rompy.schism.namelists.cosine.COSINE

pydantic model rompy.schism.namelists.cosine.COSINE

This file was auto generated from a schism namelist file on 2023-11-20. The full contents of the namelist file are shown below providing associated documentation for the objects:

!parameter inputs via namelist convention. !(1) Use ‘ ‘ (single quotes) for chars; !(2) integer values are fine for real vars/arrays; !(3) if multiple entries for a parameter are found, the last one wins - please avoid this !(4) array inputs follow column major (like FORTRAN) and can spill to multiple lines !(5) space allowed before/after ‘=’

&MARCO !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ !switches and marco parameters !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

!———————————————————————– !idelay: a 7-day delay for zooplankton predation !———————————————————————– idelay = 0 ndelay = 7

!———————————————————————– !ibgraze: bottom grazing function !———————————————————————– ibgraze = 0

!———————————————————————– !idapt: light adaptation !———————————————————————– idapt = 0 alpha_corr= 1.25 zeptic= 10.0

!———————————————————————– !iz2graze=0 : shut down Z2 grazing on S2, Z1, and DN !———————————————————————– iz2graze = 1

!———————————————————————– !CoSiNE model station output option (need cstation.in with *.bp format) ! iout_cosine=0: turn off this option ! iout_cosine=1: all available diagnostic variables ! iout_cosine=2: state variables ! iout_cosine=3: state variables + source/sink terms ! iout_cosine=4: state variables + misc diagnostics ! iout_cosine=5: state variables + surface/bottom fluxes ! nspool_cosine: output interval (number of time step) !———————————————————————– iout_cosine=0 nspool_cosine=30

!———————————————————————– !ico2s=0: no CO2 limitation on phytoplankton growth !———————————————————————– ico2s = 0

!———————————————————————– !ispm=0: constant Suspended Particlate Matter spm0 is used for while domain !ispm=1: spatial varying SPM from SPM.gr3 is used !ispm=2: use SED model to calculate SPM !———————————————————————– ispm = 0 spm0 = 20.0

!———————————————————————– !ised=1 : sediment flux model !———————————————————————– ised = 1 /

&CORE !———————————————————————— !phytoplankton !———————————————————————— gmaxs = 2.0 2.5 !maximum growth rate gammas = 0.2 0.075 !mortality rate pis = 1.5 1.5 !ammonium inhibition kno3s = 1.0 3.0 !NO3 half saturation knh4s = 0.15 0.45 !NH4 half saturation kpo4s = 0.1 0.1 !PO4 half saturation kco2s = 50.0 50.0 !CO2 half saturation ksio4 = 4.5 !SiO4 half saturation for diatom kns = 0.0 0.0 !nighttime uptake rate of NH4 alphas = 0.1 0.1 !initial slopes of P-I curve betas = 0.0 0.0 !slope for photo-inhibition aks = 0.75 0.03 0.066 !light extinction coefficients: rKe=ak1+ak2*(S1+S2)+ak3*SPM

!———————————————————————— !zooplankton !———————————————————————— betaz = 1.35 0.4 !maximum grazing rate alphaz = 0.75 0.75 !assimilation rate gammaz = 0.2 0.2 !mortality rate kez = 0.2 0.2 !excretion rate kgz = 0.5 0.25 !reference prey concentration for grazing rhoz = 0.6 0.3 0.1 !prey preference factors of Z2 on (S2,Z1,DN)

!———————————————————————— !other !———————————————————————— ipo4 = 1 !add additional PO4 from biogenic silica dissolution TR = 20.0 !Reference temperature for temperature adjust for CoSiNE sink and source kox = 30.0 !reference oxygen concentration for oxidation wss2 = 0.2 !settling velocity of S2 wsdn = 1.0 !settling velocity of DN wsdsi = 1.0 !settling velocity of DSi si2n = 1.2 !silica to nitrogen conversion coefficient p2n = 0.0625 !phosphorus to nitrogen conversion coefficient (1/16) o2no = 8.625 !oxygen to nitrogen (NO3) conversion coefficient (138/16) o2nh = 6.625 !oxygen to nitrogen (NH4) conversion coefficient (106/16) c2n = 7.3 !carbon to nitrogen conversion coefficient gamman= 0.07 !nitrification coefficent pco2a = 391.63 !atmospheric CO2 concentration kmdn = 0.009 0.075 !remineralization coefficients for DN: rate=kmdn(1)*T+kmdn(2) kmdsi = 0.0114 0.015 !remineralization coefficients for DSi: rate=kmdsi(1)*T+kmdsi(2) /

&MISC !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ !diatom sinking velocity depends on NO3 !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ iws=0 NO3c=2.0 !mmol/m3 ws1=2.5 ws2=2.0

!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ !clam grazing model !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ iclam=0 deltaZ= 1 !meter kcex=0.002 !day-1 Nperclam=0.39032 !mmol[N] Wclam=5.45e-3 !clam weigh (g) Fclam=40 !L.g[AFDW]-1.day-1, filtration rate nclam0=2000

!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ !sediment model !+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

!———————————————————————– !parameters related to S2 in sediment !fS2: partitioning coefficient from S2 in water column into sediment S2 !rkS2: changing rate of remineralization rate for sediment S2 !mkS2: maximum remineralization rate for sediment S2 !———————————————————————– fS2= 0.1 0.1 0.8 rkS2= 4e-3 1.0e-4 0.0 !time delay of 63 day mkS2= 0.1 0.01 0.0

!———————————————————————– !parameters related to DN in sediment !fdDN: partitioning coefficient from DN in water column into sediment DN !rkDN: changing rate of remineralization rate for sediment DN !mkDN: maximum remineralization rate for sediment DN !———————————————————————– fDN= 0.15 0.10 0.75 rkDN= 4e-3 1.0e-4 0.0 !time delay of 63 day mkDN= 0.1 0.01 0.0

!———————————————————————– !parameters related to DSi in sediment !fDSi: partitioning coefficient from DSi in water column into sediment DSi !rkDSi: changing rate of remineralization rate for sediment DSi !mkDSi: maximum remineralization rate for sediment DSi !———————————————————————– fDSi= 0.3 0.3 0.4 rkDSi= 0.004 1e-4 0.0 !time delay of about half a month mkDSi= 0.1 0.01 0.0 /

Fields:

• core (rompy.schism.namelists.cosine.CORE)

• marco (rompy.schism.namelists.cosine.MARCO)

• misc (rompy.schism.namelists.cosine.MISC)

field core: CORE = CORE(gmaxs=[2.0, 2.5], gammas=[0.2, 0.075], pis=[1.5, 1.5], kno3s=[1.0, 3.0], knh4s=[0.15, 0.45], kpo4s=[0.1, 0.1], kco2s=[50.0, 50.0], ksio4=4.5, kns=[0.0, 0.0], alphas=[0.1, 0.1], betas=[0.0, 0.0], aks=[0.75, 0.03, 0.066], betaz=[1.35, 0.4], alphaz=[0.75, 0.75], gammaz=[0.2, 0.2], kez=[0.2, 0.2], kgz=[0.5, 0.25], rhoz=[0.6, 0.3, 0.1], ipo4=1, TR=20.0, kox=30.0, wss2=0.2, wsdn=1.0, wsdsi=1.0, si2n=1.2, p2n=0.0625, o2no=8.625, o2nh=6.625, c2n=7.3, gamman=0.07, pco2a=391.63, kmdn=[0.009, 0.075], kmdsi=[0.0114, 0.015])

field marco: MARCO = MARCO(idelay=0, ndelay=7, ibgraze=0, idapt=0, alpha_corr=1.25, zeptic=10.0, iz2graze=1, iout_cosine=0, nspool_cosine=30, ico2s=0, ispm=0, spm0=20.0, ised=1)

field misc: MISC = MISC(iws=0, NO3c=2.0, ws1=2.5, ws2=2.0, iclam=0, deltaZ=1, kcex=0.002, Nperclam=0.39032, Wclam='5.45e-3', Fclam=40, nclam0=2000, fS2=[0.1, 0.1, 0.8], rkS2=['4e-3', '1.0e-4', 0.0], mkS2=[0.1, 0.01, 0.0], fDN=[0.15, 0.1, 0.75], rkDN=['4e-3', '1.0e-4', 0.0], mkDN=[0.1, 0.01, 0.0], fDSi=[0.3, 0.3, 0.4], rkDSi=[0.004, '1e-4', 0.0], mkDSi=[0.1, 0.01, 0.0])