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Add carbonateconversion!, clean up other metal/oxide conversions
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@brenhinkeller
brenhinkeller committed Mar 6, 2024
1 parent 70a5081 commit 7bd7280
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119 changes: 75 additions & 44 deletions src/utilities/Geochemistry.jl
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"""
```julia
dataset = oxideconversion(dataset::Dict; unitratio::Number=10000)
converted_dataset = oxideconversion(dataset::Union{Dict,NamedTuple}; unitratio::Number=10000)
```
Convert major elements (Ti, Al, etc.) into corresponding oxides (TiO2, Al2O3, ...).
If metals are as PPM, set unitratio=10000 (default); if metals are as wt%,
set unitratio = 1
As `oxideconversion!`, but returning a copy rather than modifying in-place
"""
function oxideconversion(dataset::Dict; unitratio::Number=10000)
result = copy(dataset)
return oxideconversion!(result)
end
oxideconversion(ds::Union{Dict,NamedTuple}; kwargs...) = oxideconversion!(deepcopy(ds); kwargs...)
export oxideconversion

"""
```julia
dataset = oxideconversion!(dataset::Dict; unitratio::Number=10000)
oxideconversion!(dataset::Dict; unitratio::Number=10000)
```
Convert major elements (Ti, Al, etc.) into corresponding oxides (TiO2, Al2O3, ...) in place.
Convert major elements (Ti, Al, etc.) into corresponding oxides (TiO2, Al2O3, ...) in place if extant.
If metals are as PPM, set unitratio=10000 (default); if metals are as wt%,
If metals are expected as PPM, set unitratio=10000 (default); if metals are as wt%,
set unitratio = 1
"""
function oxideconversion!(dataset::Dict; unitratio::Number=10000)
# Convert major elements (Ti, Al, etc.) into corresponding oxides (TiO2, Al2O3)...
# for i ∈ eachindex(source)
# conversionfactor(i)=mass.percation.(dest[i])./mass.(source[i]);
# end
# Array of elements to convert
source = ("Si","Ti","Al","Fe","Fe","Mg","Ca","Mn","Li","Na","K","P","Cr","Ni","Co","C","S","H")
dest = ("SiO2","TiO2","Al2O3","FeOT","Fe2O3T","MgO","CaO","MnO","Li2O","Na2O","K2O","P2O5","Cr2O3","NiO","CoO","CO2","SO2","H2O")
See also `oxideconversion`, c.f. `metalconversion!`
"""
function oxideconversion!(dataset::NamedTuple; unitratio::Number=10000)
# List of elements to convert
source = (:Si, :Ti, :Al, :Fe, :Fe, :Mg, :Ca, :Mn, :Li, :Na, :K, :P, :Cr, :Ni, :Co, :C, :S, :H)
dest = (:SiO2, :TiO2, :Al2O3, :FeOT, :Fe2O3T, :MgO, :CaO, :MnO, :Li2O, :Na2O, :K2O, :P2O5, :Cr2O3, :NiO, :CoO, :CO2, :SO2, :H2O)
conversionfactor = (2.13932704290547,1.66847584248889,1.88944149488507,1.28648836426407,1.42973254639611,1.65825961736268,1.39919258253823,1.29121895771597,2.1526657060518732,1.34795912485574,1.20459963614796,2.29133490474735,1.46154369861159,1.27258582901258,1.27147688434143,3.66405794688203,1.99806612601372,8.93601190476191)

# If source field exists, fill in destination from source
for i ∈ eachindex(source)
if haskey(dataset, source[i])
if ~haskey(dataset, dest[i]) # If destination field doesn't exist, make it.
dataset[dest[i]] = fill(NaN, size(dataset[source[i]]))
if haskey(dataset, "elements")
dataset["elements"] = dataset["elements"] ∪ (dest[i],)
end
if haskey(dataset, dest[i]) # If destination field doesn't exist, make it.
oxide, metal = dataset[dest[i]], dataset[source[i]]
fillifnan!(oxide, metal, conversionfactor[i]/unitratio)
end
oxide = dataset[dest[i]]
metal = dataset[source[i]]
fillifnan!(oxide, metal, conversionfactor[i]/unitratio)
end
end

return dataset
end
oxideconversion!(ds::Dict; kwargs...) = (oxideconversion!(TupleDataset(ds); kwargs...); ds)
export oxideconversion!

function oxideconversion!(dataset::NamedTuple; unitratio::Number=10000)
# Convert major elements (Ti, Al, etc.) into corresponding oxides (TiO2, Al2O3)...
# for i ∈ eachindex(source)
# conversionfactor(i)=mass.percation.(dest[i])./mass.(source[i]);
# end

# Array of elements to convert
source = (:Si, :Ti, :Al, :Fe, :Fe, :Mg, :Ca, :Mn, :Li, :Na, :K, :P, :Cr, :Ni, :Co, :C, :S, :H)
dest = (:SiO2, :TiO2, :Al2O3, :FeOT, :Fe2O3T, :MgO, :CaO, :MnO, :Li2O, :Na2O, :K2O, :P2O5, :Cr2O3, :NiO, :CoO, :CO2, :SO2, :H2O)
conversionfactor = (2.13932704290547,1.66847584248889,1.88944149488507,1.28648836426407,1.42973254639611,1.65825961736268,1.39919258253823,1.29121895771597,2.1526657060518732,1.34795912485574,1.20459963614796,2.29133490474735,1.46154369861159,1.27258582901258,1.27147688434143,3.66405794688203,1.99806612601372,8.93601190476191)
"""
```julia
converted_dataset = metalconversion(dataset::Union{Dict,NamedTuple}; unitratio::Number=10000)
```
As `metalconversion!`, but returning a copy rather than modifying in-place
"""
metalconversion(ds::Union{Dict,NamedTuple}; kwargs...) = metalconversion!(copy(ds); kwargs...)
export metalconversion

"""
```julia
dataset = metalconversion!(dataset::Union{Dict,NamedTuple}; unitratio::Number=10000)
```
Convert minor element oxides (MnO, Cr2O3, NiO, ...) into corresponding metals (Mn, Cr, Ni, ...) in place if extant.
If metals are expected as parts per million (ppm), set unitratio=10000 (default); if metals are as wt%, set unitratio = 1
See also `metalconversion`, c.f. `oxideconversion!`
"""
function metalconversion!(dataset::NamedTuple; unitratio::Number=10000)
# List of elements to convert
dest = (:Mn, :P, :Cr, :Ni, :Co, :Sr, :Ba, :Li, :S,)
source = (:MnO, :P2O5, :Cr2O3, :NiO, :CoO, :SrO, :BaO, :Li2O, :SO3)
conversionfactor = (0.7744619872751028, 0.4364268173666496, 0.6842080746199798, 0.785801615263874, 0.786486968277016, 0.8455993051534453, 0.8956541815613328, 0.46454031259412965, 0.4004646689233921)

# If source field exists, fill in destination from source
for i ∈ eachindex(source)
if haskey(dataset, source[i])
if haskey(dataset, dest[i]) # If destination field doesn't exist, make it.
oxide = dataset[dest[i]]
metal = dataset[source[i]]
fillifnan!(oxide, metal, conversionfactor[i]/unitratio)
metal, oxide = dataset[dest[i]], dataset[source[i]]
fillifnan!(metal, oxide, conversionfactor[i]*unitratio)
end
end
end

return dataset
end
export oxideconversion!
metalconversion!(ds::Dict; kwargs...) = (metalconversion!(TupleDataset(ds); kwargs...); ds)
export metalconversion!



"""
```julia
carbonateconversion!(dataset::NamedTuple)
```
Convert carbonates (CaCO3, MgCO3) into corresponding metal oxides and CO2 if extant, in place.
"""
function carbonateconversion!(ds::NamedTuple)
source = (:CaCO3, :CaCO3, :MgCO3, :MgCO3, :TIC,)
dest = (:CaO, :CO2, :MgO, :CO2, :CO2)
conversionfactor = (0.5602899095181764, 0.43971009048182363, 0.4780282993132732, 0.5219717006867268, 3.664057946882025)
if haskey(ds, :CaCO3) && haskey(ds, :MgCO3)
t = .!(isnan.(ds.CaCO3) .| isnan.(ds.MgCO3))
if haskey(ds, :CO2)
fillifnan!(ds.CO2, ds.CaCO3*0.43971009048182363 .+ ds.MgCO3*0.5219717006867268, 1)
end
end
for i in eachindex(source)
if haskey(ds, source[i])
if haskey(ds, dest[i])
d, s = ds[dest[i]], ds[source[i]]
fillifnan!(d, s, conversionfactor[i])
end
end
end
return ds
end
carbonateconversion!(ds::Dict) = (carbonateconversion!(TupleDataset(ds)); ds)
export carbonateconversion!

## --- Chemical Index of Alteration

# Chemical Index of Alteration as defined by Nesbitt and Young, 1982
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10 changes: 5 additions & 5 deletions src/utilities/Import.jl
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La = Vector{Float64}(100,) [0.44094669199955616 ... 0.5371416189174069]
```
"""
function TupleDataset(d::Dict, elements=keys(d))
function TupleDataset(d::Dict, elements=haskey(d,"elements") ? d["elements"] : keys(d))
symbols = symboltuple(sanitizevarname.(elements))
return NamedTuple{symbols}(d[e] for e in elements)
end
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```
"""
concatenatedatasets(args...; kwargs...) = concatenatedatasets((args...,); kwargs...)
function concatenatedatasets(dst::Tuple; elements=Symbol[])
function concatenatedatasets(dst::Tuple; kwargs...)
if length(dst) == 1
only(dst)
elseif length(dst) == 2
concatenatedatasets(dst[1], dst[2]; elements)
concatenatedatasets(dst[1], dst[2]; kwargs...)
else
c = concatenatedatasets(dst[1], dst[2]; elements)
concatenatedatasets((c, dst[3:end]...); elements)
c = concatenatedatasets(dst[1], dst[2]; kwargs...)
concatenatedatasets((c, dst[3:end]...); kwargs...)
end
end
function concatenatedatasets(d1::AbstractDict, d2::AbstractDict; elements=String[])
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39 changes: 26 additions & 13 deletions test/testGeochemistry.jl
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@test eustar(34.7773, 6.5433, 5.9037, 0.8904) ≈ 2.0825737578695205

# Iron oxide conversions

@test feoconversion(3.5, NaN, NaN, NaN) == 3.5
@test feoconversion(3.5, NaN, 7.5, NaN) == 7.5
@test feoconversion(3.5, NaN, 7.5, 10) == 7.5
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@test isnan(feoconversion(NaN, NaN, NaN, NaN))

# Other oxide conversion
D = elementify(["Fe" "Mg" "Ca" "P"; 10000 10000 10000 10000; 10000 10000 10000 10000], importas=:Dict)
D = oxideconversion(D)
@test all(D["FeOT"] .≈ (molarmass["Fe"]+molarmass["O"])/molarmass["Fe"])
@test all(D["MgO"] .≈ (molarmass["Mg"]+molarmass["O"])/molarmass["Mg"])
@test all(D["CaO"] .≈ (molarmass["Ca"]+molarmass["O"])/molarmass["Ca"])
@test all(D["P2O5"] .≈ (molarmass["P"]+2.5*molarmass["O"])/molarmass["P"])


DT = elementify(unelementify(D), importas=:Tuple)
for e in (:FeOT, :MgO, :CaO, :P2O5)
DT[e] .= NaN
end
D = ["Fe" "Mg" "Ca" "P" "FeOT" "MgO" "CaO" "P2O5"; 10000 10000 10000 10000 NaN NaN NaN NaN; 10000 10000 10000 10000 NaN NaN NaN NaN]
M = elementify(D, importas=:Dict)
O = oxideconversion(M)
@test all(O["FeOT"] .≈ (molarmass["Fe"]+molarmass["O"])/molarmass["Fe"])
@test all(O["MgO"] .≈ (molarmass["Mg"]+molarmass["O"])/molarmass["Mg"])
@test all(O["CaO"] .≈ (molarmass["Ca"]+molarmass["O"])/molarmass["Ca"])
@test all(O["P2O5"] .≈ (molarmass["P"]+2.5*molarmass["O"])/molarmass["P"])

DT = deepcopy(TupleDataset(M))
oxideconversion!(DT)
@test all(DT.FeOT .≈ (molarmass["Fe"]+molarmass["O"])/molarmass["Fe"])
@test all(DT.MgO .≈ (molarmass["Mg"]+molarmass["O"])/molarmass["Mg"])
@test all(DT.CaO .≈ (molarmass["Ca"]+molarmass["O"])/molarmass["Ca"])
@test all(DT.P2O5 .≈ (molarmass["P"]+2.5*molarmass["O"])/molarmass["P"])

D = ["NiO" "CoO" "BaO" "SO3" "Ni" "Co" "Ba" "S"; 1 1 1 1 NaN NaN NaN NaN; 1 1 1 1 NaN NaN NaN NaN]
O = elementify(D, importas=:Dict)
M = metalconversion(O)
@test all(M["Ni"] .≈ 10000molarmass["Ni"]/(molarmass["Ni"]+molarmass["O"]))
@test all(M["Co"] .≈ 10000molarmass["Co"]/(molarmass["Co"]+molarmass["O"]))
@test all(M["Ba"] .≈ 10000molarmass["Ba"]/(molarmass["Ba"]+molarmass["O"]))
@test all(M["S"] .≈ 10000molarmass["S"]/(molarmass["S"]+3molarmass["O"]))


# Carbonate conversions
D = ["CaCO3" "MgCO3" "CaO" "MgO" "CO2"; 1 1 NaN NaN NaN; 1 1 NaN NaN NaN]
C = elementify(D, importas=:Dict)
carbonateconversion!(C)
@test all(C["MgO"] .≈ (molarmass["Mg"]+molarmass["O"])/(molarmass["Mg"]+molarmass["C"]+3molarmass["O"]))
@test all(C["CaO"] .≈ (molarmass["Ca"]+molarmass["O"])/(molarmass["Ca"]+molarmass["C"]+3molarmass["O"]))
@test all(C["CO2"] .≈ (molarmass["C"]+2molarmass["O"])/(molarmass["Ca"]+molarmass["C"]+3molarmass["O"]) + (molarmass["C"]+2molarmass["O"])/(molarmass["Mg"]+molarmass["C"]+3molarmass["O"]))

# Weathering indices
@test CIA(14.8577, 4.5611, 3.29641, 2.3992) ≈ 47.66582778067264
@test WIP(3.2964, 4.5611, 2.3992, 5.9121) ≈ 78.40320264846837
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