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cosine.nml
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!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 = 1
ndelay = 7
!-----------------------------------------------------------------------
!ibgraze: bottom grazing function
!-----------------------------------------------------------------------
ibgraze = 0
!-----------------------------------------------------------------------
!idapt: light adaptation
!-----------------------------------------------------------------------
idapt = 1
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=1
nspool_cosine=24
!-----------------------------------------------------------------------
!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 = 1
spm0 = 20.0
!-----------------------------------------------------------------------
!ised=1 : sediment flux model
!-----------------------------------------------------------------------
ised = 1
/
&CORE
!------------------------------------------------------------------------
!phytoplankton
!------------------------------------------------------------------------
gmaxs = 2.0 2.0 !maximum growth rate
gammas = 0.25 0.25 !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 = 0.0625 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 = 0.01 0.01 !slope for photo-inhibition
aks = 0.1 0.03 0.05 !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 = 0 !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 = 0.1 !settling velocity of S2
wsdn = 4 !settling velocity of DN
wsdsi = 5 !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 0.05 !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= 6e-3 4.0e-3 2.0e-3 !time delay of 63 day
mkDN= 0.25 0.25 0.25
!-----------------------------------------------------------------------
!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= 4e-3 1e-4 0.0 !time delay of about half a month
mkDSi= 0.01 0.01 0.0
/