FESDIAparms {FESDIA} | R Documentation |
PHDIAparms, FESDIAparms
retrieve the parameters PHDIA and FESDIA model solutions.
FESDIAdepth, FESDIAdx
retrieve the sediment depths and layer thicknesses of PHDIA or FESDIA model solutions.
FESDIAbiot, FESDIApor, FESDIAirr
retrieve the bioturbation, porosity, and irrigation profiles of PHDIA and FESDIA model solutions.
FESDIAparms(out = NULL, as.vector = FALSE, which = NULL) PHDIAparms(out = NULL, as.vector = FALSE, which = NULL) FESDIAdepth(out = NULL) FESDIAgrid(out = NULL) FESDIAbiot(out) FESDIApor(out) FESDIAirr(out)
out |
an output object returned by FESDIAsolve or FESDIAdyna. If |
as.vector |
if |
which |
if not |
The parameters and their meaning are the following (with default values):
Cflux = 20*1e5/12/365 , nmolC/cm2/d - Carbon deposition
rFast = 25/365 , /d , decay rate fast decay detritus
rSlow = 0.5/365 , /d , decay rate slow decay detritus
pFast = 0.9 , - , fraction fast detritus in flux
NCrFdet = 0.16 , molN/molC , NC ratio fast decay detritus
NCrSdet = 0.13 , molN/molC , NC ratio slow decay detritus
PCrFdet = 9.75e-03 , molP/molC , PC ratio fast decay det.
PCrSdet = 9.75e-03 , molP/molC , PC ratio slow decay det.
FeOH3flux = 1 , nmol/cm2/d , FeOH3 deposition rate
CaPflux = 0 , nmolP/cm2/d , deposition rate of CaP
O2bw = 300 , mmol/m3 Oxygen conc in bottom water
NO3bw = 10 , mmol/m3 Nitrate
NH3bw = 1 , mmol/m3 Ammonium
CH4bw = 0 , mmol/m3 Methane
PO4bw = 0.5 , mmol/m3 Phoshpate
DICbw = 2200 , mmol/m3 dissolved inorganic carbon
Febw = 0 , mmol/m3 dissolved iron
H2Sbw = 0 , mmol/m3 sulphide
SO4bw = 30000 , mmol/m3 sulphate
w = 0.1/365000, cm/D , advection rate
mixL = 5 , cm , the depth of bioturbation layer
biot = 1 , cm2/yr , the bioturbation rate
irr = 0 , /d , the irrigation rate
gasflux = 0 , cm/d , piston velocity for dry flats - exchange of O2 and DIC only+deposition
MPBprod = 0 , mmol/m3/d , maximal rate of picrophytobenthos production - range: 5000-5e4
kMPB = 4 , /cm , exponential decay
ksDIN = 0.01 , mmol/m3 , N limitation constant
ksPO4 = 0.001 , mmol/m3 , P limitation constant
ksDIC = 1 , mmol/m3 , C limitation constant
NH3Ads = 1.3 , - , Adsorption coeff ammonium
rnit = 20. , /d , Max nitrification rate
ksO2nitri = 1. , umolO2/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 = 1. , mmolO2/m3 , half-sat O2 inhib anoxic min
temperature = 10 , dgC - for estimation of diffusion coefficients
salinity = 35 ,
TOC0 = 0.5 , the background C concentration,
rFePadsorp = 1e-5 , /d, FeP adsorption rate
rCaPprod = 0 , /d, CaP production rate
rCaPdiss = 0 , /d, CaP dissolution rate
CPrCaP = 0.2869565 , Ca:P ratio (mol/mol) - Ca10(PO4)4.6(CO3)1.32F1.87(OH)1.45
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)
por0 = 0.9 , - surface porosity
pordeep = 0.5 , - deep porosity
porcoeff = 0.3 , cm porosity coefficient
gridtype = 1 , 1 = cartesian, 2 = cylindrical, 3 = spherical
FESDIA0D
and FESDIA1D
return the output variables of the solution as a vector or data.frame.
For dynamic runs, the output is averaged over the mean of the run.
FESDIA1D
always returns the sediment depth and the porosity as the first two columns.
Karline Soetaert
Soetaert K, PMJ Herman and JJ Middelburg, 1996a. A model of early diagenetic processes from the shelf to abyssal depths. Geochimica Cosmochimica Acta, 60(6):1019-1040.
Soetaert K, PMJ Herman and JJ Middelburg, 1996b. Dynamic response of deep-sea sediments to seasonal variation: a model. Limnol. Oceanogr. 41(8): 1651-1668.
# default parameters defparms <- FESDIAparms(as.vector = TRUE) defparms # Some runs to work with defsteady <- FESDIAsolve() defdyn <- FESDIAdyna() # altered steady-state run out <- FESDIAdyna(parms = list(Cflux = 10), CfluxForc = list(amp = 1)) cbind(default = defparms, out = FESDIAparms(out)) # grid used for outputs pm <- par(mfrow = c(2, 2)) plot(FESDIApor(out), FESDIAdepth(out), ylim = c(10,0), type = "l", ylab = "cm", xlab = "-", main = "porosity") plot(FESDIAbiot(out), FESDIAdepth(out), ylim = c(10,0), type = "l", ylab = "cm", xlab = "cm2/d", main = "bioturbation") image(out, which = "NH3", grid = FESDIAdepth(out), ylim = c(10,0), main = "NH3", mfrow = NULL, legend = TRUE, ylab = "cm") matplot.1D(out, which = "NH3", xyswap = TRUE, grid = FESDIAdepth(out), type = "l", col = "grey", ylim = c(10,0), mfrow = NULL, ylab = "cm", xlab = "mmol/m3") par(mfrow = pm)