diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 7dda31d..1df935d 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-12-17T09:55:25","documenter_version":"1.8.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-12-22T18:31:57","documenter_version":"1.8.0"}} \ No newline at end of file diff --git a/dev/Carbonate chemistry/index.html b/dev/Carbonate chemistry/index.html index b35b2dc..8971403 100644 --- a/dev/Carbonate chemistry/index.html +++ b/dev/Carbonate chemistry/index.html @@ -1,5 +1,5 @@ -Carbonate chemistry · PALEOaqchem Documentation
GitHub

Carbonate chemistry

Marine carbonate chemistry is implemented by the PALEO CarbChem.ReactionCO2SYS which uses an implementation provided by the PALEOcarbchem module.

PALEOaqchem.CarbChem.ReactionCO2SYS — Type
ReactionCO2SYS

Carbonate chemistry using PALEOcarbchem.

Two different pH solver approaches are supported, set by Parameter solve_pH:

  • solve: iterative solution for pH using an internal Newton solver, at given TAlk (eg TAlk is a StateExplicit Variable, using explicit ODE solver)
  • speciation: calculate speciation given pHfree.
  • speciationTAlk: calculate speciation given pHfree, also add alkalinity contributions to TAlk_calc (eg for use in combination with a ReactionConstraintReservoir that provides a total variable TAlk and H (as pHfree) as a primary species, for use with a DAE solver to solve the algebraic constraint for pHfree at a given TAlk).

NB: Two options have been removed from Parameter solve_pH:

  • constraint: additional State Variable for pH and algebraic Constraint for TAlk (requires DAE solver). [replace with speciationTAlk and a ReactionConstraintReservoir]
  • implicit: TAlk is a Total Variable, a function of a State Variable for pH (requires DAE solver) [replace with speciationTAlk and a ReactionImplicitReservoir]

Parameters

  • WhichKs[Int64]=10, default_value=10, description="PALEOcarbchem WhichKs choice of eqb constant data"
  • WhoseKSO4[Int64]=1, default_value=1, description="PALEOcarbchem WhoseKSO4 choice of eqb constant data"
  • components[Vector{String}]=["Ci", "S", "F", "B", "Omega"], default_value=["Ci", "S", "F", "B", "Omega"], allowed_values=["Ci", "S", "F", "P", "B", "Si", "H2S", "NH3", "Omega"], description="PALEOcarbchem optional contributions to TAlk"
  • defaultconcs[Vector{String}]=["TS", "TF", "TB", "Ca"], default_value=["TS", "TF", "TB", "Ca"], allowed_values=["TS", "TF", "TB", "Ca"], description="PALEOcarbchem default concentrations (modern values calculated from salinity)"
  • outputs[Vector{String}]=["pCO2", "xCO2dryinp"], default_value=["pCO2", "xCO2dryinp"], allowed_values=["H", "OH", "TS", "HSO4", "TF", "HF", "TCi", "CO2", "HCO3", "CO3", "CAlk", "fCO2", "pCO2", "xCO2dryinp", "TB", "BAlk", "TP", "H3PO4", "H2PO4", "HPO4", "PO4", "PAlk", "TSi", "SiAlk", "TH2S", "H2S", "HSAlk", "TNH3", "NH4", "NH3Alk", "Ca", "OmegaCA", "OmegaAR"], description="PALEOcarbchem output concentrations etc to include as output variables"
  • output_pHtot[Bool]=true, default_value=true, description="true to output pHtot (requires TS_conc and TF_conc)"
  • solve_pH[String]="solve", default_value="solve", allowed_values=["solve", "speciation", "speciationTAlk"], description="'solve' to solve iteratively for pH, 'speciation' to just provide speciation at supplied [pHfree], 'speciationTAlk' to provide speciation and add to TAlk_calc"
  • pHtol[Float64]=2.220446049250313e-14, default_value=2.220446049250313e-14, description="with parameter solve_pH=solve only (internal Newton solver): pH tolerance for iterative solution"
  • simd_width[String]="1", default_value="1", allowed_values=["1", "FP64P2", "FP64P4", "FP32P4", "FP32P8"], description="with parameter solve_pH=solve only (internal Newton solver): use SIMD ("1" - no SIMD, "FP64P4" - 4 x Float64, etc)"

Methods and Variables for default Parameters

  • do_modern_default_concs
    • volume (m^3), VT_ReactDependency, description="Cell volume"
    • rho_ref (kg m^-3), VT_ReactDependency, description="density conversion factor"
    • temp (K), VT_ReactDependency, description="temperature"
    • pressure (dbar), VT_ReactDependency, description="pressure"
    • sal (psu), VT_ReactDependency, description="salinity"
    • TS_conc (mol m^-3), VT_ReactProperty, description="TS_conc modern default scaled from salinity"
    • TF_conc (mol m^-3), VT_ReactProperty, description="TF_conc modern default scaled from salinity"
    • TB_conc (mol m^-3), VT_ReactProperty, description="TB_conc modern default scaled from salinity"
    • Ca_conc (mol m^-3), VT_ReactProperty, description="Ca_conc modern default scaled from salinity"
  • do_carbchem
    • volume (m^3), VT_ReactDependency, description="Cell volume"
    • rho_ref (kg m^-3), VT_ReactDependency, description="density conversion factor"
    • temp (K), VT_ReactDependency, description="temperature"
    • pressure (dbar), VT_ReactDependency, description="pressure"
    • sal (psu), VT_ReactDependency, description="salinity"
    • pHfree (), VT_ReactProperty, description="-log10(hydrogen ion concentration), this is used to keep previous value as a starting value for internal Newton solver"
    • TAlk_conc (mol m^-3), VT_ReactDependency, description="total TAlk concentration"
    • pHtot (), VT_ReactProperty, description="-log10([H] + [HS]), pH on total scale"
    • TCi_conc (mol m^-3), VT_ReactDependency, description="TCi_concinput concentration"
    • TS_conc (mol m^-3), VT_ReactDependency, description="TS_concinput concentration"
    • TF_conc (mol m^-3), VT_ReactDependency, description="TF_concinput concentration"
    • TB_conc (mol m^-3), VT_ReactDependency, description="TB_concinput concentration"
    • Ca_conc (mol m^-3), VT_ReactDependency, description="Ca_concinput concentration"
    • pCO2 –> %reaction%pCO2 (atm), VT_ReactProperty, description="CO2 partial pressure (fugacity corrected)"
    • xCO2dryinp –> %reaction%xCO2dryinp (), VT_ReactProperty, description="mixing ratio of CO2 in dry air at 1 atm (always > pCO2 due to H2O vapour pressure)"
source

PALEOcarbchem

PALEOaqchem.PALEOcarbchem — Module
PALEOcarbchem

Carbonate chemistry equilibrium translated from Matlab CO2SYS v1.1 (van Heuven et al., 2011), (Lewis and Wallace, 1998) and refactored for speed.

Implementation based on CO2SYS constants, with reimplemented equilibrium calculation.

NB:

require constants to be on the free pH scale.

  • Effective equilibrium constants are empirical measurements hence are only accurate for modern seawater composition.

Example usage with default choice of constants, all components enabled:

julia> PALEOcarbchem.ComponentsAllStrings  # all available components
+Carbonate chemistry · PALEOaqchem Documentation
GitHub
Carbonate chemistry
Marine carbonate chemistry is implemented by the PALEO CarbChem.ReactionCO2SYS which uses an implementation provided by the PALEOcarbchem module.
PALEOaqchem.CarbChem.ReactionCO2SYS — Type
ReactionCO2SYS
Carbonate chemistry using PALEOcarbchem.
Two different pH solver approaches are supported, set by Parameter solve_pH:
  • solve: iterative solution for pH using an internal Newton solver, at given TAlk (eg TAlk is a StateExplicit Variable, using explicit ODE solver)
  • speciation: calculate speciation given pHfree.
  • speciationTAlk: calculate speciation given pHfree, also add alkalinity contributions to TAlk_calc (eg for use in combination with a ReactionConstraintReservoir that provides a total variable TAlk and H (as pHfree) as a primary species, for use with a DAE solver to solve the algebraic constraint for pHfree at a given TAlk).
NB: Two options have been removed from Parameter solve_pH:
  • constraint: additional State Variable for pH and algebraic Constraint for TAlk (requires DAE solver). [replace with speciationTAlk and a ReactionConstraintReservoir]
  • implicit: TAlk is a Total Variable, a function of a State Variable for pH (requires DAE solver) [replace with speciationTAlk and a ReactionImplicitReservoir]
Parameters
  • WhichKs[Int64]=10, default_value=10, description="PALEOcarbchem WhichKs choice of eqb constant data"
  • WhoseKSO4[Int64]=1, default_value=1, description="PALEOcarbchem WhoseKSO4 choice of eqb constant data"
  • components[Vector{String}]=["Ci", "S", "F", "B", "Omega"], default_value=["Ci", "S", "F", "B", "Omega"], allowed_values=["Ci", "S", "F", "P", "B", "Si", "H2S", "NH3", "Omega"], description="PALEOcarbchem optional contributions to TAlk"
  • defaultconcs[Vector{String}]=["TS", "TF", "TB", "Ca"], default_value=["TS", "TF", "TB", "Ca"], allowed_values=["TS", "TF", "TB", "Ca"], description="PALEOcarbchem default concentrations (modern values calculated from salinity)"
  • outputs[Vector{String}]=["pCO2", "xCO2dryinp"], default_value=["pCO2", "xCO2dryinp"], allowed_values=["H", "OH", "TS", "HSO4", "TF", "HF", "TCi", "CO2", "HCO3", "CO3", "CAlk", "fCO2", "pCO2", "xCO2dryinp", "TB", "BAlk", "TP", "H3PO4", "H2PO4", "HPO4", "PO4", "PAlk", "TSi", "SiAlk", "TH2S", "H2S", "HSAlk", "TNH3", "NH4", "NH3Alk", "Ca", "OmegaCA", "OmegaAR"], description="PALEOcarbchem output concentrations etc to include as output variables"
  • output_pHtot[Bool]=true, default_value=true, description="true to output pHtot (requires TS_conc and TF_conc)"
  • solve_pH[String]="solve", default_value="solve", allowed_values=["solve", "speciation", "speciationTAlk"], description="'solve' to solve iteratively for pH, 'speciation' to just provide speciation at supplied [pHfree], 'speciationTAlk' to provide speciation and add to TAlk_calc"
  • pHtol[Float64]=2.220446049250313e-14, default_value=2.220446049250313e-14, description="with parameter solve_pH=solve only (internal Newton solver): pH tolerance for iterative solution"
  • simd_width[String]="1", default_value="1", allowed_values=["1", "FP64P2", "FP64P4", "FP32P4", "FP32P8"], description="with parameter solve_pH=solve only (internal Newton solver): use SIMD ("1" - no SIMD, "FP64P4" - 4 x Float64, etc)"
Methods and Variables for default Parameters
  • do_modern_default_concs
    • volume  (m^3), VT_ReactDependency, description="Cell volume"
    • rho_ref  (kg m^-3), VT_ReactDependency, description="density conversion factor"
    • temp  (K), VT_ReactDependency, description="temperature"
    • pressure  (dbar), VT_ReactDependency, description="pressure"
    • sal  (psu), VT_ReactDependency, description="salinity"
    • TS_conc  (mol m^-3), VT_ReactProperty, description="TS_conc modern default scaled from salinity"
    • TF_conc  (mol m^-3), VT_ReactProperty, description="TF_conc modern default scaled from salinity"
    • TB_conc  (mol m^-3), VT_ReactProperty, description="TB_conc modern default scaled from salinity"
    • Ca_conc  (mol m^-3), VT_ReactProperty, description="Ca_conc modern default scaled from salinity"
  • do_carbchem
    • volume  (m^3), VT_ReactDependency, description="Cell volume"
    • rho_ref  (kg m^-3), VT_ReactDependency, description="density conversion factor"
    • temp  (K), VT_ReactDependency, description="temperature"
    • pressure  (dbar), VT_ReactDependency, description="pressure"
    • sal  (psu), VT_ReactDependency, description="salinity"
    • pHfree  (), VT_ReactProperty, description="-log10(hydrogen ion concentration), this is used to keep previous value as a starting value for internal Newton solver"
    • TAlk_conc  (mol m^-3), VT_ReactDependency, description="total TAlk concentration"
    • pHtot  (), VT_ReactProperty, description="-log10([H] + [HS]), pH on total scale"
    • TCi_conc  (mol m^-3), VT_ReactDependency, description="TCi_concinput concentration"
    • TS_conc  (mol m^-3), VT_ReactDependency, description="TS_concinput concentration"
    • TF_conc  (mol m^-3), VT_ReactDependency, description="TF_concinput concentration"
    • TB_conc  (mol m^-3), VT_ReactDependency, description="TB_concinput concentration"
    • Ca_conc  (mol m^-3), VT_ReactDependency, description="Ca_concinput concentration"
    • pCO2 –> %reaction%pCO2  (atm), VT_ReactProperty, description="CO2 partial pressure (fugacity corrected)"
    • xCO2dryinp –> %reaction%xCO2dryinp  (), VT_ReactProperty, description="mixing ratio of CO2 in dry air at 1 atm (always > pCO2 due to H2O vapour pressure)"
source
PALEOcarbchem
PALEOaqchem.PALEOcarbchem — Module
PALEOcarbchem
Carbonate chemistry equilibrium translated from Matlab CO2SYS v1.1 (van Heuven et al., 2011), (Lewis and Wallace, 1998) and refactored for speed.
Implementation based on CO2SYS constants, with reimplemented equilibrium calculation.
NB: 
require constants to be on the free pH scale.
  • Effective equilibrium constants are empirical measurements hence are only accurate for modern seawater composition.
Example usage with default choice of constants, all components enabled:
julia> PALEOcarbchem.ComponentsAllStrings  # all available components
 ("Ci", "S", "F", "B", "P", "Si", "H2S", "NH3", "Omega")
 
 julia> comps, concinputs = PALEOcarbchem.get_components_inputs(["Ci", "S", "F", "B", "P", "Si", "H2S", "NH3", "Omega"])
@@ -45,12 +45,12 @@
 julia> pHtot = PALEOcarbchem.mappHscale(C, pHfree, Val(3), Val(1), res_NT.TS, res_NT.TF);
 
 julia> @printf("%.14f", pHtot)
-7.94544626702045
source
Inputs and equilibrium constants
Inputs and equilibrium constants
PALEOaqchem.PALEOcarbchem.ComponentsAll — Constant
ComponentsAll::NamedTuple
 ComponentsAllStrings::Vector{String}
All available components
julia> PALEOcarbchem.ComponentsAll
 (Ci = Val{true}(), S = Val{true}(), F = Val{true}(), B = Val{true}(), P = Val{true}(), Si = Val{true}(), H2S = Val{true}(), NH3 = Val{true}(), Omega = Val{true}())
 
 julia> PALEOcarbchem.ComponentsAllStrings  # all available components
-("Ci", "S", "F", "B", "P", "Si", "H2S", "NH3", "Omega")
source
PALEOaqchem.PALEOcarbchem.get_components_inputs — Function
get_components_inputs(compstoenable) -> (components::NamedTuple, concinputs::Vector{String})
Returns components and concinputs required for specified compstoenable
compstoenable is a list (Vector or Tuple) with component names as Strings, eg ["Ci", "B", "Si"] 
Returns:
  • a NamedTuple components with those components present in compstoenable as Val{true} and others as Val{false}
  • a Vector concinputs of input concentrations required (P requires TP etc).
Examples
All components:
julia> compsall, concinputsall = PALEOcarbchem.get_components_inputs(["Ci", "S", "F", "B", "P", "Si", "H2S", "NH3", "Omega"])
+("Ci", "S", "F", "B", "P", "Si", "H2S", "NH3", "Omega")
source
PALEOaqchem.PALEOcarbchem.get_components_inputs — Function
get_components_inputs(compstoenable) -> (components::NamedTuple, concinputs::Vector{String})
Returns components and concinputs required for specified compstoenable
compstoenable is a list (Vector or Tuple) with component names as Strings, eg ["Ci", "B", "Si"] 
Returns:
  • a NamedTuple components with those components present in compstoenable as Val{true} and others as Val{false}
  • a Vector concinputs of input concentrations required (P requires TP etc).
Examples
All components:
julia> compsall, concinputsall = PALEOcarbchem.get_components_inputs(["Ci", "S", "F", "B", "P", "Si", "H2S", "NH3", "Omega"])
 ((Ci = Val{true}(), S = Val{true}(), F = Val{true}(), B = Val{true}(), P = Val{true}(), Si = Val{true}(), H2S = Val{true}(), NH3 = Val{true}(), Omega = Val{true}()), ["TCi", "TS", "TF", "TB", "TP", "TSi", "TH2S", "TNH3", "Ca"])
 
 julia> compsall
@@ -61,7 +61,7 @@
 ((Ci = Val{false}(), S = Val{false}(), F = Val{false}(), B = Val{false}(), P = Val{false}(), Si = Val{false}(), H2S = Val{false}(), NH3 = Val{false}(), Omega = Val{false}()), String[])
 
 julia> println(concinputsminimal)
-String[]
source
PALEOaqchem.PALEOcarbchem.calc_constants! — Function
calc_constants!(
     Cout, TempC_input, Pdbar, Sal_input; 
     Options=(; WhichKs=Val(10), WhoseKSO4=Val(1), pHScale=Val(3), Components=ComponentsAll))
Calculate carbonate chemistry constants, results are returned in Cout.
Arguments:
  • Cout::Vector:  (output) Vector of length length(ConstNames) with calculated equilibrium constants
  • TempC_input:  temperature deg C. Will be limited to valid range for constants in use (from calc_limits)
  • Pdbar:  pressure, dbar. 
  • Sal_input:      salinity.   Will be limited to valid range for constants in use (from calc_limits)
  • Options: NamedTuple with fields:
WhichKs:
K1 K2 dissociation constants that are to be used. Val(Int) where Int is:
  • 1 = Roy, 1993											T:    0-45  S:  5-45. Total scale. Artificial seawater.
  • 2 = Goyet & Poisson										T:   -1-40  S: 10-50. Seaw. scale. Artificial seawater.
  • 3 = HANSSON              refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 4 = MEHRBACH             refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 5 = HANSSON and MEHRBACH refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 6 = GEOSECS (i.e., original Mehrbach)					T:    2-35  S: 19-43. NBS scale.   Real seawater.
  • 7 = Peng	(i.e., originam Mehrbach but without XXX)	T:    2-35  S: 19-43. NBS scale.   Real seawater.
  • 8 = Millero, 1979, FOR PURE WATER ONLY (i.e., Sal=0)	T:    0-50  S:     0.
  • 9 = Cai and Wang, 1998									T:    2-35  S:  0-49. NBS scale.   Real and artificial seawater.
  • 10 = Lueker et al, 2000									T:    2-35  S: 19-43. Total scale. Real seawater.
  • 11 = Mojica Prieto and Millero, 2002.					T:    0-45  S:  5-42. Seaw. scale. Real seawater
  • 12 = Millero et al, 2002									T: -1.6-35  S: 34-37. Seaw. scale. Field measurements.
  • 13 = Millero et al, 2006									T:    0-50  S:  1-50. Seaw. scale. Real seawater.
  • 14 = Millero et al, 2010									T:    0-50  S:  1-50. Seaw. scale. Real seawater.
WhichKs=Val(10) (Lueker etal (2000) parameters.)
Recommended as 'best practice' by Dickson (2007)  (as cited in Orr, J. C., Epitalon, J-M., & Gattuso, J-P. (2014).  Comparison of seven packages that compute ocean carbonate chemistry.  Biogeosciences Discussions, 11(4), 5327�5397. doi:10.5194/bgd-11-5327-2014 )
WhoseKSO4:
KSO4 dissociation constants that are to be used, in combination with the formulation of the borate-to-salinity ratio to be used. Having both these choices in a single argument is somewhat awkward, but it maintains syntax compatibility with the previous version. Val(Int) where Int is:
  • 1 = KSO4 of Dickson & TB of Uppstrom 1979  (PREFERRED)
  • 2 = KSO4 of Khoo    & TB of Uppstrom 1979
  • 3 = KSO4 of Dickson & TB of Lee 2010
  • 4 = KSO4 of Khoo    & TB of Lee 2010
pHScale: Set pH scale.
Val(Int) where Int is:
  • 1 = Total scale
  • 2 = Seawater scale
  • 3 = Free scale   [required for PALEOcarbchem solvers]
  • 4 = NBS scale
Implementation
Modified CO2SYS Constants, split into functions for maintainability
Comments from the original code:
% SUB Constants, version 04.01, 10-13-97, written by Ernie Lewis.
 % Inputs: pHScale%, WhichKs%, WhoseKSO4%, Sali, TempCi, Pdbar
@@ -80,7 +80,7 @@
 %       PROGRAMMER'S NOTE: all Constants are converted to the pH scale
 %               pHScale% (the chosen one) in units of mol/kg-SW
 %               except KS and KF are on the free scale
-%               and KW is in units of (mol/kg-SW)^2
Julia-specific details:
WhichKs, WhoseKSO4, pHScale are passed as Types (using Val(Int)), not integer values, so that Julia can work out which constants and functions to call at compile time. Similarly, Comps is a Type which encodes the selection of components, so the appropriate code is generated (components included or excluded) at compile time.
source
PALEOaqchem.PALEOcarbchem.calc_limits — Function
calc_limits( Val{WhichKs::Int}) -> (TminC, TmaxC, salmin, salmax)
Return range limits for  constant set WhichKs:
  • 1 = Roy, 1993											T:    0-45  S:  5-45. Total scale. Artificial seawater.
  • 2 = Goyet & Poisson										T:   -1-40  S: 10-50. Seaw. scale. Artificial seawater.
  • 3 = HANSSON              refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 4 = MEHRBACH             refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 5 = HANSSON and MEHRBACH refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 6 = GEOSECS (i.e., original Mehrbach)					T:    2-35  S: 19-43. NBS scale.   Real seawater.
  • 7 = Peng	(i.e., originam Mehrbach but without XXX)	T:    2-35  S: 19-43. NBS scale.   Real seawater.
  • 8 = Millero, 1979, FOR PURE WATER ONLY (i.e., Sal=0)	T:    0-50  S:     0.
  • 9 = Cai and Wang, 1998									T:    2-35  S:  0-49. NBS scale.   Real and artificial seawater.
  • 10 = Lueker et al, 2000									T:    2-35  S: 19-43. Total scale. Real seawater.
  • 11 = Mojica Prieto and Millero, 2002.					T:    0-45  S:  5-42. Seaw. scale. Real seawater
  • 12 = Millero et al, 2002									T: -1.6-35  S: 34-37. Seaw. scale. Field measurements.
  • 13 = Millero et al, 2006									T:    0-50  S:  1-50. Seaw. scale. Real seawater.
  • 14 = Millero et al, 2010									T:    0-50  S:  1-50. Seaw. scale. Real seawater.
source
PALEOaqchem.PALEOcarbchem.calc_modern_default_concs — Function
calc_modern_default_concs(Sal_input, Options=(; WhichKs=Val(10), WhoseKSO4=Val(1)) -> (; TF, TS, TB, Ca)
Calculate modern seawater default concentrations as a function of salinity Sal_input
See calc_constants! for documentation for Options.
Returns
- TF: (mol kg-1) Total Fluorine modern value from salinity
+%               and KW is in units of (mol/kg-SW)^2
Julia-specific details:
WhichKs, WhoseKSO4, pHScale are passed as Types (using Val(Int)), not integer values, so that Julia can work out which constants and functions to call at compile time. Similarly, Comps is a Type which encodes the selection of components, so the appropriate code is generated (components included or excluded) at compile time.
source
PALEOaqchem.PALEOcarbchem.calc_limits — Function
calc_limits( Val{WhichKs::Int}) -> (TminC, TmaxC, salmin, salmax)
Return range limits for  constant set WhichKs:
  • 1 = Roy, 1993											T:    0-45  S:  5-45. Total scale. Artificial seawater.
  • 2 = Goyet & Poisson										T:   -1-40  S: 10-50. Seaw. scale. Artificial seawater.
  • 3 = HANSSON              refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 4 = MEHRBACH             refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 5 = HANSSON and MEHRBACH refit BY DICKSON AND MILLERO	T:    2-35  S: 20-40. Seaw. scale. Artificial seawater.
  • 6 = GEOSECS (i.e., original Mehrbach)					T:    2-35  S: 19-43. NBS scale.   Real seawater.
  • 7 = Peng	(i.e., originam Mehrbach but without XXX)	T:    2-35  S: 19-43. NBS scale.   Real seawater.
  • 8 = Millero, 1979, FOR PURE WATER ONLY (i.e., Sal=0)	T:    0-50  S:     0.
  • 9 = Cai and Wang, 1998									T:    2-35  S:  0-49. NBS scale.   Real and artificial seawater.
  • 10 = Lueker et al, 2000									T:    2-35  S: 19-43. Total scale. Real seawater.
  • 11 = Mojica Prieto and Millero, 2002.					T:    0-45  S:  5-42. Seaw. scale. Real seawater
  • 12 = Millero et al, 2002									T: -1.6-35  S: 34-37. Seaw. scale. Field measurements.
  • 13 = Millero et al, 2006									T:    0-50  S:  1-50. Seaw. scale. Real seawater.
  • 14 = Millero et al, 2010									T:    0-50  S:  1-50. Seaw. scale. Real seawater.
source
PALEOaqchem.PALEOcarbchem.calc_modern_default_concs — Function
calc_modern_default_concs(Sal_input, Options=(; WhichKs=Val(10), WhoseKSO4=Val(1)) -> (; TF, TS, TB, Ca)
Calculate modern seawater default concentrations as a function of salinity Sal_input
See calc_constants! for documentation for Options.
Returns
- TF: (mol kg-1) Total Fluorine modern value from salinity
 - TS: (mol kg-1) Total Sulphate modern value from salinity
 - TB: (mol kg-1) Total Boron modern value from salinity
 - Ca: (mol kg-1) Ca modern value from salinity
Example
julia> options = (; WhichKs=Val(10), WhoseKSO4=Val(1));
@@ -88,7 +88,7 @@
 julia> modern_concs = PALEOcarbchem.calc_modern_default_concs(35.0, Options=options);
 
 julia> map(x -> @sprintf("%.14e", x), modern_concs)
-(TF = "6.83258396883673e-05", TS = "2.82354341328601e-02", TB = "4.15700000000000e-04", Ca = "1.02845697008497e-02")
source
Solvers and outputs
PALEOaqchem.PALEOcarbchem.calculateTAfromTCpHfree! — Function
calculateTAfromTCpHfree!(res, C, Options, concs, pHfree; do_dTAdpH=Val(false)) -> (TA, dTAdpH)
Calculate TAlk, and speciation, given pH and conserved concentrations (total DIC, Si, P, SO4, B, F, ...)
Returns:
  • TA:  Total Alk, mol/kg-sw      
  • dTAdpH: derivative, or NaN if do_dTAdpH=Val(false)
Arguments:
  • res:  (output) Vector res of length length(ResultNames) with details of TA contributions etc
  • C: constants from calc_constants!. NB: must be on Free pH scale.
  • concs::NamedTuple: (mol kg-sw)  total concentrations for sulphate, fluoride, and each optional component of alkalinity enabled in C
  • pHfree: pH on free scale
Implementation
modified from Matlab CO2SYS CalculateTAfromTCpH(TCi, pHi) to use Free pH scale
source
Solvers and outputs
PALEOaqchem.PALEOcarbchem.calculateTAfromTCpHfree! — Function
calculateTAfromTCpHfree!(res, C, Options, concs, pHfree; do_dTAdpH=Val(false)) -> (TA, dTAdpH)
Calculate TAlk, and speciation, given pH and conserved concentrations (total DIC, Si, P, SO4, B, F, ...)
Returns:
  • TA:  Total Alk, mol/kg-sw      
  • dTAdpH: derivative, or NaN if do_dTAdpH=Val(false)
Arguments:
  • res:  (output) Vector res of length length(ResultNames) with details of TA contributions etc
  • C: constants from calc_constants!. NB: must be on Free pH scale.
  • concs::NamedTuple: (mol kg-sw)  total concentrations for sulphate, fluoride, and each optional component of alkalinity enabled in C
  • pHfree: pH on free scale
Implementation
modified from Matlab CO2SYS CalculateTAfromTCpH(TCi, pHi) to use Free pH scale
source
PALEOaqchem.PALEOcarbchem.calculatepHfromTATC! — Function
calculatepHfromTATC!(
     res, C, Options, conc_TAx, concs; 
     pHstart=8.0, pHTol=100*eps()
-) -> (pHfree, steps)
Call calculateTAfromTCpHfree! to iteratively solve for pH given (i) a starting value and pH tolerance,  and (ii) Alk and conserved concentrations (total DIC, Si, P, SO4, B, F, ...)
Intended for use eg in an ocean model to enable a single Newton-Raphson step each model timestep (ie pHstart from previous value in that grid cell, pHtol set to some large number)
Returns:
  • pHfree: pH on free scale
  • steps: number of Newton iterations
Arguments:
  • res:  (output) Vector res of length length(ResultNames) with details of TA contributions etc
  • C: constants from calc_constants!. NB: must be on Free pH scale.
  • conc_TAx: total Alk, mol kg-sw
  • concs: other input total concentrations, see calculateTAfromTCpHfree!
  • pHstart: starting value (free pH scale)
  • pHtol: tolerance (accuracy required)
Implementation
Modified from CO2SYS  SUB CalculatepHfromTATC, version 04.01, 10-13-96, written by Ernie Lewis. NB: recoded here to use calculateTAfromTCpHfree!, hence works on free pH scale.
Units: mol / kg-sw 
source
PALEOaqchem.PALEOcarbchem.calculateOmega — Function
calculateOmega(C, CO3,Ca) -> (OmegaCA, OmegaAR)
Calculate carbonate saturation.
Returns omega, the solubility ratio, for calcite and aragonite. This is defined by: Omega = [CO3–]*[Ca++]./Ksp, where Ksp is the solubility product (either KCa or KAr).
Arguments:
  • C    - constants from calc_constants!
  • CO3  - carbonate ion concentration, mol/kg-sw
  • Ca   - calcium concentration, mol/kg-sw
source
PALEOaqchem.PALEOcarbchem.mappHscale — Function
mappHscale(C, pHin, scalein, scaleout, TS, TF) -> pHout
Map pH scale at pressure, temperature, salinity defined by constants C
NB: Total, SW scale are not well defined unless using default contemporary values for TS (sulphate) and TF (fluorine)
Arguments:
  • C:  constants Vector from calc_constants!
  • pHin: input pH on scale scalein
  • scalein, scaleout :
    • Val(1) = Total scale
    • Val(2) = Seawater scale
    • Val(3) = Free scale
    • not implemented: Val(4) = NBS scale
  • TS: total sulphate (mol kg-1)
  • TF: total fluoride (mol kg-1)
source

+) -> (pHfree, steps)

Call calculateTAfromTCpHfree! to iteratively solve for pH given (i) a starting value and pH tolerance, and (ii) Alk and conserved concentrations (total DIC, Si, P, SO4, B, F, ...)

Intended for use eg in an ocean model to enable a single Newton-Raphson step each model timestep (ie pHstart from previous value in that grid cell, pHtol set to some large number)

Returns:

  • pHfree: pH on free scale
  • steps: number of Newton iterations

Arguments:

  • res: (output) Vector res of length length(ResultNames) with details of TA contributions etc
  • C: constants from calc_constants!. NB: must be on Free pH scale.
  • conc_TAx: total Alk, mol kg-sw
  • concs: other input total concentrations, see calculateTAfromTCpHfree!
  • pHstart: starting value (free pH scale)
  • pHtol: tolerance (accuracy required)

Implementation

Modified from CO2SYS SUB CalculatepHfromTATC, version 04.01, 10-13-96, written by Ernie Lewis. NB: recoded here to use calculateTAfromTCpHfree!, hence works on free pH scale.

Units: mol / kg-sw

source
PALEOaqchem.PALEOcarbchem.calculateOmega — Function
calculateOmega(C, CO3,Ca) -> (OmegaCA, OmegaAR)

Calculate carbonate saturation.

Returns omega, the solubility ratio, for calcite and aragonite. This is defined by: Omega = [CO3–]*[Ca++]./Ksp, where Ksp is the solubility product (either KCa or KAr).

Arguments:

  • C - constants from calc_constants!
  • CO3 - carbonate ion concentration, mol/kg-sw
  • Ca - calcium concentration, mol/kg-sw
source
PALEOaqchem.PALEOcarbchem.mappHscale — Function
mappHscale(C, pHin, scalein, scaleout, TS, TF) -> pHout

Map pH scale at pressure, temperature, salinity defined by constants C

NB: Total, SW scale are not well defined unless using default contemporary values for TS (sulphate) and TF (fluorine)

Arguments:

  • C: constants Vector from calc_constants!
  • pHin: input pH on scale scalein
  • scalein, scaleout :
    • Val(1) = Total scale
    • Val(2) = Seawater scale
    • Val(3) = Free scale
    • not implemented: Val(4) = NBS scale
  • TS: total sulphate (mol kg-1)
  • TF: total fluoride (mol kg-1)
source
diff --git a/dev/Generic Chemistry/index.html b/dev/Generic Chemistry/index.html index e045320..0440dfd 100644 --- a/dev/Generic Chemistry/index.html +++ b/dev/Generic Chemistry/index.html @@ -1,6 +1,6 @@ Generic Chemistry · PALEOaqchem Documentation
GitHub

Generic Chemistry

Generic chemical equilibrium and kinetic reactions following the standard approach used by reaction-transport codes such as PHREEQ and CrunchFlow, see eg (Steefel et al., 2015). This exploits timescale separation between "fast" (assumed instantaneous) chemical equilibrium reactions, and "slow" kinetic reactions or transport.

  • The chemical system is represented by a small number of totals

(or components) and an equal number of primary species concentrations, with secondary species concentrations calculated from the primary species via a set of equilibrium reactions. Primary species concentrations are determined by solving the set of algebraic equations given by the constraints on total concentrations.

  • Kinetic reactions (with any species, primary or secondary as reactants) are then written with totals as products.
  • Bulk transport (eg ocean advection or eddy diffusivity) transports totals. Molecular diffusivity (eg in a sediment) transports primary or secondary species and accumulates fluxes into totals.

Reservoirs

PALEOaqchem.ReservoirsAq.ReactionConstraintReservoir — Type
ReactionConstraintReservoir

A primary species and (algebraic) constraint on a corresponding total or component.

The primary species concentration or amount is defined as a PALEO State Variable, which depending on the primary_variable parameter, may be:

  • Primary_conc: (mol m-3)
  • Primary: (mol)
  • Primary_pconc: -log 10 (concentration (mol kg-1))

The corresponding R_constraint_conc or R_constraint (mol) defining the algebraic constraint on the corresponding total (for use by the numerical solver) is defined as a PALEO Constraint Variable.

This ReactionConstraintReservoir would usually be used in combination with a ReactionReservoir that provides the required total component concentration or amount as an ODE variable (where as usual reaction source and sink fluxes are applied to the corresponding _sms variable). Depending on the constraint_variable parameter, the total component may be supplied as either a per-cell concentration or amount:

  • R_conc: (mol m-3)
  • R: (mol)

Equilibrium reactions defining secondary species should add their contributions to the total to R_calc (mol). A primary species contribution R_calc += primary_total_stoich * Primary_conc * primary_volume is added to R_calc (where for the usual case parameter primary_total_stoich should be set to 1.0). Primary species contributions to other totals can be included by setting the primary_other_components parameter.

The numerical solver then solves for the primary species (and hence the secondary species concentrations) that (depending on the constraint_variable parameter) satisfy one of:

0 = R_constraint_conc = R_conc - R_calc/volume
-0 = R_constraint = R - R_calc

Volume conversions

The total species concentration R_conc and primary species concentration Primary_conc use (potentially different) volume conversions provided in volume and primary_volume respectively.

This allows for cases eg equilibrium partitioning between solute and solid phases by surface complexation, where R_conc refers to a cell total volume, and Primary_conc to a solute concentration.

Parameters

  • primary_total_stoich[Float64]=1.0, default_value=1.0, description="stoichiometric factor R_calc_conc += primary_total_stoich * Primary_conc"
  • primary_other_components[Vector{String}]=String[], default_value=String[], description="contribution of primary species to other element or component total concentrations"
  • primary_variable[String]="concentration", default_value="concentration", allowed_values=["concentration", "amount", "p_concentration"], description="units for primary variable"
  • constraint_variable[String]="concentration", default_value="concentration", allowed_values=["concentration", "amount"], description="units for constraint variable"

Methods and Variables for default Parameters

  • do_constraintreservoir_primary
    • R_calc (mol), VT_ReactContributor, description="contributions to total R_calc_conc (NB: a total, not concentration, to generalize to multiphase eqb)"
    • primary_volume –> volume (m3), VT_ReactDependency, description="cell volume (as used by Primary_conc)"
    • Primary_conc (mol m-3), VT_ReactDependency, VF_State, description="concentration of primary species"
  • do_constraintreservoir_constraint
    • R_calc (mol), VT_ReactTarget, description="contributions to total R_calc_conc (NB: a total, not concentration, to generalize to multiphase eqb)"
    • R_constraint_conc (mol m-3), VT_ReactContributor, VF_Constraint, description="algebraic constraint on R_conc (= 0)"
    • R_conc (mol m-3), VT_ReactDependency, description="total R_conc"
    • volume (m3), VT_ReactDependency, description="cell volume (as used by total variable)"
source
PALEOaqchem.ReservoirsAq.ReactionImplicitReservoir — Type
ReactionImplicitReservoir

A primary species and corresponding total or component as an 'implicit' ODE variable.

This provides an implementation of the 'Direct Substitution Approach' to chemical speciation, where the total or component is a function of the primary species concentration.

The primary species concentration or amount is defined as a PALEO StateTotal Variable, which depending on the primary_variable parameter, may be:

  • Primary_conc: (mol m-3)
  • Primary: (mol)
  • Primary_pconc: -log 10 (concentration (mol kg-1))

The corresponding total component R_conc or R is defined as a PALEO Total Variable, which depending on the constraint_variable parameter, may be provided to the solver either as a per-cell concentration or amount:

  • R_conc = R_calc/volume: (mol m-3)
  • R = R_calc: (mol)

Equilibrium reactions defining secondary species should add their contributions to the total to R_calc (mol). A primary species contribution R_calc += primary_total_stoich * Primary_conc * primary_volume is added to R_calc (where for the usual case parameter primary_total_stoich should be set to 1.0). Primary species contributions to other totals can be included by setting the primary_other_components parameter.

Source - sink fluxes eg kinetic reactions should be added to R_sms (mol yr-1) defined as a PALEO Deriv Variable.

Volume conversions

The total species concentration R_conc and primary species concentration Primary_conc use (potentially different) volume conversions provided in volume and primary_volume respectively.

This allows for cases eg equilibrium partitioning between solute and solid phases by surface complexation, where R_conc refers to a cell total volume, and Primary_conc to a solute concentration.

Parameters

  • primary_total_stoich[Float64]=1.0, default_value=1.0, description="stoichiometric factor R_calc_conc += primary_total_stoich * Primary_conc"
  • primary_other_components[Vector{String}]=String[], default_value=String[], description="contribution of primary species to other element or component total concentrations"
  • primary_variable[String]="concentration", default_value="concentration", allowed_values=["concentration", "amount", "pconcentration"], description="units for primary variable (specifies Primary\conc, Primary, Primary_pconc as StateTotal variable)"
  • total_variable[String]="concentration", default_value="concentration", allowed_values=["concentration", "amount"], description="units for total variable (specifies R_conc, R as Total variable)"
  • total[Bool]=false, default_value=false, description="true to calculate R_total = sum(R)"

Methods and Variables for default Parameters

  • do_implicitreservoir_primary
    • R_calc (mol), VT_ReactContributor, description="contributions to total R_calc_conc (NB: a total, not concentration, to generalize to multiphase eqb)"
    • primary_volume –> volume (m3), VT_ReactDependency, description="cell volume (as used by Primary_conc)"
    • Primary_conc (mol m-3), VT_ReactDependency, VF_StateTotal, description="concentration of primary species"
  • do_implicitreservoir_sms
    • R_sms (mol yr-1), VT_ReactTarget, description="total or component R source - sink"
    • R_conc_sms (mol m-3 yr-1), VT_ReactContributor, VF_Deriv, description="total or component R_conc source - sink"
    • volume (m3), VT_ReactDependency, description="cell volume (as used by total variable)"
  • do_implicitreservoir_total
    • R_calc (mol), VT_ReactTarget, description="contributions to total R_calc_conc (NB: a total, not concentration, to generalize to multiphase eqb)"
    • volume (m3), VT_ReactDependency, description="cell volume (as used by total variable)"
    • R (mol), VT_ReactProperty, description="total or component R"
    • R_conc (mol m-3), VT_ReactContributor, VF_Total, description="total or component R_conc"
source
PALEOaqchem.ReservoirsAq.ReactionAqConcSum — Type
ReactionAqConcSum

A sum of concentration variables (eg to get an element total)

Parameters

  • vars_to_add[Vector{String}]=["2\myvar", "myothervar", "-1\mythirdvar"], default_value=["2\myvar", "myothervar", "-1\mythirdvar"], description="vector of variable names to add, eg [2*myvar, myothervar, -1*mythirdvar]"
  • add_to_sum_volume[Bool]=false, default_value=false, description="true to also add to a 'sum' Variable += 'sum_conc * volume"
  • define_sum_volume[Bool]=false, default_value=false, description="only if 'add_to_sum_volume == true': true to also define the 'sum' Variable"

Methods and Variables for default Parameters

  • do_aqconcsum
    • sum_conc (mol m-3), VT_ReactProperty, description="sum of specified variables"
    • myvar (), VT_ReactDependency, description=""
    • myothervar (), VT_ReactDependency, description=""
    • mythirdvar (), VT_ReactDependency, description=""
source

Equilibrium reactions

PALEOaqchem.GenericReactions.ReactionAqEqb — Type
ReactionAqEqb

Define a new equilibrium species N 

N + a A <--> b B + c C
+0 = R_constraint = R - R_calc

Volume conversions

The total species concentration R_conc and primary species concentration Primary_conc use (potentially different) volume conversions provided in volume and primary_volume respectively.

This allows for cases eg equilibrium partitioning between solute and solid phases by surface complexation, where R_conc refers to a cell total volume, and Primary_conc to a solute concentration.

Parameters

  • primary_total_stoich[Float64]=1.0, default_value=1.0, description="stoichiometric factor R_calc_conc += primary_total_stoich * Primary_conc"
  • primary_other_components[Vector{String}]=String[], default_value=String[], description="contribution of primary species to other element or component total concentrations"
  • primary_variable[String]="concentration", default_value="concentration", allowed_values=["concentration", "amount", "p_concentration"], description="units for primary variable"
  • constraint_variable[String]="concentration", default_value="concentration", allowed_values=["concentration", "amount"], description="units for constraint variable"

Methods and Variables for default Parameters

  • do_constraintreservoir_primary
    • R_calc (mol), VT_ReactContributor, description="contributions to total R_calc_conc (NB: a total, not concentration, to generalize to multiphase eqb)"
    • primary_volume –> volume (m3), VT_ReactDependency, description="cell volume (as used by Primary_conc)"
    • Primary_conc (mol m-3), VT_ReactDependency, VF_State, description="concentration of primary species"
  • do_constraintreservoir_constraint
    • R_calc (mol), VT_ReactTarget, description="contributions to total R_calc_conc (NB: a total, not concentration, to generalize to multiphase eqb)"
    • R_constraint_conc (mol m-3), VT_ReactContributor, VF_Constraint, description="algebraic constraint on R_conc (= 0)"
    • R_conc (mol m-3), VT_ReactDependency, description="total R_conc"
    • volume (m3), VT_ReactDependency, description="cell volume (as used by total variable)"
source
PALEOaqchem.ReservoirsAq.ReactionImplicitReservoir — Type
ReactionImplicitReservoir

A primary species and corresponding total or component as an 'implicit' ODE variable.

This provides an implementation of the 'Direct Substitution Approach' to chemical speciation, where the total or component is a function of the primary species concentration.

The primary species concentration or amount is defined as a PALEO StateTotal Variable, which depending on the primary_variable parameter, may be:

  • Primary_conc: (mol m-3)
  • Primary: (mol)
  • Primary_pconc: -log 10 (concentration (mol kg-1))

The corresponding total component R_conc or R is defined as a PALEO Total Variable, which depending on the constraint_variable parameter, may be provided to the solver either as a per-cell concentration or amount:

  • R_conc = R_calc/volume: (mol m-3)
  • R = R_calc: (mol)

Equilibrium reactions defining secondary species should add their contributions to the total to R_calc (mol). A primary species contribution R_calc += primary_total_stoich * Primary_conc * primary_volume is added to R_calc (where for the usual case parameter primary_total_stoich should be set to 1.0). Primary species contributions to other totals can be included by setting the primary_other_components parameter.

Source - sink fluxes eg kinetic reactions should be added to R_sms (mol yr-1) defined as a PALEO Deriv Variable.

Volume conversions

The total species concentration R_conc and primary species concentration Primary_conc use (potentially different) volume conversions provided in volume and primary_volume respectively.

This allows for cases eg equilibrium partitioning between solute and solid phases by surface complexation, where R_conc refers to a cell total volume, and Primary_conc to a solute concentration.

Parameters

  • primary_total_stoich[Float64]=1.0, default_value=1.0, description="stoichiometric factor R_calc_conc += primary_total_stoich * Primary_conc"
  • primary_other_components[Vector{String}]=String[], default_value=String[], description="contribution of primary species to other element or component total concentrations"
  • primary_variable[String]="concentration", default_value="concentration", allowed_values=["concentration", "amount", "pconcentration"], description="units for primary variable (specifies Primary\conc, Primary, Primary_pconc as StateTotal variable)"
  • total_variable[String]="concentration", default_value="concentration", allowed_values=["concentration", "amount"], description="units for total variable (specifies R_conc, R as Total variable)"
  • total[Bool]=false, default_value=false, description="true to calculate R_total = sum(R)"

Methods and Variables for default Parameters

  • do_implicitreservoir_primary
    • R_calc (mol), VT_ReactContributor, description="contributions to total R_calc_conc (NB: a total, not concentration, to generalize to multiphase eqb)"
    • primary_volume –> volume (m3), VT_ReactDependency, description="cell volume (as used by Primary_conc)"
    • Primary_conc (mol m-3), VT_ReactDependency, VF_StateTotal, description="concentration of primary species"
  • do_implicitreservoir_sms
    • R_sms (mol yr-1), VT_ReactTarget, description="total or component R source - sink"
    • R_conc_sms (mol m-3 yr-1), VT_ReactContributor, VF_Deriv, description="total or component R_conc source - sink"
    • volume (m3), VT_ReactDependency, description="cell volume (as used by total variable)"
  • do_implicitreservoir_total
    • R_calc (mol), VT_ReactTarget, description="contributions to total R_calc_conc (NB: a total, not concentration, to generalize to multiphase eqb)"
    • volume (m3), VT_ReactDependency, description="cell volume (as used by total variable)"
    • R (mol), VT_ReactProperty, description="total or component R"
    • R_conc (mol m-3), VT_ReactContributor, VF_Total, description="total or component R_conc"
source
PALEOaqchem.ReservoirsAq.ReactionAqConcSum — Type
ReactionAqConcSum

A sum of concentration variables (eg to get an element total)

Parameters

  • vars_to_add[Vector{String}]=["2\myvar", "myothervar", "-1\mythirdvar"], default_value=["2\myvar", "myothervar", "-1\mythirdvar"], description="vector of variable names to add, eg [2*myvar, myothervar, -1*mythirdvar]"
  • add_to_sum_volume[Bool]=false, default_value=false, description="true to also add to a 'sum' Variable += 'sum_conc * volume"
  • define_sum_volume[Bool]=false, default_value=false, description="only if 'add_to_sum_volume == true': true to also define the 'sum' Variable"

Methods and Variables for default Parameters

  • do_aqconcsum
    • sum_conc (mol m-3), VT_ReactProperty, description="sum of specified variables"
    • myvar (), VT_ReactDependency, description=""
    • myothervar (), VT_ReactDependency, description=""
    • mythirdvar (), VT_ReactDependency, description=""
source

Equilibrium reactions

PALEOaqchem.GenericReactions.ReactionAqEqb — Type
ReactionAqEqb

Define a new equilibrium species N 

N + a A <--> b B + c C
 
 [N] = K_eqb'^K_power ([B]^b [C]^c) / ([A]^a)

where to convert density units for K_eqb:

K_eqb' = K_eqb * rho_ref^K_density_power

The first name in the Reactants list is the new species concentration N: other species concentrations in Reactants and Products lists must already be defined elsewhere in the model configuration.

The contribution of the new species to element totals or components is defined by the N_components vector, which may be empty eg to just calculate an Omega or a gas partial pressure etc.

Examples

Gas partial pressure from concentration

solubility_H2:
     class: ReactionAqEqb
@@ -10,5 +10,5 @@
         K_eqb:      7.8e-1   # mol m-3 atm-1 at 298.15 K (Henry's law coefficent)
         K_power:   -1.0  #  pH2 = H2_conc * K_eqb^-1
     variable_attributes:
-        pH2%units:   atm

Compilation of Henry's law coefficients: https://www.henrys-law.org/ which is R. Sander: Compilation of Henry's law constants (version 5.0.0) for water as solvent, Atmos. Chem. Phys., 23, 10901-12440 (2023), doi:10.5194/acp-23-10901-2023

Unit conversions: 1 mol m^-3 Pa-1 = 1.01325e5 mol m-3 atm-1

Parameters

  • Reactants[Vector{String}]=["N\conc", "A\conc^2"], default_value=["N\conc", "A\conc^2"], description="concentrations or activities of new species followed by other reactants, write powers as X^2 etc"
  • Products[Vector{String}]=["B\conc", "C\conc"], default_value=["B\conc", "C\conc"], description="concentrations or activities of products, write powers as X^2 etc"
  • K_eqb[Float64]=0.00018629779999999998, default_value=0.00018629779999999998, description="equilibrium constant"
  • K_density_power[Float64]=0.0, default_value=0.0, description="multiple K_eqb * rho_ref^K_density_power to convert units: 0.0 for K_eqb in mol m-3, 1.0 for K_eqb in mol kg-1, etc"
  • K_power[Float64]=-1.0, default_value=-1.0, description="exponent of K_eqb"
  • N_components[Vector{String}]=String[], default_value=String[], description="contribution of new species to element or component total eg '["2*TN_calc"]' to add 2\*N\_conc\*volume to TN\_calc (or empty vector to just define an Omega)"

Methods and Variables for default Parameters

  • do_aqeqb
    • N_conc (mol m-3), VT_ReactProperty, description="aqueous concentration or activity"
    • A_conc (mol m-3), VT_ReactDependency, description="aqueous concentration or activity"
    • B_conc (mol m-3), VT_ReactDependency, description="aqueous concentration or activity"
    • C_conc (mol m-3), VT_ReactDependency, description="aqueous concentration or activity"
source

Kinetic reactions

PALEOaqchem.GenericReactions.ReactionAqKinetic — Type
ReactionAqKinetic

Define a kinetic reaction with rate dependent on concentrations

a A + b B --> c C + d D

Rate (default) is:

R = K * [A] * [B]

where this can be modified to different functional form by defining a vector of Rate_functions to apply to each concentration variable.

Parameters Reactants and Products should be the vectors of stoichiometry * <name> of (total) species to accumulate fluxes into <name>_sms variables.

Parameter Reactant_concs should be an empty vector to take default concentration variable names from Reactants, or a Vector of names to specify concentration species names explicitly (required when eg where Reactants refers to totals which are partioned into multiple species).

Parameters

  • Reactants[Vector{String}]=["A", "2\B"], default_value=["A", "2\B"], description="reactant species"
  • Products[Vector{String}]=["2\C", "D"], default_value=["2\C", "D"], description="product species"
  • Reactant_concs[Vector{String}]=String[], default_value=String[], description="names of concentration variables to calculate rate eg '[`"A_conc"]' etc, empty vector to used defaults from 'Reactants' eg 'A_conc', 'B_conc' ..."
  • Rate_functions[Vector{String}]=String[], default_value=String[], allowed_values=["linear", "sqrt", "monod"], description="functional form for rate function of each concentration (empty vector for default 'linear')"
  • K[Float64]=NaN, default_value=NaN, description="rate constant"
  • K_lim[Float64]=NaN (mol m-3), default_value=NaN, description="limiting concentration for 'monod' rate function"

Methods and Variables for default Parameters

  • do_aqkinetic
    • redox_A_B_C_D (mol yr-1), VT_ReactProperty, description="rate variable"
    • A_conc (mol m-3), VT_ReactDependency, description="aqueous concentration or activity"
    • B_conc (mol m-3), VT_ReactDependency, description="aqueous concentration or activity"
    • volume (m3), VT_ReactDependency, description="cell solute volume"
  • RateStoich_redox_A_B_C_D
    • redox_A_B_C_D (mol yr-1), VT_ReactDependency, description="rate variable"
    • [A_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_A_B_C_D"
    • [B_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_A_B_C_D"
    • [C_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_A_B_C_D"
    • [D_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_A_B_C_D"
  • totals
    • redox_A_B_C_D (mol yr-1), VT_ReactDependency, description="rate variable"
    • redox_A_B_C_D_total (mol yr-1), VT_ReactProperty, description="total rate variable"
source

Precipitation-dissolution reactions

PALEOaqchem.GenericReactions.ReactionAqPrecipDissol — Type
ReactionAqPrecipDissol

Define a precipitation and dissolution reaction for solid S

a A + b B <--> s S + d D

Rate for the precipitation and dissolution reactions are:

R_precip = K_precip * (Ω - 1)               (Ω > 1)
-R_dissol = K_dissol * S_conc * (1 - Ω)      (Ω < 1)

Parameters Reactants and Products should be the vectors of stoichiometry * name of (total) species to accumulate fluxes into _sms variables.

Solid_conc should be the name of the concentration variable for S, or an empty string to use default 'S_conc'.

Parameters

  • Reactants[Vector{String}]=["A", "2\B"], default_value=["A", "2\B"], description="reactant species"
  • Products[Vector{String}]=["S", "0.5\D"], default_value=["S", "0.5\D"], description="product species (solid S first)"
  • Solid_conc[String]="", default_value="", description="name of solid S concentration variable (empty string to default to 'S_conc')"
  • K_precip[Float64]=0.0 (mol m-3 yr-1), default_value=0.0, description="rate constant for precipitation reaction"
  • K_dissol[Float64]=0.0 (yr-1), default_value=0.0, description="rate constant for dissolution reaction"
  • dissol_rolloff_conc[Float64]=0.0 (mol m-3), default_value=0.0, description="limiting concentration below which dissolution rate is rolled off to zero as Solid_conc^2"

Methods and Variables for default Parameters

  • do_aqprecipdissol
    • precipdissol_A_B_S_D (mol yr-1), VT_ReactProperty, description="rate variable"
    • S_conc (mol m-3), VT_ReactDependency, description="solid concentration or activity"
    • Omega (), VT_ReactDependency, description="saturation state"
    • volume (m3), VT_ReactDependency, description="cell solid phase volume"
  • RateStoich_precipdissol_A_B_S_D
    • precipdissol_A_B_S_D (mol yr-1), VT_ReactDependency, description="rate variable"
    • [A_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=precipdissol_A_B_S_D"
    • [B_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=precipdissol_A_B_S_D"
    • [S_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=precipdissol_A_B_S_D"
    • [D_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=precipdissol_A_B_S_D"
  • totals
    • precipdissol_A_B_S_D (mol yr-1), VT_ReactDependency, description="rate variable"
    • precipdissol_A_B_S_D_total (mol yr-1), VT_ReactProperty, description="total rate variable"
source

Particulate fluxes

PALEOaqchem.Particle.ReactionParticleDecay — Type
ReactionParticleDecay

Decay (eg organic matter to remineralization) at rate 1.0/decay_timescale of eg an organic matter dissolved/particulate phase in Reservoir Particle, to decayflux. Particle may have isotope_type. The Reservoir Particle may have the :vsink attribute set to represent a marine sinking particulate phase.

Parameters

  • decay_timescale[Float64]=0.5 (yr), default_value=0.5, description="particle decay timescale"
  • decay_threshold[Float64]=-Inf (mol m-3), default_value=-Inf, description="particle decay concentration below which decay stops"
  • show_decayrate[Bool]=false, default_value=false, description="true to create a 'decayrate' variable to record decay rate"
  • field_data[DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable isotopes and specify isotope type"

Methods and Variables

  • do_particle_decay
    • Particle (mol), VT_ReactDependency, description="Particle amount"
    • Particle_sms (mol yr-1), VT_ReactContributor, description="Particle source-sink"
    • decayflux (mol yr-1), VT_ReactContributor, description="Particle decay flux"
source
PALEOaqchem.Particle.ReactionFluxToComponents — Type
ReactionFluxToComponents

Distribute a single input_flux (eg an organic matter flux) to output_fluxnames components with stoichiometry output_fluxstoich. input_flux may have an isotope type (set by field_data) in which case the isotopic composition will be sent to (usually one) output_fluxname with ::Isotope suffix.

Parameters

  • outputflux_prefix[String]="", default_value="", description="Prefix for output flux names"
  • outputflux_names[Vector{String}]=["Corg", "N", "P"], default_value=["Corg", "N", "P"], description="Suffixes for output flux names. Use ::Isotope suffix to identify a flux with 'isotope_type'"
  • outputflux_stoich[Vector{Float64}]=[106.0, 16.0, 1.0], default_value=[106.0, 16.0, 1.0], description="Stoichiometry for output fluxes relative to input flux"
  • allow_unlinked_outputflux[Bool]=false, default_value=false, description="true to allow (and ignore) unlinked outputflux Variables, false to error if any outputflux Variable is not linked"
  • field_data[DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_flux_to_components
    • inputflux (mol yr-1), VT_ReactTarget, description="input flux"
    • Corg (mol yr-1), VT_ReactContributor, description="flux Corg"
    • N (mol yr-1), VT_ReactContributor, description="flux N"
    • P (mol yr-1), VT_ReactContributor, description="flux P"
source

Co-precipitation

PALEOaqchem.CoPrecip.ReactionPACoPrecip — Type
ReactionPACoPrecip

Co-precipitation of P (eg iron-bound phosphorus) with A (eg Fe oxide) formation

P -> P=A

at a rate gamma * A_formation_rate_<n>, with limitation at low P concentration

P_components defines solution totals or components that should be modified when P is consumed (eg ["-1*P"] to remove "P" from solution)

Parameters

  • A_rate_stoich_factors[Vector{Float64}]=[1.0], default_value=[1.0], description="stoichiometry factor to multiply each A formation rate variable to convert to mol A"
  • gamma[Float64]=0.15 (mol/mol), default_value=0.15, description="P:A molar ratio"
  • P_limit[Float64]=1.0e-6 (mol m-3), default_value=1.0e-6, description="limiting P concentration below which co-precipitation is inhibited"
  • P_components[Vector{String}]=["-1\P", "TAlk"], default_value=["-1\P", "TAlk"], description="totals or components that should be modified when P is consumed from solution"

Methods and Variables for default Parameters

  • do_PA_coprecip
    • rate_PA_coprecip (mol P yr-1), VT_ReactProperty, description="rate of P co-precipitation"
    • P_conc (mol m-3), VT_ReactDependency, description="P concentration"
    • A_formation_rate_1 (mol m-3 yr-1), VT_ReactDependency, description="substance A formation rate"
  • RateStoich_rate_PA_coprecip
    • rate_PA_coprecip (mol P yr-1), VT_ReactDependency, description="rate of P co-precipitation"
    • [P_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_coprecip"
    • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_coprecip"
    • [PA_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_coprecip"
  • totals
    • rate_PA_coprecip (mol P yr-1), VT_ReactDependency, description="rate of P co-precipitation"
    • rate_PA_coprecip_total (mol P yr-1), VT_ReactProperty, description="total rate of P co-precipitation"
source
PALEOaqchem.CoPrecip.ReactionPARelease — Type
ReactionPARelease

Release of P (eg iron-bound phosphorus) with A (eg Fe oxide) destruction

P=A -> P

at a rate Prelease = theta * A_destruction_rate_<n>, where theta = PA_conc / A_conc

P_components defines totals or components that should be modified when P is released (eg ["P"] to return P to solution).

Parameters

  • A_rate_stoich_factors[Vector{Float64}]=[1.0], default_value=[1.0], description="stoichiometry factor to multiply each A destruction rate variable to convert to mol A"
  • P_components[Vector{String}]=["P", "-1\TAlk"], default_value=["P", "-1\TAlk"], description="totals or components that should be modified when P is released"

Methods and Variables for default Parameters

  • do_PA_release
    • rate_PA_release (mol P yr-1), VT_ReactProperty, description="rate of coprecipitated P dissolution"
    • PA_conc (mol m-3), VT_ReactDependency, description="adsorbed P concentration"
    • A_conc (mol m-3), VT_ReactDependency, description="adsorbant concentration"
    • PA_theta (mol/mol), VT_ReactProperty, description="P:A molar ratio of adsorbed of coprecipitated P"
    • A_destruction_rate_1 (mol m-3 yr-1), VT_ReactDependency, description="substance A destruction rate"
  • RateStoich_rate_PA_release
    • rate_PA_release (mol P yr-1), VT_ReactDependency, description="rate of coprecipitated P dissolution"
    • [PA_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_release"
    • [P_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_release"
    • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_release"
  • totals
    • rate_PA_release (mol P yr-1), VT_ReactDependency, description="rate of coprecipitated P dissolution"
    • rate_PA_release_total (mol P yr-1), VT_ReactProperty, description="total rate of coprecipitated P dissolution"
source
+ pH2%units: atm

Compilation of Henry's law coefficients: https://www.henrys-law.org/ which is R. Sander: Compilation of Henry's law constants (version 5.0.0) for water as solvent, Atmos. Chem. Phys., 23, 10901-12440 (2023), doi:10.5194/acp-23-10901-2023

Unit conversions: 1 mol m^-3 Pa-1 = 1.01325e5 mol m-3 atm-1

Parameters

Methods and Variables for default Parameters

source

Kinetic reactions

PALEOaqchem.GenericReactions.ReactionAqKinetic — Type
ReactionAqKinetic

Define a kinetic reaction with rate dependent on concentrations

a A + b B --> c C + d D

Rate (default) is:

R = K * [A] * [B]

where this can be modified to different functional form by defining a vector of Rate_functions to apply to each concentration variable.

Parameters Reactants and Products should be the vectors of stoichiometry * <name> of (total) species to accumulate fluxes into <name>_sms variables.

Parameter Reactant_concs should be an empty vector to take default concentration variable names from Reactants, or a Vector of names to specify concentration species names explicitly (required when eg where Reactants refers to totals which are partioned into multiple species).

Parameters

  • Reactants[Vector{String}]=["A", "2\B"], default_value=["A", "2\B"], description="reactant species"
  • Products[Vector{String}]=["2\C", "D"], default_value=["2\C", "D"], description="product species"
  • Reactant_concs[Vector{String}]=String[], default_value=String[], description="names of concentration variables to calculate rate eg '[`"A_conc"]' etc, empty vector to used defaults from 'Reactants' eg 'A_conc', 'B_conc' ..."
  • Rate_functions[Vector{String}]=String[], default_value=String[], allowed_values=["linear", "sqrt", "monod"], description="functional form for rate function of each concentration (empty vector for default 'linear')"
  • K[Float64]=NaN, default_value=NaN, description="rate constant"
  • K_lim[Float64]=NaN (mol m-3), default_value=NaN, description="limiting concentration for 'monod' rate function"

Methods and Variables for default Parameters

  • do_aqkinetic
    • redox_A_B_C_D (mol yr-1), VT_ReactProperty, description="rate variable"
    • A_conc (mol m-3), VT_ReactDependency, description="aqueous concentration or activity"
    • B_conc (mol m-3), VT_ReactDependency, description="aqueous concentration or activity"
    • volume (m3), VT_ReactDependency, description="cell solute volume"
  • RateStoich_redox_A_B_C_D
    • redox_A_B_C_D (mol yr-1), VT_ReactDependency, description="rate variable"
    • [A_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_A_B_C_D"
    • [B_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_A_B_C_D"
    • [C_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_A_B_C_D"
    • [D_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_A_B_C_D"
  • totals
    • redox_A_B_C_D (mol yr-1), VT_ReactDependency, description="rate variable"
    • redox_A_B_C_D_total (mol yr-1), VT_ReactProperty, description="total rate variable"
source

Precipitation-dissolution reactions

PALEOaqchem.GenericReactions.ReactionAqPrecipDissol — Type
ReactionAqPrecipDissol

Define a precipitation and dissolution reaction for solid S

a A + b B <--> s S + d D

Rate for the precipitation and dissolution reactions are:

R_precip = K_precip * (Ω - 1)               (Ω > 1)
+R_dissol = K_dissol * S_conc * (1 - Ω)      (Ω < 1)

Parameters Reactants and Products should be the vectors of stoichiometry * name of (total) species to accumulate fluxes into _sms variables.

Solid_conc should be the name of the concentration variable for S, or an empty string to use default 'S_conc'.

Parameters

  • Reactants[Vector{String}]=["A", "2\B"], default_value=["A", "2\B"], description="reactant species"
  • Products[Vector{String}]=["S", "0.5\D"], default_value=["S", "0.5\D"], description="product species (solid S first)"
  • Solid_conc[String]="", default_value="", description="name of solid S concentration variable (empty string to default to 'S_conc')"
  • K_precip[Float64]=0.0 (mol m-3 yr-1), default_value=0.0, description="rate constant for precipitation reaction"
  • K_dissol[Float64]=0.0 (yr-1), default_value=0.0, description="rate constant for dissolution reaction"
  • dissol_rolloff_conc[Float64]=0.0 (mol m-3), default_value=0.0, description="limiting concentration below which dissolution rate is rolled off to zero as Solid_conc^2"

Methods and Variables for default Parameters

  • do_aqprecipdissol
    • precipdissol_A_B_S_D (mol yr-1), VT_ReactProperty, description="rate variable"
    • S_conc (mol m-3), VT_ReactDependency, description="solid concentration or activity"
    • Omega (), VT_ReactDependency, description="saturation state"
    • volume (m3), VT_ReactDependency, description="cell solid phase volume"
  • RateStoich_precipdissol_A_B_S_D
    • precipdissol_A_B_S_D (mol yr-1), VT_ReactDependency, description="rate variable"
    • [A_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=precipdissol_A_B_S_D"
    • [B_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=precipdissol_A_B_S_D"
    • [S_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=precipdissol_A_B_S_D"
    • [D_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=precipdissol_A_B_S_D"
  • totals
    • precipdissol_A_B_S_D (mol yr-1), VT_ReactDependency, description="rate variable"
    • precipdissol_A_B_S_D_total (mol yr-1), VT_ReactProperty, description="total rate variable"
source

Particulate fluxes

PALEOaqchem.Particle.ReactionParticleDecay — Type
ReactionParticleDecay

Decay (eg organic matter to remineralization) at rate 1.0/decay_timescale of eg an organic matter dissolved/particulate phase in Reservoir Particle, to decayflux. Particle may have isotope_type. The Reservoir Particle may have the :vsink attribute set to represent a marine sinking particulate phase.

Parameters

  • decay_timescale[Float64]=0.5 (yr), default_value=0.5, description="particle decay timescale"
  • decay_threshold[Float64]=-Inf (mol m-3), default_value=-Inf, description="particle decay concentration below which decay stops"
  • show_decayrate[Bool]=false, default_value=false, description="true to create a 'decayrate' variable to record decay rate"
  • field_data[DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable isotopes and specify isotope type"

Methods and Variables

  • do_particle_decay
    • Particle (mol), VT_ReactDependency, description="Particle amount"
    • Particle_sms (mol yr-1), VT_ReactContributor, description="Particle source-sink"
    • decayflux (mol yr-1), VT_ReactContributor, description="Particle decay flux"
source
PALEOaqchem.Particle.ReactionFluxToComponents — Type
ReactionFluxToComponents

Distribute a single input_flux (eg an organic matter flux) to output_fluxnames components with stoichiometry output_fluxstoich. input_flux may have an isotope type (set by field_data) in which case the isotopic composition will be sent to (usually one) output_fluxname with ::Isotope suffix.

Parameters

  • outputflux_prefix[String]="", default_value="", description="Prefix for output flux names"
  • outputflux_names[Vector{String}]=["Corg", "N", "P"], default_value=["Corg", "N", "P"], description="Suffixes for output flux names. Use ::Isotope suffix to identify a flux with 'isotope_type'"
  • outputflux_stoich[Vector{Float64}]=[106.0, 16.0, 1.0], default_value=[106.0, 16.0, 1.0], description="Stoichiometry for output fluxes relative to input flux"
  • allow_unlinked_outputflux[Bool]=false, default_value=false, description="true to allow (and ignore) unlinked outputflux Variables, false to error if any outputflux Variable is not linked"
  • field_data[DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_flux_to_components
    • inputflux (mol yr-1), VT_ReactTarget, description="input flux"
    • Corg (mol yr-1), VT_ReactContributor, description="flux Corg"
    • N (mol yr-1), VT_ReactContributor, description="flux N"
    • P (mol yr-1), VT_ReactContributor, description="flux P"
source

Co-precipitation

PALEOaqchem.CoPrecip.ReactionPACoPrecip — Type
ReactionPACoPrecip

Co-precipitation of P (eg iron-bound phosphorus) with A (eg Fe oxide) formation

P -> P=A

at a rate gamma * A_formation_rate_<n>, with limitation at low P concentration

P_components defines solution totals or components that should be modified when P is consumed (eg ["-1*P"] to remove "P" from solution)

Parameters

  • A_rate_stoich_factors[Vector{Float64}]=[1.0], default_value=[1.0], description="stoichiometry factor to multiply each A formation rate variable to convert to mol A"
  • gamma[Float64]=0.15 (mol/mol), default_value=0.15, description="P:A molar ratio"
  • P_limit[Float64]=1.0e-6 (mol m-3), default_value=1.0e-6, description="limiting P concentration below which co-precipitation is inhibited"
  • P_components[Vector{String}]=["-1\P", "TAlk"], default_value=["-1\P", "TAlk"], description="totals or components that should be modified when P is consumed from solution"

Methods and Variables for default Parameters

  • do_PA_coprecip
    • rate_PA_coprecip (mol P yr-1), VT_ReactProperty, description="rate of P co-precipitation"
    • P_conc (mol m-3), VT_ReactDependency, description="P concentration"
    • A_formation_rate_1 (mol m-3 yr-1), VT_ReactDependency, description="substance A formation rate"
  • RateStoich_rate_PA_coprecip
    • rate_PA_coprecip (mol P yr-1), VT_ReactDependency, description="rate of P co-precipitation"
    • [P_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_coprecip"
    • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_coprecip"
    • [PA_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_coprecip"
  • totals
    • rate_PA_coprecip (mol P yr-1), VT_ReactDependency, description="rate of P co-precipitation"
    • rate_PA_coprecip_total (mol P yr-1), VT_ReactProperty, description="total rate of P co-precipitation"
source
PALEOaqchem.CoPrecip.ReactionPARelease — Type
ReactionPARelease

Release of P (eg iron-bound phosphorus) with A (eg Fe oxide) destruction

P=A -> P

at a rate Prelease = theta * A_destruction_rate_<n>, where theta = PA_conc / A_conc

P_components defines totals or components that should be modified when P is released (eg ["P"] to return P to solution).

Parameters

  • A_rate_stoich_factors[Vector{Float64}]=[1.0], default_value=[1.0], description="stoichiometry factor to multiply each A destruction rate variable to convert to mol A"
  • P_components[Vector{String}]=["P", "-1\TAlk"], default_value=["P", "-1\TAlk"], description="totals or components that should be modified when P is released"

Methods and Variables for default Parameters

  • do_PA_release
    • rate_PA_release (mol P yr-1), VT_ReactProperty, description="rate of coprecipitated P dissolution"
    • PA_conc (mol m-3), VT_ReactDependency, description="adsorbed P concentration"
    • A_conc (mol m-3), VT_ReactDependency, description="adsorbant concentration"
    • PA_theta (mol/mol), VT_ReactProperty, description="P:A molar ratio of adsorbed of coprecipitated P"
    • A_destruction_rate_1 (mol m-3 yr-1), VT_ReactDependency, description="substance A destruction rate"
  • RateStoich_rate_PA_release
    • rate_PA_release (mol P yr-1), VT_ReactDependency, description="rate of coprecipitated P dissolution"
    • [PA_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_release"
    • [P_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_release"
    • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=rate_PA_release"
  • totals
    • rate_PA_release (mol P yr-1), VT_ReactDependency, description="rate of coprecipitated P dissolution"
    • rate_PA_release_total (mol P yr-1), VT_ReactProperty, description="total rate of coprecipitated P dissolution"
source
diff --git a/dev/Isotopes/index.html b/dev/Isotopes/index.html index 2c170f4..f20c370 100644 --- a/dev/Isotopes/index.html +++ b/dev/Isotopes/index.html @@ -1,2 +1,2 @@ -Isotope systems · PALEOaqchem Documentation
GitHub

Isotope systems

Boron

PALEOaqchem.Boron.ReactionBoronIsotope — Type
ReactionBoronIsotope

Calculate d11B for aqueous B(OH)4- and B(OH)3 species from mass balance, given d11B for total B, total B concentration B_conc and B(OH)4- concentration BOH4_conc.

See eg (Zeebe and Wolf-Gladrow, 2001), p220.

Parameters

  • alphaB[Float64]=1.0272, default_value=1.0272, description="isotopic fractionation factor B(OH)4m <-> B(OH)3"
  • BIsotope[external, UnionAll]=PALEOboxes.IsotopeLinear, default_value=PALEOboxes.IsotopeLinear, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable boron isotopes and specify isotope type"

Methods and Variables

  • do_boron_isotope
    • B_conc (mol m-3), VT_ReactDependency, description="B concentration"
    • BOH4_conc (mol m-3), VT_ReactDependency, description="B(OH)4m concentration"
    • B_delta (per mil), VT_ReactDependency, description="d11B delta for total B"
    • BOH4_delta (per mil), VT_ReactProperty, description="d11B delta for B(OH)4- species"
source
+Isotope systems · PALEOaqchem Documentation
GitHub

Isotope systems

Boron

PALEOaqchem.Boron.ReactionBoronIsotope — Type
ReactionBoronIsotope

Calculate d11B for aqueous B(OH)4- and B(OH)3 species from mass balance, given d11B for total B, total B concentration B_conc and B(OH)4- concentration BOH4_conc.

See eg (Zeebe and Wolf-Gladrow, 2001), p220.

Parameters

  • alphaB[Float64]=1.0272, default_value=1.0272, description="isotopic fractionation factor B(OH)4m <-> B(OH)3"
  • BIsotope[external, UnionAll]=PALEOboxes.IsotopeLinear, default_value=PALEOboxes.IsotopeLinear, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable boron isotopes and specify isotope type"

Methods and Variables

  • do_boron_isotope
    • B_conc (mol m-3), VT_ReactDependency, description="B concentration"
    • BOH4_conc (mol m-3), VT_ReactDependency, description="B(OH)4m concentration"
    • B_delta (per mil), VT_ReactDependency, description="d11B delta for total B"
    • BOH4_delta (per mil), VT_ReactProperty, description="d11B delta for B(OH)4- species"
source
diff --git a/dev/Molecular Diffusivity/index.html b/dev/Molecular Diffusivity/index.html index c94993f..796c876 100644 --- a/dev/Molecular Diffusivity/index.html +++ b/dev/Molecular Diffusivity/index.html @@ -1,3 +1,3 @@ Molecular diffusivity · PALEOaqchem Documentation
GitHub

Molecular diffusivity

PALEOaqchem.MolecularDiffusion.create_solute_diffusivity_func — Function
create_solute_diffusivity_func(species_or_constant::AbstractString) -> f_diffcoeff

Molecular diffusivity for species_or_constant in water

Based on data compiled by (Boudreau, 1997) Ch. 4

If species_or_constant is a species name, returns a function f_diffcoeff, which calculates:

f_diffcoeff(TdegK, Pbar, S) -> Dmol (cm^2/s)

If species_or_constant can be parsed into a Float64, returns a function which provides this constant value (units cm^2/s).

The effect of pressure and salinity is approximated by assuming viscosity (calculated by MolecularDiffusion.sw_dynamic_viscosity) is the primary consideration, (Boudreau, 1997) eqn. 4.107 and Table 4.10.

Example

To test from the Julia REPL:

julia> PALEOaqchem.MolecularDiffusion.create_solute_diffusivity_func("O2")(273.15+25, 1.0, 35)
-2.211824368650775e-5
source
PALEOaqchem.MolecularDiffusion.sw_dynamic_viscosity — Function
sw_dynamic_viscosity(TdegC, Pbar, S) -> mu

Seawater dynamic viscosity ((Boudreau, 1997) p94) 'claimed to accurate to within 7% over T (0 - 30C), P (1 - 1000 bar), S (0 36)'

Returns mu (10^-2 g/cm/s) (centipoise)

Arguments:

  • T: deg C (0 - 30C) temperature
  • P: bar (1 1000) pressure
  • S: salinity (0 - 36)

See check values for salinity effect Table 4.10 p.125

source
PALEOaqchem.MolecularDiffusion.ReactionAqMolecularDiffusivity — Type
ReactionAqMolecularDiffusivity

Calculate molecular diffusivity (cm^s s-1) from :diffusivity_speciesname attributes of aqueous solution concentration Variables

A Variable <species>_moldiff is created for each <species>_conc Variable with non-empty :diffusivity_speciesname attribute.

:diffusivity_speciesname may either be a known species (in which case it is looked up in create_solute_diffusivity_func), or a constant value in cm^2 s-1 supplied as a String.

source
+2.211824368650775e-5source
PALEOaqchem.MolecularDiffusion.sw_dynamic_viscosity — Function
sw_dynamic_viscosity(TdegC, Pbar, S) -> mu

Seawater dynamic viscosity ((Boudreau, 1997) p94) 'claimed to accurate to within 7% over T (0 - 30C), P (1 - 1000 bar), S (0 36)'

Returns mu (10^-2 g/cm/s) (centipoise)

Arguments:

  • T: deg C (0 - 30C) temperature
  • P: bar (1 1000) pressure
  • S: salinity (0 - 36)

See check values for salinity effect Table 4.10 p.125

source
PALEOaqchem.MolecularDiffusion.ReactionAqMolecularDiffusivity — Type
ReactionAqMolecularDiffusivity

Calculate molecular diffusivity (cm^s s-1) from :diffusivity_speciesname attributes of aqueous solution concentration Variables

A Variable <species>_moldiff is created for each <species>_conc Variable with non-empty :diffusivity_speciesname attribute.

:diffusivity_speciesname may either be a known species (in which case it is looked up in create_solute_diffusivity_func), or a constant value in cm^2 s-1 supplied as a String.

source
diff --git a/dev/Organic matter and remineralization/index.html b/dev/Organic matter and remineralization/index.html index 420038a..054e106 100644 --- a/dev/Organic matter and remineralization/index.html +++ b/dev/Organic matter and remineralization/index.html @@ -1,2 +1,2 @@ -Organic matter and remineralization · PALEOaqchem Documentation
GitHub

Organic matter and remineralization

Particulate organic carbon fluxes

PALEOaqchem.RCmultiG.ReactionRCmultiG — Type
ReactionRCmultiG

Discrete representation of organic matter reaction-continuum model from Dale (2015)

The fraction of POC having reactivity k (yr-1) in interval dk at time zero is given by the PDF:

$f(k, 0) dk = \frac{a^{\nu} k^{\nu-1} e^{-a k}}{\Gamma(\nu)} dk$

This is represented by a discrete distribution in n-2 bins spaced logarithmically in k, with additional bins at the start and end to represent POC with reactivity below and above the first and last bin.

This Reaction:

  • Defines n state variables Corg_<n> with corresponding concentrations Corg_<n>_conc and source-sink Corg_<n>_sms, and also calculates total concentration (summed over POC fractions) Corg_conc.
  • Applies POC degradation to each discrete fraction and accumulates to variable POC_decay.
  • If do_rc_distribution = true, distributes input POC defined by Corg_sms into the Corg_<n> state variables, according to the discretised RC continuum distribution, optionally modified by multipliers specified by parameter k_dist_modifier.

References

Parameters

  • k_bin_edges[Vector{Float64}]=[1.0e-10, 1.0e-9, 1.0e-8, 1.0e-7, 1.0e-6, 1.0e-5, 0.0001, 0.001, 0.01, 0.1, 1.0, 10.0, 100.0] (yr-1), default_value=[1.0e-10, 1.0e-9, 1.0e-8, 1.0e-7, 1.0e-6, 1.0e-5, 0.0001, 0.001, 0.01, 0.1, 1.0, 10.0, 100.0], description="n-1 rate-bin edges. Organic matter reactivity is represented an initial bin for k < k_bin_edges[1], n-2 bins centered in log(k), and a final bin for k > bin_edges[end]"
  • do_RC_distribution[Bool]=true, default_value=true, description="true to transfer Corg_sms to Corg_<n>_sms according to RC initial reactivity distribution, false to just define fractions and decay"
  • k_dist_modifier[Vector{Float64}]=[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], default_value=[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], description="n multipliers for distribution of Corg input to reactivity bins (1.0 to use unmodified RC distribution)"
  • a[Float64]=0.0003 (yr-1), default_value=0.0003, description="reactive-continuum model average lifetime"
  • v[Float64]=0.125, default_value=0.125, description="reactive-continuum model shape parameter"
  • oxidant_dependent_rate[Bool]=false, default_value=false, description="true to scale decomposition rates by factor 'freminOrgTot'"
  • field_data[DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_RCmultiG_conc
    • volume (m3), VT_ReactDependency, description="cell volume (or cell phase volume eg for a sediment with solid and liquid phases)"
    • Corg_conc (mol m-3), VT_ReactProperty, description="total Corg concentration from multi G reservoirs"
    • Corg_1 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_2 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_3 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_4 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_5 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_6 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_7 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_8 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_9 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_10 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_11 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_12 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_13 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_14 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_1_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_2_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_3_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_4_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_5_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_6_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_7_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_8_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_9_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_10_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_11_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_12_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_13_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_14_conc (mol m-3), VT_ReactProperty, description="concentration"
  • do_RCmultiG_distribute_input_flux
    • Corg_sms (mol yr-1), VT_ReactTarget, description="total organic carbon reservoir source - sink (to distribute to RC fractions)"
    • Corg_1_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_2_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_3_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_4_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_5_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_6_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_7_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_8_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_9_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_10_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_11_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_12_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_13_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_14_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
  • do_RCmultiG_POC_decay
    • POC_decay (mol C yr-1), VT_ReactContributor, description="decay flux"
    • Corg_1 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_2 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_3 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_4 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_5 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_6 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_7 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_8 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_9 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_10 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_11 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_12 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_13 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_14 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_1_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_2_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_3_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_4_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_5_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_6_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_7_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_8_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_9_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_10_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_11_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_12_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_13_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_14_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
  • totals
    • Corg_4 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_11 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_9 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_1 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_14 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_10 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_2 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_8 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_5 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_12 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_3 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_6 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_7 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_13 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_4_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_11_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_9_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_1_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_14_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_10_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_2_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_8_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_5_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_12_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_3_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_6_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_7_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_13_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
source

Remin

PALEOaqchem.Remin.ReactionReminPonly — Type
ReactionReminPonly

Organic particulate matter remineralization (no oxidant use)

Parameters

  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_Ponly
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
source
PALEOaqchem.Remin.ReactionReminO2 — Type
ReactionReminO2

Organic particulate matter remineralization (O2 oxidant only)

Parameters

  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • totals
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_SO4 — Type
ReactionReminO2_SO4

Organic particulate matter remineralization (O2, SO4 oxidants)

Parameters

  • oxreminlimit[Float64]=0.008 (mol m-3), default_value=0.008, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_SO4
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_SO4_CH4 — Type
ReactionReminO2_SO4_CH4

Organic particulate matter remineralization (O2, SO4 oxidants, remaining Corg to CH4)

Parameters

  • oxreminlimit[Float64]=0.008 (mol m-3), default_value=0.008, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • SO4reminlimit[Float64]=1.0 (mol m-3), default_value=1.0, description="sulphate concentration below which use of SO4 for remineralisation is inhibited"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_SO4_CH4
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactProperty, description="2 * DIC -> methane (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • RateStoich_reminOrgOxCH4
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
    • [soluteflux_CH4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * DIC -> methane (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_Fe_SO4_CH4 — Type
ReactionReminO2_Fe_SO4_CH4

Organic particulate matter remineralization (O2, FeIIIOx, SO4 oxidants, remaining Corg to CH4)

FeIIIOxreminlimit is from (Van Cappellen and Wang, 1996), 100 umol Fe(OH)3 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 100e-6*2.5e6 = 250 mol m-3 solid phase

Parameters

  • oxreminlimit[Float64]=0.008 (mol m-3), default_value=0.008, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • FeIIIOxreminlimit[Float64]=250.0 (mol m-3), default_value=250.0, description="FeIII oxide concentration below which use of FeIII for remineralisation is inhibited"
  • SO4reminlimit[Float64]=1.0 (mol m-3), default_value=1.0, description="sulphate concentration below which use of SO4 for remineralisation is inhibited"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_Fe_SO4_CH4
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • FeIIIOx_conc (mol m-3), VT_ReactDependency, description="FeIII oxide concentration"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactProperty, description="2 * DIC -> methane (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxFeIIIOx
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_FeIIIOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_FeII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • RateStoich_reminOrgOxCH4
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
    • [soluteflux_CH4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxFeIIIOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_NN_Mn_Fe_SO4_CH4 — Type
ReactionReminO2_NN_Mn_Fe_SO4_CH4

Organic particulate matter remineralization (succesive use of O2, NO2, NO3, MnIVOx, FeIIIOx, SO4 oxidants, remaining Corg to CH4)

  • FeIIIOxreminlimit is from (Van Cappellen and Wang, 1996), 100 umol Fe(OH)3 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 100e-6*2.5e6 = 250 mol m-3 solid phase
  • MnIVOxreminlimit is from (Van Cappellen and Wang, 1996), 16 umol MnO2 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 16e-6*2.5e6 = 40 mol m-3 solid phase

Parameters

  • oxreminlimit[Float64]=0.001 (mol m-3), default_value=0.001, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • NO2reminlimit[Float64]=0.01 (mol m-3), default_value=0.01, description="NO2 concentration below which use of NO2 for remineralisation is inhibited"
  • NO3reminlimit[Float64]=0.01 (mol m-3), default_value=0.01, description="NO3 concentration below which use of NO3 for remineralisation is inhibited"
  • MnIVOxreminlimit[Float64]=40.0 (mol m-3), default_value=40.0, description="MnIV oxide concentration below which use of MnIV oxide for remineralisation is inhibited"
  • FeIIIOxreminlimit[Float64]=250.0 (mol m-3), default_value=250.0, description="FeIII oxide concentration below which use of FeIII oxide for remineralisation is inhibited"
  • SO4reminlimit[Float64]=0.5 (mol m-3), default_value=0.5, description="sulphate concentration below which use of SO4 for remineralisation is inhibited"
  • aSO4[Float64]=1.0, default_value=1.0, description="attenuation factor for sulphate reduction"
  • oxidant_dependent_rate[Bool]=false, default_value=false, description="true to scale decomposition rates by factor 'freminOrgTot'"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_NN_Mn_Fe_SO4_CH4_ox_frac
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • NO2_conc (mol m-3), VT_ReactDependency, description="NO2 concentration"
    • NO3_conc (mol m-3), VT_ReactDependency, description="NO3 concentration"
    • MnIVOx_conc (mol m-3), VT_ReactDependency, description="MnIV oxide concentration"
    • FeIIIOx_conc (mol m-3), VT_ReactDependency, description="FeIII oxide concentration"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • freminOrgO2 (), VT_ReactProperty, description="fraction of remineralization by O2"
    • freminOrgNO2 (), VT_ReactProperty, description="fraction of remineralization by NO2"
    • freminOrgNO3 (), VT_ReactProperty, description="fraction of remineralization by NO3"
    • freminOrgMnIVOx (), VT_ReactProperty, description="fraction of remineralization by MnIVOx"
    • freminOrgFeIIIOx (), VT_ReactProperty, description="fraction of remineralization by FeIIIOx"
    • freminOrgSO4 (), VT_ReactProperty, description="fraction of remineralization by SO4"
    • freminOrgCH4 (), VT_ReactProperty, description="fraction of remineralization by CH4"
  • do_remin_O2_NN_Mn_Fe_SO4_CH4_rates
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • freminOrgO2 (), VT_ReactDependency, description="fraction of remineralization by O2"
    • freminOrgNO2 (), VT_ReactDependency, description="fraction of remineralization by NO2"
    • freminOrgNO3 (), VT_ReactDependency, description="fraction of remineralization by NO3"
    • freminOrgMnIVOx (), VT_ReactDependency, description="fraction of remineralization by MnIVOx"
    • freminOrgFeIIIOx (), VT_ReactDependency, description="fraction of remineralization by FeIIIOx"
    • freminOrgSO4 (), VT_ReactDependency, description="fraction of remineralization by SO4"
    • freminOrgCH4 (), VT_ReactDependency, description="fraction of remineralization by CH4"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxNO2 (mol O2eq yr-1), VT_ReactProperty, description="3/4 NO2 consumption (-ve) by remineralization"
    • reminOrgOxNO3NO2 (mol O2eq yr-1), VT_ReactProperty, description="1/2 NO3 consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactProperty, description="2 * DIC -> methane (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxNO3NO2
    • reminOrgOxNO3NO2 (mol O2eq yr-1), VT_ReactDependency, description="1/2 NO3 consumption (-ve) by remineralization"
    • [soluteflux_NO3] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3NO2"
    • [soluteflux_NO2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3NO2"
  • RateStoich_reminOrgOxNO2
    • reminOrgOxNO2 (mol O2eq yr-1), VT_ReactDependency, description="3/4 NO2 consumption (-ve) by remineralization"
    • [soluteflux_NO2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO2"
    • [soluteflux_N2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO2"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO2"
  • RateStoich_reminOrgOxMnIVOx
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_MnIVOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
    • [soluteflux_MnII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
  • RateStoich_reminOrgOxFeIIIOx
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_FeIIIOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_FeII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • RateStoich_reminOrgOxCH4
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
    • [soluteflux_CH4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxNO2 (mol O2eq yr-1), VT_ReactDependency, description="3/4 NO2 consumption (-ve) by remineralization"
    • reminOrgOxNO3NO2 (mol O2eq yr-1), VT_ReactDependency, description="1/2 NO3 consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxNO2_total (mol O2eq yr-1), VT_ReactProperty, description="total 3/4 NO2 consumption (-ve) by remineralization"
    • reminOrgOxNO3NO2_total (mol O2eq yr-1), VT_ReactProperty, description="total 1/2 NO3 consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxFeIIIOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_NO3_Mn_Fe_SO4_CH4 — Type
ReactionReminO2_NO3_Mn_Fe_SO4_CH4

Organic particulate matter remineralization (succesive use of O2, NO3, MnIVOx, FeIIIOx, SO4 oxidants, remaining Corg to CH4)

  • FeIIIOxreminlimit is from (Van Cappellen and Wang, 1996), 100 umol Fe(OH)3 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 100e-6*2.5e6 = 250 mol m-3 solid phase
  • MnIVOxreminlimit is from (Van Cappellen and Wang, 1996), 16 umol MnO2 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 16e-6*2.5e6 = 40 mol m-3 solid phase

Parameters

  • oxreminlimit[Float64]=0.001 (mol m-3), default_value=0.001, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • NO3reminlimit[Float64]=0.01 (mol m-3), default_value=0.01, description="NO3 concentration below which use of NO3 for remineralisation is inhibited"
  • MnIVOxreminlimit[Float64]=40.0 (mol m-3), default_value=40.0, description="MnIV oxide concentration below which use of MnIV oxide for remineralisation is inhibited"
  • FeIIIOxreminlimit[Float64]=250.0 (mol m-3), default_value=250.0, description="FeIII oxide concentration below which use of FeIII oxide for remineralisation is inhibited"
  • SO4reminlimit[Float64]=0.5 (mol m-3), default_value=0.5, description="sulphate concentration below which use of SO4 for remineralisation is inhibited"
  • aSO4[Float64]=1.0, default_value=1.0, description="attenuation factor for sulphate reduction"
  • oxidant_dependent_rate[Bool]=false, default_value=false, description="true to scale decomposition rates by factor 'freminOrgTot'"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_NO3_Mn_Fe_SO4_CH4_ox_frac
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • NO3_conc (mol m-3), VT_ReactDependency, description="NO3 concentration"
    • MnIVOx_conc (mol m-3), VT_ReactDependency, description="MnIV oxide concentration"
    • FeIIIOx_conc (mol m-3), VT_ReactDependency, description="FeIII oxide concentration"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • freminOrgO2 (), VT_ReactProperty, description="fraction of remineralization by O2"
    • freminOrgNO3 (), VT_ReactProperty, description="fraction of remineralization by NO3"
    • freminOrgMnIVOx (), VT_ReactProperty, description="fraction of remineralization by MnIVOx"
    • freminOrgFeIIIOx (), VT_ReactProperty, description="fraction of remineralization by FeIIIOx"
    • freminOrgSO4 (), VT_ReactProperty, description="fraction of remineralization by SO4"
    • freminOrgCH4 (), VT_ReactProperty, description="fraction of remineralization by CH4"
  • do_remin_O2_NO3_Mn_Fe_SO4_CH4_rates
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • freminOrgO2 (), VT_ReactDependency, description="fraction of remineralization by O2"
    • freminOrgNO3 (), VT_ReactDependency, description="fraction of remineralization by NO3"
    • freminOrgMnIVOx (), VT_ReactDependency, description="fraction of remineralization by MnIVOx"
    • freminOrgFeIIIOx (), VT_ReactDependency, description="fraction of remineralization by FeIIIOx"
    • freminOrgSO4 (), VT_ReactDependency, description="fraction of remineralization by SO4"
    • freminOrgCH4 (), VT_ReactDependency, description="fraction of remineralization by CH4"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxNO3only (mol O2eq yr-1), VT_ReactProperty, description="5/4 NO3 consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactProperty, description="2 * DIC -> methane (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxNO3only
    • reminOrgOxNO3only (mol O2eq yr-1), VT_ReactDependency, description="5/4 NO3 consumption (-ve) by remineralization"
    • [soluteflux_NO3] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3only"
    • [soluteflux_N2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3only"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3only"
  • RateStoich_reminOrgOxMnIVOx
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_MnIVOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
    • [soluteflux_MnII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
  • RateStoich_reminOrgOxFeIIIOx
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_FeIIIOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_FeII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • RateStoich_reminOrgOxCH4
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
    • [soluteflux_CH4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxNO3only (mol O2eq yr-1), VT_ReactDependency, description="5/4 NO3 consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxNO3only_total (mol O2eq yr-1), VT_ReactProperty, description="total 5/4 NO3 consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
+Organic matter and remineralization · PALEOaqchem Documentation
GitHub

Organic matter and remineralization

Particulate organic carbon fluxes

PALEOaqchem.RCmultiG.ReactionRCmultiG — Type
ReactionRCmultiG

Discrete representation of organic matter reaction-continuum model from Dale (2015)

The fraction of POC having reactivity k (yr-1) in interval dk at time zero is given by the PDF:

$f(k, 0) dk = \frac{a^{\nu} k^{\nu-1} e^{-a k}}{\Gamma(\nu)} dk$

This is represented by a discrete distribution in n-2 bins spaced logarithmically in k, with additional bins at the start and end to represent POC with reactivity below and above the first and last bin.

This Reaction:

  • Defines n state variables Corg_<n> with corresponding concentrations Corg_<n>_conc and source-sink Corg_<n>_sms, and also calculates total concentration (summed over POC fractions) Corg_conc.
  • Applies POC degradation to each discrete fraction and accumulates to variable POC_decay.
  • If do_rc_distribution = true, distributes input POC defined by Corg_sms into the Corg_<n> state variables, according to the discretised RC continuum distribution, optionally modified by multipliers specified by parameter k_dist_modifier.

References

Parameters

  • k_bin_edges[Vector{Float64}]=[1.0e-10, 1.0e-9, 1.0e-8, 1.0e-7, 1.0e-6, 1.0e-5, 0.0001, 0.001, 0.01, 0.1, 1.0, 10.0, 100.0] (yr-1), default_value=[1.0e-10, 1.0e-9, 1.0e-8, 1.0e-7, 1.0e-6, 1.0e-5, 0.0001, 0.001, 0.01, 0.1, 1.0, 10.0, 100.0], description="n-1 rate-bin edges. Organic matter reactivity is represented an initial bin for k < k_bin_edges[1], n-2 bins centered in log(k), and a final bin for k > bin_edges[end]"
  • do_RC_distribution[Bool]=true, default_value=true, description="true to transfer Corg_sms to Corg_<n>_sms according to RC initial reactivity distribution, false to just define fractions and decay"
  • k_dist_modifier[Vector{Float64}]=[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], default_value=[1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], description="n multipliers for distribution of Corg input to reactivity bins (1.0 to use unmodified RC distribution)"
  • a[Float64]=0.0003 (yr-1), default_value=0.0003, description="reactive-continuum model average lifetime"
  • v[Float64]=0.125, default_value=0.125, description="reactive-continuum model shape parameter"
  • oxidant_dependent_rate[Bool]=false, default_value=false, description="true to scale decomposition rates by factor 'freminOrgTot'"
  • field_data[DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_RCmultiG_conc
    • volume (m3), VT_ReactDependency, description="cell volume (or cell phase volume eg for a sediment with solid and liquid phases)"
    • Corg_conc (mol m-3), VT_ReactProperty, description="total Corg concentration from multi G reservoirs"
    • Corg_1 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_2 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_3 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_4 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_5 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_6 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_7 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_8 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_9 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_10 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_11 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_12 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_13 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_14 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_1_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_2_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_3_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_4_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_5_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_6_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_7_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_8_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_9_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_10_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_11_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_12_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_13_conc (mol m-3), VT_ReactProperty, description="concentration"
    • Corg_14_conc (mol m-3), VT_ReactProperty, description="concentration"
  • do_RCmultiG_distribute_input_flux
    • Corg_sms (mol yr-1), VT_ReactTarget, description="total organic carbon reservoir source - sink (to distribute to RC fractions)"
    • Corg_1_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_2_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_3_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_4_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_5_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_6_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_7_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_8_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_9_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_10_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_11_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_12_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_13_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_14_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
  • do_RCmultiG_POC_decay
    • POC_decay (mol C yr-1), VT_ReactContributor, description="decay flux"
    • Corg_1 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_2 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_3 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_4 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_5 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_6 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_7 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_8 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_9 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_10 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_11 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_12 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_13 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_14 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_1_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_2_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_3_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_4_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_5_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_6_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_7_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_8_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_9_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_10_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_11_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_12_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_13_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
    • Corg_14_sms (mol yr-1), VT_ReactContributor, VF_Deriv, description="organic carbon reservoir discrete RC fraction source - sink"
  • totals
    • Corg_4 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_11 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_9 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_1 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_14 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_10 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_2 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_8 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_5 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_12 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_3 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_6 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_7 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_13 (mol), VT_ReactDependency, VF_StateExplicit, description="organic carbon reservoir discrete RC fraction"
    • Corg_4_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_11_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_9_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_1_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_14_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_10_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_2_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_8_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_5_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_12_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_3_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_6_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_7_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
    • Corg_13_total (mol), VT_ReactProperty, description="total organic carbon reservoir discrete RC fraction"
source

Remin

PALEOaqchem.Remin.ReactionReminPonly — Type
ReactionReminPonly

Organic particulate matter remineralization (no oxidant use)

Parameters

  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_Ponly
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
source
PALEOaqchem.Remin.ReactionReminO2 — Type
ReactionReminO2

Organic particulate matter remineralization (O2 oxidant only)

Parameters

  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • totals
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_SO4 — Type
ReactionReminO2_SO4

Organic particulate matter remineralization (O2, SO4 oxidants)

Parameters

  • oxreminlimit[Float64]=0.008 (mol m-3), default_value=0.008, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_SO4
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_SO4_CH4 — Type
ReactionReminO2_SO4_CH4

Organic particulate matter remineralization (O2, SO4 oxidants, remaining Corg to CH4)

Parameters

  • oxreminlimit[Float64]=0.008 (mol m-3), default_value=0.008, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • SO4reminlimit[Float64]=1.0 (mol m-3), default_value=1.0, description="sulphate concentration below which use of SO4 for remineralisation is inhibited"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_SO4_CH4
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactProperty, description="2 * DIC -> methane (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • RateStoich_reminOrgOxCH4
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
    • [soluteflux_CH4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * DIC -> methane (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_Fe_SO4_CH4 — Type
ReactionReminO2_Fe_SO4_CH4

Organic particulate matter remineralization (O2, FeIIIOx, SO4 oxidants, remaining Corg to CH4)

FeIIIOxreminlimit is from (Van Cappellen and Wang, 1996), 100 umol Fe(OH)3 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 100e-6*2.5e6 = 250 mol m-3 solid phase

Parameters

  • oxreminlimit[Float64]=0.008 (mol m-3), default_value=0.008, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • FeIIIOxreminlimit[Float64]=250.0 (mol m-3), default_value=250.0, description="FeIII oxide concentration below which use of FeIII for remineralisation is inhibited"
  • SO4reminlimit[Float64]=1.0 (mol m-3), default_value=1.0, description="sulphate concentration below which use of SO4 for remineralisation is inhibited"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_Fe_SO4_CH4
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • FeIIIOx_conc (mol m-3), VT_ReactDependency, description="FeIII oxide concentration"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactProperty, description="2 * DIC -> methane (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxFeIIIOx
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_FeIIIOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_FeII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • RateStoich_reminOrgOxCH4
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
    • [soluteflux_CH4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxFeIIIOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_NN_Mn_Fe_SO4_CH4 — Type
ReactionReminO2_NN_Mn_Fe_SO4_CH4

Organic particulate matter remineralization (succesive use of O2, NO2, NO3, MnIVOx, FeIIIOx, SO4 oxidants, remaining Corg to CH4)

  • FeIIIOxreminlimit is from (Van Cappellen and Wang, 1996), 100 umol Fe(OH)3 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 100e-6*2.5e6 = 250 mol m-3 solid phase
  • MnIVOxreminlimit is from (Van Cappellen and Wang, 1996), 16 umol MnO2 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 16e-6*2.5e6 = 40 mol m-3 solid phase

Parameters

  • oxreminlimit[Float64]=0.001 (mol m-3), default_value=0.001, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • NO2reminlimit[Float64]=0.01 (mol m-3), default_value=0.01, description="NO2 concentration below which use of NO2 for remineralisation is inhibited"
  • NO3reminlimit[Float64]=0.01 (mol m-3), default_value=0.01, description="NO3 concentration below which use of NO3 for remineralisation is inhibited"
  • MnIVOxreminlimit[Float64]=40.0 (mol m-3), default_value=40.0, description="MnIV oxide concentration below which use of MnIV oxide for remineralisation is inhibited"
  • FeIIIOxreminlimit[Float64]=250.0 (mol m-3), default_value=250.0, description="FeIII oxide concentration below which use of FeIII oxide for remineralisation is inhibited"
  • SO4reminlimit[Float64]=0.5 (mol m-3), default_value=0.5, description="sulphate concentration below which use of SO4 for remineralisation is inhibited"
  • aSO4[Float64]=1.0, default_value=1.0, description="attenuation factor for sulphate reduction"
  • oxidant_dependent_rate[Bool]=false, default_value=false, description="true to scale decomposition rates by factor 'freminOrgTot'"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_NN_Mn_Fe_SO4_CH4_ox_frac
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • NO2_conc (mol m-3), VT_ReactDependency, description="NO2 concentration"
    • NO3_conc (mol m-3), VT_ReactDependency, description="NO3 concentration"
    • MnIVOx_conc (mol m-3), VT_ReactDependency, description="MnIV oxide concentration"
    • FeIIIOx_conc (mol m-3), VT_ReactDependency, description="FeIII oxide concentration"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • freminOrgO2 (), VT_ReactProperty, description="fraction of remineralization by O2"
    • freminOrgNO2 (), VT_ReactProperty, description="fraction of remineralization by NO2"
    • freminOrgNO3 (), VT_ReactProperty, description="fraction of remineralization by NO3"
    • freminOrgMnIVOx (), VT_ReactProperty, description="fraction of remineralization by MnIVOx"
    • freminOrgFeIIIOx (), VT_ReactProperty, description="fraction of remineralization by FeIIIOx"
    • freminOrgSO4 (), VT_ReactProperty, description="fraction of remineralization by SO4"
    • freminOrgCH4 (), VT_ReactProperty, description="fraction of remineralization by CH4"
  • do_remin_O2_NN_Mn_Fe_SO4_CH4_rates
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • freminOrgO2 (), VT_ReactDependency, description="fraction of remineralization by O2"
    • freminOrgNO2 (), VT_ReactDependency, description="fraction of remineralization by NO2"
    • freminOrgNO3 (), VT_ReactDependency, description="fraction of remineralization by NO3"
    • freminOrgMnIVOx (), VT_ReactDependency, description="fraction of remineralization by MnIVOx"
    • freminOrgFeIIIOx (), VT_ReactDependency, description="fraction of remineralization by FeIIIOx"
    • freminOrgSO4 (), VT_ReactDependency, description="fraction of remineralization by SO4"
    • freminOrgCH4 (), VT_ReactDependency, description="fraction of remineralization by CH4"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxNO2 (mol O2eq yr-1), VT_ReactProperty, description="3/4 NO2 consumption (-ve) by remineralization"
    • reminOrgOxNO3NO2 (mol O2eq yr-1), VT_ReactProperty, description="1/2 NO3 consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactProperty, description="2 * DIC -> methane (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxNO3NO2
    • reminOrgOxNO3NO2 (mol O2eq yr-1), VT_ReactDependency, description="1/2 NO3 consumption (-ve) by remineralization"
    • [soluteflux_NO3] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3NO2"
    • [soluteflux_NO2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3NO2"
  • RateStoich_reminOrgOxNO2
    • reminOrgOxNO2 (mol O2eq yr-1), VT_ReactDependency, description="3/4 NO2 consumption (-ve) by remineralization"
    • [soluteflux_NO2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO2"
    • [soluteflux_N2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO2"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO2"
  • RateStoich_reminOrgOxMnIVOx
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_MnIVOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
    • [soluteflux_MnII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
  • RateStoich_reminOrgOxFeIIIOx
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_FeIIIOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_FeII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • RateStoich_reminOrgOxCH4
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
    • [soluteflux_CH4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxNO2 (mol O2eq yr-1), VT_ReactDependency, description="3/4 NO2 consumption (-ve) by remineralization"
    • reminOrgOxNO3NO2 (mol O2eq yr-1), VT_ReactDependency, description="1/2 NO3 consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxNO2_total (mol O2eq yr-1), VT_ReactProperty, description="total 3/4 NO2 consumption (-ve) by remineralization"
    • reminOrgOxNO3NO2_total (mol O2eq yr-1), VT_ReactProperty, description="total 1/2 NO3 consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxFeIIIOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
PALEOaqchem.Remin.ReactionReminO2_NO3_Mn_Fe_SO4_CH4 — Type
ReactionReminO2_NO3_Mn_Fe_SO4_CH4

Organic particulate matter remineralization (succesive use of O2, NO3, MnIVOx, FeIIIOx, SO4 oxidants, remaining Corg to CH4)

  • FeIIIOxreminlimit is from (Van Cappellen and Wang, 1996), 100 umol Fe(OH)3 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 100e-6*2.5e6 = 250 mol m-3 solid phase
  • MnIVOxreminlimit is from (Van Cappellen and Wang, 1996), 16 umol MnO2 g-1, assuming dry density is 2.5 g/cm^3 (= 2.5e6 g m^-3) = 16e-6*2.5e6 = 40 mol m-3 solid phase

Parameters

  • oxreminlimit[Float64]=0.001 (mol m-3), default_value=0.001, description="oxygen concentration below which use of O2 for remineralisation is inhibited"
  • NO3reminlimit[Float64]=0.01 (mol m-3), default_value=0.01, description="NO3 concentration below which use of NO3 for remineralisation is inhibited"
  • MnIVOxreminlimit[Float64]=40.0 (mol m-3), default_value=40.0, description="MnIV oxide concentration below which use of MnIV oxide for remineralisation is inhibited"
  • FeIIIOxreminlimit[Float64]=250.0 (mol m-3), default_value=250.0, description="FeIII oxide concentration below which use of FeIII oxide for remineralisation is inhibited"
  • SO4reminlimit[Float64]=0.5 (mol m-3), default_value=0.5, description="sulphate concentration below which use of SO4 for remineralisation is inhibited"
  • aSO4[Float64]=1.0, default_value=1.0, description="attenuation factor for sulphate reduction"
  • oxidant_dependent_rate[Bool]=false, default_value=false, description="true to scale decomposition rates by factor 'freminOrgTot'"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_remin_O2_NO3_Mn_Fe_SO4_CH4_ox_frac
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • NO3_conc (mol m-3), VT_ReactDependency, description="NO3 concentration"
    • MnIVOx_conc (mol m-3), VT_ReactDependency, description="MnIV oxide concentration"
    • FeIIIOx_conc (mol m-3), VT_ReactDependency, description="FeIII oxide concentration"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • freminOrgO2 (), VT_ReactProperty, description="fraction of remineralization by O2"
    • freminOrgNO3 (), VT_ReactProperty, description="fraction of remineralization by NO3"
    • freminOrgMnIVOx (), VT_ReactProperty, description="fraction of remineralization by MnIVOx"
    • freminOrgFeIIIOx (), VT_ReactProperty, description="fraction of remineralization by FeIIIOx"
    • freminOrgSO4 (), VT_ReactProperty, description="fraction of remineralization by SO4"
    • freminOrgCH4 (), VT_ReactProperty, description="fraction of remineralization by CH4"
  • do_remin_O2_NO3_Mn_Fe_SO4_CH4_rates
    • remin_P (mol yr-1), VT_ReactTarget, description="flux P"
    • remin_N (mol yr-1), VT_ReactTarget, description="flux N"
    • remin_Corg (mol yr-1), VT_ReactTarget, description="flux Corg"
    • remin_Ccarb (mol yr-1), VT_ReactTarget, description="flux Ccarb"
    • soluteflux_P (mol yr-1), VT_ReactContributor, description="flux P"
    • [soluteflux_TNH3] (mol yr-1), VT_ReactContributor, description="flux TNH3"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="flux DIC"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="flux TAlk"
    • freminOrgO2 (), VT_ReactDependency, description="fraction of remineralization by O2"
    • freminOrgNO3 (), VT_ReactDependency, description="fraction of remineralization by NO3"
    • freminOrgMnIVOx (), VT_ReactDependency, description="fraction of remineralization by MnIVOx"
    • freminOrgFeIIIOx (), VT_ReactDependency, description="fraction of remineralization by FeIIIOx"
    • freminOrgSO4 (), VT_ReactDependency, description="fraction of remineralization by SO4"
    • freminOrgCH4 (), VT_ReactDependency, description="fraction of remineralization by CH4"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxNO3only (mol O2eq yr-1), VT_ReactProperty, description="5/4 NO3 consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactProperty, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactProperty, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactProperty, description="2 * DIC -> methane (-ve) by remineralization"
  • RateStoich_reminOrgOxO2
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_O2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxO2"
  • RateStoich_reminOrgOxNO3only
    • reminOrgOxNO3only (mol O2eq yr-1), VT_ReactDependency, description="5/4 NO3 consumption (-ve) by remineralization"
    • [soluteflux_NO3] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3only"
    • [soluteflux_N2] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3only"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxNO3only"
  • RateStoich_reminOrgOxMnIVOx
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_MnIVOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
    • [soluteflux_MnII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxMnIVOx"
  • RateStoich_reminOrgOxFeIIIOx
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • [soluteflux_FeIIIOx] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_FeII] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxFeIIIOx"
  • RateStoich_reminOrgOxSO4
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • [soluteflux_SO4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_H2S] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
    • [soluteflux_TAlk] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxSO4"
  • RateStoich_reminOrgOxCH4
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • [soluteflux_DIC] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
    • [soluteflux_CH4] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=reminOrgOxCH4"
  • totals
    • reminOrgOxSO4 (mol O2eq yr-1), VT_ReactDependency, description="2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4 (mol O2eq yr-1), VT_ReactDependency, description="2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxNO3only (mol O2eq yr-1), VT_ReactDependency, description="5/4 NO3 consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx (mol O2eq yr-1), VT_ReactDependency, description="oxygen consumption (-ve) by remineralization"
    • reminOrgOxSO4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * sulphate consumption (-ve) by remineralization"
    • reminOrgOxO2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxMnIVOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
    • reminOrgOxCH4_total (mol O2eq yr-1), VT_ReactProperty, description="total 2 * DIC -> methane (-ve) by remineralization"
    • reminOrgOxNO3only_total (mol O2eq yr-1), VT_ReactProperty, description="total 5/4 NO3 consumption (-ve) by remineralization"
    • reminOrgOxFeIIIOx_total (mol O2eq yr-1), VT_ReactProperty, description="total oxygen consumption (-ve) by remineralization"
source
diff --git a/dev/References/index.html b/dev/References/index.html index 66399c0..020f249 100644 --- a/dev/References/index.html +++ b/dev/References/index.html @@ -1,2 +1,2 @@ -References · PALEOaqchem Documentation
GitHub

References

+References · PALEOaqchem Documentation
GitHub

References

diff --git a/dev/Secondary Redox/index.html b/dev/Secondary Redox/index.html index 586410f..b16a41f 100644 --- a/dev/Secondary Redox/index.html +++ b/dev/Secondary Redox/index.html @@ -1,2 +1,2 @@ -Secondary redox · PALEOaqchem Documentation
GitHub

Secondary redox

NB: this is just a minimal set of predefined secondary redox reactions for H2S and CH4. Use GenericReactions.ReactionAqKinetic to define additional reactions.

Sulphur

PALEOaqchem.SecondaryRedox.ReactionRedoxH2S_O2 — Type
ReactionRedoxH2S_O2

Sulphide oxidation by oxygen.

O2 + 0.5 H2S -> 0.5 SO4 + H+

Rate:

R_H2S_O2 * O2_conc * H2S_conc (mol O2 m-3 yr-1)
Rate R_H2S_O2UnitsRefNotes
1.6e5(mol l-1)-1 yr-1(Van Cappellen and Wang, 1996)
3.65e6(mol l-1)-1 yr-1(Ozaki et al., 2011)
54e6(mol l-1)-1 yr-1(Romaniello and Derry, 2010)

Parameters

  • R_H2S_O2[Float64]=3650.0 ((mol m-3)-1 yr-1), default_value=3650.0, description="rate constant"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_redox_O2_H2S
    • redox_H2S_O2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (+ve) by H2S oxidation"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • H2S_conc (mol m-3), VT_ReactDependency, description="H2S concentration"
    • volume (m3), VT_ReactDependency, description="box fluid volume"
  • RateStoich_redox_H2S_O2
    • redox_H2S_O2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (+ve) by H2S oxidation"
    • [O2_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_H2S_O2"
    • [H2S_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_H2S_O2"
    • [SO4_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_H2S_O2"
    • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_H2S_O2"
  • totals
    • redox_H2S_O2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (+ve) by H2S oxidation"
    • redox_H2S_O2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (+ve) by H2S oxidation"
source

Methane

PALEOaqchem.SecondaryRedox.ReactionRedoxCH4_O2 — Type
ReactionRedoxCH4_O2

Methane oxidation by oxygen.

O2 + 0.5 CH4 -> 0.5 DIC (CO2) + H2O

Rate:

R_CH4_O2 * O2_conc * CH4_conc (mol O2 m-3 yr-1)
Rate R_CH4_O2UnitsRefNotes
1e10(mol l-1)-1 yr-1(Van Cappellen and Wang, 1996)
10e6(mol l-1)-1 yr-1TODO

Parameters

  • R_CH4_O2[Float64]=10000.0 ((mol m-3)-1 yr-1), default_value=10000.0, description="rate constant"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_redox_O2_CH4
    • redox_CH4_O2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (+ve) by CH4 oxidation"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • CH4_conc (mol m-3), VT_ReactDependency, description="CH4 concentration"
    • volume (m3), VT_ReactDependency, description="box fluid volume"
  • RateStoich_redox_CH4_O2
    • redox_CH4_O2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (+ve) by CH4 oxidation"
    • [O2_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_O2"
    • [CH4_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_O2"
    • [DIC_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_O2"
  • totals
    • redox_CH4_O2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (+ve) by CH4 oxidation"
    • redox_CH4_O2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (+ve) by CH4 oxidation"
source
PALEOaqchem.SecondaryRedox.ReactionRedoxCH4_SO4 — Type
ReactionRedoxCH4_SO4

Methane oxidation by sulphate (anaerobic methane oxidation).

SO4-- + CH4 + 2 H+ -> DIC + H2S + 2H2O

Rate

R_CH4_SO4 * SO4_conc * CH4_conc (mol C m-3 yr-1)
Rate R_CH4_SO4UnitsRefNotes
1e4(mol l-1)-1 yr-1(Van Cappellen and Wang, 1996)k17

Parameters

  • R_CH4_SO4[Float64]=10.0 ((mol m-3)-1 yr-1), default_value=10.0, description="rate constant"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_redox_SO4_CH4
    • redox_CH4_SO4 (mol CH4/SO4 yr-1), VT_ReactProperty, description="sulphate consumption (+ve) by CH4 oxidation"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • CH4_conc (mol m-3), VT_ReactDependency, description="CH4 concentration"
    • volume (m3), VT_ReactDependency, description="box fluid volume"
  • RateStoich_redox_CH4_SO4
    • redox_CH4_SO4 (mol CH4/SO4 yr-1), VT_ReactDependency, description="sulphate consumption (+ve) by CH4 oxidation"
    • [SO4_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
    • [CH4_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
    • [DIC_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
    • [H2S_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
    • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
  • totals
    • redox_CH4_SO4 (mol CH4/SO4 yr-1), VT_ReactDependency, description="sulphate consumption (+ve) by CH4 oxidation"
    • redox_CH4_SO4_total (mol CH4/SO4 yr-1), VT_ReactProperty, description="total sulphate consumption (+ve) by CH4 oxidation"
source
+Secondary redox · PALEOaqchem Documentation
GitHub

Secondary redox

NB: this is just a minimal set of predefined secondary redox reactions for H2S and CH4. Use GenericReactions.ReactionAqKinetic to define additional reactions.

Sulphur

PALEOaqchem.SecondaryRedox.ReactionRedoxH2S_O2 — Type
ReactionRedoxH2S_O2

Sulphide oxidation by oxygen.

O2 + 0.5 H2S -> 0.5 SO4 + H+

Rate:

R_H2S_O2 * O2_conc * H2S_conc (mol O2 m-3 yr-1)
Rate R_H2S_O2UnitsRefNotes
1.6e5(mol l-1)-1 yr-1(Van Cappellen and Wang, 1996)
3.65e6(mol l-1)-1 yr-1(Ozaki et al., 2011)
54e6(mol l-1)-1 yr-1(Romaniello and Derry, 2010)

Parameters

  • R_H2S_O2[Float64]=3650.0 ((mol m-3)-1 yr-1), default_value=3650.0, description="rate constant"
  • SIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable sulphur isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_redox_O2_H2S
    • redox_H2S_O2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (+ve) by H2S oxidation"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • H2S_conc (mol m-3), VT_ReactDependency, description="H2S concentration"
    • volume (m3), VT_ReactDependency, description="box fluid volume"
  • RateStoich_redox_H2S_O2
    • redox_H2S_O2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (+ve) by H2S oxidation"
    • [O2_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_H2S_O2"
    • [H2S_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_H2S_O2"
    • [SO4_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_H2S_O2"
    • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_H2S_O2"
  • totals
    • redox_H2S_O2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (+ve) by H2S oxidation"
    • redox_H2S_O2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (+ve) by H2S oxidation"
source

Methane

PALEOaqchem.SecondaryRedox.ReactionRedoxCH4_O2 — Type
ReactionRedoxCH4_O2

Methane oxidation by oxygen.

O2 + 0.5 CH4 -> 0.5 DIC (CO2) + H2O

Rate:

R_CH4_O2 * O2_conc * CH4_conc (mol O2 m-3 yr-1)
Rate R_CH4_O2UnitsRefNotes
1e10(mol l-1)-1 yr-1(Van Cappellen and Wang, 1996)
10e6(mol l-1)-1 yr-1TODO

Parameters

  • R_CH4_O2[Float64]=10000.0 ((mol m-3)-1 yr-1), default_value=10000.0, description="rate constant"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_redox_O2_CH4
    • redox_CH4_O2 (mol O2 yr-1), VT_ReactProperty, description="oxygen consumption (+ve) by CH4 oxidation"
    • O2_conc (mol m-3), VT_ReactDependency, description="O2 concentration"
    • CH4_conc (mol m-3), VT_ReactDependency, description="CH4 concentration"
    • volume (m3), VT_ReactDependency, description="box fluid volume"
  • RateStoich_redox_CH4_O2
    • redox_CH4_O2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (+ve) by CH4 oxidation"
    • [O2_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_O2"
    • [CH4_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_O2"
    • [DIC_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_O2"
  • totals
    • redox_CH4_O2 (mol O2 yr-1), VT_ReactDependency, description="oxygen consumption (+ve) by CH4 oxidation"
    • redox_CH4_O2_total (mol O2 yr-1), VT_ReactProperty, description="total oxygen consumption (+ve) by CH4 oxidation"
source
PALEOaqchem.SecondaryRedox.ReactionRedoxCH4_SO4 — Type
ReactionRedoxCH4_SO4

Methane oxidation by sulphate (anaerobic methane oxidation).

SO4-- + CH4 + 2 H+ -> DIC + H2S + 2H2O

Rate

R_CH4_SO4 * SO4_conc * CH4_conc (mol C m-3 yr-1)
Rate R_CH4_SO4UnitsRefNotes
1e4(mol l-1)-1 yr-1(Van Cappellen and Wang, 1996)k17

Parameters

  • R_CH4_SO4[Float64]=10.0 ((mol m-3)-1 yr-1), default_value=10.0, description="rate constant"
  • CIsotope[external, DataType]=PALEOboxes.ScalarData, default_value=PALEOboxes.ScalarData, allowed_values=Type[PALEOboxes.ScalarData, PALEOboxes.IsotopeLinear], description="disable / enable carbon isotopes and specify isotope type"

Methods and Variables for default Parameters

  • do_redox_SO4_CH4
    • redox_CH4_SO4 (mol CH4/SO4 yr-1), VT_ReactProperty, description="sulphate consumption (+ve) by CH4 oxidation"
    • SO4_conc (mol m-3), VT_ReactDependency, description="SO4 concentration"
    • CH4_conc (mol m-3), VT_ReactDependency, description="CH4 concentration"
    • volume (m3), VT_ReactDependency, description="box fluid volume"
  • RateStoich_redox_CH4_SO4
    • redox_CH4_SO4 (mol CH4/SO4 yr-1), VT_ReactDependency, description="sulphate consumption (+ve) by CH4 oxidation"
    • [SO4_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
    • [CH4_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
    • [DIC_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
    • [H2S_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
    • [TAlk_sms] (mol yr-1), VT_ReactContributor, description="generated by RateStoich rate=redox_CH4_SO4"
  • totals
    • redox_CH4_SO4 (mol CH4/SO4 yr-1), VT_ReactDependency, description="sulphate consumption (+ve) by CH4 oxidation"
    • redox_CH4_SO4_total (mol CH4/SO4 yr-1), VT_ReactProperty, description="total sulphate consumption (+ve) by CH4 oxidation"
source
diff --git a/dev/functions/index.html b/dev/functions/index.html index 43c3f8d..2b1fde5 100644 --- a/dev/functions/index.html +++ b/dev/functions/index.html @@ -6,4 +6,4 @@ (-138.0, -17.0) julia> PALEOaqchem.O2AlkUptakeRemin(106.0, (0.0, 16.0, 0.0), 1.0, 0.0) # Corg:TNH3:P = 106:16:1 -(-106.0, 15.0)source +(-106.0, 15.0)source diff --git a/dev/index.html b/dev/index.html index f73c8cd..aea1a36 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,3 +1,3 @@ PALEOaqchem.jl · PALEOaqchem Documentation
GitHub

PALEOaqchem.jl

Aquatic biogeochemistry components for the PALEOtoolkit biogeochemical model framework.

The PALEOaqchem package implements biogeochemistry components that provide:

  • representation of organic matter phases (as discrete reactivity fractions or as a reactive-continuum model) and remineralization by oxygen, nitrogen, manganese, iron, sulphur and disproportionation to methane.
  • generic equilibrium, kinetic, and precipitation-dissolution reactions, which can be configured into reaction networks using the PALEO YAML configuration file.
  • pre-packaged reactions to simplify implementation of marine carbonate chemistry and a subset of secondary redox reactions, including support for carbon and sulphur isotope systems.

It can be used in two main ways:

  • to construct arbitrary aqueous biogeochemical models, including equilibrium, kinetic and precipitation-dissolution reactions for a configurable set of solute and solid-phase species.
  • to construct more-or-less standard ocean or sediment biogeochemical models (with commonly used carbonate chemistry, primary and secondary redox reactions) out of predefined components.

Installation

The PALEOaqchem Reactions are available to the PALEOtoolkit framework when the registered PALEOaqchem package is installed and loaded:

julia> Pkg.add("PALEOaqchem")  # install PALEOaqchem in currently active Julia environment
-julia> import PALEOaqchem

Examples of usage

The PALEOtutorials repository includes a minimal model of the marine carbonate system implementated using PALEOaqchem generic chemistry.

The PALEOocean and PALEOsediment include examples of water column and sediment biogeochemistry.

+julia> import PALEOaqchem

Examples of usage

The PALEOtutorials repository includes a minimal model of the marine carbonate system implementated using PALEOaqchem generic chemistry.

The PALEOocean and PALEOsediment include examples of water column and sediment biogeochemistry.

diff --git a/dev/indexpage/index.html b/dev/indexpage/index.html index 408d619..2b3f887 100644 --- a/dev/indexpage/index.html +++ b/dev/indexpage/index.html @@ -1,2 +1,2 @@ -Index · PALEOaqchem Documentation
GitHub

Index

+Index · PALEOaqchem Documentation
GitHub

Index

diff --git a/dev/objects.inv b/dev/objects.inv index b66c9e1..c22211e 100644 Binary files a/dev/objects.inv and b/dev/objects.inv differ