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Geochemistry.jl
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Geochemistry.jl
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## --- Calculate Eu*
"""
```julia
eustar(Nd::Number, Sm::Number, Gd::Number, Tb::Number)
```
Calculate expected europium concentration, Eu*, based on abundance of
adjacent rare earths.
Full four-element log-linear interpolation, assuming 3+ ionic radii and the
chondritic abundances of Sun and McDonough 1989 (doi: 10.1144/gsl.sp.1989.042.01.19)
"""
function eustar(Nd::Number, Sm::Number, Gd::Number, Tb::Number)
# Ionic radii, in pm [Tb, Gd, Sm, Nd]
r = [106.3, 107.8, 109.8, 112.3] # or x = [1, 2, 4, 6]
# Normalize to chondrite
y = log.([Tb/0.0374, Gd/0.2055, Sm/0.1530, Nd/0.4670])
notnan = .!isnan.(y)
# Make sure we're interpolating and not extrapolating
if any(view(notnan, 1:2)) && any(view(notnan, 3:4))
# Fit a straight line through the chondrite-normalized values
x = r[notnan]
(a,b) = hcat(fill!(similar(x), 1), x) \ y[notnan]
# De-dormalize output for Eu, interpolating at r = 108.7 pm or x = 3
eu_interp = 0.0580*exp(a + b*108.7)
else
eu_interp = NaN
end
return eu_interp
end
"""
```julia
eustar(Sm::Number, Gd::Number)
```
Calculate expected europium concentration, Eu*, based on abundance of
adjacent rare earths.
Simple geometric mean interpolation from Sm and Gd alone, assuming the chondritic
abundances of Sun and McDonough 1989 (doi: 10.1144/gsl.sp.1989.042.01.19), that is
Eu* = `0.0580*sqrt(Sm/0.1530 * Gd/0.2055)`
"""
function eustar(Sm::Number, Gd::Number)
# Geometric mean in regular space is equal to the arithmetic mean in log space. Fancy that!
return 0.0580*sqrt(Sm/0.1530 * Gd/0.2055)
end
export eustar
## --- CIPW norm
"""
```julia
cipw_norm(SiO2, TiO2, Al2O3, Fe2O3, FeO, MnO, MgO, CaO, Na2O, K2O, P2O5)
```
Returns
```
quartz, orthoclase, plagioclase, corundum, nepheline, diopside, orthopyroxene, olivine, magnetite, ilmenite, apatite
```
"""
function cipw_norm(SiO2, TiO2, Al2O3, Fe2O3, FeO, MnO, MgO, CaO, Na2O, K2O, P2O5)
SiO2 /= 60.0843
TiO2 /= 79.8988
Al2O3 /= 101.9613
Fe2O3 /= 159.6922
FeO /= 71.8464
MnO /= 70.9374
MgO /= 40.3044
CaO /= 56.0794
Na2O /= 61.9789
K2O /= 94.1960
P2O5 /= 141.9445
FeO = nanadd(FeO, MnO)
CaO -= 3.333333333333333 * P2O5
apatite = 0.6666666666666666 * P2O5
# P2O5 = 0
FeO -= TiO2
ilmenite = TiO2
FeO -= Fe2O3
magnetite = Fe2O3
# Fe2O3 = 0
Al2O3 -= K2O
orthoclase = K2O
# K2O = 0
Al2O3 -= Na2O
albite = Na2O
if CaO > Al2O3
CaO -= Al2O3
anorthite = Al2O3
Al2O3 = 0
else
Al2O3 -= CaO
anorthite = CaO
CaO = 0
end
if Al2O3 > 0
corundum = Al2O3
Al2O3 = 0
else
corundum = 0
end
Mg′ = MgO / (MgO + FeO)
FMO = FeO + MgO
FMO_weight = (Mg′*40.3044)+((1-Mg′)*71.8464)
if CaO > 0
FMO -= CaO
diopside = CaO
else
diopside = 0
end
orthopyroxene = FMO
pSi1 = 6orthoclase + 6albite + 2anorthite + 2diopside + orthopyroxene
if pSi1 < SiO2
quartz = SiO2 - pSi1
nepheline = 0
olivine = 0
else
quartz = 0
pSi2 = 6orthoclase + 6albite + 2anorthite + 2diopside
pSi3 = SiO2 - pSi2
if FMO > 2pSi3
orthopyroxene = 0
olivine = FMO
FMO = 0
pSi4 = 6orthoclase + 2anorthite + 2diopside + 0.5olivine
pSi5 = SiO2 - pSi4
Albite = (pSi5-(2*Na2O))/4
nepheline = Na2O-Albite
else
nepheline = 0
orthopyroxene = 2pSi3 - FMO
olivine = FMO - pSi3
end
end
orthoclase *= 2
nepheline *= 2
albite *= 2
An′ = anorthite/(anorthite+albite)
plag_weight = (An′*278.2093)+((1-An′)*262.2230)
plagioclase = albite+anorthite
quartz *= 60.0843
orthoclase *= 278.3315
plagioclase *= plag_weight
corundum *= 101.9613
nepheline *= 142.0544
diopside *= (172.248 + FMO_weight)
orthopyroxene *= (60.0843 + FMO_weight)
olivine *= (60.0843 + 2FMO_weight)
magnetite *= 231.5386
ilmenite *= 151.7452
apatite *= 504.3152
return (quartz=quartz, orthoclase=orthoclase, plagioclase=plagioclase,
corundum=corundum, nepheline=nepheline, diopside=diopside,
orthopyroxene=orthopyroxene, olivine=olivine, magnetite=magnetite,
ilmenite=ilmenite, apatite=apatite)
end
# export cipw_norm
## --- Fe oxide conversions
"""
```julia
feoconversion(FeO::Number=NaN, Fe2O3::Number=NaN, FeOT::Number=NaN, Fe2O3T::Number=NaN)
```
Compiles data from FeO, Fe2O3, FeOT, and Fe2O3T into a single FeOT value.
"""
function feoconversion(FeO::Number=NaN, Fe2O3::Number=NaN, FeOT::Number=NaN, Fe2O3T::Number=NaN)
# To convert from Fe2O3 wt % to FeO wt %, multiply by
conversionfactor = (55.845+15.999) / (55.845+1.5*15.999)
# If FeOT or Fe2O3T already exists, use that
if isnan(FeOT)
if isnan(Fe2O3T)
if isnan(Fe2O3)
FeOT = FeO
elseif isnan(FeO)
FeOT = Fe2O3*conversionfactor
else
FeOT = Fe2O3*conversionfactor + FeO
end
else
FeOT=Fe2O3T*conversionfactor
end
end
return FeOT
end
export feoconversion
## --- Oxide conversions
function fillifnan!(dest::AbstractArray, source::AbstractArray)
@inbounds for i in eachindex(dest, source)
if isnan(dest[i]) && !isnan(source[i])
dest[i] = source[i]
end
end
return dest
end
function fillifnan!(dest::AbstractArray, source::AbstractArray, factor::Number)
@inbounds for i in eachindex(dest, source)
if isnan(dest[i]) && !isnan(source[i])
dest[i] = source[i] * factor
end
end
return dest
end
function nannegative!(a::AbstractArray)
@inbounds for i in eachindex(a)
if a[i] < 0
a[i] = NaN
end
end
return a
end
"""
```julia
converted_dataset = oxideconversion(dataset::Union{Dict,NamedTuple}; unitratio::Number=10000)
```
As `oxideconversion!`, but returning a copy rather than modifying in-place
"""
oxideconversion(ds::Union{Dict,NamedTuple}; kwargs...) = oxideconversion!(deepcopy(ds); kwargs...)
export oxideconversion
"""
```julia
oxideconversion!(dataset::Dict; unitratio::Number=10000)
```
Convert major elements (Ti, Al, etc.) into corresponding oxides (TiO2, Al2O3, ...) in place if extant.
If metals are expected as PPM, set unitratio=10000 (default); if metals are as wt%,
set unitratio = 1
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, :S, :H)
dest = (:SiO2, :TiO2, :Al2O3, :FeOT, :Fe2O3T, :MgO, :CaO, :MnO, :Li2O, :Na2O, :K2O, :P2O5, :Cr2O3, :NiO, :CoO, :SO3, :H2O)
conversionfactor = (2.13932704290547,1.66847584248889,1.88944149488507,1.28648836426407,1.42973254639611,1.65825961736268,1.39919258253823,1.29121895771597,2.1526657060518732,1.34795912485574,1.20459963614796,2.29133490474735,1.46154369861159,1.27258582901258,1.27147688434143,2.4970991890205863,8.93601190476191)
@assert eachindex(source) == eachindex(dest) == eachindex(conversionfactor)
# 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, metal = dataset[dest[i]], dataset[source[i]]
fillifnan!(oxide, metal, conversionfactor[i]/unitratio)
end
end
end
return dataset
end
oxideconversion!(ds::Dict; kwargs...) = (oxideconversion!(TupleDataset(ds); kwargs...); ds)
export oxideconversion!
"""
```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.
metal, oxide = dataset[dest[i]], dataset[source[i]]
fillifnan!(metal, oxide, conversionfactor[i]*unitratio)
end
end
end
return dataset
end
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,
as well as synchonizing TIC, TOC, TC, C and CO2. All are assumed to be reported in the same units,
(likely wt. %) except for C, which is assumed to be equivalent to unitratio * TC,
"""
function carbonateconversion!(ds::NamedTuple; unitratio=10000)
# Calculate CO2 if both CaCO3 and MgCO3 are reported
if haskey(ds, :CaCO3) && haskey(ds, :MgCO3) && haskey(ds, :CO2)
fillifnan!(ds.CO2, ds.CaCO3*0.43971009048182363 .+ ds.MgCO3*0.5219717006867268)
end
# Populate oxides and CO2 from carbonates and TIC
source = (:CaCO3, :CaCO3, :MgCO3, :MgCO3, :TIC,)
dest = (:CaO, :CO2, :MgO, :CO2, :CO2)
conversionfactor = (0.5602899095181764, 0.43971009048182363, 0.4780282993132732, 0.5219717006867268, 3.664057946882025)
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
# Fill TC from C and TIC from CO2
if haskey(ds,:TC) && haskey(ds, :C)
fillifnan!(ds.TC, ds.C, 1e-4)
end
if haskey(ds,:TIC) && haskey(ds, :CO2)
fillifnan!(ds.TIC, ds.CO2, 0.27292144788565975)
end
# Synchronise TOC, TIC, TC
if haskey(ds, :TC) && haskey(ds, :TOC) && haskey(ds, :TIC)
fillifnan!(ds.TC, ds.TOC + ds.TIC)
fillifnan!(ds.TOC, ds.TC - ds.TIC)
nannegative!(ds.TOC)
fillifnan!(ds.TIC, ds.TC - ds.TOC)
nannegative!(ds.TIC)
if haskey(ds, :CO2)
# If we have new TIC values, fill CO2 again
fillifnan!(ds.CO2, ds.TIC, 3.664057946882025)
end
end
# Fill C from any available source
if haskey(ds,:TC) && haskey(ds, :C)
fillifnan!(ds.C, ds.TC, 1e4)
end
if haskey(ds,:TOC) && haskey(ds,:TIC) && haskey(ds, :C)
fillifnan!(ds.C, ds.TOC + ds.TIC, 1e4)
end
if haskey(ds,:TOC) && haskey(ds,:CO2) && haskey(ds, :C)
fillifnan!(ds.C, ds.TOC + ds.CO2/3.664057946882025, 1e4)
end
if haskey(ds,:TOC) && haskey(ds, :C)
fillifnan!(ds.C, ds.TOC, 1e4)
end
if haskey(ds,:TIC) && haskey(ds, :C)
fillifnan!(ds.C, ds.TIC, 1e4)
end
if haskey(ds,:CO2) && haskey(ds, :C)
fillifnan!(ds.C, ds.CO2, 1e4/3.664057946882025)
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
# Note that CaO should be only igneous CaO excluding any Ca from calcite or apatite
function CIA(Al2O3::Number, CaO::Number, Na2O::Number, K2O::Number)
A = Al2O3 / 101.96007714
C = CaO / 56.0774
N = Na2O / 61.978538564
K = K2O / 94.19562
return A / (A + C + N + K) * 100
end
export CIA
# "Weathering Index of Parker" as defined by Parker, 1970
function WIP(Na2O::Number, MgO::Number, K2O::Number, CaO::Number)
Na = Na2O / 30.9895
Mg = MgO / 40.3044
K = K2O / 47.0980
Ca = CaO / 56.0774
# Denominator for each element is a measure of Nicholls' bond strengths
return (Na/0.35 + Mg/0.9 + K/0.25 + Ca/0.7) * 100
end
export WIP
## --- MELTS interface
"""
```julia
melts_configure(meltspath::String, scratchdir::String, composition::Collection{Number},
\telements::Collection{String},
\tT_range=(1400, 600),
\tP_range=(10000,10000);)
```
Configure and run a MELTS simulation using alphaMELTS.
Optional keyword arguments and defaults include:
batchstring::String = "1\nsc.melts\n10\n1\n3\n1\nliquid\n1\n1.0\n0\n10\n0\n4\n0\n"
A string defining the sequence of options that would be entered to produce
the desired calculation if running alphaMELTS at the command line. The
default string specifies a batch calculation starting at the liquidus.
dT = -10
The temperature step, in degrees, between each step of the MELTS calculation
dP = 0
The pressure step, in bar, between each step of the MELTS calculation
index = 1
An optional variable used to specify a unique suffix for the run directory name
version::String = "pMELTS"
A string specifying the desired version of MELTS. Options include `MELTS` and `pMELTS`.
mode::String = "isobaric"
A string specifying the desired calculation mode for MELTS. Options include
`isothermal`, `isobaric`, `isentropic`, `isenthalpic`, `isochoric`,
`geothermal` and `PTPath`.
fo2path::String = "FMQ"
A string specifying the oxygen fugacity buffer to follow, e.g., `FMQ` or `NNO+1`.
Available buffers include `IW`,`COH`,`FMQ`,`NNO`,`HM`, and `None`
fractionatesolids::Bool = false
Fractionate all solids? default is `false`
suppress::Collection{String} = String[]
Supress individual phases (specify as strings in array, i.e. `["leucite"]`)
verbose::Bool = true
Print verbose MELTS output to terminal (else, write it to `melts.log`)
"""
function melts_configure(meltspath::String, scratchdir::String, composition::Collection{Number},
elements::Collection{String}, T_range::Collection{Number}=(1400, 600), P_range::Collection{Number}=(10000,10000);
batchstring::String="1\nsc.melts\n10\n1\n3\n1\nliquid\n1\n1.0\n0\n10\n0\n4\n0\n",
dT=-10, dP=0, index=1, version="pMELTS",mode="isobaric",fo2path="FMQ",
fractionatesolids::Bool=false, suppress::Collection{String}=String[], verbose::Bool=true)
############################ Default Settings ###############################
##MELTS or pMELTS
#version = "pMELTS"
##Mode (isothermal, isobaric, isentropic, isenthalpic, isochoric, geothermal or PTPath)
#mode = "isobaric"
## Set fO2 constraint, i.e. "IW","COH","FMQ","NNO","HM","None" as a string
#fo2path = "FMQ"
## Fractionate all solids? ("!" for no, "" for yes)
#fractionatesolids = "!"
# Mass retained during fractionation
massin = 0.001
# Ouptut temperatures in celcius? ("!" for no, "" for yes)
celciusoutput = ""
# Save all output? ("!" for no, "" for yes)
saveall = "!"
# Fractionate all water? ("!" for no, "" for yes)
fractionatewater = "!"
# Fractionate individual phases (specify as strings in cell array, i.e. {"olivine","spinel"})
fractionate = String[]
# Coninuous (fractional) melting? ("!" for no, "" for yes)
continuous = "!"
# Threshold above which melt is extracted (if fractionation is turned on)
minf = 0.005
# Do trace element calculations
dotrace = "!"
# Treat water as a trace element
dotraceh2o = "!"
# Initial trace compositionT
tsc = Float64[]
# Initial trace elements
telements = String[]
# Default global constraints
Pmax = 90000
Pmin = 2
Tmax = 3000
Tmin = 450
# Simulation number (for folder, etc)
########################## end Default Settings ############################
# Guess if intention is for calculation to end at Tf or Pf as a min or max
if last(T_range)<first(T_range)
Tmin=last(T_range)
end
if last(T_range)>first(T_range)
Tmax=last(T_range)
end
if last(P_range)<first(P_range)
Pmin=last(P_range)
end
if last(P_range)>first(P_range)
Pmax=last(P_range)
end
if fractionatesolids
fractionatesolids = ""
else
fractionatesolids = "!"
end
# Normalize starting composition
composition = composition./sum(composition)*100
# output prefixectory name
prefix = joinpath(scratchdir, "out$(index)/")
# Ensure directory exists and is empty
system("rm -rf $prefix; mkdir -p $prefix")
# Make .melts file containing the starting composition you want to run simulations on
fp = open(prefix*"sc.melts", "w")
for i ∈ eachindex(elements)
write(fp,"Initial Composition: $(elements[i]) $(trunc(composition[i],digits=4))\n")
end
for i ∈ eachindex(telements)
write(fp, "Initial Trace: $(telements[i]) $(trunc(tsc[i],digits=4))\n")
end
write(fp, "Initial Temperature: $(trunc(first(T_range),digits=2))\nInitial Pressure: $(trunc(first(P_range),digits=2))\nlog fo2 Path: $fo2path\n")
for i ∈ eachindex(fractionate)
write(fp,"Fractionate: $(fractionate[i])\n")
end
for i ∈ eachindex(suppress)
write(fp,"Suppress: $(suppress[i])\n")
end
close(fp)
# Make melts_env file to specify type of MELTS calculation
fp = open(prefix*"/melts_env.txt", "w")
write(fp, "! *************************************\n! Julia-generated environment file\n! *************************************\n\n" *
"! this variable chooses MELTS or pMELTS; for low-pressure use MELTS\n" *
"ALPHAMELTS_VERSION $version\n\n" *
"! do not use this unless fO2 anomalies at the solidus are a problem\n" *
"!ALPHAMELTS_ALTERNATIVE_FO2 true\n\n" *
"! use this if you want to buffer fO2 for isentropic, isenthalpic or isochoric mode\n! e.g. if you are doing isenthalpic AFC\n" *
"!ALPHAMELTS_IMPOSE_FO2 true\n\n" *
"! use if you want assimilation and fractional crystallization (AFC)\n" *
"!ALPHAMELTS_ASSIMILATE true\n\n" *
"! isothermal, isobaric, isentropic, isenthalpic, isochoric, geothermal or PTPath\n" *
"ALPHAMELTS_MODE $mode\n" *
"!ALPHAMELTS_PTPATH_FILE ptpath.txt\n\n" *
"! need to set DELTAP for polybaric paths; DELTAT for isobaric paths\nALPHAMELTS_DELTAP $(trunc(dP,digits=1))\n" *
"ALPHAMELTS_DELTAT $(trunc(dT,digits=1))\n" *
"ALPHAMELTS_MAXP $(trunc(Pmax,digits=1))\n" *
"ALPHAMELTS_MINP $(trunc(Pmin,digits=1))\n" *
"ALPHAMELTS_MAXT $(trunc(Tmax,digits=1))\n" *
"ALPHAMELTS_MINT $(trunc(Tmin,digits=1))\n\n" *
"! this one turns on fractional crystallization for all solids\n! use Fractionate: in the melts file instead for selective fractionation\n" *
"$(fractionatesolids)ALPHAMELTS_FRACTIONATE_SOLIDS true\n" *
"$(fractionatesolids)ALPHAMELTS_MASSIN $massin\n\n" *
"! free water is unlikely but can be extracted\n" *
"$(fractionatewater)ALPHAMELTS_FRACTIONATE_WATER true\n" *
"$(fractionatewater)ALPHAMELTS_MINW 0.005\n\n" *
"! the next one gives an output file that is always updated, even for single calculations\n" *
"$(saveall)ALPHAMELTS_SAVE_ALL true\n" *
"!ALPHAMELTS_SKIP_FAILURE true\n\n" *
"! this option converts the output temperature to celcius, like the input\n" *
"$(celciusoutput)ALPHAMELTS_CELSIUS_OUTPUT true\n\n" *
"! the next two turn on and off fractional melting\n" *
"$(continuous)ALPHAMELTS_CONTINUOUS_MELTING true\n" *
"$(continuous)ALPHAMELTS_MINF $minf\n" *
"$(continuous)ALPHAMELTS_INTEGRATE_FILE integrate.txt\n\n" *
"! the next two options refer to the trace element engine\n" *
"$(dotrace)ALPHAMELTS_DO_TRACE true\n" *
"$(dotraceh2o)ALPHAMELTS_DO_TRACE_H2O true\n")
close(fp)
# Make a batch file to run the above .melts file starting from the liquidus
fp = open(prefix*"/batch.txt", "w")
write(fp,batchstring)
close(fp)
# Run the command
# Edit the following line(s to make sure you have a correct path to the "run_alphamelts.command" perl script
if verbose
system("cd " * prefix * "; " * meltspath * " -f melts_env.txt -b batch.txt")
else
system("cd " * prefix * "; " * meltspath * " -f melts_env.txt -b batch.txt &>./melts.log")
end
return 0
end
export melts_configure
"""
```julia
melts_query(scratchdir::String; index=1)
```
Read all phase proportions from `Phase_main_tbl.txt` in specified MELTS run directory
Returns an elementified dictionary
"""
function melts_query(scratchdir::String; index=1, importas=:Dict)
prefix = joinpath(scratchdir, "out$(index)/") # path to data files
if importas==:Dict
melts = Dict{String, Union{Vector{String}, Dict}}()
else
melts = Dict{String, Union{Vector{String}, NamedTuple}}()
end
if isfile(prefix*"/Phase_main_tbl.txt")
data = readdlm(prefix*"/Phase_main_tbl.txt", ' ', skipblanks=false)
pos = findall(all(isempty.(data), dims=2) |> vec)
melts["minerals"] = Array{String}(undef, length(pos)-1)
for i=1:(length(pos)-1)
name = data[pos[i]+1,1]
melts[name] = elementify(data[pos[i]+2:pos[i+1]-1,:], skipnameless=true, importas=importas)
melts["minerals"][i] = name
end
end
return melts
end
export melts_query
"""
```julia
melts_query_modes(scratchdir::String; index=1)
```
Read modal phase proportions from `Phase_mass_tbl.txt` in specified MELTS run
Returns an elementified dictionary
"""
function melts_query_modes(scratchdir::String; index=1, importas=:Dict)
prefix = joinpath(scratchdir, "out$(index)/") # path to data files
# Read results and return them if possible
if isfile(prefix*"/Phase_mass_tbl.txt")
# Read data as an Array{Any}
data = readdlm(prefix*"Phase_mass_tbl.txt", ' ', skipstart=1)
# Convert to a dictionary
data = elementify(data, standardize=true, skipnameless=true, importas=importas)
else
# Return empty dictionary if file doesn't exist
data = importas==:Dict ? Dict() : ()
end
return data
end
export melts_query_modes
"""
```julia
melts_clean_modes(scratchdir::String; index=1)
```
Read and parse / clean-up modal phase proportions from specified MELTS run directory
Returns an elementified dictionary
"""
function melts_clean_modes(scratchdir::String; index=1)
prefix = joinpath(scratchdir, "out$(index)/") # path to data files
# Read results and return them if possible
if isfile(prefix*"/Phase_mass_tbl.txt")
# Read data as an Array{Any}
data = readdlm(prefix*"Phase_mass_tbl.txt", ' ', skipstart=1)
# Convert to a dictionary
data = elementify(data, standardize=true, skipnameless=true, importas=:Dict)
# Start by transferring over all the non-redundant elements
modes = typeof(data)()
for e in data["elements"]
m = replace(e, r"_.*" => s"")
if haskey(modes, m)
modes[m] .+= data[e]
else
modes[m] = copy(data[e])
end
end
# Add the sum of all solids
modes["solids"] = zeros(size(data["Temperature"]))
for e in data["elements"][4:end]
if !contains(e, "water") && !contains(e, "liquid")
modes["solids"] .+= data[e]
end
end
# Get full mineral compositions, add feldspar and oxides
melts = melts_query(scratchdir, index=index)
if containsi(melts["minerals"],"feldspar")
modes["anorthite"] = zeros(size(modes["Temperature"]))
modes["albite"] = zeros(size(modes["Temperature"]))
modes["orthoclase"] = zeros(size(modes["Temperature"]))
end
An_Ca = (238.12507+40.0784) / (15.999+40.0784)
Ab_Na = (239.22853+22.98977*2) / (15.999+22.98977*2)
Or_K = (239.22853+39.09831*2) / (15.999+39.09831*2)
if containsi(melts["minerals"],"rhm_oxide")
modes["ilmenite"] = zeros(size(modes["Temperature"]))
modes["magnetite"] = zeros(size(modes["Temperature"]))
modes["hematite"] = zeros(size(modes["Temperature"]))
end
for m in melts["minerals"]
if containsi(m,"feldspar")
t = vec(findclosest(melts[m]["Temperature"],modes["Temperature"]))
AnAbOr = [melts[m]["CaO"]*An_Ca melts[m]["Na2O"]*Ab_Na melts[m]["K2O"]*Or_K] |> x -> x ./ sum(x, dims=2)
modes["anorthite"][t] .+= AnAbOr[:,1] .* melts[m]["mass"]
modes["albite"][t] .+= AnAbOr[:,2] .* melts[m]["mass"]
modes["orthoclase"][t] .+= AnAbOr[:,3] .* melts[m]["mass"]
elseif containsi(m,"rhm_oxide")
t = vec(findclosest(melts[m]["Temperature"],modes["Temperature"]))
Ilmenite = Vector{Float64}(undef, length(t))
Magnetite = Vector{Float64}(undef, length(t))
if haskey(melts[m],"MnO")
Ilmenite .= (melts[m]["TiO2"] + melts[m]["MnO"]+(melts[m]["TiO2"]*(71.8444/79.8768) - melts[m]["MnO"]*(71.8444/70.9374))) / 100
Magnetite .= (melts[m]["FeO"] - (melts[m]["TiO2"])*71.8444/79.8768) * (1+159.6882/71.8444)/100
else
Ilmenite .= (melts[m]["TiO2"] + melts[m]["TiO2"]*71.8444/79.8768) / 100
Magnetite .= (melts[m]["FeO"] - melts[m]["TiO2"]*71.8444/79.8768) * (1+159.6882/71.8444)/100
end
Magnetite[Magnetite.<0] .= 0
Hematite = (melts[m]["Fe2O3"] - Magnetite*100*159.6882/231.5326)/100
modes["ilmenite"][t] .+= melts[m]["mass"] .* Ilmenite
modes["magnetite"][t] .+= melts[m]["mass"] .* Magnetite
modes["hematite"][t] .+= melts[m]["mass"] .* Hematite
end
end
minerals = sort(collect(keys(modes)))
modes["elements"] = ["Pressure","Temperature","mass","solids","liquid"] ∪ minerals[.!containsi.(minerals, "feldspar") .& .!containsi.(minerals, "rhm")]
else
# Return empty dictionary if file doesn't exist
modes = Dict()
end
return modes
end
export melts_clean_modes
"""
```julia
melts_query_liquid(scratchdir::String; index=1)
```
Read liquid composition from `Liquid_comp_tbl.txt` in specified MELTS run directory
Returns an elementified dictionary
"""
function melts_query_liquid(scratchdir::String; index=1, importas=:Dict)
prefix = joinpath(scratchdir, "out$(index)/") # path to data files
# Read results and return them if possible
if isfile(prefix*"/Liquid_comp_tbl.txt")
# Read data as an Array{Any}
data = readdlm(prefix*"Liquid_comp_tbl.txt", ' ', skipstart=1)
# Convert to a dictionary
data = elementify(data, standardize=true, skipnameless=true, importas=importas)
else
# Return empty dictionary if file doesn't exist
data = importas==:Dict ? Dict() : ()
end
return data
end
export melts_query_liquid
"""
```julia
melts_query_solid(scratchdir::String; index=1)
```
Read solid composition from `Solid_comp_tbl.txt` in specified MELTS run directory
Returns an elementified dictionary
"""
function melts_query_solid(scratchdir::String; index=1, importas=:Dict)
prefix = joinpath(scratchdir, "out$(index)/") # path to data files
# Read results and return them if possible
if isfile(prefix*"/Solid_comp_tbl.txt")
# Read data as an Array{Any}
data = readdlm(prefix*"Solid_comp_tbl.txt", ' ', skipstart=1)
# Convert to a dictionary
data = elementify(data, standardize=true, skipnameless=true, importas=importas)
else
# Return empty dictionary if file doesn't exist
data = importas==:Dict ? Dict() : ()
end
return data
end
export melts_query_solid
"""
```julia
melts_query_system(scratchdir::String; index=1, importas=:Dict)
```
Read system thermodynamic and composition data from `System_main_tbl.txt` in
specified MELTS run directory. Returns an elementified dictionary or tuple.
"""
function melts_query_system(scratchdir::String; index=1, importas=:Dict)
prefix = joinpath(scratchdir, "out$(index)/") # path to data files
# Read results and return them if possible
if isfile(prefix*"/System_main_tbl.txt")
# Read data as an Array{Any}
data = readdlm(prefix*"System_main_tbl.txt", ' ', skipstart=1)
# Convert to a dictionary
data = elementify(data, standardize=true, skipnameless=true, importas=importas)
else
# Return empty dictionary if file doesn't exist
data = importas==:Dict ? Dict() : ()
end
return data
end
export melts_query_system
## -- Perplex interface: 1. Configuration
"""
```julia
perplex_configure_geotherm(perplexdir::String, scratchdir::String, composition::Collection{Number},
\telements::String=["SIO2","TIO2","AL2O3","FEO","MGO","CAO","NA2O","K2O","H2O"],
\tP_range=(280,28000), T_surf::Number=273.15, geotherm::Number=0.1;
\tdataset::String="hp02ver.dat",
\tindex::Integer=1,
\tnpoints::Integer=100,
\tsolution_phases::String="O(HP)\\nOpx(HP)\\nOmph(GHP)\\nGt(HP)\\noAmph(DP)\\ncAmph(DP)\\nT\\nB\\nChl(HP)\\nBio(TCC)\\nMica(CF)\\nCtd(HP)\\nIlHm(A)\\nSp(HP)\\nSapp(HP)\\nSt(HP)\\nfeldspar_B\\nDo(HP)\\nF\\n",
\texcludes::String="ts\\nparg\\ngl\\nged\\nfanth\\ng\\n",
\tmode_basis::String="vol", #["vol", "wt", "mol"]
\tcomposition_basis::String="wt", #["vol", "wt", "mol"]
\tfluid_eos::Integer=5)
```
Set up a PerpleX calculation for a single bulk composition along a specified
geothermal gradient and pressure (depth) range. P specified in bar and T_surf
in Kelvin, with geothermal gradient in units of Kelvin/bar
"""
function perplex_configure_geotherm(perplexdir::String, scratchdir::String, composition::Collection{Number},
elements::Collection{String}=["SIO2","TIO2","AL2O3","FEO","MGO","CAO","NA2O","K2O","H2O"],
P_range::NTuple{2,Number}=(280,28000), T_surf::Number=273.15, geotherm::Number=0.1;
dataset::String="hp02ver.dat",
index::Integer=1,
npoints::Integer=100,
solution_phases::String="O(HP)\nOpx(HP)\nOmph(GHP)\nGt(HP)\noAmph(DP)\ncAmph(DP)\nT\nB\nChl(HP)\nBio(TCC)\nMica(CF)\nCtd(HP)\nIlHm(A)\nSp(HP)\nSapp(HP)\nSt(HP)\nfeldspar_B\nDo(HP)\nF\n",
excludes::String="ts\nparg\ngl\nged\nfanth\ng\n",
mode_basis::String="vol",
composition_basis::String="wt",
fluid_eos::Integer=5
)
build = joinpath(perplexdir, "build")# path to PerpleX build
vertex = joinpath(perplexdir, "vertex")# path to PerpleX vertex
#Configure working directory
prefix = joinpath(scratchdir, "out$(index)/")
system("rm -rf $prefix; mkdir -p $prefix")
# Place required data files
system("cp $(joinpath(perplexdir,dataset)) $prefix")
system("cp $(joinpath(perplexdir,"perplex_option.dat")) $prefix")
system("cp $(joinpath(perplexdir,"solution_model.dat")) $prefix")
# Edit perplex_option.dat to specify number of nodes at which to solve
system("sed -e \"s/1d_path .*|/1d_path $npoints $npoints |/\" -i.backup $(prefix)perplex_option.dat")
# Edit perplex_option.dat to output all seismic properties
#println("editing perplex options ")
system("sed -e \"s/seismic_output .*|/seismic_output all |/\" -i.backup $(prefix)perplex_option.dat")
# Specify whether we want volume or weight percentages
system("sed -e \"s/proportions .*|/proportions $mode_basis |/\" -i.backup $(prefix)perplex_option.dat")
system("sed -e \"s/composition_system .*|/composition_system $composition_basis |/\" -i.backup $(prefix)perplex_option.dat")
system("sed -e \"s/composition_phase .*|/composition_phase $composition_basis |/\" -i.backup $(prefix)perplex_option.dat")
# Create build batch file.
fp = open(prefix*"build.bat", "w")
# Name, components, and basic options. P-T conditions.
# default fluid_eos = 5: Holland and Powell (1998) "CORK" fluid equation of state
elementstring = join(elements .* "\n")
write(fp,"$index\n$dataset\nperplex_option.dat\nn\n3\nn\nn\nn\n$elementstring\n$fluid_eos\nn\ny\n2\n1\n$T_surf\n$geotherm\n$(first(P_range))\n$(last(P_range))\ny\n") # v6.8.7
# write(fp,"$index\n$dataset\nperplex_option.dat\nn\nn\nn\nn\n$elementstring\n5\n3\nn\ny\n2\n1\n$T_surf\n$geotherm\n$(first(P_range))\n$(last(P_range))\ny\n") # v6.8.1
# Whole-rock composition
for i ∈ eachindex(composition)
write(fp,"$(composition[i]) ")
end
# Solution model
if length(excludes) > 0
write(fp,"\nn\ny\nn\n$excludes\ny\nsolution_model.dat\n$solution_phases\nGeothermal")
else
write(fp,"\nn\nn\ny\nsolution_model.dat\n$(solution_phases)\nGeothermal")
end
close(fp)
# build PerpleX problem definition
system("cd $prefix; $build < build.bat > build.log")
println("Built problem definition")
# Run PerpleX vertex calculations
result = system("cd $prefix; echo $index | $vertex > vertex.log")
return result
end
export perplex_configure_geotherm
"""
```julia
perplex_configure_isobar(perplexdir::String, scratchdir::String, composition::Collection{Number},
\telements::String=["SIO2","TIO2","AL2O3","FEO","MGO","CAO","NA2O","K2O","H2O"]
\tP::Number=10000, T_range::NTuple{2,Number}=(500+273.15, 1500+273.15);
\tdataset::String="hp11ver.dat",
\tindex::Integer=1,
\tnpoints::Integer=100,
\tsolution_phases::String="O(HP)\\nOpx(HP)\\nOmph(GHP)\\nGt(HP)\\noAmph(DP)\\ncAmph(DP)\\nT\\nB\\nChl(HP)\\nBio(TCC)\\nMica(CF)\\nCtd(HP)\\nIlHm(A)\\nSp(HP)\\nSapp(HP)\\nSt(HP)\\nfeldspar_B\\nDo(HP)\\nF\\n",
\texcludes::String="ts\\nparg\\ngl\\nged\\nfanth\\ng\\n",
\tmode_basis::String="wt", #["vol", "wt", "mol"]
\tcomposition_basis::String="wt", #["vol", "wt", "mol"]
\tnonlinear_subdivision::Bool=false,
\tfluid_eos::Integer=5)
```
Set up a PerpleX calculation for a single bulk composition along a specified
isobaric temperature gradient. P specified in bar and T_range in Kelvin
"""
function perplex_configure_isobar(perplexdir::String, scratchdir::String, composition::Collection{Number},
elements::Collection{String}=("SIO2","TIO2","AL2O3","FEO","MGO","CAO","NA2O","K2O","H2O"),
P::Number=10000, T_range::NTuple{2,Number}=(500+273.15, 1500+273.15);
dataset::String="hp11ver.dat",
index::Integer=1,
npoints::Integer=100,
solution_phases::String="O(HP)\nOpx(HP)\nOmph(GHP)\nGt(HP)\noAmph(DP)\ncAmph(DP)\nT\nB\nChl(HP)\nBio(TCC)\nMica(CF)\nCtd(HP)\nIlHm(A)\nSp(HP)\nSapp(HP)\nSt(HP)\nfeldspar_B\nDo(HP)\nF\n",
excludes::String="ts\nparg\ngl\nged\nfanth\ng\n",
mode_basis::String="wt",
composition_basis::String="wt",
nonlinear_subdivision::Bool=false,
fluid_eos::Integer=5
)
build = joinpath(perplexdir, "build")# path to PerpleX build
vertex = joinpath(perplexdir, "vertex")# path to PerpleX vertex
#Configure working directory
prefix = joinpath(scratchdir, "out$(index)/")
system("rm -rf $prefix; mkdir -p $prefix")
# Place required data files
system("cp $(joinpath(perplexdir,dataset)) $prefix")
system("cp $(joinpath(perplexdir,"perplex_option.dat")) $prefix")
system("cp $(joinpath(perplexdir,"solution_model.dat")) $prefix")
# Edit perplex_option.dat to specify number of nodes at which to solve
system("sed -e \"s/1d_path .*|/1d_path $npoints $npoints |/\" -i.backup $(prefix)perplex_option.dat")
# Specify whether we want volume or weight percentages
system("sed -e \"s/proportions .*|/proportions $mode_basis |/\" -i.backup $(prefix)perplex_option.dat")
system("sed -e \"s/composition_system .*|/composition_system $composition_basis |/\" -i.backup $(prefix)perplex_option.dat")
system("sed -e \"s/composition_phase .*|/composition_phase $composition_basis |/\" -i.backup $(prefix)perplex_option.dat")
# Turn on nonlinear subdivision and change resolution
if nonlinear_subdivision
system("sed -e \"s/non_linear_switch .*|/non_linear_switch T |/\" -i.backup $(prefix)perplex_option.dat")
system("sed -e \"s:initial_resolution .*|:initial_resolution 1/2 1/4 |:\" -i.backup $(prefix)perplex_option.dat")
end
# Create build batch file
# Options based on Perplex v6.8.7
fp = open(prefix*"build.bat", "w")
# Name, components, and basic options. P-T conditions.
# default fluid_eos = 5: Holland and Powell (1998) "CORK" fluid equation of state
elementstring = join(elements .* "\n")
write(fp,"$index\n$dataset\nperplex_option.dat\nn\n3\nn\nn\nn\n$elementstring\n$fluid_eos\nn\nn\n2\n$(first(T_range))\n$(last(T_range))\n$P\ny\n") # v6.8.7
# write(fp,"$index\n$dataset\nperplex_option.dat\nn\nn\nn\nn\n$elementstring\n$fluid_eos\n3\nn\nn\n2\n$(first(T_range))\n$(last(T_range))\n$P\ny\n") # v6.8.1
# Whole-rock composition
for i ∈ eachindex(composition)
write(fp,"$(composition[i]) ")
end
# Solution model
write(fp,"\nn\ny\nn\n$excludes\ny\nsolution_model.dat\n$solution_phases\nIsobaric")
close(fp)
# build PerpleX problem definition
system("cd $prefix; $build < build.bat > build.log")
# Run PerpleX vertex calculations
result = system("cd $prefix; printf \"$index\ny\ny\ny\ny\ny\ny\ny\ny\n\" | $vertex > vertex.log")
return result
end
export perplex_configure_isobar
"""
```julia