CNPDIAparms: Functions to retrieve parameters, porosity, depth and...

In CNPDIA: Diagenetic Model with Simple Nitrogen, Carbon, Phosphorus Dynamics

Description

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

Usage

  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)

Arguments

out	an output object returned by CNPDIAsolve, MPBDIAsolve, or CNPDIAdyna, MPBDIAdyna. If NULL, CNPDIAparms or MPBDIAparms will return the default (parameter) values.
as.vector	if TRUE will return the parameter vector, else a data.frame that also contains the units.
which	if not NULL, a vector with names of the variables/parameters to return.

Details

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

Author(s)

Karline Soetaert

References

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.

Examples

# 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)

CNPDIA documentation built on April 15, 2021, 3 p.m.