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namelist_pisces
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namelist_pisces
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!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!! PISCES : 1 - air-sea exchange (nampisext)
!! namelists 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)
!! 9 - parameters for Kriest parameterization (nampiskrp, nampiskrs)
!! 10 - additional 2D/3D diagnostics (nampisdia)
!! 11 - Damping (nampisdmp)
!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&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 !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing !
sn_patm = 'presatm' , -1 , 'patm' , .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)
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampisbio ! biological parameters
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
nrdttrc = 3 ! time step frequency for biology
wsbio = 2. ! POC sinking speed
xkmort = 2.E-7 ! half saturation constant for mortality
ferat3 = 10.E-6 ! Fe/C in zooplankton
wsbio2 = 30. ! Big particles sinking speed
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampislim ! parameters for nutrient limitations
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
conc0 = 1.e-6 ! Phosphate half saturation
conc1 = 8E-6 ! Phosphate half saturation for diatoms
conc2 = 1E-9 ! Iron half saturation for phyto
conc2m = 3E-9 ! Max iron half saturation for phyto
conc3 = 3E-9 ! Iron half saturation for diatoms
conc3m = 8E-9 ! Maxi iron half saturation for diatoms
xsizedia = 1.E-6 ! Minimum size criteria for diatoms
xsizephy = 1.E-6 ! Minimum size criteria for phyto
concnnh4 = 1.E-7 ! NH4 half saturation for phyto
concdnh4 = 8.E-7 ! NH4 half saturation for diatoms
xksi1 = 2.E-6 ! half saturation constant for Si uptake
xksi2 = 3.33E-6 ! half saturation constant for Si/C
xkdoc = 417.E-6 ! half-saturation constant of DOC remineralization
concfebac = 1.E-11 ! Half-saturation for Fe limitation of Bacteria
qnfelim = 7.E-6 ! Optimal quota of phyto
qdfelim = 7.E-6 ! Optimal quota of diatoms
caco3r = 0.16 ! mean rain ratio
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampisprod ! parameters for phytoplankton growth
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
pislope = 2. ! P-I slope
pislope2 = 2. ! P-I slope for diatoms
excret = 0.05 ! excretion ratio of phytoplankton
excret2 = 0.05 ! excretion ratio of diatoms
ln_newprod = .false. ! Enable new parame. of production (T/F)
bresp = 0.00333 ! Basal respiration rate
chlcnm = 0.033 ! Minimum Chl/C in nanophytoplankton
chlcdm = 0.05 ! Minimum Chl/C in diatoms
chlcmin = 0.0033 ! Maximum Chl/c in phytoplankton
fecnm = 40E-6 ! Maximum Fe/C in nanophytoplankton
fecdm = 40E-6 ! Minimum Fe/C in diatoms
grosip = 0.151 ! mean Si/C ratio
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampismort ! parameters for phytoplankton sinks
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
wchl = 0.001 ! quadratic mortality of phytoplankton
wchld = 0.02 ! maximum quadratic mortality of diatoms
mprat = 0.01 ! phytoplankton mortality rate
mprat2 = 0.01 ! Diatoms mortality rate
mpratm = 0.01 ! Phytoplankton minimum mortality rate
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampismes ! parameters for mesozooplankton
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
part2 = 0.75 ! part of calcite not dissolved in mesozoo guts
grazrat2 = 0.7 ! maximal mesozoo grazing rate
resrat2 = 0.005 ! exsudation rate of mesozooplankton
mzrat2 = 0.03 ! mesozooplankton mortality rate
xprefc = 1. ! zoo preference for phyto
xprefp = 0.3 ! zoo preference for POC
xprefz = 1. ! zoo preference for zoo
xprefpoc = 0.3 ! zoo preference for poc
xthresh2zoo = 1.E-8 ! zoo feeding threshold for mesozooplankton
xthresh2dia = 1.E-8 ! diatoms feeding threshold for mesozooplankton
xthresh2phy = 1.E-8 ! nanophyto feeding threshold for mesozooplankton
xthresh2poc = 1.E-8 ! poc feeding threshold for mesozooplankton
xthresh2 = 2.E-7 ! Food threshold for grazing
xkgraz2 = 20.E-6 ! half sturation constant for meso grazing
epsher2 = 0.3 ! Efficicency of Mesozoo growth
sigma2 = 0.6 ! Fraction of mesozoo excretion as DOM
unass2 = 0.3 ! non assimilated fraction of P by mesozoo
grazflux = 2.e3 ! flux-feeding rate
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampiszoo ! parameters for microzooplankton
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
part = 0.5 ! part of calcite not dissolved in microzoo gutsa
grazrat = 3.0 ! maximal zoo grazing rate
resrat = 0.03 ! exsudation rate of zooplankton
mzrat = 0.001 ! zooplankton mortality rate
xpref2c = 0.1 ! Microzoo preference for POM
xpref2p = 1. ! Microzoo preference for Nanophyto
xpref2d = 0.5 ! 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 = 2.E-7 ! Food threshold for feeding
xkgraz = 20.E-6 ! half sturation constant for grazing
epsher = 0.3 ! Efficiency of microzoo growth
sigma1 = 0.6 ! Fraction of microzoo excretion as DOM
unass = 0.3 ! non assimilated fraction of phyto by zoo
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampisrem ! parameters for remineralization
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
xremik = 0.25 ! remineralization rate of DOC
xremip = 0.025 ! remineralisation rate of POC
nitrif = 0.05 ! NH4 nitrification rate
xsirem = 0.003 ! remineralization rate of Si
xsiremlab = 0.025 ! fast remineralization rate of Si
xsilab = 0.31 ! Fraction of labile biogenic silica
xlam1 = 0.005 ! scavenging rate of Iron
oxymin = 1.E-6 ! Half-saturation constant for anoxia
ligand = 0.6E-9 ! Ligands concentration
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampiscal ! parameters for Calcite chemistry
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
kdca = 6. ! calcite dissolution rate constant (1/time)
nca = 1. ! order of dissolution reaction (dimensionless)
/
!Joan
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampissed ! parameters for inputs deposition
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
! ! file name ! frequency (hours) ! variable ! time interp. ! clim ! 'yearly'/ ! weights ! rotation !
! ! ! (if <0 months) ! name ! (logical) ! (T/F) ! 'monthly' ! filename ! pairing !
sn_dust = 'dust.orca' , -1 , 'dust' , .true. , .true. , 'yearly' , '' , ''
sn_riverdic = 'river.orca' , -12 , 'riverdic' , .false. , .true. , 'yearly' , '' , ''
sn_riverdoc = 'river.orca' , -12 , 'riverdoc' , .false. , .true. , 'yearly' , '' , ''
sn_ndepo = 'ndeposition.orca', -12 , 'ndep' , .false. , .true. , 'yearly' , '' , ''
sn_ironsed = 'bathy.orca' , -12 , 'bathy' , .false. , .true. , 'yearly' , '' , ''
!
cn_dir = './' ! root directory for the location of the dynamical files
ln_dust = .true. ! boolean for dust input from the atmosphere
ln_river = .true. ! boolean for river input of nutrients
ln_ndepo = .true. ! boolean for atmospheric deposition of N
ln_ironsed = .false. ! boolean for Fe input from sediments
!end_Joan
sedfeinput = 1E-9 ! Coastal release of Iron
dustsolub = 0.02 ! Solubility of the dust
wdust = 2.0 ! Dust sinking speed
nitrfix = 1E-7 ! Nitrogen fixation rate
diazolight = 50. ! Diazotrophs sensitivity to light (W/m2)
concfediaz = 1.E-10 ! Diazotrophs half-saturation Cste for Iron
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampiskrp ! Kriest parameterization : parameters "key_kriest"
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
xkr_eta = 1.17 ! Sinking exponent
xkr_zeta = 2.28 ! N content exponent
xkr_mass_min = 0.0002 ! Minimum mass for Aggregates
xkr_mass_max = 1. ! Maximum mass for Aggregates
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampiskrs ! Kriest parameterization : size classes "key_kriest"
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
xkr_sfact = 942. ! Sinking factor
xkr_stick = 0.5 ! Stickiness
xkr_nnano = 2.337 ! Nbr of cell in nano size class
xkr_ndiat = 3.718 ! Nbr of cell in diatoms size class
xkr_nmeso = 7.147 ! Nbr of cell in mesozoo size class
xkr_naggr = 9.877 ! Nbr of cell in aggregates size class
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampisdia ! additional 2D/3D tracers diagnostics
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
! ! name ! title of the field ! units !
! ! ! ! !
pisdia2d(1) = 'Cflx ' , 'DIC flux ', 'molC/m2/s '
pisdia2d(2) = 'Oflx ' , 'Oxygen flux ', 'molC/m2/s '
pisdia2d(3) = 'Kg ' , 'Gas transfer ', 'mol/m2/s/uatm'
pisdia2d(4) = 'Delc ' , 'Delta CO2 ', 'uatm '
pisdia2d(5) = 'PMO ' , 'POC export ', 'molC/m2/s '
pisdia2d(6) = 'PMO2 ' , 'GOC export ', 'molC/m2/s '
pisdia2d(7) = 'ExpFe1 ' , 'Nano iron export ', 'molFe/m2/s '
pisdia2d(8) = 'ExpFe2 ' , 'Diatoms iron export ', 'molFe/m2/s '
pisdia2d(9) = 'ExpSi ' , 'Silicate export ', 'molSi/m2/s '
pisdia2d(10) = 'ExpCaCO3 ' , 'Calcite export ', 'molC/m2/s '
pisdia2d(11) = 'heup ' , 'euphotic layer depth ', 'm '
pisdia2d(12) = 'Fedep ' , 'Iron dep ', 'molFe/m2/s '
pisdia2d(13) = 'Nfix ' , 'Nitrogen Fixation ', 'molN/m2/s '
pisdia3d(1) = 'PH ' , 'PH ', '- '
pisdia3d(2) = 'CO3 ' , 'Bicarbonates ', 'mol/l '
pisdia3d(3) = 'CO3sat ' , 'CO3 saturation ', 'mol/l '
pisdia3d(4) = 'PAR ' , 'light penetration ', 'W/m2 '
pisdia3d(5) = 'PPPHY ' , 'Primary production of nanophyto ', 'molC/m3/s '
pisdia3d(6) = 'PPPHY2 ' , 'Primary production of diatoms ', 'molC/m3/s '
pisdia3d(7) = 'PPNEWN ' , 'New Primary production of nano ', 'molC/m3/s '
pisdia3d(8) = 'PPNEWD ' , 'New Primary production of diat ', 'molC/m3/s '
pisdia3d(9) = 'PBSi ' , 'Primary production of Si diatoms ', 'molSi/m3/s '
pisdia3d(10) = 'PFeN ' , 'Primary production of nano iron ', 'molFe/m3/s '
pisdia3d(11) = 'PFeD ' , 'Primary production of diatoms iron', 'molFe/m3/s '
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampisdmp ! Damping
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
ln_pisdmp = .true. ! Relaxation fo some tracers to a mean value
nn_pisdmp = 2400 ! Frequency of Relaxation
/
!'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
&nampismass ! Mass conservation
!,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
ln_check_mass = .true. ! Check mass conservation
/