CNPDIAparms {CNPDIA} | R Documentation |
CNPDIAparms, CNPDIAdepth, CNPDIAdx
retrieve the parameters, sediment depths and layer thicknesses of CNPDIA model solutions.
CNPDIAbiot, CNPDIApor, CNPDIAirr
retrieve the bioturbation, porosity, and irrigation profiles of CNPDIA model solutions.
MPBDIAparms
retrieves the parameters of the MPBDIA model
CNPDIAparms(out = NULL, as.vector = FALSE, which = NULL) MPBDIAparms(out = NULL, as.vector = FALSE, which = NULL) CNPDIAdepth(out = NULL) CNPDIAgrid(out = NULL) CNPDIAdx(out = NULL) CNPDIApor(out) CNPDIAbiot(out) CNPDIAirr(out)
out |
an output object returned by CNPDIAsolve, MPBDIAsolve,
or CNPDIAdyna, MPBDIAdyna.
If |
as.vector |
if |
which |
if not |
For the CNPDIA model, the parameters and their meaning are the following (with default values):
Cflux , 5.00e+02 , nmolC/cm2/d , total organic C deposition
pFast , 9.00e-01 , - , part FDET in carbon flux
FePflux , 0.00e+00 , nmolP/cm2/d , deposition rate of FeP
CaPflux , 0.00e+00 , nmolP/cm2/d , deposition rate of CaP
rFast , 6.85e-02 , /d , decay rate FDET
rSlow , 1.37e-04 , /d , decay rate SDET
NCrFdet , 1.51e-01 , molN/molC , NC ratio FDET
NCrSdet , 1.51e-01 , molN/molC , NC ratio SDET
PCrFdet , 9.43e-03 , molP/molC , PC ratio FDET
PCrSdet , 9.43e-03 , molP/molC , PC ratio SDET
BCupLiq , 2.00e+00 , - , upper boundary liq. 1:flux, 2:conc, 3:0-grad
BCdownLiq , 3.00e+00 , - , lower boundary liq. 1:flux, 2:conc, 3:0-grad
O2bw , 3.00e+02 , mmol/m3 , upper boundary O2 -if BC=1: flux, 2:conc
NO3bw , 1.00e+01 , mmol/m3 , upper boundary NO3 -if BC=1: flux, 2:conc
NO2bw , 0.00e+00 , mmol/m3 , upper boundary NO2 -if BC=1: flux, 2:conc
NH3bw , 1.00e+00 , mmol/m3 , upper boundary NH3 -if BC=1: flux, 2:conc
ODUbw , 0.00e+00 , mmol/m3 , upper boundary ODU -if BC=1: flux, 2:conc
PO4bw , 5.00e-01 , mmol/m3 , upper boundary PO4 -if BC=1: flux, 2:conc
DICbw , 2.20e+03 , mmol/m3 , upper boundary DIC -if BC=1: flux, 2:conc
O2dw , NA , mmol/m3 , lower boundary O2 -if BC=1: flux, 2:conc
NO3dw , NA , mmol/m3 , lower boundary NO3 -if BC=1: flux, 2:conc
NO2dw , NA , mmol/m3 , lower boundary NO2 -if BC=1: flux, 2:conc
NH3dw , NA , mmol/m3 , lower boundary NH3 -if BC=1: flux, 2:conc
ODUdw , NA , mmol/m3 , lower boundary ODU -if BC=1: flux, 2:conc
PO4dw , NA , mmol/m3 , lower boundary PO4 -if BC=1: flux, 2:conc
DICdw , NA , mmol/m3 , lower boundary DIC -if BC=1: flux, 2:conc
w , 2.74e-07 , cm/d , advection rate
biot , 2.74e-03 , cm2/d , bioturbation coefficient
biotdepth , 5.00e+00 , cm , depth of mixed layer
biotatt , 1.00e+00 , cm , attenuation coeff below biotdepth
irr , 0.00e+00 , /d , bio-irrigation rate
irrdepth , 5.00e+00 , cm , depth of irrigated layer
irratt , 1.00e+00 , cm , attenuation coeff below irrdepth
gasflux , 0.00e+00 , cm/d , piston velocity for dry flats
NH3Ads , 1.30e+00 , - , Adsorption coeff ammonium
rnitri1 , 2.00e+01 , /d , Max nitrification rate step1 (NH3ox)
rnitri2 , 2.00e+01 , /d , Max nitrification rate step2 (NO2ox)
ksO2nitri , 1.00e+00 , mmolO2/m3 , half-sat O2 in nitrification
ranammox , 1.00e-01 , /d , Anammox rate
ksNO2anammox, 1.00e-01 , mmolN/m3 , half-sat NO2 in anammox
rODUox , 2.00e+01 , /d , Max rate ODU oxidation in one layer
rSurfODUox , 0.00e+00 , /d , Max rate ODU oxidation with BW O2
ODUoxdepth , 5.00e+00 , cm , Max depth ODU oxidation with BW O2
ODUoxatt , 1.00e+00 , cm , depth attenuation ODU oxidation
ksO2oduox , 1.00e+00 , mmolO2/m3 , half-sat O2 in oxidation of ODU
ksO2oxic , 3.00e+00 , mmolO2/m3 , half-sat O2 in oxic mineralisation
ksNO3denit , 3.00e+01 , mmolNO3/m3 , half-sat NO3 in denitrification
kinO2denit , 1.00e+00 , mmolO2/m3 , half-sat O2 inhib denitrification
kinNO3anox , 1.00e+00 , mmolNO3/m3 , half-sat NO3 inhib anoxic degr
kinO2anox , 1.00e+00 , mmolO2/m3 , half-sat O2 inhib anoxic min
pdepo , NA , - , part ODU prod lost (NA:estimated from w)
rdepo , 0.00e+00 , /d , ODU removal rate
temperature , 1.00e+01 , dgC , temperature
salinity , 3.50e+01 , psu , salinity
TOC0 , 5.00e-01 ,
rFePdesorp , 1.00e-02 , /d , rate FeP desorption
rFePadsorp , 3.00e-01 , /d , rate FeP adsorption
rCaPprod , 0.00e+00 , /d , rate CaP production
rCaPdiss , 0.00e+00 , /d , rate CaP dissolution
CPrCaP , 2.87e-01 , molC/molP , C:Pratio in CaP
rPads , 0.00e+00 , /d , adsorption rate PO4
rPdes , 0.00e+00 , /d , desorption rate of adsorbed P
maxPads , 1.00e+03 ,mmolP/m3solid , Max adsorbed P concentration
por0 , 9.00e-01 , - , surface porosity
pordeep , 5.00e-01 , - , deep porosity
porcoeff , 3.00e-01 , cm , porosity decay coefficient
formationtype, 1.00e+00 , - , formationfactor, 1=sand,2=fine sand,3=general
dilution , 0.00e+00 , /d , relaxation towards background conc
Hwater , 1.00e+01 , cm , height of water over core
Cfall , 1.00e+02 , cm/d , fall speed of organic C (FDET, SDET)
FePfall , 1.00e+02 , cm/d , fall speed of FeP
CaPfall , 1.00e+02 , cm/d , fall speed of CaP
MPBprod , 0.00e+00 , mmol/m3/d , maximal MPB production rate
kdSed , 2.00e+01 , /cm , light extinction coefficient
kNO3upt , 3.00e+00 , mmolN/m3 , NO3 limitation constant MPB
kNH3upt , 3.00e+00 , mmolN/m3 , NH3 limitation constant MPB
kPO4upt , 1.00e-01 , mmolP/m3 , P limitation constant MPB
kDICupt , 1.00e+00 , mmolC/m3 , C limitation constant MPB
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.
# defaults defparms <- CNPDIAparms(as.vector = TRUE) defparms # a run to work with defsteady <- CNPDIAsolve() defdyn <- CNPDIAdyna() out <- CNPDIAdyna(parms = list(Cflux = 1000), CfluxForc = list(amp = 0.8)) # grid used for outputs pm <- par(mfrow = c(2, 2)) plot(CNPDIApor(out), CNPDIAdepth(out), ylim = c(10,0), type = "l", ylab = "cm", xlab = "-", main = "porosity") plot(CNPDIAbiot(out), CNPDIAdepth(out), ylim = c(10,0), type = "l", ylab = "cm", xlab = "cm2/d", main = "bioturbation") image(out, which = "NH3", grid = CNPDIAdepth(out), ylim = c(10,0), main = "NH3", mfrow = NULL, legend = TRUE, ylab = "cm", clab = "mmol/m3") matplot.1D(out, which = "NH3", xyswap = TRUE, grid = CNPDIAdepth(out), type = "l", col = "grey", ylim = c(10,0), mfrow = NULL, ylab = "cm", xlab = "mmol/m3") par(mfrow = pm)