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cgem.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.
! Values can be separated by commas or spaces.
!(5) space allowed before/after '='
&nosp
!------------------------------------------------------------------------
!Number of Phyto and Zooplankton species
!------------------------------------------------------------------------
nospA = 1
nospZ = 2
skipcgem = 0 !1==Run as tracers with sinking
checkwindrad = 0 !1==For checking, write Rad and Wind to stdout
debug = 0 !Extra write statments, 0=none, 1=interface, 2=components, 3=fluxes, 4=light
sinkwcgem = .TRUE. !If true, do sinking internally, else use SCHISM
cgemcoords = .FALSE. !Set .TRUE. and pick fixed coords if you don't use hgrid.ll
cgemlat = 30. !If SCHISM doesn't define ylat_el, xlon_el
cgemlon = 88. !Mocsy and getSolar use East, not negative
!------------------------------------------------------------------------
/
&switches
!------------------------------------------------------------------------
!Switches in CGEM
!------------------------------------------------------------------------
Which_fluxes = 1 1 0 !Which_fluxes: Toggle on(1) off(0): O2surf, DICsurf, Instant Remineralization
Which_temperature = 1 !Which_temperature: 1==Sigmoidal, 2==Optimum Temp. Thresh., 3==Arrenhius
Which_uptake = 1 !Which_uptake: 1==Michaelis-Menten, 2==Geider (needs nfQs), 3==Roelke, Nutrient uptake rate
Which_quota = 1 !Which_quota: 1==Droop, 2==Nyholm, 3==Flynn, Nutrient dependent growth
Which_photosynthesis = 1 !Which_photosynthesis: 1==photoinhibition, 2==without photoinhibition, 3==nutrient dependent
Which_growth = 1 !Which_growth: 1==minimum, 2==product formulation, 3==umax nutrient dependent
Which_rad = 1 !Which_rad: 0==getsolar, 1==use schism solar fluxes, in W/m2
Which_wind = 1 !Which_wind: 0==constant 5m/s, 1==use schism wind
sinkTr = 0.01 !Sinking rate for tracer
!------------------------------------------------------------------------
/
&optics
!------------------------------------------------------------------------
!optics - needed for the light model
!------------------------------------------------------------------------
Kw = 0.146 !Kw: AOP, light attenuation due to water
Kcdom = 0.001 !Kcdom: AOP, light attenuation due to CDOM
Kspm = 0.029 !Kspm: AOP, light attenuation due to SPM
Kchla = 0.024 !Kchla: AOP, light attenuation due to chla
astar490 = 0.0375 !astar490: Chla specific absorption at 490 nm
aw490 = 0.015 !aw490: seawater absorption at 490 nm
astarOMA = 0.01 !astarOMA: OM_A specific absorption at 490 nm
astarOMZ = 0.01 !astarOMZ: OM_Z specific absorption at 490 nm
astarOMR = 0.01 !astarOMR: OM_R specific absorption at 490 nm
astarOMBC = 0.01 !astarOMBC: OM_BC specific absorption at 490 nm
PARfac = 1. !PARfac: Multiplies surface PAR
sinkCDOM = 0. !sinkCDOM: sinking rate of CDOM
!------------------------------------------------------------------------
/
&temperature
!--------------------------------------------------------------------------
!temperature - phyto/zooplankton growth
!--------------------------------------------------------------------------
Tref = 17. 22. 26. !Tref(nospA+nospZ): Optimum temperature for growth(C)
KTg1 = 0.0035 0.0035 0.0035 !KTg1(nospA+nospZ): Effect of T below Topt(C^2)
KTg2 = 0.001 0.001 0.001 !KTg2(nospA+nospZ): Effect of T above Topt(C^2)
Ea = 0.61 0.61 0.61 !Ea(nospA+nospZ): Slope of Arrhenius plot(eV)
!------------------------------------------------------------------------
/
&phytoplankton
!------------------------------------------------------------------------
!Phytoplankton, up to 3 types
!------------------------------------------------------------------------
umax = 1.12 !umax: maximum growth rate
CChla = 181.477 !CChla: Fixed C:Chla ratio
alpha = 3.96e-16 !alpha: initial slope of the photosynthesis-irradiance relationship
beta = 1.1e-18 !beta: photoinhibition constant
respg = 0.1 !respg: phytoplankton growth respiration coefficient
respb = 0.02 !respb: phytoplankton basal respiration coefficient
QminN = 1.53e-10 !QminN: minimum N cell-quota
QminP = 1.07e-11 !QminP: minimum P cell-quota
QmaxN = 6.85e-9 !QmaxN: maximum N cell-quota
QmaxP = 4.28e-10 !QmaxP: maximum P cell-quota
Kn = 1.13 !Kn: half-saturation constant for N
Kp = 0.51 !Kp: half-saturation constant for P
Ksi = 1.13 !Ksi: half-saturation constant for Si uptake
KQn = 5. !KQn: Qn constant for Flynn nutrient dependent growth model
KQp = 0.2 !KQp: Qp constant for Flynn nutrient dependent growth model
nfQs = 1. !nfQs: exponent for Geider nutrient uptake model
vmaxN = 1.33e-09 !vmaxN: N-uptake rate measured at umax
vmaxP = 4.07e-10 !vmaxP: P-uptake rate measured at umax
vmaxSi = 1.33e-09 !vmaxSi: Si-uptake rate measured at umax
aN = 1. !aN: coefficient for non-limiting nutrient
volcell = 513. !volcell: phytoplankton volume/cell
Qc = 4.54e-08 !Qc: phytoplankton carbon/cell
Athresh = 7e+07 !Athresh: Phytoplankton threshold for grazing, is multiplied by VOLcell
sinkA = 0.0029 !sinkA: sinking rate of phytoplankton cells
mA = 0.11 !mA: mortality coefficient
A_wt = 1. !A_wt: Relative proportion of total chlA for initializing phytoplankton
!------------------------------------------------------------------------
/
&zooplankton
!------------------------------------------------------------------------
!Zooplankton - up to 2 types
!------------------------------------------------------------------------
ediblevector = 0.4 0.4 !edibility vector for Z1(A1), Z2(A2)
Zeffic = 0.4 0.4 !Zeffic: assimilation efficiency as a fraction of ingestion
Zslop = 0.25 .0 !Zslop: proportion of grazed phytoplankton lost to sloppy feeding
Zvolcell = 2.98e+07 6.74e5 !Zvolcell: zooplankton volume/individual
ZQc = 3.13e-4 7.08e-07 !ZQc: zooplankton carbon/individual
ZQn = 6.95e-05 1.57e-07 !ZQn: zooplankton nitrogen/individual
ZQp = 3.77e-06 8.53e-09 !ZQp: zooplankton phosphorus/individual
ZKa = 1.12e+12 1.12e+12 !ZKa: half saturation coefficient for grazing
Zrespg = 0.2 0.3 !Zrespg: Zooplankton growth-dependent respiration factor
Zrespb = 0.1 0.416 !Zrespb: Zooplankton biomass-dependent respiration factor
Zumax = 9.45e+08 2.98e+07 !Zumax: maximum growth rate of zooplankton
Zm = 0.00072 0.00072 !Zm: Zooplankton mortality constant for quadratic mortality
!------------------------------------------------------------------------
/
&OM
!------------------------------------------------------------------------
!Organic Matter
!------------------------------------------------------------------------
KG1 = 30. !KG1: turnover rate for OM1_A and OM1_Z
KG2 = 30. !KG2: turnover rate for OM2_A and OM2_Z
KG1R = 11. !KG1_R: OM1 turnover rate for riverine
KG2R = 3.7 !KG2_R: OM2 turnover rate for riverine
KG1BC = 1. !KG1_BC: OM1 turnover rate for initial and bc
KG2BC = 1. !KG2_BC: OM2 turnover rate for initial and bc
KNH4 = 1. !KNH4: NH4 rate constant for nitrification
nitmax = 0.52 !nitmax: maximum rate of nitrification per day
KO2 = 10. !KO2: half-saturation concentration for O2 utilization
KstarO2 = 10. !KstarO2: O2 concentration that inhibits denitrification
KNO3 = 5. !KNO3: half-saturation concentration for NO3 used in denitrification
pCO2 = 380. !pCO2: atmospheric CO2
!--Initialize stoichiometry: CNP to P ratios (P:P = 1)
sx1R = 51. !stoich_x1R: initial ratio C:P
sy1R = 4.5 !stoich_y1R: initial ratio N:P
sx2R = 700. !stoich_x2R: initial ratio C:P
sy2R = 50. !stoich_y2R: initial ratio N:P
sx1BC= 106. !stoich_x1BC:initial ratio C:P
sy1BC= 16. !stoich_y1BC:initial ratio N:P
sx2BC= 106. !stoich_x2BC:initial ratio C:P
sy2BC= 16. !stoich_y2BC:initial ratio N:P
!--OM sinking rates
sinkOM1A = 0.01 !sinkOM1_A: sinking rate
sinkOM2A = 0. !sinkOM2_A: sinking rate
sinkOM1Z = 0.01 !sinkOM1_Z: sinking rate
sinkOM2Z = 0. !sinkOM2_Z: sinking rate
sinkOM1R = 0.01 !sinkOM1_R: sinking rate
sinkOM2R = 0. !sinkOM2_R: sinking rate
sinkOM1BC = 0.01 !sinkOM1_BC: sinking rate
sinkOM2BC = 0. !sinkOM2_BC: sinking rate
KGcdom = 0.01 !KGcdom: decay rate of CDOM, 1/day
CF_SPM = 0.018 !CF_SPM: conversion factor for river OM to river SPM
KGbot = 10950. !KG_bot, turnover rate for k=20 if Instant Remineralization is used (see Which_fluxes above)
/
&init
!Initialize ff
!Not read by SCHISM, used in write_initial_condition.py
A_init = 6.e7 !A
Qn_init = 0.30649887E-8 !Qn
Qp_init = 0.19438481E-9 !Qp
Z_init = 150. 1505. !Z1 Z2
NO3_init = 5. !NO3
NH4_init = 1. !NH4
PO4_init = 2. !PO4
DIC_init = 2134. !DIC
O2_init = 172. !O2
OM1CA_init = 1.E-5 !OM1CA
OM1NA_init = 1.5E-6 !OM1NA
OM1PA_init = 1.E-7 !OM1PA
OM2CA_init = 1.E-5 !OM2CA
OM2NA_init = 1.5E-6 !OM2NA
OM2PA_init = 1.E-7 !OM2PA
OM1CZ_init = 1.E-5 !OM1CZ
OM1NZ_init = 1.5E-6 !OM1NZ
OM1PZ_init = 1.E-7 !OM1PZ
OM2CZ_init = 1.E-5 !OM2CZ
OM2NZ_init = 1.5E-6 !OM2NZ
OM2PZ_init = 1.E-7 !OM2PZ
OM1_R_init = 0.00001 !OM1_rp
OM2_R_init = 0.00001 !OM2_rp
CDOM_init = 2. !CDOM
Si_init = 15. !Si
OM1_BC_init = 0.00001 !OM1_bc
OM2_BC_init = 0.00001 !OM2_bc
ALK_init = 2134. !ALK
Tr_init = 1. !Tr
/