Nothing
R/aaa.R
In FESDIA: Diagenetic model including Fe, S and CH4 dynamics
## ====================================================================
## A local environment for non user-visible data,
## ====================================================================
.FESDIA <- new.env()
.FESDIA$N <- 100
.FESDIA$Grid <- setup.grid.1D(x.up=0, dx.1 = 0.01, N = .FESDIA$N, L = 100)
##------------------------------------
## Parameters
##------------------------------------
.FESDIA$Parms <- c(
## organic matter dynamics #
Cflux = 20*1e5/12/365 , # nmolC/cm2/d - Carbon deposition: 20gC/m2/yr
pFast = 0.9 , # - fraction fast detritus in flux
FeOH3flux = 1 , # nmol/cm2/d FeOH3 deposition rate
CaPflux = 0 , # nmolP/cm2/d deposition rate of CaP
rFast = 25/365 , # /d decay rate fast decay detritus
rSlow = 0.05/365 , # /d decay rate slow decay detritus
NCrFdet = 16/106 , # molN/molC NC ratio fast decay detritus
NCrSdet = 16/106 , # molN/molC NC ratio slow decay detritus
PCrFdet = 1/106 , # molP/molC PC ratio fast decay det.
PCrSdet = 1/106 , # molP/molC PC ratio slow decay det.
## Nutrient bottom water conditions
BCupLiq = 2 , # upper boundary condition for liquid; 1= flux, 2=conc, 3 = 0-grad
BCdownLiq = 3 , # lower boundary condition; default = 0-gradient
O2bw = 300 , # mmol/m3 Oxygen conc in bottom water
NO3bw = 10 , # mmol/m3
NO2bw = 0 , # mmol/m3
NH3bw = 1 , # mmol/m3
CH4bw = 0 , # mmol/m3
PO4bw = 0.5 , # mmol/m3
DICbw = 2100 ,
Febw = 0 ,
H2Sbw = 0 ,
SO4bw = 31000 ,
ALKbw = 2400 ,
O2dw = NA , # mmol/m3 deep boundary concentrations
NO3dw = NA , # mmol/m3
NO2dw = NA , # mmol/m3
NH3dw = NA , # mmol/m3
CH4dw = NA , # mmol/m3
PO4dw = NA , # mmol/m3
DICdw = NA ,
Fedw = NA ,
H2Sdw = NA ,
SO4dw = NA ,
ALKdw = NA ,
## Bioturbation, advection, bio-irrigation
w = 1/365000 , # cm/d advection rate
biot = 1/365 , # cm2/d bioturbation coefficient
biotdepth = 5 , # cm depth of mixed layer
biotatt = 1 , # cm depth attenuation coefficient below biotdepth
irr = 0 , # /d bio-irrigation rate
irrdepth = 5 , # cm depth of irrigates layer
irratt = 1 , # cm depth attenuation coefficient below irrdepth
gasflux = 0 , # cm/d piston velocity for dry flats - exchange of O2 and DIC only+deposition
## Nutrient parameters
NH3Ads = 1.3 , # - Adsorption coeff ammonium
rnitri1 = 20 , #/d Max nitrification rate (step1) - oxidation of ammonium
rnitri2 = 20. , #/d Max nitrification rate (step2) - oxidation of nitrite
ranammox = 0.1 , # /(mmol/m3)/d Anammox rate
ksO2nitri = 1. , # mmolO2/m3 half-sat O2 in nitrification
ksO2oxic = 3. , # mmolO2/m3 half-sat O2 in oxic mineralisation
ksNO3denit = 30. , # mmolNO3/m3 half-sat NO3 in denitrification
kinO2denit = 1. , # mmolO2/m3 half-sat O2 inhib denitrification
kinNO3anox = 1. , # mmolNO3/m3 half-sat NO3 inhib anoxic degr
kinO2anox = 0.001 , # mmolO2/m3 half-sat O2 inhib anoxic min
## To estimate diffusion coefficients
temperature = 10 , # temperature
salinity = 35 , #
TOC0 = 0.5 , # % TOC concentration at depth
rFePadsorp = 1e-6 , # /(nmolLiq/cm3)/day
rCaPprod = 0.0 ,
rCaPdiss = 0.0 ,
CPrCaP = 1.32/4.6 , # Ca10(PO4)4.6(CO3)1.32F1.87(OH)1.45 Jilbert and Slomp
rPads = 0.0 , # /day - adsorption rate of phosphate
rPdes = 0.0 , # /day - desorption rate of adsorbed P
maxPads = 1e3 , # Max adsorbed P concentration - mmolP/m3 solid
ksFeOH3 = 12500. , # mmolFeOH3/m3 half-sat FeOH3 in iron red
kinFeOH3 = 12500. , # mmolFeOH3/m3 half-sat FeOH3 inhib BSR
ksSO4BSR = 1600. , # mmolSO4/m3 half-sat SO4 in sulfate reduction
kinSO4Met = 1000 , # mmolSO4/m3 half-sat SO4 inhibition for methanogenesis
rFeox = 0.3 , # /d/nmol/cm3 oxidation constant for iron by O2 (bimolecular rate law)
rH2Sox = 5e-4 , # /d/nmol/cm3 oxidation constant for diss Sulfide by O2 (bimolecular rate law)
rFeS = 1e-3 , # /d/nmol/cm3 oxidation constant for diss Sulfide by O2 (bimolecular rate law)
rCH4ox = 27 , # /d/nmol/cm3 oxidation constant for CH4 by O2 (bimolecular rate law)
rAOM = 3e-5 , # /d/nmol/cm3 oxidation constant for AOM CH4 by SO4 (bimolecular rate law)
rSurfH2Sox = 0. , # /d Max rate oxidation of deep H2S with surface O2 - 0 to toggle it off
rSurfCH4ox = 0. , # /d Max rate oxidation of deep CH4 with surface O2 - 0 to toggle it off
ksSurfALK = 3000. , # mmol/m3 half-sat alkalinity in reoxidation of CH4 or H2S with O2
ksO2reox = 1. , # mmolO2/m3 half-sat O2 in reoxidation of CH4 or H2S with O2
ODUoxdepth = 5. , # cm Depth where oxidation of H2S/ODU with surface water O2 is possible
ODUoxatt = 1. , # /cm the depth attenuation coefficient of H2S/ODU oxidation below ODUoxdepth.
# NOT USED rFeS2 = 8.9^10-6, # cm3 liquid/nmol/d - Rickard (1997a)
por0 = 0.9 , # - surface porosity
pordeep = 0.5 , # - deep porosity
porcoeff = 0.3 , # cm porosity coefficient
formationtype = 1 , # to estimate effective diffusion, 1=sand, 2=mud, 3=general
# parameters if bottom water is dynamically described
dilution = 0 , # /day relaxation towards background conc dissolved
Hwater = 10 , # cm height of water over core
Cfall = 100 , # cm/day fall speed of organic carbon (FDET, SDET)
FePfall = 100 , # cm/day fall speed of FeP
FeOH3fall = 100 , # cm/day fall speed of FeP
CaPfall = 100 , # cm/day fall speed of FeP
addalk = 1. , # if 1: alkalinity dyanmically modeled
## MPB production
MPBprod = 0 , # mmol/m3/d maximal rate - range: 5000-5e4
kMPB = 4 , # /cm, exponential decay
kDINupt = 0.01 , # mmol/m3, DIN limitation constant
kPO4upt = 0.001 , # mmol/m3, P limitation constant
kDICupt = 1 # mmol/m3, C limitation constant
)
# parameter units
.FESDIA$Parunit <- c("nmolC/cm2/d", "-", "nmol/cm2/d", "nmol/cm2/d", "/d", "/d",
"molN/molC", "molN/molC", "molP/molC", "molP/molC", "-", "-",
rep("mmol/m3", times=11), rep("mmol/m3",times=11), "cm/d",
"cm2/d", "cm", "/cm", "/d", "cm", "cm", "cm/d",
"-", "/d","/d", "/(mmol/m3)/d", "mmolO2/m3", "mmolO2/m3",
"mmolNO3/m3", "mmolO2/m3", "mmolNO3/m3", "mmolO2/m3",
"dgC", "psu", "%",
"/d", "/d", "/d", "mol/mol", "/d", "/d", "mmolP/m3solid", "mmolFeOH3/m3","mmolFeOH3/m3",
"mmolS/m3", "mmolS/m3", "/(mmol/m3)/d", "/(mmol/m3)/d", "/(mmol/m3)/d",
"/(mmol/m3)/d", "/(mmol/m3)/d", "/d", "/d", "mmol/m3", "mmolO2/m3", "cm", "/cm", "-", "-", "cm",
"-", "/d", "cm", "cm/d", "cm/d", "cm/d", "cm/d", "-", "mmol/m3/d", "/cm", "mmol/m3",
"mmol/m3", "mmol/m3")
.FESDIA$Pardesc <- c("total organic C deposition","part FDET in carbon flux",
"deposition rate of FeOH3", "deposition rate of CaP",
"decay rate FDET", "decay rate SDET", "NC ratio FDET", "NC ratio SDET",
"PC ratio FDET", "PC ratio SDET",
"upper boundary liq. 1:flux, 2:conc, 3:0-grad",
"lower boundary liq. 1:flux, 2:conc, 3:0-grad",
"upper boundary O2 -if BC=1: flux, 2:conc",
"upper boundary NO3 -if BC=1: flux, 2:conc",
"upper boundary NO2 -if BC=1: flux, 2:conc",
"upper boundary NH3 -if BC=1: flux, 2:conc",
"upper boundary CH4 -if BC=1: flux, 2:conc",
"upper boundary PO4 -if BC=1: flux, 2:conc",
"upper boundary DIC -if BC=1: flux, 2:conc",
"upper boundary Fe2+ -if BC=1: flux, 2:conc",
"upper boundary H2S -if BC=1: flux, 2:conc",
"upper boundary SO4 -if BC=1: flux, 2:conc",
"upper boundary alkalinity -if BC=1: flux, 2:conc",
"lower boundary O2 -if BC=1: flux, 2:conc",
"lower boundary NO3 -if BC=1: flux, 2:conc",
"lower boundary NO2 -if BC=1: flux, 2:conc",
"lower boundary NH3 -if BC=1: flux, 2:conc",
"lower boundary CH3 -if BC=1: flux, 2:conc",
"lower boundary PO4 -if BC=1: flux, 2:conc",
"lower boundary DIC -if BC=1: flux, 2:conc",
"lower boundary Fe2+ -if BC=1: flux, 2:conc",
"lower boundary H2S -if BC=1: flux, 2:conc",
"lower boundary SO4 -if BC=1: flux, 2:conc",
"lower boundary alkalinity -if BC=1: flux, 2:conc",
"advection rate", "bioturbation coefficient", "depth of mixed layer",
"attenuation coeff below biotdepth", "bio-irrigation rate",
"depth of irrigated layer", "attenuation coeff below irrdepth",
"piston velocity for dry flats", "Adsorption coeff ammonium",
"Max nitrification rate step1 (NH3ox)", "Max nitrification rate step2 (NO2ox)",
"Anammox rate", "half-sat O2 in nitrification", "half-sat O2 in oxic mineralisation",
"half-sat NO3 in denitrification", "half-sat O2 inhib denitrification",
"half-sat NO3 inhib anoxic degr", "half-sat O2 inhib anoxic min",
"temperature", "salinity", "refractory Carbon conc",
"rate FeP adsorption",
"rate CaP production", "rate CaP dissolution","C:Pratio in CaP",
"adsorption rate PO4", "desorption rate of adsorbed P", "Max adsorbed P concentration",
"half-sat FeOH3 conc in iron reduction", "half-sat FeOH3 inhibition S reduction",
"half-sat SO4 conc in sulphate reduction", "half-sat SO4 inhibition methanogenesis",
"Max rate Fe oxidation", "Max rate H2S oxidation", "maximum rate FeS production",
"Max rate CH4 oxidation with O2", "Max rate anaerobic oxidation Methane",
"Max rate H2S oxidation with BW O2",
"Max rate CH4 oxidation with BW O2",
"half-sat Alkalinity in oxidation of H2S/CH4 with bwO2",
"half-sat Oxygen in oxidation of H2S/CH4 with bwO2",
"Max depth H2S/CH4 oxidation with BW O2", "depth attenuation ODU oxidation",
"surface porosity", "deep porosity", "porosity decay coefficient",
"formationfactor, 1=sand,2=fine sand,3=general",
"relaxation towards background conc ", "height of water over core",
"fall speed of organic C (FDET, SDET)", "fall speed of FeP", "fall speed of FeOH3",
"fall speed of CaP", "solve for alkalinity",
"maximal MPB production rate", "sedimentary light extinction coefficient",
"DIN limitation constant MPB",
"P limitation constant MPB",
"C limitation constant MPB")
##------------------------------------
## State variables
##------------------------------------
.FESDIA$ynames <- c("FDET", "SDET", "O2",
"NO3", "NO2", "NH3", "DIC",
"Fe", "FeOH3", "H2S",
"SO4", "CH4", "PO4",
"FeP", "CaP", "Pads", "ALK")
.FESDIA$svar <- .FESDIA$ynames
.FESDIA$yunits <- c("mmolC/m3 solid", "mmolC/m3 solid", "mmolO/m3 liquid",
"mmolN/m3 liquid", "mmolN/m3 liquid", "mmolN/m3 liquid", "mmolC/m3 liquid",
"mmolFe/m3 liquid", "mmolFe/m3 solid", "mmolS/m3 liquid",
"mmolS/m3 liquid", "mmolC/m3 liquid", "mmolP/m3 liquid",
"mmolP/m3 solid", "mmolP/m3 solid", "mmolP/m3 solid", "mmol/m3 liquid")
.FESDIA$ydescrip <- c("Fast decaying Detritus (solid)",
"Slow decaying Detritus (solid)",
"Oxygen (liquid)",
"Nitrate (liquid)", "Nitrite (liquid)",
"Ammonium/ammonia (liquid)",
"Dissolved Inorganic Carbon (liquid)",
"Fe2+ (liquid)",
"Fe-oxide (solid)",
"Sulphide (liquid)",
"Sulphate (liquid)",
"Methane (liquid)",
"Phosphate (liquid)",
"Iron-bound P (solid)",
"Ca-bound P (solid)",
"Adsorbed P (solid)",
"Alpkalinity (liquid)")
.FESDIA$ynamesall <- as.vector(sapply(.FESDIA$ynames, FUN = function(x) rep(x, times = .FESDIA$N)))
##------------------------------------
## 0-D Variables
##------------------------------------
.FESDIA$var0D <- c("O2flux", "O2deepflux",
"NO3flux", "NO3deepflux",
"NO2flux", "NO2deepflux",
"NH3flux", "NH3deepflux",
"PO4flux", "PO4deepflux",
"DICflux", "DICdeepflux",
"Feflux", "Fedeepflux",
"H2Sflux", "H2Sdeepflux",
"SO4flux", "SO4deepflux",
"CH4flux", "CH4deepflux",
"ALKflux", "ALKdeepflux",
"FDETflux", "FDETdeepflux",
"SDETflux", "SDETdeepflux",
"FePsurfflux", "FePdeepflux",
"CaPsurfflux", "CaPdeepflux",
"FeOH3surfflux", "FeOH3deepflux",
"OrgCflux", "OrgNflux", "OrgPflux",
"DINDIPflux", "DINDIPmean", "DINDIPdeep",
"TotMin", "TotOxic", "TotDenit",
"TotFered", "TotBSR", "TotMeth",
"PartOxic", "PartDenit",
"PartFered", "PartBSR", "PartMethano",
"TotNitri1", "TotNitri2", "TotAnammox", "TotFeoxid",
"TotH2Soxid", "TotCH4oxid", "TotAOM",
"TotFeSprod", "TotFePprod", "TotCaPprod",
"TotFePdesorp", "TotCaPdiss", "TotPadsorb",
"TotNH3prod", "TotPO4prod", "TotNH3ads", "TotO2prod", "TotH2Soxsurf",
"TotCH4oxsurf", "TotALkprod", "PartPremoved", "PartNremoved",
"TotMPBNO3uptake", "TotMPBNH3uptake", "TotMPBPO4uptake", "TotMPBDICuptake",
"TotMPBO2prod","TotalFDET", "TotalSDET", "TotalO2",
"TotalNO3", "TotalNO2", "TotalNH3",
"TotalDIC", "TotalFe", "TotalFeOH3", "TotalH2S", "TotalSO4",
"TotalCH4", "TotalPO4", "TotalFeP", "TotalCaP", "TotalPads")
.FESDIA$unit0D <- c("nmolO2/cm2/d", "nmolO2/cm2/d", "nmolN/cm2/d", "nmolN/cm2/d",
"nmolN/cm2/d", "nmolN/cm2/d", "nmolN/cm2/d", "nmolN/cm2/d",
"nmolP/cm2/d", "nmolP/cm2/d",
"nmolC/cm2/d", "nmolC/cm2/d", "nmolFe/cm2/d", "nmolFe/cm2/d",
"nmolS/cm2/d", "nmolS/cm2/d", "nmolS/cm2/d", "nmolS/cm2/d",
"nmolC/cm2/d", "nmolC/cm2/d", "nmol/cm2/d", "nmol/cm2/d",
"nmolC/cm2/d", "nmolC/cm2/d", "nmolC/cm2/d", "nmolC/cm2/d",
"nmolP/cm2/d", "nmolP/cm2/d", "nmolP/cm2/d", "nmolP/cm2/d",
"nmolFe/cm2/d", "nmolFe/cm2/d", "nmolC/cm2/d", "nmolN/cm2/d",
"nmolP/cm2/d", "molN/molP", "molN/molP", "molN/molP",
"nmolC/cm2/d", "nmolC/cm2/d", "nmolC/cm2/d",
"nmolC/cm2/d", "nmolC/cm2/d", "nmolC/cm2/d",
"-", "-", "-", "-", "-",
"nmolN/cm2/d", "nmolN/cm2/d", "nmolN/cm2/d", "nmolFe/cm2/d",
"nmolS/cm2/d", "nmolC/cm2/d", "nmolS/cm2/d",
"nmolFe/cm2/d", "nmolFe/cm2/d", "nmolP/cm2/d",
"nmolP/cm2/d", "nmolP/cm2/d", "nmolP/cm2/d",
"nmolN/cm2/d", "nmolP/cm2/d", "nmolN/cm2/d", "nmolO/cm2/d",
"nmolS/cm2/d", "nmolC/cm2/d", "nmol/cm2/d", "-", "-",
"nmolN/cm2/d", "nmolN/cm2/d", "nmolP/cm2/d", "nmolC/cm2/d",
"nmolO2/cm2/d", "nmolC/cm2", "nmolC/cm2",
"nmolO/cm2", "nmolN/cm2", "nmolN/cm2", "nmolN/cm2", "nmolC/cm2",
"nmolFe/cm2", "nmolFe/cm2", "nmolS/cm2", "nmolS/cm2",
"nmolC/cm2", "nmolP/cm2", "nmolP/cm2",
"nmolP/cm2", "nmolP/cm2")
.FESDIA$descrip0D <- c("O2 influx sediment-water", "O2 efflux lower boundary",
"NO3 influx sediment-water", "NO3 efflux lower boundary",
"NO2 influx sediment-water", "NO2 efflux lower boundary",
"NH3 influx sediment-water", "NH3 efflux lower boundary",
"PO4 influx sediment-water", "PO4 efflux lower boundary",
"DIC influx sediment-water", "DIC efflux lower boundary",
"Fe2+ influx sediment-water", "Fe2+ efflux lower boundary",
"H2S influx sediment-water", "H2S efflux lower boundary",
"SO4 influx sediment-water", "SO4 efflux lower boundary",
"CH4 influx sediment-water", "CH4 efflux lower boundary",
"Alkalinity influx sediment-water", "Alkalinity efflux lower boundary",
"FDET flux to sediment", "FDET efflux lower boundary",
"SDET flux to sediment", "SDET efflux lower boundary",
"FeP flux upper boundary", "FeP efflux lower boundary",
"CaP flux upper boundary", "CaP efflux lower boundary",
"FeOH3 flux upper boundary", "FeOH3 efflux lower boundary",
"OrgC influx to sediment", "OrgN influx to sediment",
"OrgP influx to sediment",
# "O2:DIC ratio flux sediment-water",
# "(O2+ODUflux): (DIC flux) sediment-water",
"DIN:DIP ratio flux sediment-water",
"DIN:DIP mean concentration",
"DIN:DIP deep concentration",
"Vertically integrated Mineralisation",
"Vertically integrated oxic Mineralisation",
"Vertically integrated Denitrification",
"Vertically integrated Iron reduction",
"Vertically integrated Sulphate reduction",
"Vertically integrated Methanogenesis",
"Part of mineralisation by oxic min",
"Part of mineralisation by denitrification",
"Part of mineralisation by iron reduction",
"Part of mineralisation by sulphate reduction",
"Part of mineralisation by methanogenisis",
"Vertically integrated nitrification step 1 (NH3 ox)",
"Vertically integrated nitrification step 2 (NO2 ox)",
"Vertically integrated anammox",
"Vertically integrated Fe2+ oxidation",
"Vertically integrated H2S oxidation",
"Vertically integrated CH4 oxidation",
"Vertically integrated Anaerobic oxidation methane",
"Vertically integrated FeS production",
"Vertically integrated FeP production",
"Vertically integrated CaP production",
"Vertically integrated FeP desorption",
"Vertically integrated CaP dissolution",
"Vertically integrated P adsorption",
"Vertically integrated NH3 production",
"Vertically integrated PO4 production",
"Vertically integrated NH3 adsorption",
"Vertically integrated O2 production (?)",
"Vertically integrated H2S oxidation by surface O2",
"Vertically integrated CH4 oxidation by surface O2",
"Total alkalinity production",
"Part P removed", "Part N removed",
"Vertically integrated MPB NO3 uptake",
"Vertically integrated MPB NH3 uptake",
"Vertically integrated MPB PO4 uptake",
"Vertically integrated MPB DIC uptake",
"Vertically integrated MPB O2 production",
"Vertically integrated Fast decaying Detritus",
"Vertically integrated Slow decaying Detritus",
"Vertically integrated Oxygen",
"Vertically integrated Nitrate",
"Vertically integrated Nitrite",
"Vertically integrated Ammonium/ammonia",
"Vertically integrated Dissolved Inorganic Carbon",
"Vertically integrated Fe",
"Vertically integrated FeOH3",
"Vertically integrated H2S",
"Vertically integrated SO4",
"Vertically integrated CH4",
"Vertically integrated Phosphate",
"Vertically integrated Iron-bound P",
"Vertically integrated Ca-bound P",
"Vertically integrated Adsorbed P")
##------------------------------------
## forcing functions
##------------------------------------
.FESDIA$varforc <- c("Cflux", "FeOH3flux", "CaPflux", "w", "biotfac", "irrfac",
"rFast", "rSlow", "pFast", "MPBprod",
"gasflux", "bwO2", "bwNO3", "bwNO2", "bwNH3",
"bwCH4", "bwFe", "bwH2S", "bwSO4",
"bwPO4", "bwDIC", "bwALK", "Hwater", "Ratefactor")
.FESDIA$unitforc <- c("nmolC/cm2/d", "nmolP/cm2/d", "nmolP/cm2/d",
"cm/d", "-", "-", "/d", "/d",
"-", "mmol/m3/d", "cm/d", rep("mmol/m3", times=11), "cm", "-")
.FESDIA$descripforc <- c( "Carbon flux to sediment",
"FeOH3 flux to sediment", "CaP flux to sediment",
"Sedimentation rate",
"Bioturbation multiplication factor",
"Irrigation multiplication factor",
"Decay rate FDET",
"Decay rate SDET",
"Part FDET in flux",
"MicroPhytoBenthos forcing",
"Gas exchange flux (piston velocity)",
"Bottom water O2 concentration",
"Bottom water NO3 concentration",
"Bottom water NO2 concentration",
"Bottom water NH3 concentration",
"Bottom water CH4 concentration",
"Bottom water Fe concentration",
"Bottom water H2S concentration",
"Bottom water SO4 concentration",
"Bottom water PO4 concentration",
"Bottom water DIC concentration",
"Bottom water alkalinity concentration",
"Height of water above the sediment",
"Rate multiplication factor"
)
##------------------------------------
## 1D variables
##------------------------------------
.FESDIA$var1D <- c("TOC", "DICprodMin", "DINprodMin", "DIPprodMin", "O2prod",
"Oxicmin", "Denitrific", "Feredmin",
"BSRmin", "Methmin", "nitri1", "nitri2", "Anammox",
"Feoxid", "H2Soxid", "CH4oxid",
"AOM", "FeSprod", "FePadsorp", "FePdesorp",
"CaPprod", "CaPdiss","Padsorb",
"H2Soxsurf", "CH4oxsurf",
"O2distConsump", "ALKprod", "DICprodCH4",
"MPBCprod", "MPBuptakeNO3", "MPBuptakeNH3",
"MPBuptakePO4", "MPBuptakeDIC")
.FESDIA$unit1D <- c("%", "nmolC/cm3 liquid/d", "nmolN/cm3 liquid/d",
"nmolP/cm3 liquid/d", "nmolO/cm3 liquid/d",
"nmolC/cm3 liquid/d", "nmolC/cm3 liquid/d", "nmolC/cm3 liquid/d",
"nmolC/cm3 liquid/d", "nmolC/cm3 liquid/d",
"nmolN/cm3 liquid/d", "nmolN/cm3 liquid/d", "nmolN/cm3 liquid/d",
"nmolFe/cm3 liquid/d", "nmolS/cm3 liquid/d",
"nmolC/cm3 liquid/d", "nmolS/cm3 liquid/d", "nmolFe/cm3 liquid/d",
"nmolFe/cm3 liquid/d", "nmolP/cm3 solid/d", "nmolP/cm3 liquid/d",
"nmolP/cm3 solid/d", "nmolP/cm3 solid/d",
"nmolS/cm3 liquid/d", "nmolC/cm3 liquid/d", "nmolO/cm3 liquid/d",
"nmol/cm3 liquid/d", "nmolC/cm3 liquid/d", "nmolC/cm3 solid/d",
"nmolN/cm3 liquid/d", "nmolN/cm3 liquid/d",
"nmolP/cm3 liquid/d", "nmolC/cm3 liquid/d")
.FESDIA$descrip1D <- c("Total Organic Carbon % profile",
"DIC production profile (mineralisation)",
"DIN production profile (mineralisation)",
"DIP production profile (mineralisation)",
"O2 production profile (microphytobenthos)",
"Oxic mineralisation profile", "Denitrification profile",
"Fe reduction mineralisation profile", "Sulphate reduction mineralisation profile",
"Methanogensis mineralisation profile",
"Nitrification step 1 profile (NH3 oxidation)",
"Nitrification step 2 profile (NO2 oxidation)",
"Anammox profile", "Fe2+ oxidation profile", "H2S oxidaton profile",
"CH4 oxidation profile",
"Anaerobic oxidation of methane profile", "FeS production profile",
"FeP adsorption profile", "FeP desorption profile",
"CaP production profile", "CaP dissolution profile",
"P adsorption profile",
"H2S oxidation with surface O2 profile",
"CH4 oxidation with surface O2 profile",
"O2 uptake oxidation with surface O2 profile",
"Alkalinity production profile", "DIC production via Methane profile",
"MPB production profile",
"MPB NO3 uptake profile", "MPB NH3 uptake profile",
"MPB PO4 uptake profile", "MPB DIC uptake profile")
.FESDIA$var1Dall <- as.vector(sapply(.FESDIA$var1D, FUN = function(x) rep(x, times = .FESDIA$N)))
.FESDIA$outnames <- c(.FESDIA$var0D, .FESDIA$var1Dall,.FESDIA$varforc)
.FESDIA$nout <- length(.FESDIA$outnames)
# how to plot the units
.FESDIA$labels <- data.frame(
Units = c("%", "nmolC/cm3 liquid/d", "nmolN/cm3 liquid/d",
"nmolP/cm3 liquid/d", "nmolO/cm3 liquid/d", "nmolFe/cm3 liquid/d",
"nmolS/cm3 liquid/d", "nmolP/cm3 solid/d", "nmolC/cm3 solid/d",
"nmol/cm3 liquid/d",
"nmolO2/cm2/d", "nmolN/cm2/d", "nmolP/cm2/d", "nmolC/cm2/d",
"nmolFe/cm2/d", "nmolS/cm2/d", "nmol/cm2/d", "molN/molP", "-",
"nmolO/cm2/d" , "cm/d", "/d", "mmol/m3/d", "mmol/m3",
"cm", "mmolC/m3 solid",
"mmolO/m3 liquid", "mmolN/m3 liquid", "mmolC/m3 liquid",
"mmolFe/m3 liquid", "mmolFe/m3 solid",
"mmolS/m3 liquid", "mmolP/m3 liquid", "mmolP/m3 solid", "mmol/m3 liquid",
"nmolC/cm2", "nmolO/cm2", "nmolN/cm2", "nmolFe/cm2", "nmolS/cm2"),
Labels = c("%", "mmol/m3.l/d", "mmol/m3.l/d",
"mmol/m3.l/d", "mmol/m3.l/d", "mmol/m3.l/d",
"mmol/m3.l/d", "mmol/m3.s/d", "mmol/m3.s/d", "mmol/m3.l/d",
"nmol/cm2/d", "nmol/cm2/d", "nmol/cm2/d", "nmol/cm2/d",
"nmol/cm2/d", "nmol/cm2/d", "nmol/cm2/d", "mol/mol", "-",
"nmol/cm2/d" , "cm/d", "/d", "mmol/m3/d", "mmol/m3", "cm", "mmol/m3.s",
"mmol/m3.l", "mmol/m3.l", "mmol/m3.l", "mmol/m3.l", "mmol/m3.s",
"mmol/m3.l", "mmol/m3.l", "mmol/m3.s", "mmol/m3.l",
"nmol/cm2", "nmol/cm2", "nmol/cm2", "nmol/cm2", "nmol/cm2") )
row.names(.FESDIA$labels) <- .FESDIA$labels$Units
.FESDIA$getplot1D <-
rbind(data.frame(names = .FESDIA$ynames, units = .FESDIA$labels[.FESDIA$yunits,2]),
data.frame(names = .FESDIA$var1D, units = .FESDIA$labels[.FESDIA$unit1D,2]))
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FESDIA documentation built on April 22, 2021, 3 p.m.
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## ====================================================================
## A local environment for non user-visible data,
## ====================================================================
.FESDIA <- new.env()
.FESDIA$N <- 100
.FESDIA$Grid <- setup.grid.1D(x.up=0, dx.1 = 0.01, N = .FESDIA$N, L = 100)
##------------------------------------
## Parameters
##------------------------------------
.FESDIA$Parms <- c(
## organic matter dynamics #
Cflux = 20*1e5/12/365 , # nmolC/cm2/d - Carbon deposition: 20gC/m2/yr
pFast = 0.9 , # - fraction fast detritus in flux
FeOH3flux = 1 , # nmol/cm2/d FeOH3 deposition rate
CaPflux = 0 , # nmolP/cm2/d deposition rate of CaP
rFast = 25/365 , # /d decay rate fast decay detritus
rSlow = 0.05/365 , # /d decay rate slow decay detritus
NCrFdet = 16/106 , # molN/molC NC ratio fast decay detritus
NCrSdet = 16/106 , # molN/molC NC ratio slow decay detritus
PCrFdet = 1/106 , # molP/molC PC ratio fast decay det.
PCrSdet = 1/106 , # molP/molC PC ratio slow decay det.
## Nutrient bottom water conditions
BCupLiq = 2 , # upper boundary condition for liquid; 1= flux, 2=conc, 3 = 0-grad
BCdownLiq = 3 , # lower boundary condition; default = 0-gradient
O2bw = 300 , # mmol/m3 Oxygen conc in bottom water
NO3bw = 10 , # mmol/m3
NO2bw = 0 , # mmol/m3
NH3bw = 1 , # mmol/m3
CH4bw = 0 , # mmol/m3
PO4bw = 0.5 , # mmol/m3
DICbw = 2100 ,
Febw = 0 ,
H2Sbw = 0 ,
SO4bw = 31000 ,
ALKbw = 2400 ,
O2dw = NA , # mmol/m3 deep boundary concentrations
NO3dw = NA , # mmol/m3
NO2dw = NA , # mmol/m3
NH3dw = NA , # mmol/m3
CH4dw = NA , # mmol/m3
PO4dw = NA , # mmol/m3
DICdw = NA ,
Fedw = NA ,
H2Sdw = NA ,
SO4dw = NA ,
ALKdw = NA ,
## Bioturbation, advection, bio-irrigation
w = 1/365000 , # cm/d advection rate
biot = 1/365 , # cm2/d bioturbation coefficient
biotdepth = 5 , # cm depth of mixed layer
biotatt = 1 , # cm depth attenuation coefficient below biotdepth
irr = 0 , # /d bio-irrigation rate
irrdepth = 5 , # cm depth of irrigates layer
irratt = 1 , # cm depth attenuation coefficient below irrdepth
gasflux = 0 , # cm/d piston velocity for dry flats - exchange of O2 and DIC only+deposition
## Nutrient parameters
NH3Ads = 1.3 , # - Adsorption coeff ammonium
rnitri1 = 20 , #/d Max nitrification rate (step1) - oxidation of ammonium
rnitri2 = 20. , #/d Max nitrification rate (step2) - oxidation of nitrite
ranammox = 0.1 , # /(mmol/m3)/d Anammox rate
ksO2nitri = 1. , # mmolO2/m3 half-sat O2 in nitrification
ksO2oxic = 3. , # mmolO2/m3 half-sat O2 in oxic mineralisation
ksNO3denit = 30. , # mmolNO3/m3 half-sat NO3 in denitrification
kinO2denit = 1. , # mmolO2/m3 half-sat O2 inhib denitrification
kinNO3anox = 1. , # mmolNO3/m3 half-sat NO3 inhib anoxic degr
kinO2anox = 0.001 , # mmolO2/m3 half-sat O2 inhib anoxic min
## To estimate diffusion coefficients
temperature = 10 , # temperature
salinity = 35 , #
TOC0 = 0.5 , # % TOC concentration at depth
rFePadsorp = 1e-6 , # /(nmolLiq/cm3)/day
rCaPprod = 0.0 ,
rCaPdiss = 0.0 ,
CPrCaP = 1.32/4.6 , # Ca10(PO4)4.6(CO3)1.32F1.87(OH)1.45 Jilbert and Slomp
rPads = 0.0 , # /day - adsorption rate of phosphate
rPdes = 0.0 , # /day - desorption rate of adsorbed P
maxPads = 1e3 , # Max adsorbed P concentration - mmolP/m3 solid
ksFeOH3 = 12500. , # mmolFeOH3/m3 half-sat FeOH3 in iron red
kinFeOH3 = 12500. , # mmolFeOH3/m3 half-sat FeOH3 inhib BSR
ksSO4BSR = 1600. , # mmolSO4/m3 half-sat SO4 in sulfate reduction
kinSO4Met = 1000 , # mmolSO4/m3 half-sat SO4 inhibition for methanogenesis
rFeox = 0.3 , # /d/nmol/cm3 oxidation constant for iron by O2 (bimolecular rate law)
rH2Sox = 5e-4 , # /d/nmol/cm3 oxidation constant for diss Sulfide by O2 (bimolecular rate law)
rFeS = 1e-3 , # /d/nmol/cm3 oxidation constant for diss Sulfide by O2 (bimolecular rate law)
rCH4ox = 27 , # /d/nmol/cm3 oxidation constant for CH4 by O2 (bimolecular rate law)
rAOM = 3e-5 , # /d/nmol/cm3 oxidation constant for AOM CH4 by SO4 (bimolecular rate law)
rSurfH2Sox = 0. , # /d Max rate oxidation of deep H2S with surface O2 - 0 to toggle it off
rSurfCH4ox = 0. , # /d Max rate oxidation of deep CH4 with surface O2 - 0 to toggle it off
ksSurfALK = 3000. , # mmol/m3 half-sat alkalinity in reoxidation of CH4 or H2S with O2
ksO2reox = 1. , # mmolO2/m3 half-sat O2 in reoxidation of CH4 or H2S with O2
ODUoxdepth = 5. , # cm Depth where oxidation of H2S/ODU with surface water O2 is possible
ODUoxatt = 1. , # /cm the depth attenuation coefficient of H2S/ODU oxidation below ODUoxdepth.
# NOT USED rFeS2 = 8.9^10-6, # cm3 liquid/nmol/d - Rickard (1997a)
por0 = 0.9 , # - surface porosity
pordeep = 0.5 , # - deep porosity
porcoeff = 0.3 , # cm porosity coefficient
formationtype = 1 , # to estimate effective diffusion, 1=sand, 2=mud, 3=general
# parameters if bottom water is dynamically described
dilution = 0 , # /day relaxation towards background conc dissolved
Hwater = 10 , # cm height of water over core
Cfall = 100 , # cm/day fall speed of organic carbon (FDET, SDET)
FePfall = 100 , # cm/day fall speed of FeP
FeOH3fall = 100 , # cm/day fall speed of FeP
CaPfall = 100 , # cm/day fall speed of FeP
addalk = 1. , # if 1: alkalinity dyanmically modeled
## MPB production
MPBprod = 0 , # mmol/m3/d maximal rate - range: 5000-5e4
kMPB = 4 , # /cm, exponential decay
kDINupt = 0.01 , # mmol/m3, DIN limitation constant
kPO4upt = 0.001 , # mmol/m3, P limitation constant
kDICupt = 1 # mmol/m3, C limitation constant
)
# parameter units
.FESDIA$Parunit <- c("nmolC/cm2/d", "-", "nmol/cm2/d", "nmol/cm2/d", "/d", "/d",
"molN/molC", "molN/molC", "molP/molC", "molP/molC", "-", "-",
rep("mmol/m3", times=11), rep("mmol/m3",times=11), "cm/d",
"cm2/d", "cm", "/cm", "/d", "cm", "cm", "cm/d",
"-", "/d","/d", "/(mmol/m3)/d", "mmolO2/m3", "mmolO2/m3",
"mmolNO3/m3", "mmolO2/m3", "mmolNO3/m3", "mmolO2/m3",
"dgC", "psu", "%",
"/d", "/d", "/d", "mol/mol", "/d", "/d", "mmolP/m3solid", "mmolFeOH3/m3","mmolFeOH3/m3",
"mmolS/m3", "mmolS/m3", "/(mmol/m3)/d", "/(mmol/m3)/d", "/(mmol/m3)/d",
"/(mmol/m3)/d", "/(mmol/m3)/d", "/d", "/d", "mmol/m3", "mmolO2/m3", "cm", "/cm", "-", "-", "cm",
"-", "/d", "cm", "cm/d", "cm/d", "cm/d", "cm/d", "-", "mmol/m3/d", "/cm", "mmol/m3",
"mmol/m3", "mmol/m3")
.FESDIA$Pardesc <- c("total organic C deposition","part FDET in carbon flux",
"deposition rate of FeOH3", "deposition rate of CaP",
"decay rate FDET", "decay rate SDET", "NC ratio FDET", "NC ratio SDET",
"PC ratio FDET", "PC ratio SDET",
"upper boundary liq. 1:flux, 2:conc, 3:0-grad",
"lower boundary liq. 1:flux, 2:conc, 3:0-grad",
"upper boundary O2 -if BC=1: flux, 2:conc",
"upper boundary NO3 -if BC=1: flux, 2:conc",
"upper boundary NO2 -if BC=1: flux, 2:conc",
"upper boundary NH3 -if BC=1: flux, 2:conc",
"upper boundary CH4 -if BC=1: flux, 2:conc",
"upper boundary PO4 -if BC=1: flux, 2:conc",
"upper boundary DIC -if BC=1: flux, 2:conc",
"upper boundary Fe2+ -if BC=1: flux, 2:conc",
"upper boundary H2S -if BC=1: flux, 2:conc",
"upper boundary SO4 -if BC=1: flux, 2:conc",
"upper boundary alkalinity -if BC=1: flux, 2:conc",
"lower boundary O2 -if BC=1: flux, 2:conc",
"lower boundary NO3 -if BC=1: flux, 2:conc",
"lower boundary NO2 -if BC=1: flux, 2:conc",
"lower boundary NH3 -if BC=1: flux, 2:conc",
"lower boundary CH3 -if BC=1: flux, 2:conc",
"lower boundary PO4 -if BC=1: flux, 2:conc",
"lower boundary DIC -if BC=1: flux, 2:conc",
"lower boundary Fe2+ -if BC=1: flux, 2:conc",
"lower boundary H2S -if BC=1: flux, 2:conc",
"lower boundary SO4 -if BC=1: flux, 2:conc",
"lower boundary alkalinity -if BC=1: flux, 2:conc",
"advection rate", "bioturbation coefficient", "depth of mixed layer",
"attenuation coeff below biotdepth", "bio-irrigation rate",
"depth of irrigated layer", "attenuation coeff below irrdepth",
"piston velocity for dry flats", "Adsorption coeff ammonium",
"Max nitrification rate step1 (NH3ox)", "Max nitrification rate step2 (NO2ox)",
"Anammox rate", "half-sat O2 in nitrification", "half-sat O2 in oxic mineralisation",
"half-sat NO3 in denitrification", "half-sat O2 inhib denitrification",
"half-sat NO3 inhib anoxic degr", "half-sat O2 inhib anoxic min",
"temperature", "salinity", "refractory Carbon conc",
"rate FeP adsorption",
"rate CaP production", "rate CaP dissolution","C:Pratio in CaP",
"adsorption rate PO4", "desorption rate of adsorbed P", "Max adsorbed P concentration",
"half-sat FeOH3 conc in iron reduction", "half-sat FeOH3 inhibition S reduction",
"half-sat SO4 conc in sulphate reduction", "half-sat SO4 inhibition methanogenesis",
"Max rate Fe oxidation", "Max rate H2S oxidation", "maximum rate FeS production",
"Max rate CH4 oxidation with O2", "Max rate anaerobic oxidation Methane",
"Max rate H2S oxidation with BW O2",
"Max rate CH4 oxidation with BW O2",
"half-sat Alkalinity in oxidation of H2S/CH4 with bwO2",
"half-sat Oxygen in oxidation of H2S/CH4 with bwO2",
"Max depth H2S/CH4 oxidation with BW O2", "depth attenuation ODU oxidation",
"surface porosity", "deep porosity", "porosity decay coefficient",
"formationfactor, 1=sand,2=fine sand,3=general",
"relaxation towards background conc ", "height of water over core",
"fall speed of organic C (FDET, SDET)", "fall speed of FeP", "fall speed of FeOH3",
"fall speed of CaP", "solve for alkalinity",
"maximal MPB production rate", "sedimentary light extinction coefficient",
"DIN limitation constant MPB",
"P limitation constant MPB",
"C limitation constant MPB")
##------------------------------------
## State variables
##------------------------------------
.FESDIA$ynames <- c("FDET", "SDET", "O2",
"NO3", "NO2", "NH3", "DIC",
"Fe", "FeOH3", "H2S",
"SO4", "CH4", "PO4",
"FeP", "CaP", "Pads", "ALK")
.FESDIA$svar <- .FESDIA$ynames
.FESDIA$yunits <- c("mmolC/m3 solid", "mmolC/m3 solid", "mmolO/m3 liquid",
"mmolN/m3 liquid", "mmolN/m3 liquid", "mmolN/m3 liquid", "mmolC/m3 liquid",
"mmolFe/m3 liquid", "mmolFe/m3 solid", "mmolS/m3 liquid",
"mmolS/m3 liquid", "mmolC/m3 liquid", "mmolP/m3 liquid",
"mmolP/m3 solid", "mmolP/m3 solid", "mmolP/m3 solid", "mmol/m3 liquid")
.FESDIA$ydescrip <- c("Fast decaying Detritus (solid)",
"Slow decaying Detritus (solid)",
"Oxygen (liquid)",
"Nitrate (liquid)", "Nitrite (liquid)",
"Ammonium/ammonia (liquid)",
"Dissolved Inorganic Carbon (liquid)",
"Fe2+ (liquid)",
"Fe-oxide (solid)",
"Sulphide (liquid)",
"Sulphate (liquid)",
"Methane (liquid)",
"Phosphate (liquid)",
"Iron-bound P (solid)",
"Ca-bound P (solid)",
"Adsorbed P (solid)",
"Alpkalinity (liquid)")
.FESDIA$ynamesall <- as.vector(sapply(.FESDIA$ynames, FUN = function(x) rep(x, times = .FESDIA$N)))
##------------------------------------
## 0-D Variables
##------------------------------------
.FESDIA$var0D <- c("O2flux", "O2deepflux",
"NO3flux", "NO3deepflux",
"NO2flux", "NO2deepflux",
"NH3flux", "NH3deepflux",
"PO4flux", "PO4deepflux",
"DICflux", "DICdeepflux",
"Feflux", "Fedeepflux",
"H2Sflux", "H2Sdeepflux",
"SO4flux", "SO4deepflux",
"CH4flux", "CH4deepflux",
"ALKflux", "ALKdeepflux",
"FDETflux", "FDETdeepflux",
"SDETflux", "SDETdeepflux",
"FePsurfflux", "FePdeepflux",
"CaPsurfflux", "CaPdeepflux",
"FeOH3surfflux", "FeOH3deepflux",
"OrgCflux", "OrgNflux", "OrgPflux",
"DINDIPflux", "DINDIPmean", "DINDIPdeep",
"TotMin", "TotOxic", "TotDenit",
"TotFered", "TotBSR", "TotMeth",
"PartOxic", "PartDenit",
"PartFered", "PartBSR", "PartMethano",
"TotNitri1", "TotNitri2", "TotAnammox", "TotFeoxid",
"TotH2Soxid", "TotCH4oxid", "TotAOM",
"TotFeSprod", "TotFePprod", "TotCaPprod",
"TotFePdesorp", "TotCaPdiss", "TotPadsorb",
"TotNH3prod", "TotPO4prod", "TotNH3ads", "TotO2prod", "TotH2Soxsurf",
"TotCH4oxsurf", "TotALkprod", "PartPremoved", "PartNremoved",
"TotMPBNO3uptake", "TotMPBNH3uptake", "TotMPBPO4uptake", "TotMPBDICuptake",
"TotMPBO2prod","TotalFDET", "TotalSDET", "TotalO2",
"TotalNO3", "TotalNO2", "TotalNH3",
"TotalDIC", "TotalFe", "TotalFeOH3", "TotalH2S", "TotalSO4",
"TotalCH4", "TotalPO4", "TotalFeP", "TotalCaP", "TotalPads")
.FESDIA$unit0D <- c("nmolO2/cm2/d", "nmolO2/cm2/d", "nmolN/cm2/d", "nmolN/cm2/d",
"nmolN/cm2/d", "nmolN/cm2/d", "nmolN/cm2/d", "nmolN/cm2/d",
"nmolP/cm2/d", "nmolP/cm2/d",
"nmolC/cm2/d", "nmolC/cm2/d", "nmolFe/cm2/d", "nmolFe/cm2/d",
"nmolS/cm2/d", "nmolS/cm2/d", "nmolS/cm2/d", "nmolS/cm2/d",
"nmolC/cm2/d", "nmolC/cm2/d", "nmol/cm2/d", "nmol/cm2/d",
"nmolC/cm2/d", "nmolC/cm2/d", "nmolC/cm2/d", "nmolC/cm2/d",
"nmolP/cm2/d", "nmolP/cm2/d", "nmolP/cm2/d", "nmolP/cm2/d",
"nmolFe/cm2/d", "nmolFe/cm2/d", "nmolC/cm2/d", "nmolN/cm2/d",
"nmolP/cm2/d", "molN/molP", "molN/molP", "molN/molP",
"nmolC/cm2/d", "nmolC/cm2/d", "nmolC/cm2/d",
"nmolC/cm2/d", "nmolC/cm2/d", "nmolC/cm2/d",
"-", "-", "-", "-", "-",
"nmolN/cm2/d", "nmolN/cm2/d", "nmolN/cm2/d", "nmolFe/cm2/d",
"nmolS/cm2/d", "nmolC/cm2/d", "nmolS/cm2/d",
"nmolFe/cm2/d", "nmolFe/cm2/d", "nmolP/cm2/d",
"nmolP/cm2/d", "nmolP/cm2/d", "nmolP/cm2/d",
"nmolN/cm2/d", "nmolP/cm2/d", "nmolN/cm2/d", "nmolO/cm2/d",
"nmolS/cm2/d", "nmolC/cm2/d", "nmol/cm2/d", "-", "-",
"nmolN/cm2/d", "nmolN/cm2/d", "nmolP/cm2/d", "nmolC/cm2/d",
"nmolO2/cm2/d", "nmolC/cm2", "nmolC/cm2",
"nmolO/cm2", "nmolN/cm2", "nmolN/cm2", "nmolN/cm2", "nmolC/cm2",
"nmolFe/cm2", "nmolFe/cm2", "nmolS/cm2", "nmolS/cm2",
"nmolC/cm2", "nmolP/cm2", "nmolP/cm2",
"nmolP/cm2", "nmolP/cm2")
.FESDIA$descrip0D <- c("O2 influx sediment-water", "O2 efflux lower boundary",
"NO3 influx sediment-water", "NO3 efflux lower boundary",
"NO2 influx sediment-water", "NO2 efflux lower boundary",
"NH3 influx sediment-water", "NH3 efflux lower boundary",
"PO4 influx sediment-water", "PO4 efflux lower boundary",
"DIC influx sediment-water", "DIC efflux lower boundary",
"Fe2+ influx sediment-water", "Fe2+ efflux lower boundary",
"H2S influx sediment-water", "H2S efflux lower boundary",
"SO4 influx sediment-water", "SO4 efflux lower boundary",
"CH4 influx sediment-water", "CH4 efflux lower boundary",
"Alkalinity influx sediment-water", "Alkalinity efflux lower boundary",
"FDET flux to sediment", "FDET efflux lower boundary",
"SDET flux to sediment", "SDET efflux lower boundary",
"FeP flux upper boundary", "FeP efflux lower boundary",
"CaP flux upper boundary", "CaP efflux lower boundary",
"FeOH3 flux upper boundary", "FeOH3 efflux lower boundary",
"OrgC influx to sediment", "OrgN influx to sediment",
"OrgP influx to sediment",
# "O2:DIC ratio flux sediment-water",
# "(O2+ODUflux): (DIC flux) sediment-water",
"DIN:DIP ratio flux sediment-water",
"DIN:DIP mean concentration",
"DIN:DIP deep concentration",
"Vertically integrated Mineralisation",
"Vertically integrated oxic Mineralisation",
"Vertically integrated Denitrification",
"Vertically integrated Iron reduction",
"Vertically integrated Sulphate reduction",
"Vertically integrated Methanogenesis",
"Part of mineralisation by oxic min",
"Part of mineralisation by denitrification",
"Part of mineralisation by iron reduction",
"Part of mineralisation by sulphate reduction",
"Part of mineralisation by methanogenisis",
"Vertically integrated nitrification step 1 (NH3 ox)",
"Vertically integrated nitrification step 2 (NO2 ox)",
"Vertically integrated anammox",
"Vertically integrated Fe2+ oxidation",
"Vertically integrated H2S oxidation",
"Vertically integrated CH4 oxidation",
"Vertically integrated Anaerobic oxidation methane",
"Vertically integrated FeS production",
"Vertically integrated FeP production",
"Vertically integrated CaP production",
"Vertically integrated FeP desorption",
"Vertically integrated CaP dissolution",
"Vertically integrated P adsorption",
"Vertically integrated NH3 production",
"Vertically integrated PO4 production",
"Vertically integrated NH3 adsorption",
"Vertically integrated O2 production (?)",
"Vertically integrated H2S oxidation by surface O2",
"Vertically integrated CH4 oxidation by surface O2",
"Total alkalinity production",
"Part P removed", "Part N removed",
"Vertically integrated MPB NO3 uptake",
"Vertically integrated MPB NH3 uptake",
"Vertically integrated MPB PO4 uptake",
"Vertically integrated MPB DIC uptake",
"Vertically integrated MPB O2 production",
"Vertically integrated Fast decaying Detritus",
"Vertically integrated Slow decaying Detritus",
"Vertically integrated Oxygen",
"Vertically integrated Nitrate",
"Vertically integrated Nitrite",
"Vertically integrated Ammonium/ammonia",
"Vertically integrated Dissolved Inorganic Carbon",
"Vertically integrated Fe",
"Vertically integrated FeOH3",
"Vertically integrated H2S",
"Vertically integrated SO4",
"Vertically integrated CH4",
"Vertically integrated Phosphate",
"Vertically integrated Iron-bound P",
"Vertically integrated Ca-bound P",
"Vertically integrated Adsorbed P")
##------------------------------------
## forcing functions
##------------------------------------
.FESDIA$varforc <- c("Cflux", "FeOH3flux", "CaPflux", "w", "biotfac", "irrfac",
"rFast", "rSlow", "pFast", "MPBprod",
"gasflux", "bwO2", "bwNO3", "bwNO2", "bwNH3",
"bwCH4", "bwFe", "bwH2S", "bwSO4",
"bwPO4", "bwDIC", "bwALK", "Hwater", "Ratefactor")
.FESDIA$unitforc <- c("nmolC/cm2/d", "nmolP/cm2/d", "nmolP/cm2/d",
"cm/d", "-", "-", "/d", "/d",
"-", "mmol/m3/d", "cm/d", rep("mmol/m3", times=11), "cm", "-")
.FESDIA$descripforc <- c( "Carbon flux to sediment",
"FeOH3 flux to sediment", "CaP flux to sediment",
"Sedimentation rate",
"Bioturbation multiplication factor",
"Irrigation multiplication factor",
"Decay rate FDET",
"Decay rate SDET",
"Part FDET in flux",
"MicroPhytoBenthos forcing",
"Gas exchange flux (piston velocity)",
"Bottom water O2 concentration",
"Bottom water NO3 concentration",
"Bottom water NO2 concentration",
"Bottom water NH3 concentration",
"Bottom water CH4 concentration",
"Bottom water Fe concentration",
"Bottom water H2S concentration",
"Bottom water SO4 concentration",
"Bottom water PO4 concentration",
"Bottom water DIC concentration",
"Bottom water alkalinity concentration",
"Height of water above the sediment",
"Rate multiplication factor"
)
##------------------------------------
## 1D variables
##------------------------------------
.FESDIA$var1D <- c("TOC", "DICprodMin", "DINprodMin", "DIPprodMin", "O2prod",
"Oxicmin", "Denitrific", "Feredmin",
"BSRmin", "Methmin", "nitri1", "nitri2", "Anammox",
"Feoxid", "H2Soxid", "CH4oxid",
"AOM", "FeSprod", "FePadsorp", "FePdesorp",
"CaPprod", "CaPdiss","Padsorb",
"H2Soxsurf", "CH4oxsurf",
"O2distConsump", "ALKprod", "DICprodCH4",
"MPBCprod", "MPBuptakeNO3", "MPBuptakeNH3",
"MPBuptakePO4", "MPBuptakeDIC")
.FESDIA$unit1D <- c("%", "nmolC/cm3 liquid/d", "nmolN/cm3 liquid/d",
"nmolP/cm3 liquid/d", "nmolO/cm3 liquid/d",
"nmolC/cm3 liquid/d", "nmolC/cm3 liquid/d", "nmolC/cm3 liquid/d",
"nmolC/cm3 liquid/d", "nmolC/cm3 liquid/d",
"nmolN/cm3 liquid/d", "nmolN/cm3 liquid/d", "nmolN/cm3 liquid/d",
"nmolFe/cm3 liquid/d", "nmolS/cm3 liquid/d",
"nmolC/cm3 liquid/d", "nmolS/cm3 liquid/d", "nmolFe/cm3 liquid/d",
"nmolFe/cm3 liquid/d", "nmolP/cm3 solid/d", "nmolP/cm3 liquid/d",
"nmolP/cm3 solid/d", "nmolP/cm3 solid/d",
"nmolS/cm3 liquid/d", "nmolC/cm3 liquid/d", "nmolO/cm3 liquid/d",
"nmol/cm3 liquid/d", "nmolC/cm3 liquid/d", "nmolC/cm3 solid/d",
"nmolN/cm3 liquid/d", "nmolN/cm3 liquid/d",
"nmolP/cm3 liquid/d", "nmolC/cm3 liquid/d")
.FESDIA$descrip1D <- c("Total Organic Carbon % profile",
"DIC production profile (mineralisation)",
"DIN production profile (mineralisation)",
"DIP production profile (mineralisation)",
"O2 production profile (microphytobenthos)",
"Oxic mineralisation profile", "Denitrification profile",
"Fe reduction mineralisation profile", "Sulphate reduction mineralisation profile",
"Methanogensis mineralisation profile",
"Nitrification step 1 profile (NH3 oxidation)",
"Nitrification step 2 profile (NO2 oxidation)",
"Anammox profile", "Fe2+ oxidation profile", "H2S oxidaton profile",
"CH4 oxidation profile",
"Anaerobic oxidation of methane profile", "FeS production profile",
"FeP adsorption profile", "FeP desorption profile",
"CaP production profile", "CaP dissolution profile",
"P adsorption profile",
"H2S oxidation with surface O2 profile",
"CH4 oxidation with surface O2 profile",
"O2 uptake oxidation with surface O2 profile",
"Alkalinity production profile", "DIC production via Methane profile",
"MPB production profile",
"MPB NO3 uptake profile", "MPB NH3 uptake profile",
"MPB PO4 uptake profile", "MPB DIC uptake profile")
.FESDIA$var1Dall <- as.vector(sapply(.FESDIA$var1D, FUN = function(x) rep(x, times = .FESDIA$N)))
.FESDIA$outnames <- c(.FESDIA$var0D, .FESDIA$var1Dall,.FESDIA$varforc)
.FESDIA$nout <- length(.FESDIA$outnames)
# how to plot the units
.FESDIA$labels <- data.frame(
Units = c("%", "nmolC/cm3 liquid/d", "nmolN/cm3 liquid/d",
"nmolP/cm3 liquid/d", "nmolO/cm3 liquid/d", "nmolFe/cm3 liquid/d",
"nmolS/cm3 liquid/d", "nmolP/cm3 solid/d", "nmolC/cm3 solid/d",
"nmol/cm3 liquid/d",
"nmolO2/cm2/d", "nmolN/cm2/d", "nmolP/cm2/d", "nmolC/cm2/d",
"nmolFe/cm2/d", "nmolS/cm2/d", "nmol/cm2/d", "molN/molP", "-",
"nmolO/cm2/d" , "cm/d", "/d", "mmol/m3/d", "mmol/m3",
"cm", "mmolC/m3 solid",
"mmolO/m3 liquid", "mmolN/m3 liquid", "mmolC/m3 liquid",
"mmolFe/m3 liquid", "mmolFe/m3 solid",
"mmolS/m3 liquid", "mmolP/m3 liquid", "mmolP/m3 solid", "mmol/m3 liquid",
"nmolC/cm2", "nmolO/cm2", "nmolN/cm2", "nmolFe/cm2", "nmolS/cm2"),
Labels = c("%", "mmol/m3.l/d", "mmol/m3.l/d",
"mmol/m3.l/d", "mmol/m3.l/d", "mmol/m3.l/d",
"mmol/m3.l/d", "mmol/m3.s/d", "mmol/m3.s/d", "mmol/m3.l/d",
"nmol/cm2/d", "nmol/cm2/d", "nmol/cm2/d", "nmol/cm2/d",
"nmol/cm2/d", "nmol/cm2/d", "nmol/cm2/d", "mol/mol", "-",
"nmol/cm2/d" , "cm/d", "/d", "mmol/m3/d", "mmol/m3", "cm", "mmol/m3.s",
"mmol/m3.l", "mmol/m3.l", "mmol/m3.l", "mmol/m3.l", "mmol/m3.s",
"mmol/m3.l", "mmol/m3.l", "mmol/m3.s", "mmol/m3.l",
"nmol/cm2", "nmol/cm2", "nmol/cm2", "nmol/cm2", "nmol/cm2") )
row.names(.FESDIA$labels) <- .FESDIA$labels$Units
.FESDIA$getplot1D <-
rbind(data.frame(names = .FESDIA$ynames, units = .FESDIA$labels[.FESDIA$yunits,2]),
data.frame(names = .FESDIA$var1D, units = .FESDIA$labels[.FESDIA$unit1D,2]))
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