ecolMod (version 1.2.2)

OMEXDIAsteady: steady-state application of the OMEXDIA diagenetic model - fortran DLL

Description

A 1-D model of Carbon, nitrogen and oxygen diagenesis in a marine sediment. The model describes six state variables, in 100 layers:

• 2 fractions of organic carbon (FDET,SDET): fast and slow decaying, solid substance
• Oxygen (O2), dissolved substance
• Nitrate (NO3), dissolved substance
• Ammonium (NH3), dissolved substance
• Oxygen demand unit (ODU), dissolved substance, as lump sum of all reduced substances other than ammonium

See Soetaert et al., 1996 for further details of the model.

This is a simplified version of the OMEXDIA model, added just to create a figure in the book. A more complete version will be published in a separate R-package that will deal with reactive transport modelling in R. The name of this package is not yet decided upon.

Usage

OMEXDIAsteady()

Value

• a list containing:
• steady
  The steady-state condition of the state variables, a vector containing steady-state concentrations of FDET(0-100), SDET(101-200), O2 (201-300), NO3 (301-400), NH3 (401-500) and ODU (501-600)
• precis
  the precision of the steady-state solution
• Solved
  a logical, TRUE when steady-state has been reached

Details

The model application just estimates the steady-state condition of the OMEXDIA model, the parameter values are such that there is almost no overlap between the oxic and anoxic zone of the sediment.

For efficiency reasons, the OMEXDIA diagenetic model was written in Fortran, and this code linked to the package.

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

N      <- 100
Depth  <- seq(0.05,by=0.1,len=100)
out    <- OMEXDIAsteady()

# Steady-state concentrations in sediment
CONC  <- out$steady

FDET  <- CONC[1:N]
SDET  <- CONC[(N+1)  :(2*N)]
O2    <- CONC[(2*N+1):(3*N)]
NO3   <- CONC[(3*N+1):(4*N)]
NH3   <- CONC[(4*N+1):(5*N)]
ODU   <- CONC[(5*N+1):(6*N)]

TOC  <- (FDET+SDET)*1200/10^9/2.5     # % organic carbon (excess)

par(mfrow=c(2,2))
plot(TOC,Depth,ylim=c(10,0),xlab="procent" ,main="TOC",
        type="l",lwd=2)
plot(O2,Depth,ylim=c(10,0),xlab="mmol/m3" ,main="O2",
        type="l",lwd=2)
plot(NO3,Depth,ylim=c(10,0),xlab="mmol/m3" ,main="NO3",
        type="l",lwd=2)
plot(NH3,Depth,ylim=c(10,0),xlab="mmol/m3" ,main="NH3",
        type="l",lwd=2)


mtext(outer=TRUE,side=3,line=-2,cex=1.5,"OMEXDIAmodel")