooplankton + xthresh2phy = 1E-8 ! nanophyto feeding threshold for mesozooplankton + xthresh2mes = 1E-8 ! meso feeding threshold for mesozooplankton + xthresh2poc = 1E-8 ! poc feeding threshold for mesozooplankton + xthresh2 = 3E-7 ! Food threshold for grazing + xkgraz2 = 20.E-6 ! half sturation constant for meso grazing + epsher2 = 0.5 ! Efficicency of Mesozoo growth + epsher2min = 0.5 ! Minimum efficiency of mesozoo growth + ssigma2 = 0.5 ! Fraction excreted as semi-labile DOM + srespir2 = 0.2 ! Active respiration + unass2c = 0.3 ! non assimilated fraction of C by mesozoo + unass2n = 0.3 ! non assimilated fraction of N by mesozoo + unass2p = 0.3 ! non assimilated fraction of P by mesozoo + xsigma2 = 0.5 ! Predation window size + xsigma2del = 1.0 ! Predation window size scaling + grazflux = 3.e3 ! flux-feeding rate + ln_dvm_meso = .false. ! Activates DVM for mesozooplankton + xfracmig = 0.25 ! Fraction of mesozooplankton performing DVM +/ +!----------------------------------------------------------------------- +&namp4zzoo ! parameters for microzooplankton for PISCES std - ln_p4z +!----------------------------------------------------------------------- + part = 0.75 ! part of calcite not dissolved in microzoo guts + grazrat = 2.0 ! maximal zoo grazing rate + resrat = 0.02 ! Linear mortality rate of zooplankton + mzrat = 0.005 ! zooplankton mortality rate + xprefc = 0.15 ! Microzoo preference for POM + xprefn = 1. ! Microzoo preference for Nanophyto + xprefd = 0.8 ! Microzoo preference for Diatoms + xthreshdia = 1.E-8 ! Diatoms feeding threshold for microzooplankton + xthreshphy = 1.E-8 ! Nanophyto feeding threshold for microzooplankton + xthreshpoc = 1.E-8 ! POC feeding threshold for microzooplankton + xthresh = 3.E-7 ! Food threshold for feeding + xkgraz = 20.E-6 ! half sturation constant for grazing + epsher = 0.4 ! Efficiency of microzoo growth + epshermin = 0.4 ! Minimum efficiency of microzoo growth + sigma1 = 0.6 ! Fraction of microzoo excretion as DOM + unass = 0.3 ! non assimilated fraction of phyto by zoo + xsigma = 0.5 ! Predation window size + xsigmadel = 1.0 ! Predation window size scaling +/ +!----------------------------------------------------------------------- +&namp5zzoo ! parameters for microzooplankton +!----------------------------------------------------------------------- + part = 0.75 ! part of calcite not dissolved in microzoo gutsa + grazrat = 2.0 ! maximal zoo grazing rate + bmetexc = .true. ! Metabolic use of excess carbon + resrat = 0.02 ! exsudation rate of zooplankton + mzrat = 0.005 ! zooplankton mortality rate + xprefc = 0.15 ! Microzoo preference for POM + xprefn = 1.0 ! Microzoo preference for Nanophyto + xprefp = 1.0 ! Microzoo preference for picophyto + xprefd = 1.0 ! Microzoo preference for Diatoms + xprefz = 0. ! Microzoo preference for microzooplankton + xthreshdia = 1.E-8 ! Diatoms feeding threshold for microzooplankton + xthreshphy = 1.E-8 ! Nanophyto feeding threshold for microzooplankton + xthreshpic = 1.E-8 ! Picophyto feeding threshold for microzooplankton + xthreshzoo = 1.E-8 ! Microzoo feeding threshold for microzooplankton + xthreshpoc = 1.E-8 ! POC feeding threshold for microzooplankton + xthresh = 3.E-7 ! Food threshold for feeding + xkgraz = 20.E-6 ! half saturation constant for grazing + epsher = 0.5 ! Efficiency of microzoo growth + epshermin = 0.5 ! Minimum efficiency of microzoo growth + ssigma = 0.5 ! Fraction excreted as semi-labile DOM + srespir = 0.2 ! Active respiration + unassc = 0.3 ! non assimilated fraction of C by zoo + unassn = 0.3 ! non assimilated fraction of N by zoo + unassp = 0.3 ! non assimilated fraction of P by zoo + xsigma = 0.5 ! Predation window size + xsigmadel = 1.0 ! Predation window size scaling +/ +!----------------------------------------------------------------------- +&nampisfer ! parameters for iron chemistry +!----------------------------------------------------------------------- + ln_ligvar = .false. ! variable ligand concentration + xlam1 = 0.02 ! scavenging rate of Iron by biogenic particles + xlamdust = 150.0 ! Scavenging rate of Iron by dust + ligand = 1E-9 ! Ligands concentration + kfep = 0.01 ! Nanoparticle formation rate constant + scaveff = 1.0 ! Fraction of scavenged Fe that goes to POFe +/ +!----------------------------------------------------------------------- +&nampisrem ! parameters for remineralization +!----------------------------------------------------------------------- + nitrif = 0.05 ! NH4 nitrification rate + xsirem = 0.003 ! remineralization rate of Si + xsiremlab = 0.03 ! fast remineralization rate of Si + xsilab = 0.5 ! Fraction of labile biogenic silica + feratb = 60.E-6 ! Fe/C quota in bacteria + xkferb = 4E-10 ! Half-saturation constant for bacteria Fe/C +! ! ln_p5z + xremikc = 0.4 ! remineralization rate of DOC + xremikn = 0.4 ! remineralization rate of DON + xremikp = 0.5 ! remineralization rate of DOP +/ +!----------------------------------------------------------------------- +&nampispoc ! parameters for organic particles +!----------------------------------------------------------------------- + xremip = 0.035 ! remineralisation rate of POC + jcpoc = 15 ! Number of lability classes + rshape = 1.0 ! Shape of the gamma function +! ! ln_p5z + xremipc = 0.028 ! remineralisation rate of POC + xremipn = 0.03 ! remineralisation rate of PON + xremipp = 0.035 ! remineralisation rate of POP +/ +!----------------------------------------------------------------------- +&nampiscal ! parameters for Calcite chemistry +!----------------------------------------------------------------------- + kdca = 100. ! calcite dissolution rate constant (1/time) + nca = 4.7 ! order of dissolution reaction (dimensionless) +/ +!----------------------------------------------------------------------- +&nampisbc ! 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.naa10km_orca', -1 , 'dust' , .true. , .true. , 'yearly' , '' , '' , '' + sn_ironsed = 'domain_cfg' , -12 , 'bathy_metry' , .false. , .true. , 'yearly' , '' , '' , '' + sn_hydrofe = 'hydrofe.orca' , -12 , 'epsdb' , .false. , .true. , 'yearly' , '' , '' , '' +! + cn_dir = './' ! root directory for the location of the dynamical files + ln_ironsed = .false. ! boolean for Fe input from sediments + ln_ironice = .false. ! boolean for Fe input from sea ice + ln_hydrofe = .false. ! boolean for from hydrothermal vents + sedfeinput = 2.e-9 ! Coastal release of Iron + distcoast = 5.e3 ! Distance off the coast for Iron from sediments + mfrac = 0.035 ! Fe mineral fraction of dust + wdust = 2.0 ! Dust sinking speed + icefeinput = 15.e-9 ! Iron concentration in sea ice + hratio = 1.e+7 ! Fe to 3He ratio assumed for vent iron supply +! ! ln_ligand + lgw_rath = 0.2 ! Weak ligand ratio from sed hydro sources +/ +!----------------------------------------------------------------------- +&nampislig ! Namelist parameters for ligands, nampislig +!----------------------------------------------------------------------- + rlgw = 300. ! Lifetime (years) of weak ligands + rlig = 1.E-4 ! Remin ligand production per unit C + prlgw = 3.E-4 ! Photolysis of weak ligand + rlgs = 1. ! Lifetime (years) of strong ligands + xklig = 1.E-9 ! 1/2 saturation constant of photolysis +/ +!----------------------------------------------------------------------- +&nampissed ! Namelist parameters for sediment mobilisation +!----------------------------------------------------------------------- + nitrfix = 2.e-7 ! Nitrogen fixation rate + diazolight = 30. ! Diazotrophs sensitivity to light (W/m2) + concfediaz = 1.e-10 ! Diazotrophs half-saturation Cste for Iron +/ +!----------------------------------------------------------------------- +&nampisice ! Prescribed sea ice tracers +!----------------------------------------------------------------------- +!======================================================================== +! constant ocean tracer concentrations are defined in trcice_pisces.F90 +! (Global, Arctic, Antarctic and Baltic) +! trc_ice_ratio : >=0 & <=1 => prescribed ice/ocean tracer concentration ratio +! : = -1 => the ice-ocean tracer concentration ratio +! follows the ice-ocean salinity ratio +! : = -2 => tracer concentration in sea ice is prescribed +! and trc_ice_prescr is used +! trc_ice_prescr : prescribed tracer concentration. used only if +! trc_ice_ratio = -2. equals -99 if not used. +! cn_trc_o : = 'GL' => use global ocean values making the Baltic +! distinction only +! : = 'AA' => use specific Arctic/Antarctic/Baltic values +!======================================================================== +! sn_tri_ ! trc_ice_ratio ! trc_ice_prescr ! cn_trc_o + sn_tri_dic = -1., -99., 'AA' + sn_tri_doc = 0., -99., 'AA' + sn_tri_tal = -1., -99., 'AA' + sn_tri_oxy = -1., -99., 'AA' + sn_tri_cal = 0., -99., 'AA' + sn_tri_po4 = -1., -99., 'AA' + sn_tri_poc = 0., -99., 'AA' + sn_tri_goc = 0., -99., 'AA' + sn_tri_bfe = 0., -99., 'AA' + sn_tri_num = 0., -99., 'AA' + sn_tri_sil = -1., -99., 'AA' + sn_tri_dsi = 0., -99., 'AA' + sn_tri_gsi = 0., -99., 'AA' + sn_tri_phy = 0., -99., 'AA' + sn_tri_dia = 0., -99., 'AA' + sn_tri_zoo = 0., -99., 'AA' + sn_tri_mes = 0., -99., 'AA' + sn_tri_fer = -2., 15E-9, 'AA' + sn_tri_sfe = 0., -99., 'AA' + sn_tri_dfe = 0., -99., 'AA' + sn_tri_nfe = 0., -99., 'AA' + sn_tri_nch = 0., -99., 'AA' + sn_tri_dch = 0., -99., 'AA' + sn_tri_no3 = -1., -99., 'AA' + sn_tri_nh4 = 1., -99., 'AA' +/ +!----------------------------------------------------------------------- +&nampisdmp ! Damping +!----------------------------------------------------------------------- + ln_pisdmp = .true. ! Relaxation for some tracers to a mean value + nn_pisdmp = 5475 ! Frequency of Relaxation +/ +!----------------------------------------------------------------------- +&nampismass ! Mass conservation +!----------------------------------------------------------------------- + ln_check_mass = .false. ! Check mass conservation +/ +!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!! PISCES reduced (key_pisces_reduced, ex LOBSTER) : namelists +!! 1 - biological parameters for phytoplankton (namlobphy) +!! 2 - biological parameters for nutrients (namlobnut) +!! 3 - biological parameters for zooplankton (namlobzoo) +!! 4 - biological parameters for detritus (namlobdet) +!! 5 - biological parameters for DOM (namlobdom) +!! 6 - parameters from aphotic layers to sediment (namlobsed) +!! 7 - general coefficients (namlobrat) +!! 8 - optical parameters (namlobopt) +!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!----------------------------------------------------------------------- +&namlobphy ! biological parameters for phytoplankton +!----------------------------------------------------------------------- + tmumax = 1.21e-5 ! maximal phytoplankton growth rate [s-1] + rgamma = 0.05 ! phytoplankton exudation fraction [%] + fphylab = 0.75 ! NH4 fraction of phytoplankton exsudation + tmminp = 5.8e-7 ! minimal phytoplancton mortality rate [0.05/86400 s-1=20 days] + aki = 33. ! light photosynthesis half saturation constant[W/m2] +/ +!----------------------------------------------------------------------- +&namlobnut ! biological parameters for nutrients +!----------------------------------------------------------------------- + akno3 = 0.7 ! nitrate limitation half-saturation value [mmol/m3] + aknh4 = 0.001 ! ammonium limitation half-saturation value [mmol/m3] + taunn = 5.80e-7 ! nitrification rate [s-1] + psinut = 3. ! inhibition of nitrate uptake by ammonium +/ +!----------------------------------------------------------------------- +&namlobzoo ! biological parameters for zooplankton +!----------------------------------------------------------------------- + rppz = 0.8 ! zooplankton nominal preference for phytoplancton food [%] + taus = 9.26E-6 ! specific zooplankton maximal grazing rate [s-1] +! ! 0.75/86400 s-1=8.680555E-6 1/86400 = 1.15e-5 + aks = 1. ! half-saturation constant for total zooplankton grazing [mmolN.m-3] + rpnaz = 0.3 ! non-assimilated phytoplankton by zooplancton [%] + rdnaz = 0.3 ! non-assimilated detritus by zooplankton [%] + tauzn = 8.1e-7 ! zooplancton specific excretion rate [0.1/86400 s-1=10 days] + fzoolab = 0.5 ! NH4 fraction of zooplankton excretion + fdbod = 0.5 ! zooplankton mortality fraction that goes to detritus + tmminz = 2.31e-6 ! minimal zooplankton mortality rate [(mmolN/m3)-1 d-1] +/ +!----------------------------------------------------------------------- +&namlobdet ! biological parameters for detritus +!----------------------------------------------------------------------- + taudn = 5.80e-7 ! detritus breakdown rate [0.1/86400 s-1=10 days] + fdetlab = 0. ! NH4 fraction of detritus dissolution +/ +!----------------------------------------------------------------------- +&namlobdom ! biological parameters for DOM +!----------------------------------------------------------------------- + taudomn = 6.43e-8 ! DOM breakdown rate [s-1] +! ! slow remineralization rate of semi-labile dom to nh4 (1 month) +/ +!----------------------------------------------------------------------- +&namlobsed ! parameters from aphotic layers to sediment +!----------------------------------------------------------------------- + sedlam = 3.86e-7 ! time coefficient of POC remineralization in sediments [s-1] + sedlostpoc = 0. ! mass of POC lost in sediments + vsed = 3.47e-5 ! detritus sedimentation speed [m/s] + xhr = -0.858 ! coeff for martin''s remineralisation profile +/ +!----------------------------------------------------------------------- +&namlobrat ! general coefficients +!----------------------------------------------------------------------- + rcchl = 60. ! Carbone/Chlorophyl ratio [mgC.mgChla-1] + redf = 6.56 ! redfield ratio (C:N) for phyto + reddom = 6.56 ! redfield ratio (C:N) for DOM +/ +!----------------------------------------------------------------------- +&namlobopt ! optical parameters +!----------------------------------------------------------------------- + xkg0 = 0.0232 ! green absorption coefficient of water + xkr0 = 0.225 ! red absorption coefficent of water + xkgp = 0.074 ! green absorption coefficient of chl + xkrp = 0.037 ! red absorption coefficient of chl + xlg = 0.674 ! green chl exposant for absorption + xlr = 0.629 ! red chl exposant for absorption + rpig = 0.7 ! chla/chla+pheo ratio +/ diff --git a/cfgs/SPITZ12/RUNDIR/namelist_top_cfg b/cfgs/SPITZ12/RUNDIR/namelist_top_cfg new file mode 100755 index 0000000..5a3da19 --- /dev/null +++ b/cfgs/SPITZ12/RUNDIR/namelist_top_cfg @@ -0,0 +1,169 @@ +!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!! NEMO/TOP1 : Configuration namelist : used to overwrite defaults values defined in SHARED/namelist_top_ref +!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!----------------------------------------------------------------------- +&namtrc_run ! run information +!----------------------------------------------------------------------- + ln_top_euler = .true. +/ +!----------------------------------------------------------------------- +&namtrc ! tracers definition +!----------------------------------------------------------------------- + jp_bgc = 24 +! + ln_pisces = .true. + ln_my_trc = .false. + ln_age = .false. + ln_cfc11 = .false. + ln_cfc12 = .false. + ln_c14 = .false. +! + ln_trcdta = .true. ! Initialisation from data input file (T) or not (F) + ln_trcbc = .true. ! Enables Boundary conditions +! ! ! ! ! ! +! ! name ! title of the field ! units ! init ! sbc ! cbc ! obc ! ais + sn_tracer(1) = 'DIC ' , 'Dissolved inorganic Concentration ', 'mol-C/L' , .true. , .false., .true. , .true. , .false. + sn_tracer(2) = 'Alkalini' , 'Total Alkalinity Concentration ', 'eq/L ' , .true. , .false., .true. , .true. , .false. + sn_tracer(3) = 'O2 ' , 'Dissolved Oxygen Concentration ', 'mol-C/L' , .true. , .false., .false., .true. , .false. + sn_tracer(4) = 'CaCO3 ' , 'Calcite Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(5) = 'PO4 ' , 'Phosphate Concentration ', 'mol-C/L' , .true. , .true. , .true. , .true. , .false. + sn_tracer(6) = 'POC ' , 'Small organic carbon Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(7) = 'Si ' , 'Silicate Concentration ', 'mol-C/L' , .true. , .true. , .true. , .true. , .false. + sn_tracer(8) = 'PHY ' , 'Nanophytoplankton Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(9) = 'ZOO ' , 'Microzooplankton Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(10) = 'DOC ' , 'Dissolved organic Concentration ', 'mol-C/L' , .false. , .false., .true. , .false. , .false. + sn_tracer(11) = 'PHY2 ' , 'Diatoms Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(12) = 'ZOO2 ' , 'Mesozooplankton Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(13) = 'DSi ' , 'Diatoms Silicate Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(14) = 'Fer ' , 'Dissolved Iron Concentration ', 'mol-C/L' , .false. , .true. , .true. , .false. , .false. + sn_tracer(15) = 'BFe ' , 'Big iron particles Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(16) = 'GOC ' , 'Big organic carbon Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(17) = 'SFe ' , 'Small iron particles Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(18) = 'DFe ' , 'Diatoms iron Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(19) = 'GSi ' , 'Sinking biogenic Silicate Concentration', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(20) = 'NFe ' , 'Nano iron Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(21) = 'NCHL ' , 'Nano chlorophyl Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(22) = 'DCHL ' , 'Diatoms chlorophyl Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. + sn_tracer(23) = 'NO3 ' , 'Nitrates Concentration ', 'mol-C/L' , .true. , .true. , .true. , .true. , .false. + sn_tracer(24) = 'NH4 ' , 'Ammonium Concentration ', 'mol-C/L' , .false. , .false., .false., .false. , .false. +/ +!----------------------------------------------------------------------- +&namage ! AGE +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namtrc_dta ! Initialisation from data input file +!----------------------------------------------------------------------- +! ! 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_trcdta(1) = 'data_DIC_nomask.nc', -1 , 'dissic' , .false. , .true. , 'yearly' , '' , '' , '' + sn_trcdta(2) = 'data_ALK_nomask.nc', -1 , 'talk' , .false. , .true. , 'yearly' , '' , '' , '' + sn_trcdta(3) = 'data_OXY_nomask.nc', -1 , 'o2' , .false. , .true. , 'yearly' , '' , '' , '' + sn_trcdta(5) = 'data_PO4_nomask.nc', -1 , 'po4' , .false. , .true. , 'yearly' , '' , '' , '' + sn_trcdta(7) = 'data_SIL_nomask.nc', -1 , 'si' , .false. , .true. , 'yearly' , '' , '' , '' + sn_trcdta(23) = 'data_NO3_nomask.nc', -1 , 'no3' , .false. , .true. , 'yearly' , '' , '' , '' + + rn_trfac(1) = 1000.e-6 ! multiplicative factor + rn_trfac(2) = 1000.e-6 ! - - - - + rn_trfac(3) = 1000.e-6 ! - - - - + rn_trfac(5) = 122000.e-6 ! - - - - + rn_trfac(7) = 1000.e-6 ! - - - - + rn_trfac(23) = 7600.e-6 ! - - - - + +/ +!----------------------------------------------------------------------- +&namtrc_adv ! advection scheme for passive tracer (default: NO selection) +!----------------------------------------------------------------------- + ln_trcadv_fct = .true. ! FCT scheme + nn_fct_h = 4 ! =2/4, horizontal 2nd / 4th order + nn_fct_v = 2 ! =2/4, vertical 2nd / COMPACT 4th order +/ +!----------------------------------------------------------------------- +&namtrc_ldf ! lateral diffusion scheme for passive tracer (default: NO selection) +!----------------------------------------------------------------------- + ln_trcldf_tra = .true. ! use active tracer setting +/ +!----------------------------------------------------------------------- +&namtrc_rad ! treatment of negative concentrations +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namtrc_snk ! sedimentation of particles +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namtrc_dmp ! passive tracer newtonian damping +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namtrc_ice ! Representation of sea ice growth & melt effects +!----------------------------------------------------------------------- +/ +!----------------------------------------------------------------------- +&namtrc_trd ! diagnostics on tracer trends ('key_trdtrc') +!---------------------------------------------------------------------- +/ +!---------------------------------------------------------------------- +&namtrc_bc ! data for boundary conditions +!----------------------------------------------------------------------- +! ! 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 ! + cn_dir_obc = './' ! root directory for the location of OPEN data files + sn_trcobc(1) = 'dissic_PISCES-NAA10KM_bdy_12m_clim', -1 , 'DIC' , .true. , .true.,'yearly' , '', '', '' + sn_trcobc(2) = 'talk_PISCES-NAA10KM_bdy_12m_clim' , -1 , 'Alkalini' , .true. , .true.,'yearly' , '', '', '' + sn_trcobc(3) = 'o2_PISCES-NAA10KM_bdy_12m_clim' , -1 , 'O2' , .true. , .true.,'yearly' , '', '', '' + sn_trcobc(5) = 'po4_PISCES-NAA10KM_bdy_12m_clim' , -1 , 'PO4' , .true. , .true.,'yearly' , '', '', '' + sn_trcobc(7) = 'si_PISCES-NAA10KM_bdy_12m_clim' , -1 , 'Si' , .true. , .true.,'yearly' , '', '', '' + sn_trcobc(23) = 'no3_PISCES-NAA10KM_bdy_12m_clim' , -1 , 'NO3' , .true. , .true.,'yearly' , '', '', '' + + + rn_trofac(1) = 1000.e-6 ! multiplicative factor + rn_trofac(2) = 1000.e-6 ! - - - - + rn_trofac(3) = 1000.e-6 ! - - - - + rn_trofac(5) = 122000.e-6 ! - - - - + rn_trofac(7) = 1000.e-6 ! - - - - + rn_trofac(23) = 7600.e-6 ! - - - - + + + cn_tronam(1) = 'dissic' ! Tracer-name to variable-name translation + cn_tronam(2) = 'talk' ! Tracer-name to variable-name translation + cn_tronam(3) = 'o2' ! Tracer-name to variable-name translation + cn_tronam(5) = 'po4' ! Tracer-name to variable-name translation + cn_tronam(7) = 'si' ! Tracer-name to variable-name translation + cn_tronam(23) = 'no3' ! Tracer-name to variable-name translation + + sn_trccbc(1) = 'river_loads_naa10km', -1 , 'riverdic' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trccbc(2) = 'river_loads_naa10km', -1 , 'riverdic' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trccbc(5) = 'river_loads_naa10km', -1 , 'riverdip' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trccbc(7) = 'river_loads_naa10km', -1 , 'riverdsi' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trccbc(10) = 'river_loads_naa10km', -1 , 'riverdoc' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trccbc(14) = 'river_loads_naa10km', -1 , 'riverdic' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trccbc(23) = 'river_loads_naa10km', -1 , 'riverdin' , .true. , .true. , 'yearly' , '' , '' , '' + rn_trcfac(1) = 8.333333e+01 ! + rn_trcfac(2) = 8.333333e+01 ! + rn_trcfac(5) = 3.774193e+03 ! + rn_trcfac(7) = 3.558719e+01 ! + rn_trcfac(10) = 8.333333e+01 ! + rn_trcfac(14) = 4.166667e-03 ! + rn_trcfac(23) = 5.223214e+02 ! + rn_cbc_time = 3.1536e+7 ! Time scaling factor for CBC data (seconds in a year) + + sn_trcsbc(5) = 'dust.naa10km_orca' , -1 , 'dustpo4' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trcsbc(7) = 'dust.naa10km_orca' , -1 , 'dustsi' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trcsbc(14) = 'dust.naa10km_orca' , -1 , 'dustfer' , .true. , .true. , 'yearly' , '' , '' , '' + sn_trcsbc(23) = 'dust.naa10km_orca' , -12 , 'ndep' , .false. , .true. , 'yearly' , '' , '' , '' + rn_trsfac(5) = 3.774194e-03 ! ( 1E-3 / 31. * 117 ) + rn_trsfac(7) = 9.572954e-03 ! ( 0.269 / 28.1 ) + rn_trsfac(14) = 6.2667860e-04 ! ( 0.035 / 55.85 ) + rn_trsfac(23) = 5.2232143e-01 ! ( From kgN m-2 s-1 to molC l-1 ====> zfact = 7.3125/14 ) + rn_sbc_time = 1. ! Time scaling factor for SBC and CBC data (seconds in a day) +/ +!---------------------------------------------------------------------- +&namtrc_bdy ! Setup of tracer boundary conditions +!----------------------------------------------------------------------- +! ! file name ! freq ! variable ! time interp. ! clim !'yearly' ! weights ! rotation | land/sea +/ +!----------------------------------------------------------------------- +&namtrc_ais ! Representation of Antarctic Ice Sheet tracers supply +!----------------------------------------------------------------------- +/ diff --git a/cfgs/SPITZ12/RUNDIR/namelist_top_ref b/cfgs/SPITZ12/RUNDIR/namelist_top_ref new file mode 100755 index 0000000..fef1d96 --- /dev/null +++ b/cfgs/SPITZ12/RUNDIR/namelist_top_ref @@ -0,0 +1,185 @@ +!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!! NEMO/TOP : Reference namelist +!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!! - tracer run information (namtrc_run) +!! - tracer definition (namtrc ) +!! - tracer data initialisation (namtrc_dta) +!! - tracer advection (namtrc_adv) +!! - tracer lateral diffusion (namtrc_ldf) +!! - tracer vertical physics (namtrc_zdf) +!! - tracer newtonian damping (namtrc_dmp) +!! - dynamical tracer trends (namtrc_trd) +!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> +!----------------------------------------------------------------------- +&namtrc_run ! run information +!----------------------------------------------------------------------- + ln_top_euler = .false. ! use Euler time-stepping for TOP + ln_rsttr = .false. ! start from a restart file (T) or not (F) + nn_rsttr = 0 ! restart control = 0 initial time step is not compared to the restart file value + ! = 1 do not use the value in the restart file + ! = 2 calendar parameters read in the restart file + cn_trcrst_in = "restart_trc" ! suffix of pass. sn_tracer restart name (input) + cn_trcrst_indir = "." ! directory from which to read input passive tracer restarts + cn_trcrst_out = "restart_trc" ! suffix of pass. sn_tracer restart name (output) + cn_trcrst_outdir = "." ! directory to which to write output passive tracer restarts +/ +!----------------------------------------------------------------------- +&namtrc ! tracers definition +!----------------------------------------------------------------------- + jp_bgc = 0 ! Number of passive tracers of the BGC model + ! + ln_pisces = .false. ! Run PISCES BGC model + ln_my_trc = .false. ! Run MY_TRC BGC model + ln_age = .false. ! Run the sea water age tracer + ln_cfc11 = .false. ! Run the CFC11 passive tracer + ln_cfc12 = .false. ! Run the CFC12 passive tracer + ln_sf6 = .false. ! Run the SF6 passive tracer + ln_c14 = .false. ! Run the Radiocarbon passive tracer + ! + ln_trcdta = .false. ! Initialisation from data input file (T) or not (F) + ln_trcdmp = .false. ! add a damping termn (T) or not (F) + ln_trcdmp_clo = .false. ! damping term (T) or not (F) on closed seas + ln_trcbc = .false. ! Surface, Lateral or Open Boundaries conditions + ln_trcais = .false. ! Antarctic Ice Sheet nutrient supply + ! + jp_dia3d = 0 ! Number of 3D diagnostic variables + jp_dia2d = 0 ! Number of 2D diagnostic variables + !_____________!___________!_________________________________________!____________!________________! + ! ! name ! title of the field ! units ! init from file ! +! sn_tracer(1) = 'tracer ', 'Tracer Concentration ', ' - ' , .false. +/ +!----------------------------------------------------------------------- +&namage ! AGE +!----------------------------------------------------------------------- + rn_age_depth = 10 ! depth over which age tracer reset to zero + rn_age_kill_rate = -0.000138888 ! = -1/7200 recip of relaxation timescale (s) for age tracer shallower than age_depth +/ +!----------------------------------------------------------------------- +&namtrc_dta ! Initialisation from data input file +!----------------------------------------------------------------------- +! ! 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 ! + ! + cn_dir = './' ! root directory for the location of the data files +/ +!----------------------------------------------------------------------- +&namtrc_adv ! advection scheme for passive tracer (default: NO selection) +!----------------------------------------------------------------------- + ln_trcadv_OFF = .false. ! No passive tracer advection + ln_trcadv_cen = .false. ! 2nd order centered scheme + nn_cen_h = 4 ! =2/4, horizontal 2nd order CEN / 4th order CEN + nn_cen_v = 4 ! =2/4, vertical 2nd order CEN / 4th order COMPACT + ln_trcadv_fct = .false. ! FCT scheme + nn_fct_h = 2 ! =2/4, horizontal 2nd / 4th order + nn_fct_v = 2 ! =2/4, vertical 2nd / COMPACT 4th order + ln_trcadv_mus = .false. ! MUSCL scheme + ln_mus_ups = .false. ! use upstream scheme near river mouths + ln_trcadv_ubs = .false. ! UBS scheme + nn_ubs_v = 2 ! =2 , vertical 2nd order FCT + ln_trcadv_qck = .false. ! QUICKEST scheme +/ +!----------------------------------------------------------------------- +&namtrc_ldf ! lateral diffusion scheme for passive tracer (default: NO selection) +!----------------------------------------------------------------------- +! ! Type of the operator: + ln_trcldf_OFF = .false. ! No explicit diffusion + ln_trcldf_tra = .false. ! use active tracer setting + ! ! Coefficient (defined with namtra_ldf coefficient) + rn_ldf_multi = 1. ! multiplier of aht for TRC mixing coefficient + rn_fact_lap = 1. ! Equatorial enhanced zonal eddy diffusivity (lap only) +/ +!----------------------------------------------------------------------- +&namtrc_rad ! treatment of negative concentrations +!----------------------------------------------------------------------- + ln_trcrad = .true. ! artificially correct negative concentrations (T) or not (F) +/ +!----------------------------------------------------------------------- +&namtrc_snk ! Sedimentation of particles +!----------------------------------------------------------------------- + nitermax = 2 ! number of iterations for sedimentation +/ +!----------------------------------------------------------------------- +&namtrc_dcy ! Diurnal cycle +!----------------------------------------------------------------------- + ln_trcdc2dm = .false. ! Diurnal cycle for TOP +/ +!----------------------------------------------------------------------- +&namtrc_opt ! light availability in the water column +!----------------------------------------------------------------------- +! ! 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_par = 'par.orca' , 24 , 'fr_par' , .true. , .true. , 'yearly' , '' , '' , '' + cn_dir = './' ! root directory for the location of the dynamical files + ln_varpar = .false. ! Read PAR from file + parlux = 0.43 ! Fraction of shortwave as PAR + light_loc = 'center' ! Light location in the water cell ('center', 'integral') +/ +!----------------------------------------------------------------------- +&namtrc_dmp ! passive tracer newtonian damping (ln_trcdmp=T) +!----------------------------------------------------------------------- + nn_zdmp_tr = 1 ! vertical shape =0 damping throughout the water column + ! =1 no damping in the mixing layer (kz criteria) + ! =2 no damping in the mixed layer (rho crieria) + cn_resto_tr = 'resto_tr.nc' ! create a damping.coeff NetCDF file (=1) or not (=0) +/ +!----------------------------------------------------------------------- +&namtrc_ice ! Representation of sea ice growth & melt effects +!----------------------------------------------------------------------- + nn_ice_tr = -1 ! tracer concentration in sea ice + ! =-1 (no vvl: identical cc in ice and ocean / vvl: cc_ice = 0) + ! = 0 (no vvl: cc_ice = zero / vvl: cc_ice = ) + ! = 1 prescribed to a namelist value (implemented in pisces only) +/ +!----------------------------------------------------------------------- +&namtrc_trd ! diagnostics on tracer trends ('key_trdtrc') +! or mixed-layer trends ('key_trdmld_trc') +!---------------------------------------------------------------------- + nn_trd_trc = 5475 ! time step frequency and tracers trends + nn_ctls_trc = 0 ! control surface type in mixed-layer trends (0,1 or n /seconds ; =86400. -> /day) + ln_trdmld_trc_restart = .false. ! restart for ML diagnostics + ln_trdmld_trc_instant = .true. ! flag to diagnose trends of instantantaneous or mean ML T/S + ln_trdtrc( 1) = .true. + ln_trdtrc( 2) = .true. + ln_trdtrc(23) = .true. +/ +!---------------------------------------------------------------------- +&namtrc_bc ! data for boundary conditions +!---------------------------------------------------------------------- +! Surface and coastal input data must be specified individually for each tracer. +! Lateral open boundary inputs are specified for each BDY segment and related inputfiles +! must contain data for the variables with active open boundary (set through &namtrc). +! By default, variable names of BDY inputfiles are the same as in &namtrc, but using +! cn_tronam it is possible to specify alternative variable names to match with inputfiles. +! ! file name ! freq ! variable ! time interp. ! clim !'yearly' ! weights ! rotation | land/sea +! sn_trcobc(1) = 'bdy_dta_trc_North_y1980', -1 , 'dummy' , .false. , .true. ,'yearly' , '', '', '' +!----------------------------------------------------------------------- + cn_dir_sbc = './' ! root directory for the location of SURFACE data files + cn_dir_cbc = './' ! root directory for the location of COASTAL data files + cn_dir_obc = './' ! root directory for the location of OPEN data files + ln_rnf_ctl = .false. ! Remove runoff dilution on tracers with absent river load + rn_sbc_time = 86400. ! Time scaling factor for SBC data (seconds in a day) + rn_cbc_time = 86400. ! Time scaling factor for CBC data (seconds in a day) +! cn_tronam(1) = 'var1' ! Tracer-name to variable-name translation +/ +!---------------------------------------------------------------------- +&namtrc_bdy ! Setup of tracer boundary conditions +!----------------------------------------------------------------------- + cn_trc_dflt = 'neumann' ! OBC applied by default to all tracers + cn_trc = 'specified' ! Boundary conditions used for tracers with data files (selected in namtrc) + + nn_trcdmp_bdy = 0 ! Use damping timescales defined in nambdy of namelist + ! = 0 NO damping of tracers at open boudaries + ! = 1 Only for tracers forced with external data + ! = 2 Damping applied to all tracers + ln_zintobc = .false. ! T if a vertical interpolation is required. Variables gdep[t] and e3[t] must exist in the file + ! automatically defined to T if the number of vertical levels in bdy dta /= jpk +/ +!----------------------------------------------------------------------- +&namtrc_ais ! Representation of Antarctic Ice Sheet tracers supply +!----------------------------------------------------------------------- + nn_ais_tr = 1 ! tracer concentration in iceberg and ice shelf + ! = 0 (null concentrations) + ! = 1 prescribed concentrations + rn_icbdep = 120. ! Mean underwater depth of iceberg (m) +/