diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 4bcdf36..3121b3f 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-02-29T12:32:03","documenter_version":"1.2.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-02-29T12:56:04","documenter_version":"1.2.1"}} \ No newline at end of file diff --git a/dev/Equations_Units/index.html b/dev/Equations_Units/index.html index dbe8cb2..29f62e5 100644 --- a/dev/Equations_Units/index.html +++ b/dev/Equations_Units/index.html @@ -12,4 +12,4 @@ 1 M-0.5 yr-1 = 3.16e-2 (mol m-3)^-0.5 yr-1 1 M-1 h-1 = 8.766 (mol m-3)-1 yr-1 -1 M-0.5 h-1 = 277.2 (mol m-3)^-0.5 yr-1 +1 M-0.5 h-1 = 277.2 (mol m-3)^-0.5 yr-1 diff --git a/dev/PALEOsediment_Reactions/index.html b/dev/PALEOsediment_Reactions/index.html index c06078d..634f7ba 100644 --- a/dev/PALEOsediment_Reactions/index.html +++ b/dev/PALEOsediment_Reactions/index.html @@ -1,2 +1,2 @@ -PALEOsediment Reactions · PALEOsediment Documentation
GitHub

PALEOsediment Reactions

Sediment

PALEOsediment.Sediment.SedimentTransport.ReactionSedimentTransport — Type
SedimentTransport

Sediment transport for n x 1D sediment columns.

A grid with n columns is created in a Domain sediment, bounded at the top by Domain oceanfloor and at the base by Domain sedimentfloor. Boundary cells at the sediment surface are therefore in subdomain sediment.oceanfloor.

The number of columns, and column area, water depth, accumulation rate, and porosity are set by oceanfloor Variables. Bioturbation and bioirrigation rates should be supplied on the sediment grid eg by PALEOsediment.Sediment.SedimentBioRates.ReactionSedimentBioRates.

Each component <totalname> to be transported should be defined by a source-minus-sink flux <totalname>_sms, and one or more concentration Variables with names of form <rootnameN>_conc. Solute concentration Variables are identified by attributes vphase == VP_Solute and advect == true, and are transported by diffusion, bioturbation and bioirrigation, and advection. If the totalname attribute is present, then this is used to define the appropriate <totalname>_sms flux (allowing multiple species concentrations with different transport properties or phases for a single <totalname>), otherwise <totalname> is assumed to be the same as <rootnameN>. Transport fluxes are then accumulated into <totalname>_sms. Species-specific solute diffusivities are calculated based on the attribute diffusivity_speciesname of the <rootnameN>_conc solute Variables, which should be one of the names available from PALEOaqchem.MolecularDiffusion.create_solute_diffusivity_func Similarly, solid phase concentration Variables are transported by bioturbation and advection, and identified by attribute vphase == VP_Solid and advect == true.

Oceanfloor solute fluxes should be defined in the Domain fluxOceanfloor, with names fluxOceanfloor.soluteflux_<totalname>. Input particulate fluxes should be added by the fluxOceanfloor flux coupler to the surface sediment cells by linking to Variables in the sediment.oceanfloor subdomain, ie to sediment.oceanfloor.<totalname>_sms.

Burial fluxes are the base of the sediment columns are defined in the Domain fluxOceanBurial.

Parameters

  • L[Float64]=0.15 (m), default_value=0.15, description="depth of sediment column"
  • ncellspercol[Int64]=60, default_value=60, description="number of cells per column"
  • f_grid[String]="linear", default_value="linear", allowed_values=["linear", "quadratic"], description="vertical grid transformation"
  • grid_eta[Float64]=NaN (m), default_value=NaN, description="length scale for vertical grid transformation"
  • f_porosity[String]="Const", default_value="Const", allowed_values=["Const", "ExpAtten"], description="functional form for porosity vs depth"
  • zpor[Float64]=0.1 (m), default_value=0.1, description="lengthscale for porosity if f_porosity=ExpAtten"
  • zdbl[Float64]=0.0004 (m), default_value=0.0004, description="diffusive boundary layer thickness at sediment - water column interface"
  • w_solute[Bool]=false, default_value=false, description="true to assume w_solute = w_solid at base of column, false to set w_solute=0.0 (ie zero solute velocity at great depth)"

Methods and Variables for default Parameters

  • do_sediment_phys
    • volume (m^3), VT_ReactDependency, description="volume of sediment cells"
    • volume_total (m^3), VT_ReactDependency, description="total volume of sediment cells"
    • Abox (m^2), VT_ReactDependency, description="horizontal area of box"
    • zupper (m), VT_ReactDependency, description="depth of upper surface of box (m) 0 is surface, -100 is depth of 100 m"
    • zlower (m), VT_ReactDependency, description="depth of lower surface of box (m)"
    • zmid (m), VT_ReactDependency, description="mean depth of box"
    • pressure (dbar), VT_ReactDependency, description="sediment pressure"
    • rho_ref (kg m^-3), VT_ReactDependency, description="density conversion factor"
    • oceanfloor_Afloor –> oceanfloor.Afloor (m^2), VT_ReactDependency, description="horizontal area of seafloor at sediment surface"
    • oceanfloor_zfloor –> oceanfloor.zfloor (m), VT_ReactDependency, description="depth of ocean floor (m, -ve)"
    • oceanfloor_temp –> oceanfloor.temp (K), VT_ReactDependency, description="oceanfloor temperature"
    • oceanfloor_sal –> oceanfloor.sal (psu), VT_ReactDependency, description="oceanfloor salinity"
    • oceanfloor_phi –> oceanfloor.phi (), VT_ReactDependency, description="sediment surface porosity"
    • [oceanfloor_phimin] –> oceanfloor.phimin (), VT_ReactDependency, description="sediment porosity at infinite depth"
    • oceanfloor_w_accum –> oceanfloor.w_accum (m yr-1), VT_ReactDependency, description="sediment accumulation rate (+ve)"
    • phi (), VT_ReactProperty, description="porosity (volume fraction of solute phase)"
    • phi_solid (), VT_ReactProperty, description="1.0 - porosity (volume fraction of solid phase)"
    • volume_solute (m^3), VT_ReactProperty, description="solute volume of sediment cells"
    • volume_solid (m^3), VT_ReactProperty, description="solid volume of sediment cells"
    • temp (Kelvin), VT_ReactProperty, description="sediment temperature"
    • sal (psu), VT_ReactProperty, description="sediment salinity"
    • w_solid (m yr-1), VT_ReactProperty, description="solid phase advection velocity (downwards is -ve)"
    • w_solute (m yr-1), VT_ReactProperty, description="solute phase advection velocity (downwards is -ve)"
    • Dfac (), VT_ReactProperty, description="tortuoisity-dependent multiplier for solute diffusivity"
source
PALEOsediment.Sediment.SedimentBioRates.ReactionSedimentBioRates — Type
ReactionSedimentBioRates

Calculate sediment bioturbation and bioirrigation rates (for use by sediment transport).

Literature compilation of functional forms for dependency on oceanfloor oxygen, Corg flux, and depth within sediment, from (Boudreau, 1996), (Archer, 2002), (Arndt et al., 2011), (Dale et al., 2015)

Parameters

  • f_bioTurbRate[String]="Prescribed", default_value="Prescribed", allowed_values=["Prescribed", "CorgArcher2002"], description="functional form for bioturbation max rate"
  • f_bioTurbDepth[String]="ConstCutoff", default_value="ConstCutoff", allowed_values=["ConstCutoff", "ErfcCutoff", "ExpCutoff"], description="functional form of bioturbation rate with depth in sediment"
  • f_bioIrrigDepth[String]="ConstCutoff", default_value="ConstCutoff", allowed_values=["ConstCutoff", "ErfcCutoff", "ExpCutoff"], description="functional form of bioirrigation rate with depth in sediment"
  • f_bioO2[String]="None", default_value="None", allowed_values=["None", "MM", "Dale2015"], description="functional form of bioturbation and bioirrigation sensitivity to oceanfloor oxygen"
  • bioO2halfmax[Float64]=0.02 (mol m-3), default_value=0.02, description="oceanfloor [O2] for 50% decrease in bioturbation/bioirrigation"
  • bioO2decreaserate[Float64]=0.012 (mol m-3), default_value=0.012, description="oceanfloor [O2] sharpness of decrease in bioturbation/bioirrigation"

Methods and Variables for default Parameters

METHODS PALEOboxes.DocStrings.Methods(:methods_do) exception: ErrorException("PALEOsediment.Sediment.SedimentBioRates.ReactionSedimentBioRates register_methods! not implemented")

source
+PALEOsediment Reactions · PALEOsediment Documentation
GitHub

PALEOsediment Reactions

Sediment

PALEOsediment.Sediment.SedimentTransport.ReactionSedimentTransport — Type
SedimentTransport

Sediment transport for n x 1D sediment columns.

A grid with n columns is created in a Domain sediment, bounded at the top by Domain oceanfloor and at the base by Domain sedimentfloor. Boundary cells at the sediment surface are therefore in subdomain sediment.oceanfloor.

The number of columns, and column area, water depth, accumulation rate, and porosity are set by oceanfloor Variables. Bioturbation and bioirrigation rates should be supplied on the sediment grid eg by PALEOsediment.Sediment.SedimentBioRates.ReactionSedimentBioRates.

Each component <totalname> to be transported should be defined by a source-minus-sink flux <totalname>_sms, and one or more concentration Variables with names of form <rootnameN>_conc. Solute concentration Variables are identified by attributes vphase == VP_Solute and advect == true, and are transported by diffusion, bioturbation and bioirrigation, and advection. If the totalname attribute is present, then this is used to define the appropriate <totalname>_sms flux (allowing multiple species concentrations with different transport properties or phases for a single <totalname>), otherwise <totalname> is assumed to be the same as <rootnameN>. Transport fluxes are then accumulated into <totalname>_sms. Species-specific solute diffusivities are calculated based on the attribute diffusivity_speciesname of the <rootnameN>_conc solute Variables, which should be one of the names available from PALEOaqchem.MolecularDiffusion.create_solute_diffusivity_func Similarly, solid phase concentration Variables are transported by bioturbation and advection, and identified by attribute vphase == VP_Solid and advect == true.

Oceanfloor solute fluxes should be defined in the Domain fluxOceanfloor, with names fluxOceanfloor.soluteflux_<totalname>. Input particulate fluxes should be added by the fluxOceanfloor flux coupler to the surface sediment cells by linking to Variables in the sediment.oceanfloor subdomain, ie to sediment.oceanfloor.<totalname>_sms.

Burial fluxes are the base of the sediment columns are defined in the Domain fluxOceanBurial.

Parameters

  • L[Float64]=0.15 (m), default_value=0.15, description="depth of sediment column"
  • ncellspercol[Int64]=60, default_value=60, description="number of cells per column"
  • f_grid[String]="linear", default_value="linear", allowed_values=["linear", "quadratic"], description="vertical grid transformation"
  • grid_eta[Float64]=NaN (m), default_value=NaN, description="length scale for vertical grid transformation"
  • f_porosity[String]="Const", default_value="Const", allowed_values=["Const", "ExpAtten"], description="functional form for porosity vs depth"
  • zpor[Float64]=0.1 (m), default_value=0.1, description="lengthscale for porosity if f_porosity=ExpAtten"
  • zdbl[Float64]=0.0004 (m), default_value=0.0004, description="diffusive boundary layer thickness at sediment - water column interface"
  • w_solute[Bool]=false, default_value=false, description="true to assume w_solute = w_solid at base of column, false to set w_solute=0.0 (ie zero solute velocity at great depth)"

Methods and Variables for default Parameters

  • do_sediment_phys
    • volume (m^3), VT_ReactDependency, description="volume of sediment cells"
    • volume_total (m^3), VT_ReactDependency, description="total volume of sediment cells"
    • Abox (m^2), VT_ReactDependency, description="horizontal area of box"
    • zupper (m), VT_ReactDependency, description="depth of upper surface of box (m) 0 is surface, -100 is depth of 100 m"
    • zlower (m), VT_ReactDependency, description="depth of lower surface of box (m)"
    • zmid (m), VT_ReactDependency, description="mean depth of box"
    • pressure (dbar), VT_ReactDependency, description="sediment pressure"
    • rho_ref (kg m^-3), VT_ReactDependency, description="density conversion factor"
    • oceanfloor_Afloor –> oceanfloor.Afloor (m^2), VT_ReactDependency, description="horizontal area of seafloor at sediment surface"
    • oceanfloor_zfloor –> oceanfloor.zfloor (m), VT_ReactDependency, description="depth of ocean floor (m, -ve)"
    • oceanfloor_temp –> oceanfloor.temp (K), VT_ReactDependency, description="oceanfloor temperature"
    • oceanfloor_sal –> oceanfloor.sal (psu), VT_ReactDependency, description="oceanfloor salinity"
    • oceanfloor_phi –> oceanfloor.phi (), VT_ReactDependency, description="sediment surface porosity"
    • [oceanfloor_phimin] –> oceanfloor.phimin (), VT_ReactDependency, description="sediment porosity at infinite depth"
    • oceanfloor_w_accum –> oceanfloor.w_accum (m yr-1), VT_ReactDependency, description="sediment accumulation rate (+ve)"
    • phi (), VT_ReactProperty, description="porosity (volume fraction of solute phase)"
    • phi_solid (), VT_ReactProperty, description="1.0 - porosity (volume fraction of solid phase)"
    • volume_solute (m^3), VT_ReactProperty, description="solute volume of sediment cells"
    • volume_solid (m^3), VT_ReactProperty, description="solid volume of sediment cells"
    • temp (Kelvin), VT_ReactProperty, description="sediment temperature"
    • sal (psu), VT_ReactProperty, description="sediment salinity"
    • w_solid (m yr-1), VT_ReactProperty, description="solid phase advection velocity (downwards is -ve)"
    • w_solute (m yr-1), VT_ReactProperty, description="solute phase advection velocity (downwards is -ve)"
    • Dfac (), VT_ReactProperty, description="tortuoisity-dependent multiplier for solute diffusivity"
source
PALEOsediment.Sediment.SedimentBioRates.ReactionSedimentBioRates — Type
ReactionSedimentBioRates

Calculate sediment bioturbation and bioirrigation rates (for use by sediment transport).

Literature compilation of functional forms for dependency on oceanfloor oxygen, Corg flux, and depth within sediment, from (Boudreau, 1996), (Archer, 2002), (Arndt et al., 2011), (Dale et al., 2015)

Parameters

  • f_bioTurbRate[String]="Prescribed", default_value="Prescribed", allowed_values=["Prescribed", "CorgArcher2002"], description="functional form for bioturbation max rate"
  • f_bioTurbDepth[String]="ConstCutoff", default_value="ConstCutoff", allowed_values=["ConstCutoff", "ErfcCutoff", "ExpCutoff"], description="functional form of bioturbation rate with depth in sediment"
  • f_bioIrrigDepth[String]="ConstCutoff", default_value="ConstCutoff", allowed_values=["ConstCutoff", "ErfcCutoff", "ExpCutoff"], description="functional form of bioirrigation rate with depth in sediment"
  • f_bioO2[String]="None", default_value="None", allowed_values=["None", "MM", "Dale2015"], description="functional form of bioturbation and bioirrigation sensitivity to oceanfloor oxygen"
  • bioO2halfmax[Float64]=0.02 (mol m-3), default_value=0.02, description="oceanfloor [O2] for 50% decrease in bioturbation/bioirrigation"
  • bioO2decreaserate[Float64]=0.012 (mol m-3), default_value=0.012, description="oceanfloor [O2] sharpness of decrease in bioturbation/bioirrigation"

Methods and Variables for default Parameters

METHODS PALEOboxes.DocStrings.Methods(:methods_do) exception: ErrorException("PALEOsediment.Sediment.SedimentBioRates.ReactionSedimentBioRates register_methods! not implemented")

source
diff --git a/dev/References/index.html b/dev/References/index.html index 0bd1f92..125a682 100644 --- a/dev/References/index.html +++ b/dev/References/index.html @@ -1,2 +1,2 @@ -References · PALEOsediment Documentation
GitHub

References

+References · PALEOsediment Documentation
GitHub

References

diff --git a/dev/collated_examples/boudreau1996/README/index.html b/dev/collated_examples/boudreau1996/README/index.html index 821f70d..3ba68c1 100644 --- a/dev/collated_examples/boudreau1996/README/index.html +++ b/dev/collated_examples/boudreau1996/README/index.html @@ -1,3 +1,3 @@ Sediment Boudreau (1996) test cases · PALEOsediment Documentation
GitHub

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.

+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.

diff --git a/dev/collated_examples/ironsulphur/README/index.html b/dev/collated_examples/ironsulphur/README/index.html index a3802c0..121502c 100644 --- a/dev/collated_examples/ironsulphur/README/index.html +++ b/dev/collated_examples/ironsulphur/README/index.html @@ -1,3 +1,3 @@ Sediment iron-sulphur chemistry examples · PALEOsediment Documentation
GitHub

Sediment iron-sulphur chemistry examples

Implementation

Fe-S chemistry is implemented by three PALEO reactions ReactionFeSaq, ReactionFeSm, ReactionPyrH2S, see PALEOaqchem documentation for details

ReactionFeSaq: equilibrium chemistry of FeII, H2S, FeS system

Represents two equilibrium reactions as algebraic constraints to define primary species [Fe2++] and [HS-] in terms of:

  • total [S-II] = [HS-] + [H2S] + [FeSaq]
  • total [FeII] = [Fe++] + [FeSaq]

given a provided fixed value of [H+]

H2S        <--> H+ + HS-         eqb. const. K_H2S
-FeSaq + H+ <--> Fe++ + HS-       eqb. const K2_FeSaq

ReactionFeSm: FeS precipitation/dissolution

Represents 

[FeSaq] <--> [FeSm]

as a fast precipitation dissolution reaction

ReactionPyrH2S: Pyrite formation by the "H2S" (Berzelius) mechanism

FeSm + H2S -> FeS2pyr + H2

at rate 

R_Pyr_H2S * [FeSm] * [H2S]

Sediment configurations and experiments

NB: these are illustrative model test configurations only, and are not scientifically validated !!

Physical environment and organic matter input from PALEOexamples\src\sediment\boudreau1996\README.md, from (Boudreau, 1996) shelf and shelf/slope cases.

Fe reactions with FeHR, FeMR, FePR iron oxide phases from Dale (2015), Van Cappellen & Wang (1996), with Fe-S system with explicit treatment of FeS from Rickard and Luther (2007), Lenton & Daines (2017), van de Velde (2021).

TODO

  • not checked rate constants carefully
  • physical configuration and organic matter input is illustrative only
  • no Mn

Oxygen, sulphur, iron, with iron-sulphur interaction and pyrite, iron oxide burial

julia> include("PALEO_examples_sediment_Fe_pyr_x15.jl")

Set of 15 columns, all with same shelf environment, 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), excess Fe input:

  • Columns 1-5 with [SO4] 28 mM (high modern value), decreasing values of [O2], with bioturbation
  • Columns 6-10 with [SO4] 28 mM (high modern value), decreasing values of [O2], no bioturbation
  • Columns 11-15 with zero [O2], no bioturbation decreasing values of [SO4]

Demonstrates (cf van de Velde & Meysman (2016)):

  • Pyrite oxidation with modern [O2] and bioturbated sediment resulting in (2*FeS2)/(S reduction) of ~0.085, increases once [O2] drops below ~100 uM, cf Canfield & Farquar (2009)
  • (non bioturbated oxic sediment with modern [O2] stays mostly oxic with little S reduction hence low pyrite burial)
  • Zero oxygen (and non bioturbated) sediment shows high SR, (2*FeS2)/(S reduction) of ~0.5 hence high pyrite burial until [SO4] drops to ~100uM (down a factor of two at ~1 Mm), presumably set by the remin [SO4] dependence (inhibition below 1 mM), cf Habicht (2002)

Test case with pyrite burial

julia> include("PALEO_examples_sediment_Fe_pyr.jl")

Boudreau (1996) test cases with Corg, O2, SO4/H2S, P, Fe-S and pyrite burial. Three columns: shelf/slope, rise, rise (no bioturbation)

Test case with Fe only, no Fe-S or pyrite burial

julia> include("PALEO_examples_sediment_Fe.jl")

Boudreau (1996) test cases with Corg, O2, SO4/H2S, P, Fe, no Fe-S or pyrite Three columns: shelf/slope, rise, rise (no bioturbation)

References

  • Canfield & Farquar (2009) PNAS https://10.1073/pnas.0902037106
  • Habicht etal (2002) Science https://10.1126/science.1078265
  • Poulton & Canfield (2011) Elements https://10.2113/gselements.7.2.107
  • Rickard (2006) GCA https://10.1016/j.gca.2006.02.029
  • Rickard and Luther (2007) Chemical Reviews https://dx.doi.org/10.1021/cr0503658
  • Lenton and Daines (2017) Ann. Rev. Mar. Sci. https://dx.doi.org/10.1146/annurev-marine-010816-060521
  • van de Velde & Meysman (2016) Aquatic Geochem. https://dx.doi.org/10.1007/s10498-016-9301-7
  • van de Velde etal (2021) GMD https://dx.doi.org/10.5194/gmd-14-2713-2021
  • Dale etal (2015) GBC https://dx.doi.org/10.1002/2014GB005017
  • Van Cappellen & Wang Am J Sci (1996) https://dx.doi.org/10.2475/ajs.296.3.197
+FeSaq + H+ <--> Fe++ + HS- eqb. const K2_FeSaq

ReactionFeSm: FeS precipitation/dissolution

Represents 

[FeSaq] <--> [FeSm]

as a fast precipitation dissolution reaction

ReactionPyrH2S: Pyrite formation by the "H2S" (Berzelius) mechanism

FeSm + H2S -> FeS2pyr + H2

at rate 

R_Pyr_H2S * [FeSm] * [H2S]

Sediment configurations and experiments

NB: these are illustrative model test configurations only, and are not scientifically validated !!

Physical environment and organic matter input from PALEOexamples\src\sediment\boudreau1996\README.md, from (Boudreau, 1996) shelf and shelf/slope cases.

Fe reactions with FeHR, FeMR, FePR iron oxide phases from Dale (2015), Van Cappellen & Wang (1996), with Fe-S system with explicit treatment of FeS from Rickard and Luther (2007), Lenton & Daines (2017), van de Velde (2021).

TODO

Oxygen, sulphur, iron, with iron-sulphur interaction and pyrite, iron oxide burial

julia> include("PALEO_examples_sediment_Fe_pyr_x15.jl")

Set of 15 columns, all with same shelf environment, 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), excess Fe input:

Demonstrates (cf van de Velde & Meysman (2016)):

Test case with pyrite burial

julia> include("PALEO_examples_sediment_Fe_pyr.jl")

Boudreau (1996) test cases with Corg, O2, SO4/H2S, P, Fe-S and pyrite burial. Three columns: shelf/slope, rise, rise (no bioturbation)

Test case with Fe only, no Fe-S or pyrite burial

julia> include("PALEO_examples_sediment_Fe.jl")

Boudreau (1996) test cases with Corg, O2, SO4/H2S, P, Fe, no Fe-S or pyrite Three columns: shelf/slope, rise, rise (no bioturbation)

References

diff --git a/dev/collated_examples/transport_tests/README/index.html b/dev/collated_examples/transport_tests/README/index.html index bfb2f6a..27d757f 100644 --- a/dev/collated_examples/transport_tests/README/index.html +++ b/dev/collated_examples/transport_tests/README/index.html @@ -1,2 +1,2 @@ -Sediment transport test cases · PALEOsediment Documentation
GitHub
+Sediment transport test cases · PALEOsediment Documentation
GitHub
diff --git a/dev/index.html b/dev/index.html index 16c3e7d..86530dd 100644 --- a/dev/index.html +++ b/dev/index.html @@ -5,4 +5,4 @@ julia> Pkg.activate("..") # use the PALEOsediment/examples environment julia> include("PALEO_examples_sediment_x10.jl")

Using PALEOsediment Reactions from other models

The PALEO Reactions comprising the PALEOsediment models are available when the registered PALEOsediment package is loaded (without downloading the repository), ie

julia> Pkg.add("PALEOsediment")
-julia> import PALEOsediment
+julia> import PALEOsediment diff --git a/dev/indexpage/index.html b/dev/indexpage/index.html index 4caf3e8..577572e 100644 --- a/dev/indexpage/index.html +++ b/dev/indexpage/index.html @@ -1,2 +1,2 @@ -Index · PALEOsediment Documentation
GitHub
+Index · PALEOsediment Documentation
GitHub