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Sediment Boudreau (1996) test cases

To run sediment test cases from (Boudreau, 1996), assuming the Julia environment PALEOsediment/examples has already been activated:

julia> cd("examples/boundreau1996")
julia> include("PALEO_examples_sediment.jl")

This will run and plot output (NB: the first run will be slow as Julia JIT compiles the code).

The configuration includes three sediment columns, with:

  1. Shelf / slope case
  2. Rise case
  3. Rise, no bioturbation

NB: this configuration doesn't include N, so results differ in detail from the paper.

Oceanfloor [O2] and [SO4] gradients

julia> include("PALEO_examples_sediment_x10.jl")

The configuration includes ten sediment columns, with the physical environment for the (Boudreau, 1996) shelf/slope case, no bioturbation, and Corg input with two reactivity fractions (a combination of the high-reactivity fraction from the shelf/slope case, and the low reactivity fraction from the rise case).

  1. Columns 1-5: oceanfloor [O2] gradient, constant [SO4] = 28mM
  2. Columns 6-10: oceanfloor [SO4] gradient, at constant [O2] = 0

Summary plots show oceanfloor solute fluxes and remineralization pathways:

O2 and SO4 gradient summary figure

Figure 1

Oceanfloor solute fluxes and remineralization pathways vs oceanfloor [O2] and [SO4] concentration

Sulphur isotope example

julia> include("PALEO_examples_sediment_Sisotopes.jl")

Three sediment column example as PALEO_examples_sediment.jl, with sulphur isotopes enabled and low (1 mM) oceanfloor [SO4] to illustrate Rayleigh fractionation within the sediment column as [SO4] becomes limiting.

Carbonate chemistry example

julia> include("PALEO_examples_sediment_carb.jl")

Three sediment column example as PALEO_examples_sediment.jl, with carbonate chemistry.

NB: POC includes C, P only (no N) to simplify TAlk conservation check (where soluteflux_TAlk = 2*soluteflux_H2S)

julia> PALEOmodel.get_array(paleorun.output, "fluxOceanfloor.soluteflux_TAlk", (cell=1, tmodel=1e12)).values
0.014436958064622729

julia> PALEOmodel.get_array(paleorun.output, "fluxOceanfloor.soluteflux_H2S", (cell=1, tmodel=1e12)).values
0.007218479032309767

julia> PALEOmodel.get_array(paleorun.output, "fluxOceanfloor.soluteflux_SO4", (cell=1, tmodel=1e12)).values
-0.0072184790322306815