rompy.schism.namelists.icm.ICM#
- pydantic model rompy.schism.namelists.icm.ICM[source]#
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:
!———————————————————————– ! ICM model parameter inputs. ! Format rules ! (1) Lines beginning with “!” are comments; blank lines are ignored; ! (2) one line for each parameter in the format: keywords= (value1,value2,…); ! keywords are case sensitive; spaces allowed between keywords and “=” and value; ! comments starting with “!” allowed after value; ! (3) value is an integer, double, or string (no single quote needed); for double, ! any of the format is acceptable: 40 40. 4.e1; ! Use of decimal point in integers ! is OK but discouraged. ! (4) spatially varying parameters are available for most parameters when value=-999; ! spatial value will be read from “ICM_param.nc” ! dimension=(npt),(npt,d1),or (npt,d1,d2) for scalar/1D/2D param, where npt=ne/np !——————————————————————————— !—————————state variables in ICM——————————– !——————————————————————————— !Core Module ! 1 PB1 : Diatom g/m^3 ! 2 PB2 : Green Algae g/m^3 ! 3 PB3 : Cyanobacteria g/m^3 ! 4 RPOC : Refractory Particulate Organic Carbon g/m^3 ! 5 LPOC : Labile Particulate Organic Carbon g/m^3 ! 6 DOC : Dissolved Orgnaic Carbon g/m^3 ! 7 RPON : Refractory Particulate Organic Nitrogen g/m^3 ! 8 LPON : Labile Particulate Organic Nitrogen g/m^3 ! 9 DON : Dissolved Orgnaic Nitrogen g/m^3 ! 10 NH4 : Ammonium Nitrogen g/m^3 ! 11 NO3 : Nitrate Nitrogen g/m^3 ! 12 RPOP : Refractory Particulate Organic Phosphorus g/m^3 ! 13 LPOP : Labile Particulate Organic Phosphorus g/m^3 ! 14 DOP : Dissolved Orgnaic Phosphorus g/m^3 ! 15 PO4 : Total Phosphate g/m^3 ! 16 COD : Chemical Oxygen Demand g/m^3 ! 17 DOX : Dissolved Oxygen g/m^3 !Silica Module ! 1 SU : Particulate Biogenic Silica g/m^3 ! 2 SA : Available Silica g/m^3 !Zooplankton Module ! 1 ZB1 : 1st zooplankton g/m^3 ! 2 ZB2 : 2nd zooplankton g/m^3 !pH Module ! 1 TIC : Total Inorganic Carbon g/m^3 ! 2 ALK : Alkalinity g[CaCO3]/m^3 ! 3 CA : Dissolved Calcium g[CaCO3]/m^3 ! 4 CACO3 : Calcium Carbonate g[CaCO3]/m^3 !CBP Module ! 1 SRPOC : Slow Refractory Particulate Organic Carbon g/m^3 ! 2 SRPON : Slow Refractory Particulate Organic Nitro. g/m^3 ! 3 SRPOP : Slow Refractory Particulate Organic Phosp. g/m^3 ! 4 PIP : Particulate Inorganic Phosphate g/m^3 !SAV Module (no transport variables) !VEG Module (no transport variables) !SFM Module (no transport variables) !BA Module (no transport variables) !———————————————————————————
&MARCO !———————————————————————– !number of subcycles in ICM kinetics !———————————————————————– nsub=1
!———————————————————————– !options of formulations for computing light attenuation coefficients ! iKe=0: Ke=Ke0+KeC*Chl+KeS*(tss2c*POC); TSS=tss2c*POC ! iKe=1: Ke=Ke0+KeC*Chl+KeS*TSS; from SED3D or saved total_sed_conc ! iKe=2: Ke=Ke0+KeC*Chl+KeSalt*Salt; CDOM effect related to Salinity !———————————————————————– iKe = 0
Ke0 = 0.26 !backgroud light extinction coefficient (1/m) KeC = 0.017 !Light attenu. due to chlorophyll KeS = 0.07 !Light attenu. due to TSS KeSalt = -0.02 !Light attenu. due to CDOM (related to salinity) tss2c = 6.0 !TSS to carbon ratio
!———————————————————————– !options of computing light limitation factor ! iLight=0: (Carl Cerco), unit: E/m^2 ! iLight=1: todo (add other options) !———————————————————————– iLight = 0
alpha = 8.0 8.0 8.0 !init. slope of P-I curve (g[C]*m2/g[Chl]/E), (iLight=0)
!———————————————————————– !options of phytoplankton’ predation term !———————————————————————– iPR = 1 !(0: linear formulation; 1: quadratic)
PRR = 0.1 0.2 0.05 !predation rate by higher trophic level (day-1, or day-1.g-1.m3)
!———————————————————————– !ICM init. value (wqc0), settling velocity (WSP), net settling velocity (WSPn) (m.day-1) !———————————————————————– !name: (PB1,PB2,PB3) (RPOC,LPOC,DOC) (RPON,LPON,DON,NH4,NO3) (RPOP,LPOP,DOP,PO4) (COD,DO) wqc0 = 1.0 0.5 0.05 1.0 0.5 0.5 0.15 0.15 0.05 0.01 0.05 0.005 0.005 0.01 0.05 0.0 12.0 WSP = 0.3 0.10 0.0 0.25 0.25 0.0 0.25 0.25 0.0 0.0 0.0 0.25 0.25 0.0 1.0 0.0 0.0 WSPn = 0.3 0.10 0.0 0.25 0.25 0.0 0.25 0.25 0.0 0.0 0.0 0.25 0.25 0.0 1.0 0.0 0.0
!———————————————————————– !Silica model (0: OFF; 1: ON) !———————————————————————– iSilica = 0
!———————————————————————– !Zooplankton(iZB=1: use zooplankton dynamics; iZB=0: don’t use) !———————————————————————– iZB = 0
!———————————————————————– !PH model (0: OFF; 1: ON) !———————————————————————– iPh = 0
!———————————————————————– !ChesBay Program Model (0: OFF; 1: ON) !———————————————————————– iCBP = 0
!———————————————————————– !Submerged Aquatic Vegetation switch !———————————————————————– isav_icm = 0
!———————————————————————– !Intertidal vegetation switch !———————————————————————– iveg_icm = 0 !0: VEG off; 1: VEG on
!———————————————————————– !Sediment module switch. iSed=1: Use sediment flux model !benthic flux provided by sed_flux_model !———————————————————————– iSed = 1
!———————————————————————– !Benthic Algae !———————————————————————– iBA = 0
!———————————————————————– !solar radiation: dim=(npt,time) or (time,) ! iRad=0: short wave from sflux; require ihconsv =1, nws=2 ! iRad=1: short wave from ICM_rad.th.nc (unit: E.m-2.day-1) ! note: npt=1/np/ne/other; need to add “elements” number if npt=other !———————————————————————– iRad = 0
!———————————————————————– !Atmospheric and Bottom fluxes: dim=(npt,ntrs_icm,time) ! isflux/ibflux=1: additional nutrient fluxes from ICM_sflux.th.nc/ICM_bflux.th.nc ! units: g/m2,(consistent with variable units in the model) ! note: npt=1/np/ne/other; need to add “elements” number if npt=other !———————————————————————– isflux = 0 ibflux = 0
!———————————————————————– !ICM station outputs (need istation.in with *.bp format) !———————————————————————– iout_icm = 0 nspool_icm = 24
!———————————————————————– !options of nutrient limitation on phytoplankton growth ! iLimit=0: f=min[f(N),f(P)]*f(I); iLimit=1: f=min[f(N),f(P),f(I)] !———————————————————————– iLimit = 0
!———————————————————————– !idry_icm=1: turn on shallow kinetic biochemical process !idry_icm=0: jump dry elems, keep last wet value; jump won’t happen if iveg_icm is turn on and this elem is veg !———————————————————————– idry_icm = 0 /
&CORE !———————————————————————– !ICM parameters for water column; PB: phytoplankton !CBP module parameters are included: (SRPOC,SRPON,SRPOP,PIP) !———————————————————————– !phytoplankton growth GPM = 2.5 2.8 3.5 !PB growth rates (day-1) TGP = 15.0 22.0 27.0 !optimal temp. for PB growth (oC) KTGP = 0.005 0.004 0.003 0.008 0.006 0.004 !temp. dependence for PB growth; dim(PB=1:3,1:2) (oC-2)
!phytoplankton photorespiration & metabolism MTR = 0.0 0.0 0.0 !PB photorespiration coefficient (0<MTR<1) MTB = 0.01 0.02 0.03 !PB metabolism rates (day-1) TMT = 20.0 20.0 20.0 !reference temp. for PB metabolism (oC) KTMT = 0.0322 0.0322 0.0322 !temp. dependence for PB metabolism (oC-1)
!partition of phytoplankton biomass (predation) FCP = 0.35 0.30 0.20 0.55 0.50 0.50 0.10 0.20 0.30 0.0 0.0 0.0 !fractions of PB carbon into (RPOC,LPOC,DOC,SRPOC); dim(PB=1:3,3) FNP = 0.35 0.35 0.35 0.50 0.50 0.50 0.10 0.10 0.10 0.05 0.05 0.05 0.0 0.0 0.0 !fractions of PB nitrogen into (RPON,LPON,DON,NH4,SRPON) FPP = 0.10 0.10 0.10 0.20 0.20 0.20 0.50 0.50 0.50 0.20 0.20 0.20 0.0 0.0 0.0 !fractions of PB Phosphorus into (RPOP,LPOP,DOP,PO4,SRPOP)
!partition of metabolized phytoplankton biomass FCM = 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.1 0.1 0.0 0.0 0.0 !fractions of PB metabolism carbon into (RPOC,LPOC,DOC,SRPOC); dim(PB=1:3,4) FNM = 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 !fractions of PB metabolism N. into (RPON,LPON,DON,NH4,SRPON); dim(PB=1:3,5) FPM = 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 !fractions of PB metabolism P. into (RPOP,LPOP,DOP,PO4,SRPOP); dim(PB=1:3,5)
!nitrification Nit = 0.07 !maximum nitrification rate (day-1) TNit = 27.0 !optimal temp. for nitrification (oC) KTNit = 0.0045 0.0045 !temp. dependence (T<=TNit & T>TNit) for nitrification (oC-2) KhDOn = 1.0 !DO half saturation for nitrification (mg/L)
!denitrifcation KhDOox = 0.5 !DO half saturation for dentrification & DOC’s oxic respiration (mg/L) KhNO3dn = 0.1 !NO3 half saturation for denitrification (mg/L)
!decay coefficients for organic matters (C,N,P); CBP module: (KSR,TRSR,KTRSR,KPIP) KC0 = 0.005 0.075 0.2 !minimum decay rate of RPOC,LPOC,DOC (day-1) KN0 = 0.005 0.075 0.2 !minimum decay rate of RPON,LPON,DON (day-1) KP0 = 0.005 0.075 0.2 !minimum decay rate of RPOP,LPOP,DOP (day-1) KCalg = 0.0 0.0 0.0 !algae effect on RPOC,LPOC,DOC decay (day-1.m3.g[C]-1) KNalg = 0.0 0.0 0.0 !algae effect on RPON,LPON,DON decay (day-1.m3.g[C]-1) KPalg = 0.0 0.0 0.0 !algae effect on RPOP,LPOP,DOP decay (day-1.m3.g[C]-1) TRM = 20.0 20.0 20.0 !reference temp. for (RPOM,LPOM,DOM) decay (oC) KTRM = 0.069 0.069 0.069 !temp. dependence for (RPOM,LPOM,DOM) decay (oC-1) KSR0 = 0.001 0.001 0.001 !decay rates of SRPOC,SRPON,SRPOP (day-1) TRSR = 20.0 20.0 20.0 !reference temp. for (SRPOC,SRPON,SRPOP) decay (oC) KTRSR = 0.069 0.069 0.069 !temp. dependence for (SRPOC,SRPON,SRPOP) decay (oC-1) KPIP = 0.0 !dissolution rate of PIP (day-1)
!decay coefficient for chemical oxygen demand (COD) KCD = 1.0 !oxidation rate of COD at TRCOD (day-1) TRCOD = 20.0 !reference temp. for COD oxidation (oC) KTRCOD= 0.041 !temp. dependence for COD oxidation (oC-1) KhCOD= 1.5 !COD half saturation for COD oxidation (mg[O2]/L)
!nutrient limitation & salinity stress KhN = 0.01 0.01 0.01 !nitrogen half saturation (mg/L) KhP = 0.001 0.001 0.001 !phosphorus half saturation (mg/L) KhSal= 1e6 1e6 0.1 !salinity when PB growth is halved (PSU); (1e6: no salinity stress)
!conversion coeffiecients c2chl= 0.059 0.059 0.059 !carbon to chlorophyll ratio (g[C]/mg[Chl]) n2c = 0.167 0.167 0.167 !nitrogen to carbon ratio for phytoplankton p2c = 0.02 0.02 0.02 !phosphorus to carbon ratio for phytoplankton o2c = 2.67 !oxygen to carbon ratio in respiration o2n = 4.33 !oxygen to ammonium ratio (g[O2]/g[NH4]) dn2c = 0.933 !mass of NO3 consumed per mass of DOC oxidized in denit. (g[N]/g[C]) an2c = 0.5 !ratio of denit. rate to oxic DOC respiration rate
!misc KhDO = 0.5 0.5 0.5 !DO half saturation for PB’s DOC excretion (mg/L) KPO4p= 0.0 !coefficient relating PO4 sorption to TSS WRea = 0.0 !baseline wind-induced reaeration coefficient for DO (day-1) PBmin= 0.01 0.01 0.01 !minimum PB concentration (mg[C]/L) dz_flux= 1.0 1.0 !surface/bottom thikness (m) within which sflux/bflux are redistributed /
&SFM !———————————————————————– ! sediment flux model (SFM) parameter !———————————————————————– !initial sediment concentrations in lower layer (g/m3); For cold start btemp0 = 5.0 !initial temp. (oC) bstc0 = 0.1 !surface transfer coefficient bSTR0 = 0.0 !benthic stress (day) bThp0 = 0.0 !consective days of hypoxia (day) bTox0 = 0.0 !consective days of oxic condition after hypoxia event (day) bNH40 = 4.0 !NH4 bNO30 = 1.0 !NO3 bPO40 = 5.0 !PO4 bH2S0 = 250.0 !H2S bCH40 = 40.0 !CH4 bPOS0 = 500.0 !POS bSA0 = 500.0 !SA bPOC0 = 1000.0 3000.0 5000.0 !POC(G=1:3) bPON0 = 150.0 500.0 1500.0 !PON(G=1:3) bPOP0 = 30.0 300.0 500.0 !POP(G=1:3)
!basic information about sediment bdz = 0.1 !sediment thickness (m) bVb = 1.37e-5 !burial rate (m.day-1); 1 cm/yr=2.74e-5 m.day-1 bsolid = 0.5 0.5 !sediment solid conc. in Layer 1 and Layer 2 (Kg.L-1) bdiff = 1.8e-7 !diffusion coefficient for sediment temp. (m2/s) bTR = 20 !reference temp. for sediment processes
!particle mixing and diffusion coefficients, benthic stress bVpmin = 3.0e-6 !minimum particle mixing velocity coefficient (m.day-1) bVp = 1.2e-4 !particle mixing velocity coefficient (m.day-1) bVd = 1.0e-3 !diffusion velocity coefficient (m.day-1) bKTVp = 1.117 !temp. dependece of particle mixing velocity bKTVd = 1.08 !temp. dependece of diffusion velocity bKST = 0.03 !1st order decay rate of benthic stress (day-1) bSTmax = 20.0 !maximum value of benthic stress (day) (note: smaller than 1/bKST) bKhDO_Vp = 4.0 !DO half-saturation of particle mixing (mg/L) bDOc_ST = 1.0 !DO criteria for benthic stress (mg/L) banoxic = 10.0 !consective days of hypoxia causing maximum benthic stress (day) boxic = 45.0 !time lag for bethos recovery from hypoxia event (day) bp2d = 0.0 !ratio from mixing coef. to diffusion coef. (benthos enhanced effect)
!decay rates of sediment POM (diagenesis flux) bKC = 0.035 0.0018 0.00 !decay rate of POC (3G class) at bTR (day-1) bKN = 0.035 0.0018 0.00 !decay rate of PON (3G class) at bTR (day-1) bKP = 0.035 0.0018 0.00 !decay rate of POP (3G class) at bTR (day-1) bKTC = 1.10 1.150 1.17 !temp. dependence of POC decay (oC-1) bKTN = 1.10 1.150 1.17 !temp. dependence of PON decay (oC-1) bKTP = 1.10 1.150 1.17 !temp. dependence of POP decay (oC-1)
!fraction of phytoplankton into sediment 3G POM (depositional flux) bFCP = 0.35 0.55 0.01 0.35 0.55 0.01 0.35 0.55 0.01 !Phyto POC into sed POC (G3,PB=1:3) bFNP = 0.35 0.55 0.01 0.35 0.55 0.01 0.35 0.55 0.01 !Phyto PON into sed PON (G3,PB=1:3) bFPP = 0.35 0.55 0.01 0.35 0.55 0.01 0.35 0.55 0.01 !Phyto POP into sed POP (G3,PB=1:3)
!fraction of RPOM into sediment 3G POM (depositional flux, for iCBP=0); when iCBP=1, RPOM will be routed to sediment G2 pool bFCM = 0.0 0.43 0.57 !refractory POC into sed POC(3G) bFNM = 0.0 0.54 0.46 !refractory PON into sed PON(3G) bFPM = 0.0 0.43 0.57 !refractory POP into sed POP(3G)
!nitrification (NH4) bKNH4f = 0.20 !NH4 reaction rate in freshwater at bTR (1st layer) (m/day) bKNH4s = 0.140 !NH4 reaction rate in salty water at bTR (1st layer) (m/day) bKTNH4 = 1.08 !temp. dependency for NH4 reaction (oC-1) bKhNH4 = 1.5 !half-stauration NH4 for nitrification (g/m3) bKhDO_NH4 = 2.00 !half-stauration DO for nitrification (g/m3) bpieNH4 = 1.0 !partition coefficients of NH4 in Layer 1 & 2 (Kg-1.L) bsaltn = 1.0 !salinity criteria of fresh/salty water for NH4/NO3 reaction (PSU)
!denitrification (NO3) bKNO3f = 0.30 !NO3 reaction rate in freshwater at bTR (1st layer) (m/day) bKNO3s = 0.125 !NO3 reaction rate in salty water at bTR (1st layer) (m/day) bKNO3 = 0.25 !NO3 reaction rate (2nd layer) (m/day) bKTNO3 = 1.08 !temp. dependency for NO3 reaction (oC-1)
!sulfide oxidation (H2S) bKH2Sd = 0.2 !dissolved H2S reaction rate at bTR (1st layer) (m/day) bKH2Sp = 0.4 !particulate H2S reaction rate at bTR (1st layer) (m/day) bKTH2S = 1.08 !temp. dependency for H2S reaction (oC-1) bpieH2Ss = 100.0 !partition coefficient of NH4 in Layer 1 (Kg-1.L) bpieH2Sb = 100.0 !partition coefficient of NH4 in Layer 2 (Kg-1.L) bKhDO_H2S = 8.0 !O2 constant to normalize H2S oxidation (g[O2]/m3) bsaltc = 1.0 !salinity criteria of fresh/salty water for carbon reaction (PSU)
!methane oxidation (CH4) bKCH4 = 0.2 !CH4 reaction rate at bTR (1st layer) (m/day) bKTCH4 = 1.08 !temp. dependency for CH4 reaction bKhDO_CH4 = 0.2 !half-saturation DO for CH4 oxidation (g[O2]/m3) bo2n = 2.86 !oxygen to nitrogen ratio in sediment (denitrification)
!phosphate reaction (PO4) bpiePO4 = 50.0 !partition coefficient of PO4 in Layer 2 (Kg-1.L) bKOPO4f = 3000.0 !oxygen dependency for PO4 sorption in freshwater in Layer 1 bKOPO4s = 300.0 !oxygen dependency for PO4 sorption in salty water in Layer 1 bDOc_PO4 = 1.0 !DO criteria for PO4 sorptiona (g[O2]/m3) bsaltp = 1.0 !salinity criteria of fresh/salty water for PO4 partition (PSU)
!silica dissolution (SI) bKS = 0.50 !decay rate of POS (3G class) at bTR bKTS = 1.10 !temp. dependence of POS decay bSIsat = 40.0 !silica saturation conc. in pore water (g[Si]/m3) bpieSI = 100.0 !partition coefficient of silica in Layer 2 (Kg-1.L) bKOSI = 10.0 !oxygen dependency for silica sorption in Layer 1 bKhPOS = 5.0e4 !POS half saturation for POS dissolution (g/m3) bDOc_SI = 1.0 !DO criteria for silica sorptiona (g[O2]/m3) bJPOSa = 0.0 !additional POS flux associated with POM detrius beside algea (g.m-2.day-1)
!SAV and VEG contribution to sediment POM (for isav_icm=1, iveg_icm=1) bFCs = 0.65 0.255 0.095 !SAV POC into 3G sed 3G POC bFNs = 0.65 0.300 0.050 !SAV PON into 3G sed 3G PON bFPs = 0.65 0.255 0.095 !SAV POP into 3G sed 3G POP bFCv = 0.65 0.255 0.095 0.65 0.255 0.095 0.65 0.255 0.095 !VEG POC into sed POC (G3,PB=1:3) bFNv = 0.65 0.300 0.050 0.65 0.300 0.050 0.65 0.300 0.050 !VEG PON into sed PON (G3,PB=1:3) bFPv = 0.65 0.255 0.095 0.65 0.255 0.095 0.65 0.255 0.095 !VEG POP into sed POP (G3,PB=1:3) /
&Silica !———————————————————————– !Silica parameters !———————————————————————– !silica FSP = 0.90 0.10 !fractions of diatom silica into (SU,SA) FSM = 0.50 0.50 !fractions of diatom metabolism Si into (SU,SA) KS = 0.03 !dissolution rate of SU at TRS (day-1) TRS = 20.0 !reference temp. for SU dissolution (oC) KTRS = 0.092 !temp. dependence for SU dissolution (oC-1) KhS = 0.05 0.0 0.0 !silica half saturation (mg/L); (0.0: no Si limitation) s2c = 0.50 0.0 0.0 !silica to carbon ratio for phytolankton; (0.0: no Si uptake) KSAp = 0.0 !coefficient relating Silicate(SA) sorption to TSS /
&ZB !———————————————————————– !Zooplankton (ZB) parameters !ZB prey(1:8)=(ZB1,ZB2,PB1,PB2,PB3,RPOC,LPOC,DOC) !———————————————————————– !zooplankton growth zGPM = 0.0 0.0 1.75 1.75 1.75 1.75 1.75 1.75 1.0 0.0 2.0 2.0 2.0 2.0 2.0 2.0 !ZB predation rate(day-1); dim(prey=1:8, ZB=1:2) zKhG = 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 0.175 !reference prey conc.(mg/L); dim(prey=1:8, ZB=1:2) zTGP = 25.0 25.0 !optimal temp. for ZB growth (oC) zKTGP= 0.0035 0.008 0.025 0.030 !temp. dependence for ZB growth (T<=zTGP & T>zTGP); dim(ZB=1:2,1:2) (oC-2) zAG = 0.75 !ZB assimilation efficiency ratio (0-1) zRG = 0.1 !ZB respiration ratio when it grazes (0-1)
!zooplankton mortality & metabolism zMRT = 0.02 0.02 !ZB mortality rates (day-1) zMTB = 0.254 0.186 !ZB metabolism rates (day-1) zTMT = 20.0 20.0 !reference temp. for ZB metabolism (oC) zKTMT = 0.0693 0.0693 !temp. dependence for ZB metabolism (oC-1)
!partition of zooplankton biomass zFCP = 0.35 0.55 0.10 !fractions of ZB carbon into (RPOC,LPOC,DOC) zFNP = 0.35 0.50 0.10 0.05 !fractions of ZB nitrogen into (RPON,LPON,DON,NH4) zFPP = 0.10 0.20 0.50 0.20 !fractions of ZB Phosphorus into (RPOP,LPOP,DOP,PO4) zFSP = 0.70 0.25 !fractions of ZB silica into (SU,SA)
!partition of metabolized zooplankton biomass zFCM = 0.10 0.0 !fractions of ZB metabolism carbon into DOC; dim(ZB=1:2) zFNM = 0.35 0.30 0.50 0.40 0.10 0.20 0.05 0.10 !fractions of ZB metabolism N. into (RPON,LPON,DON,NH4); dim(ZB=1:2,4) zFPM = 0.35 0.30 0.50 0.40 0.10 0.20 0.05 0.10 !fractions of ZB metabolism P. into (RPOP,LPOP,DOP,PO4); dim(ZB=1:2,4) zFSM = 0.50 0.40 0.50 0.60 !fractions of ZB metabolism Si into (SU,SA); dim(ZB=1:2,2)
!misc zKhDO= 0.5 0.5 !DO half saturation for ZB’s DOC excretion (mg/L) zn2c = 0.20 0.20 !nitrogen to carbon ratio for zooplankton zp2c = 0.02 0.02 !phosphorus to carbon ratio for zooplankton zs2c = 0.50 0.50 !silica to carbon ratio for zooplankton z2pr = 0.5 0.5 !ratio converting ZB+PB biomass to predation rates on ZB (L.mg-1.day-1) p2pr = 0.25 !ratio converting ZB+PB biomass to predation rates on PB (L.mg-1.day-1) /
&PH_ICM !———————————————————————– !PH model parameter !———————————————————————– ppatch0 = -999 !region flag for pH (1: ON all elem.; -999: spatial) pKCACO3 = 60.0 !dissulution bewteen CaCO3 and Ca++ pKCA = 60.0 !sediment surface transfer coefficient from CaCO3 to Ca++ pRea = 1.0 !reaeration rate for CO2 inu_ph = 0 !nudge option for pH model /
&SAV !———————————————————————– !Submerged Aquatic Vegetation (SAV) parameters !———————————————————————– spatch0 = -999 !region flag for SAV. (1: ON all elem.; -999: spatial) stleaf0 = -999 !init conc of total sav leaf ststem0 = -999 !init conc of total sav stem stroot0 = -999 !init conc of total sav root
!growth coefficients sGPM = 0.1 !maximum growth rate (day-1) sTGP = 32 !optimal growth temperature (oC) sKTGP = 0.003 0.005 !temp. dependence for growth (T<=sTGP & T>sTGP) sFAM = 0.2 !fraction of leaf production to active metabolism sFCP = 0.6 0.3 0.1 !fractions of production to leaf/stem/root biomass
!metabolism coefficients sMTB = 0.02 0.02 0.02 !metabolism rates of leaf/stem/root sTMT = 20 20 20 !reference temp. for leaf/stem/root metabolism sKTMT = 0.069 0.069 0.069 !temp. dependence of leaf/stem/root metabolism sFCM = 0.05 0.15 0.3 0.5 !fractions of metabolism C into (RPOC,LPOC,DOC,CO2) sFNM = 0.05 0.15 0.3 0.5 !fractions of metabolism N into (RPON,LPON,DON,NH4) sFPM = 0.05 0.1 0.35 0.5 !fractions of metabolism P into (RPOP,LPOP,DOP,PO4)
!nutrient limitation sKhNw = 0.01 !nitrogen half saturation in water column sKhNs = 0.1 !nitrogen half saturation in sediments sKhNH4 = 0.1 !ammonium half saturation sKhPw = 0.001 !phosphorus half saturation in water column sKhPs = 0.01 !phosphorus half saturation in sediments
!misc. coefficients salpha = 0.006 !init. slope of P-I curve (g[C]*m2/g[Chl]/E) sKe = 0.045 !light attenuation due to sav absorption shtm = 0.054 2.0 !minimum (base) and maximium canopy height s2ht = 0.0036 0.0036 0.0 !coeffs. converting (leaf,stem,root) to canopy height sc2dw = 0.38 !carbon to dry weight ratio of SAV s2den = 10 !coeff. computing SAV density from leaf&stem sn2c = 0.09 !nitrogen to carbon ratio of sav sp2c = 0.01 !phosphorus to carbon ratio so2c = 2.67 !oxygen to carbon ratio /
&VEG !———————————————————————– !Intertidal Vegetation (VEG), paramters !———————————————————————– vpatch0 = -999 !region flag for VEG. (1: ON all elem.; -999: spatial) vtleaf0 = 100.0 100.0 100.0 !init conc to total veg leaf vtstem0 = 100.0 100.0 100.0 !init conc to total veg stem vtroot0 = 30.0 30.0 30.0 !init conc to total veg root
!growth coefficients: see description of variable meanings above vGPM = 0.1 0.1 0.1 !maximum growth rate (day-1) vFAM = 0.2 0.2 0.2 !fractions of leaf production to active metabolism vTGP = 32.0 32.0 32.0 !optimal growth temperature (oC) vKTGP = 0.003 0.003 0.003 0.005 0.005 0.005 !temp. dependence(3,2) for growth (T<=vTGP & T>vTGP) vFCP = 0.6 0.6 0.6 0.3 0.3 0.3 0.1 0.1 0.1 !fractions of production to leaf/stem/root biomass; dim(veg,leaf/stem/root)
!metabolism coefficients: see description of variable meanings above vMTB = 0.02 0.02 0.02 0.02 0.02 0.02 0.01 0.01 0.01 !metabolism rates of leaf/stem/root; dim(veg,leaf/stem/root) vTMT = 20.0 20.0 20.0 20.0 20.0 20.0 20.0 20.0 20.0 !reference temp. for leaf/stem/root metabolism vKTMT = 0.069 0.069 0.069 0.069 0.069 0.069 0.069 0.069 0.069 !temp. depdenpence for leaf/stem/root metabolism vFNM = 0.05 0.05 0.05 0.15 0.15 0.15 0.3 0.3 0.3 0.5 0.5 0.5 !fractions(3,4) of metabolism N into (RPON,LPON,DON,NH4) vFPM = 0.05 0.05 0.05 0.1 0.1 0.1 0.35 0.35 0.35 0.5 0.5 0.5 !fractions(3,4) of metabolism P into (RPOP,LPOP,DOP,PO4) vFCM = 0.05 0.05 0.05 0.15 0.15 0.15 0.3 0.3 0.3 0.5 0.5 0.5 !fractions(3,4) of metabolism N into (RPOC,LPOC,DOC,CO2) ivNc = 1 !recycled veg N goes to (0: sediment; 1: water) ivPc = 1 !recycled veg P goes to (0: sediment; 1: water)
!nutrient limitation & salinity/inundation stress vKhNs = 0.1 0.1 0.1 !nitrogen half saturation in sediments vKhPs = 0.01 0.01 0.01 !phosphorus half saturation in sediments vScr = 35.0 35.0 35.0 !reference sality for computing veg growth vSopt = 35.0 15.0 0.0 !optimal salinity for veg growth vInun = 1.0 1.0 1.0 !reference value for inundation stress (nondimensional) ivNs = 1 !N limitation on veg growth(0: OFF; 1: ON) ivPs = 1 !P limitation on veg growth(0: OFF; 1: ON)
!mortality (seasonal?) ivMRT = 0 !veg mortality term (0: OFF; 1: ON) vTMR = 17.0 17.0 17.0 17.0 17.0 17.0 !reference temp(3,2) for leaf/stem mortality vKTMR = 4.0 4.0 4.0 4.0 4.0 4.0 !temp dependence(3,2) for leaf/stem mortality vMR0 = 12.8 12.8 12.8 12.8 12.8 12.8 !base value(3,2) of temp effect on mortality (unit: None) vMRcr = 15.0 15.0 15.0 15.0 15.0 15.0 !reference value(3,2) for computing mortality (unit: None)
!misc. coefficients valpha = 0.006 0.006 0.006 !init. slope of P-I curve vKe = 0.045 0.045 0.045 !light attenuation from veg absorption vht0 = 0.054 0.054 0.054 !base veg canopy hgt (vht) vcrit = 250.0 250.0 250.0 !critical mass for computing vht v2ht = 0.0036 0.0036 0.0036 0.001 0.001 0.001 !coefs. convert mass(3,2) to canopy height vc2dw = 0.38 0.38 0.38 !carbon to dry weight ratio of VEG v2den = 10 10 10 !coeff. computing veg density vp2c = 0.01 0.01 0.01 !phosphorus to carbon ratio vn2c = 0.09 0.09 0.09 !nitrogen to carbon ratio vo2c = 2.67 2.67 2.67 !oxygen to carbon ratio /
&BAG !———————————————————————– !Benthic Algae !———————————————————————– gpatch0 = -999 !region flag for BA. (1: ON all elem.; -999: spatial) BA0 = 5.0 !initial BA concentration (g[C].m-2) gGPM = 2.25 !BA maximum growth rate (day-1) gTGP = 20.0 !optimal temp. for BA growth (oC) gKTGP = 0.004 0.006 !temp. dependence for BA growth (oC-2) gMTB = 0.05 !respiration rate at temp. of gTR (day-1) gPRR = 0.1 !predation rate at temp. of gTR (day-1) gTR = 20.0 !reference temperature for BA respiration (oC) gKTR = 0.069 !temp. dependence for BA respiration (oC-1) galpha = 0.1 !init. slope of P-I curve (m2/E) gKSED = 0.0 !light attenuation due to sediment (None) gKBA = 0.01 !light attenuation coef. due to BA self-shading (g[C]-1.m2) gKhN = 0.01 !nitrogen half saturation for BA growth (g[N]/m2) gKhP = 0.001 !phosphorus half saturation for BA growth (g[P]/2) gp2c = 0.0167 !phosphorus to carbon ratio gn2c = 0.167 !nitrogen to carbon ratio go2c = 2.67 !oxygen to carbon ratio gFCP = 0.5 0.45 0.05 !fraction of predation BA C into 3G classes in sediment gFNP = 0.5 0.45 0.05 !fraction of predation BA N into 3G classes in sediment gFPP = 0.5 0.45 0.05 !fraction of predation BA P into 3G classes in sediment /
&ERO !———————————————————————– ! benthic erosion parameter !———————————————————————– ierosion = 0 !1: H2S flux; 2: POC flux; 3: H2S&POC flux erosion = 864 !erosion rate (kg.m-2.day) etau = 1.e-6 !critical bottom shear stress (Pa) eporo = 0.8 !coefficinet in erosion formula (see code in icm_sfm.F90) efrac = 0.5 !fraction coefficinet in erosion formula (see code in icm_sfm.F90) ediso = 2.5 !H2S erosion coeffcient (see code in icm_sfm.F90) dfrac = 0.02 0.02 !deposition fraction of POC (negative value: dfrac will be computed) dWS_POC = 3.0 3.0 !coefficient in POC erosion (see code in icm_sfm.F90) /
- Fields:
- field bag: BAG = BAG(gpatch0=-999, BA0=5.0, gGPM=2.25, gTGP=20.0, gKTGP=[0.004, 0.006], gMTB=0.05, gPRR=0.1, gTR=20.0, gKTR=0.069, galpha=0.1, gKSED=0.0, gKBA=0.01, gKhN=0.01, gKhP=0.001, gp2c=0.0167, gn2c=0.167, go2c=2.67, gFCP=[0.5, 0.45, 0.05], gFNP=[0.5, 0.45, 0.05], gFPP=[0.5, 0.45, 0.05])#
- field core: CORE = CORE(GPM=[2.5, 2.8, 3.5], TGP=[15.0, 22.0, 27.0], KTGP=[0.005, 0.004, 0.003, 0.008, 0.006, 0.004], MTR=[0.0, 0.0, 0.0], MTB=[0.01, 0.02, 0.03], TMT=[20.0, 20.0, 20.0], KTMT=[0.0322, 0.0322, 0.0322], FCP=[0.35, 0.3, 0.2, 0.55, 0.5, 0.5, 0.1, 0.2, 0.3, 0.0, 0.0, 0.0], FNP=[0.35, 0.35, 0.35, 0.5, 0.5, 0.5, 0.1, 0.1, 0.1, 0.05, 0.05, 0.05, 0.0, 0.0, 0.0], FPP=[0.1, 0.1, 0.1, 0.2, 0.2, 0.2, 0.5, 0.5, 0.5, 0.2, 0.2, 0.2, 0.0, 0.0, 0.0], FCM=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.1, 0.1, 0.1, 0.0, 0.0, 0.0], FNM=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], FPM=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], Nit=0.07, TNit=27.0, KTNit=[0.0045, 0.0045], KhDOn=1.0, KhDOox=0.5, KhNO3dn=0.1, KC0=[0.005, 0.075, 0.2], KN0=[0.005, 0.075, 0.2], KP0=[0.005, 0.075, 0.2], KCalg=[0.0, 0.0, 0.0], KNalg=[0.0, 0.0, 0.0], KPalg=[0.0, 0.0, 0.0], TRM=[20.0, 20.0, 20.0], KTRM=[0.069, 0.069, 0.069], KSR0=[0.001, 0.001, 0.001], TRSR=[20.0, 20.0, 20.0], KTRSR=[0.069, 0.069, 0.069], KPIP=0.0, KCD=1.0, TRCOD=20.0, KTRCOD=0.041, KhCOD=1.5, KhN=[0.01, 0.01, 0.01], KhP=[0.001, 0.001, 0.001], KhSal=['1e6', '1e6', 0.1], c2chl=[0.059, 0.059, 0.059], n2c=[0.167, 0.167, 0.167], p2c=[0.02, 0.02, 0.02], o2c=2.67, o2n=4.33, dn2c=0.933, an2c=0.5, KhDO=[0.5, 0.5, 0.5], KPO4p=0.0, WRea=0.0, PBmin=[0.01, 0.01, 0.01], dz_flux=[1.0, 1.0])#
- field ero: ERO = ERO(ierosion=0)#
- field marco: MARCO = MARCO(nsub=1, iKe=0, Ke0=0.26, KeC=0.017, KeS=0.07, KeSalt=-0.02, tss2c=6.0, iLight=0, alpha=[8.0, 8.0, 8.0], iPR=1, PRR=[0.1, 0.2, 0.05], wqc0=[1.0, 0.5, 0.05, 1.0, 0.5, 0.5, 0.15, 0.15, 0.05, 0.01, 0.05, 0.005, 0.005, 0.01, 0.05, 0.0, 12.0], WSP=[0.3, 0.1, 0.0, 0.25, 0.25, 0.0, 0.25, 0.25, 0.0, 0.0, 0.0, 0.25, 0.25, 0.0, 1.0, 0.0, 0.0], WSPn=[0.3, 0.1, 0.0, 0.25, 0.25, 0.0, 0.25, 0.25, 0.0, 0.0, 0.0, 0.25, 0.25, 0.0, 1.0, 0.0, 0.0], iSilica=0, iZB=0, iPh=0, iCBP=0, isav_icm=0, iveg_icm=0, iSed=1, iBA=0, iRad=0, isflux=0, ibflux=0, iout_icm=0, nspool_icm=24, iLimit=0, idry_icm=0)#
- field ph_icm: PH_ICM = PH_ICM(ppatch0=-999, pKCACO3=60.0, pKCA=60.0, pRea=1.0, inu_ph=0)#
- field poc: POC = POC(erosion=864, etau='1.e-6', eporo=0.8, efrac=0.5, ediso=2.5, dfrac=[0.02, 0.02], dWS_POC=[3.0, 3.0])#
- field sav: SAV = SAV(spatch0=-999, stleaf0=-999, ststem0=-999, stroot0=-999, sGPM=0.1, sTGP=32, sKTGP=[0.003, 0.005], sFAM=0.2, sFCP=[0.6, 0.3, 0.1], sMTB=[0.02, 0.02, 0.02], sTMT=[20, 20, 20], sKTMT=[0.069, 0.069, 0.069], sFCM=[0.05, 0.15, 0.3, 0.5], sFNM=[0.05, 0.15, 0.3, 0.5], sFPM=[0.05, 0.1, 0.35, 0.5], sKhNw=0.01, sKhNs=0.1, sKhNH4=0.1, sKhPw=0.001, sKhPs=0.01, salpha=0.006, sKe=0.045, shtm=[0.054, 2.0], s2ht=[0.0036, 0.0036, 0.0], sc2dw=0.38, s2den=10)#
- field sfm: SFM = SFM(btemp0=5.0, bstc0=0.1, bSTR0=0.0, bThp0=0.0, bTox0=0.0, bNH40=4.0, bNO30=1.0, bPO40=5.0, bH2S0=250.0, bCH40=40.0, bPOS0=500.0, bSA0=500.0, bPOC0=[1000.0, 3000.0, 5000.0], bPON0=[150.0, 500.0, 1500.0], bPOP0=[30.0, 300.0, 500.0], bdz=0.1, bVb='1.37e-5', bsolid=[0.5, 0.5], bdiff='1.8e-7', bTR=20, bVpmin='3.0e-6', bVp='1.2e-4', bVd='1.0e-3', bKTVp=1.117, bKTVd=1.08, bKST=0.03, bSTmax=20.0, bKhDO_Vp=4.0, bDOc_ST=1.0, banoxic=10.0, boxic=45.0, bp2d=0.0, bKC=[0.035, 0.0018, 0.0], bKN=[0.035, 0.0018, 0.0], bKP=[0.035, 0.0018, 0.0], bKTC=[1.1, 1.15, 1.17], bKTN=[1.1, 1.15, 1.17], bKTP=[1.1, 1.15, 1.17], bFCP=[0.35, 0.55, 0.01, 0.35, 0.55, 0.01, 0.35, 0.55, 0.01], bFNP=[0.35, 0.55, 0.01, 0.35, 0.55, 0.01, 0.35, 0.55, 0.01], bFPP=[0.35, 0.55, 0.01, 0.35, 0.55, 0.01, 0.35, 0.55, 0.01], bFCM=[0.0, 0.43, 0.57], bFNM=[0.0, 0.54, 0.46], bFPM=[0.0, 0.43, 0.57], bKNH4f=0.2, bKNH4s=0.14, bKTNH4=1.08, bKhNH4=1.5, bKhDO_NH4=2.0, bpieNH4=1.0, bsaltn=1.0, bKNO3f=0.3, bKNO3s=0.125, bKNO3=0.25, bKTNO3=1.08, bKH2Sd=0.2, bKH2Sp=0.4, bKTH2S=1.08, bpieH2Ss=100.0, bpieH2Sb=100.0, bKhDO_H2S=8.0, bsaltc=1.0, bKCH4=0.2, bKTCH4=1.08, bKhDO_CH4=0.2, bo2n=2.86, bpiePO4=50.0, bKOPO4f=3000.0, bKOPO4s=300.0, bDOc_PO4=1.0, bsaltp=1.0, bKS=0.5, bKTS=1.1, bSIsat=40.0, bpieSI=100.0, bKOSI=10.0, bKhPOS='5.0e4', bDOc_SI=1.0, bJPOSa=0.0, bFCs=[0.65, 0.255, 0.095], bFNs=[0.65, 0.3, 0.05], bFPs=[0.65, 0.255, 0.095], bFCv=[0.65, 0.255, 0.095, 0.65, 0.255, 0.095, 0.65, 0.255, 0.095], bFNv=[0.65, 0.3, 0.05, 0.65, 0.3, 0.05, 0.65, 0.3, 0.05], bFPv=[0.65, 0.255, 0.095, 0.65, 0.255, 0.095, 0.65, 0.255, 0.095])#
- field silica: SILICA = SILICA(FSP=[0.9, 0.1], FSM=[0.5, 0.5], KS=0.03, TRS=20.0, KTRS=0.092, KhS=[0.05, 0.0, 0.0], s2c=[0.5, 0.0, 0.0], KSAp=0.0)#
- field stem: STEM = STEM(sn2c=0.09, sp2c=0.01, so2c=2.67)#
- field veg: VEG = VEG(vpatch0=-999, vtleaf0=[100.0, 100.0, 100.0], vtstem0=[100.0, 100.0, 100.0], vtroot0=[30.0, 30.0, 30.0], vGPM=[0.1, 0.1, 0.1], vFAM=[0.2, 0.2, 0.2], vTGP=[32.0, 32.0, 32.0], vKTGP=[0.003, 0.003, 0.003, 0.005, 0.005, 0.005], vFCP=[0.6, 0.6, 0.6, 0.3, 0.3, 0.3, 0.1, 0.1, 0.1], vMTB=[0.02, 0.02, 0.02, 0.02, 0.02, 0.02, 0.01, 0.01, 0.01], vTMT=[20.0, 20.0, 20.0, 20.0, 20.0, 20.0, 20.0, 20.0, 20.0], vKTMT=[0.069, 0.069, 0.069, 0.069, 0.069, 0.069, 0.069, 0.069, 0.069], vFNM=[0.05, 0.05, 0.05, 0.15, 0.15, 0.15, 0.3, 0.3, 0.3, 0.5, 0.5, 0.5], vFPM=[0.05, 0.05, 0.05, 0.1, 0.1, 0.1, 0.35, 0.35, 0.35, 0.5, 0.5, 0.5], vFCM=[0.05, 0.05, 0.05, 0.15, 0.15, 0.15, 0.3, 0.3, 0.3, 0.5, 0.5, 0.5], ivNc=1, ivPc=1, vKhNs=[0.1, 0.1, 0.1], vKhPs=[0.01, 0.01, 0.01], vScr=[35.0, 35.0, 35.0], vSopt=[35.0, 15.0, 0.0], vInun=[1.0, 1.0, 1.0], ivNs=1, ivPs=1, ivMRT=0, vTMR=[17.0, 17.0, 17.0, 17.0, 17.0, 17.0], vKTMR=[4.0, 4.0, 4.0, 4.0, 4.0, 4.0], vMR0=[12.8, 12.8, 12.8, 12.8, 12.8, 12.8], vMRcr=[15.0, 15.0, 15.0, 15.0, 15.0, 15.0], valpha=[0.006, 0.006, 0.006], vKe=[0.045, 0.045, 0.045], vht0=[0.054, 0.054, 0.054], vcrit=[250.0, 250.0, 250.0], v2ht=[0.0036, 0.0036, 0.0036, 0.001, 0.001, 0.001], vc2dw=[0.38, 0.38, 0.38], v2den=[10, 10, 10], vp2c=[0.01, 0.01, 0.01], vn2c=[0.09, 0.09, 0.09], vo2c=[2.67, 2.67, 2.67])#
- field zb: ZB = ZB(zGPM=[0.0, 0.0, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.0, 0.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0], zKhG=[0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175, 0.175], zTGP=[25.0, 25.0], zKTGP=[0.0035, 0.008, 0.025, 0.03], zAG=0.75, zRG=0.1, zMRT=[0.02, 0.02], zMTB=[0.254, 0.186], zTMT=[20.0, 20.0], zKTMT=[0.0693, 0.0693], zFCP=[0.35, 0.55, 0.1], zFNP=[0.35, 0.5, 0.1, 0.05], zFPP=[0.1, 0.2, 0.5, 0.2], zFSP=[0.7, 0.25], zFCM=[0.1, 0.0], zFNM=[0.35, 0.3, 0.5, 0.4, 0.1, 0.2, 0.05, 0.1], zFPM=[0.35, 0.3, 0.5, 0.4, 0.1, 0.2, 0.05, 0.1], zFSM=[0.5, 0.4, 0.5, 0.6], zKhDO=[0.5, 0.5], zn2c=[0.2, 0.2], zp2c=[0.02, 0.02], zs2c=[0.5, 0.5], z2pr=[0.5, 0.5], p2pr=0.25)#