/
PerplexExamples.jl
353 lines (275 loc) · 16.2 KB
/
PerplexExamples.jl
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################################################################################
# A few PerpleX calculation examples using the Julia-Perplex interface
## --- Import some useful packages
using StatGeochem
using Plots; gr();
using Statistics, DelimitedFiles, SpecialFunctions
## --- Configure
# Absolute paths to perplex resources
perplexdir = joinpath(resourcepath,"perplex-stable")
scratchdir = "./scratch/" # Location of directory to store output files
# Attempt to install perplex, if not already extant
if !isfile(joinpath(perplexdir,"vertex"))
# Make sure resourcepath exists
run(`mkdir -p $resourcepath`)
# Try to compile PerpleX from source; if that fails, try to download linux binaries
try
# Check if there is a fortran compiler
run(`gfortran -v`)
# Download Perplex v6.8.7 -- known to work with interface used here
file = download("https://storage.googleapis.com/statgeochem/perplex-6.8.7-source.zip", joinpath(resourcepath,"perplex-stable.zip"))
# # For a more updated perplex version, you might also try
# file = download("https://petrol.natur.cuni.cz/~ondro/perplex-sources-stable.zip", joinpath(resourcepath,"perplex-stable.zip"))
run(`unzip -u $file -d $resourcepath`) # Extract
system("cd $perplexdir; make") # Compile
catch
@warn "Failed to compile from source, trying precompiled linux binaries instead"
run(`mkdir -p $perplexdir`)
file = download("https://petrol.natur.cuni.cz/~ondro/Perple_X_6.8.7_Linux_64_gfortran.tar.gz","perplex-6.8.7-linux.tar.gz")
run(`tar -xzf $file -C $perplexdir`)
end
end
## --- # # # # # # # # # # # # # Initial composition # # # # # # # # # # # # # #
## McDonough Pyrolite
#elements = [ "SIO2", "TIO2", "AL2O3", "FEO", "MNO", "MGO", "CAO", "NA2O", "K2O", "H2O", "CO2",]
#composition = [45.1242, 0.2005, 4.4623, 8.0723, 0.1354, 37.9043, 3.5598, 0.3610, 0.0291, 0.1511, 0.0440,]
# # Kelemen (2014) primitive continental basalt. H2O and CO2 are guesses
# elements = [ "SIO2", "TIO2", "AL2O3", "FEO", "MNO", "MGO", "CAO", "NA2O", "K2O", "H2O", "CO2",]
# composition = [50.0956, 0.9564, 15.3224, 8.5103, 0.1659, 9.2520, 9.6912, 2.5472, 0.8588, 2.0000, 0.6000,]
# # Kelemen (2014) primitive continental basalt excluding Mn. H2O and CO2 are guesses
# elements = [ "SIO2", "TIO2", "AL2O3", "FEO", "MGO", "CAO", "NA2O", "K2O", "H2O", "CO2",]
# composition = [50.0956, 0.9564, 15.3224, 8.5103, 9.2520, 9.6912, 2.5472, 0.8588, 2.0000, 0.6000,]
# Kelemen (2014) primitive continental basalt excluding Mn and Ti since most melt models can"t handle them..
elements = [ "SIO2", "AL2O3", "FEO", "MGO", "CAO", "NA2O", "K2O", "H2O", "CO2",]
composition = [50.0956, 15.3224, 8.5103, 9.2520, 9.6912, 2.5472, 0.8588, 2.0000, 0.6000,]
# # Average Archean basalt (EarthChem data)
# elements = [ "SIO2", "TIO2", "AL2O3", "FEO", "MNO", "MGO", "CAO", "NA2O", "K2O", "H2O", "CO2",]
# composition = [49.2054, 0.8401, 12.0551, 11.4018, 0.2198, 12.3997, 9.3113, 1.6549, 0.4630, 1.8935, 0.5555,]
# # A random granite
# elements = [ "SIO2", "TIO2", "AL2O3", "FEO", "MGO", "CAO", "NA2O", "K2O", "H2O", "CO2",]
# composition = [ 69.16, 0.42, 14.96, 2.9064, 1.52, 1.81, 3.7, 4.95, 1.8386, 0.4407,]
## --- # # # # # # # # # # # Some solution model options # # # # # # # # # # # #
# Emphasis on phases from Green (2016) -- developed for metabasites, includes what is probably the best (and most expensive) amphibole model. Use with hp11ver.dat
G_solution_phases = "Augite(G)\nOpx(JH)\ncAmph(G)\noAmph(DP)\nO(JH)\nSp(JH)\nGrt(JH)\nfeldspar_B\nMica(W)\nBio(TCC)\nChl(W)\nCtd(W)\nCrd(W)\nSa(WP)\nSt(W)\nIlm(WPH)\nAtg(PN)\nT\nB\nF\nDo(HP)\nScap\nChum\nNeph(FB)\n"
G_excludes ="ged\nfanth\ngl\nilm\nilm_nol\n"
# Emphasis on phases from White (2014) -- developed for metapelites. Use with hp11ver.dat (though can apparenty run with hp02ver.dat without crashing)
W_solution_phases = "Omph(HP)\nOpx(W)\ncAmph(DP)\noAmph(DP)\nO(JH)\nSp(JH)\nGt(W)\nfeldspar_B\nMica(W)\nBi(W)\nChl(W)\nCtd(W)\nCrd(W)\nSa(WP)\nSt(W) \nIlm(WPH)\nAtg(PN)\nT\nB\nF\nDo(HP)\nScap\nChum\nPu(M)\n"
W_excludes = "andr\nts\nparg\ngl\nged\nfanth\n"
# Emphasis on phases from Jennings and Holland (2015) -- developed for mantle melting. Use with hp11ver.dat
JH_solution_phases = "Cpx(JH)\nOpx(JH)\ncAmph(DP)\noAmph(DP)\nO(JH)\nSp(JH)\nGrt(JH)\nfeldspar_B\nMica(W)\nBio(TCC)\nChl(W)\nCtd(W)\nCrd(W)\nSa(WP)\nSt(W)\nIlm(WPH)\nAtg(PN)\nT\nB\nF\nDo(HP)\nScap\nChum\nNeph(FB)\n"
JH_excludes = "ts\nparg\ngl\nged\nfanth\n"
# Emphasis on phases from Holland and Powell -- all phases can be used with hp02ver.dat.
HP_solution_phases = "Omph(HP)\nOpx(HP)\nGlTrTsPg\nAnth\nO(HP)\nSp(HP)\nGt(HP)\nfeldspar_B\nMica(CF)\nBio(TCC)\nChl(HP)\nCtd(HP)\nSapp(HP)\nSt(HP)\nIlHm(A)\nDo(HP)\nT\nB\nF\n"
HP_excludes = ""
## --- # # # # # # # # # # # # # Isobaric example # # # # # # # # # # # # # # # #
# Input parameters
P = 1000 # Pressure, bar
T_range = [0+273.15, 1500+273.15] # Temperature range, Kelvin
# # Configure (run build and vertex)
# melt_model = "melt(G)"
# @time perplex_configure_isobar(perplexdir, scratchdir, composition, elements, P, T_range,
# dataset="hpha11ver.dat",
# npoints=100,
# excludes=G_excludes,
# solution_phases=melt_model*"\n"*G_solution_phases
# )
melt_model = "melt(HP)"
@time perplex_configure_isobar(perplexdir, scratchdir, composition, elements, P, T_range,
dataset="hp02ver.dat",
npoints=100,
excludes=HP_excludes,
solution_phases=melt_model*"\n"*HP_solution_phases
)
## --- Query all properties at a single temperature -- results returned as text
T = 850+273.15
data_isobaric = perplex_query_point(perplexdir, scratchdir, T) |> print
## --- Query the full isobar -- results returned as dict
bulk = perplex_query_system(perplexdir, scratchdir) # Get system data for all temperatures. Set include_fluid = "n" to get solid+melt only
modes = perplex_query_modes(perplexdir, scratchdir) # || phase modes
melt = perplex_query_phase(perplexdir, scratchdir, melt_model) # || melt data
# Melt wt.% seems to be slightly inaccurate; use values from modes instead
melt["wt_pct"] = modes[melt_model]
# Create dictionary to hold solid composition and fill it using what we know from system and melt
solid = Dict()
solid["wt_pct"] = 100 .- melt["wt_pct"]
for e in ["SIO2","AL2O3","FEO","MGO","CAO","NA2O","K2O"]
solid[e] = (bulk[e] - (melt[e] .* melt["wt_pct"]/100)) ./ (solid["wt_pct"]/100)
end
renormalize!(solid,["SIO2","AL2O3","FEO","MGO","CAO","NA2O","K2O"],total=100)
## --- Plot melt composition as a function of melt percent
h = plot(xlabel="Percent melt", ylabel="Wt. % in melt", title="$melt_model + G_solution_phases, $P bar")
i = 0
for e in ["SIO2","AL2O3","FEO","MGO","CAO","NA2O","K2O"]
plot!(h, melt["wt_pct"], melt[e], label=e, color=lines[global i += 1])
plot!(h, melt["wt_pct"], bulk[e], label="", color=lines[i], linestyle=:dot)
end
plot!(h,fg_color_legend=:white, framestyle=:box)
savefig(h,"MeltComposition.pdf")
display(h)
## --- Plot melt composition as a function of melt SiO2
h = plot(xlabel="Magma SIO2 (wt.%)", ylabel="Wt. % in melt", title="$melt_model + G_solution_phases, $P bar")
i = 1
for e in ["AL2O3","FEO","MGO","CAO","NA2O","K2O"]
plot!(h,melt["SIO2"], melt[e], label=e, color = lines[global i +=1])
end
plot!(h,fg_color_legend=:white, framestyle=:box)
savefig(h,"MeltCompositionvsSiO2.pdf")
display(h)
## --- Plot solid composition as a function of melt percent
h = plot(xlabel="Percent melt", ylabel="Wt. % in solid", title="$melt_model + G_solution_phases, $P bar")
i = 0
for e in ["SIO2","AL2O3","FEO","MGO","CAO","NA2O","K2O"]
plot!(h, melt["wt_pct"], solid[e], label=e, color=lines[global i +=1])
end
plot!(h,fg_color_legend=:white, framestyle=:box, legend=:topleft)
savefig(h,"SolidComposition.pdf")
display(h)
## --- Plot modes of all phases as a function of temperature
h = plot(xlabel="T (C)", ylabel="Weight percent", title="$melt_model + G_solution_phases, $P bar")
for m in modes["elements"][3:end]
plot!(h, modes["T(K)"] .- 273.15, modes[m], label=m)
end
plot!(h,fg_color_legend=:white, framestyle=:box)
savefig(h,"PhaseModes.pdf")
display(h)
## --- Plot modes of all phases as a function of melt percent
h = plot(xlabel="Percent melt", ylabel="Weight percent", title="$melt_model + G_solution_phases, $P bar")
for m in modes["elements"][3:end]
plot!(h, modes[melt_model], modes[m], label=m)
end
plot!(h,fg_color_legend=:white, framestyle=:box)
savefig(h,"PhaseModesvsF.pdf")
display(h)
## --- Plot seismic properties
# Query seismic properties along the whole profile
seismic = perplex_query_seismic(perplexdir, scratchdir)
seismic["vp/vs"][seismic["vp/vs"] .> 100] .= NaN # Exclude cases where vs drops to zero
h = plot(xlabel="Pressure", ylabel="Property")
plot!(h,seismic["T(K)"],seismic["vp,km/s"], label="vp,km/s")
plot!(h,seismic["T(K)"],seismic["vp/vs"], label="vp/vs")
plot!(h,seismic["T(K)"],seismic["rho,kg/m3"]/1000, label="rho, g/cc")
savefig(h,"GeothermSeismicProperties.pdf")
display(h)
## --- # # # # # # # # # # # Geothermal gradient example # # # # # # # # # # # #
# Input parameters
P_range = [280, 28000] # Pressure range to explore, bar (roughly 1-100 km depth)
T_surf = 273.15 # Temperature of surface (K)
geotherm = 0.01 # Geothermal gradient of 0.1 K/bar == about 28.4 K/km
melt_model = ""
# Configure (run build and vertex)
@time perplex_configure_geotherm(perplexdir, scratchdir, composition, elements,
P_range, T_surf, geotherm, dataset="hp02ver.dat", excludes=HP_excludes,
solution_phases=HP_solution_phases, npoints=200, index=2)
# # Alternative configuration, using hpha02ver.dat
# @time perplex_configure_geotherm(perplexdir, scratchdir, composition, elements,
# P_range, T_surf, geotherm, dataset="hpha02ver.dat", excludes="qGL\n"*HP_excludes,
# solution_phases=HP_solution_phases, npoints=200, index=2)
# # Alternative configuration, using hpha02ver.dat and new phases for metapelites
# @time perplex_configure_geotherm(perplexdir, scratchdir, composition, elements,
# P_range, T_surf, geotherm, dataset="hpha02ver.dat", excludes="qGL\n"*W_excludes,
# solution_phases=W_solution_phases, npoints=200, index=2)
## --- Plot modes of all phases as a function of temperature
modes = perplex_query_modes(perplexdir, scratchdir, index=2) # || phase modes
h = plot(xlabel="T (C)", ylabel="Weight percent")
for m in modes["elements"][3:end]
plot!(h, modes["T(K)"] .- 273.15, modes[m], label=m)
end
plot!(h,fg_color_legend=:white, framestyle=:box)
savefig(h,"GeothermPhaseModes.pdf")
display(h)
## --- Plot seismic properties
# Query seismic properties along the whole profile
seismic = perplex_query_seismic(perplexdir, scratchdir, index=2)
seismic["vp/vs"][seismic["vp/vs"] .> 100] .= NaN # Exclude cases where vs drops to zero
h = plot(xlabel="Pressure", ylabel="Property")
plot!(h,seismic["P(bar)"],seismic["vp,km/s"], label="vp,km/s")
plot!(h,seismic["P(bar)"],seismic["vp/vs"], label="vp/vs")
plot!(h,seismic["P(bar)"],seismic["rho,kg/m3"]/1000, label="rho, g/cc")
plot!(h,seismic["P(bar)"],seismic["T(K)"]/1000, label="T(K)/1000")
savefig(h,"GeothermSeismicProperties.pdf")
display(h)
## --- Query all properties at a single pressure
P = 10000
data_geotherm = perplex_query_point(perplexdir, scratchdir, P, index=2) |> print
## --- Compare seismic properties for several different geotherms, as a function of Pressure
# Input parameters
P_range = [280, 14000] # Pressure range to explore, bar (roughly 1-50 km depth)
T_surf = 273.15 # Temperature of surface (K)
dataset="hp02ver.dat"
yelem = "vp,km/s"
# yelem = "rho,kg/m3"
h = plot(xlabel="Pressure (bar)", ylabel=yelem)
for i=1:5
geotherm = i/50
# Configure (run build and vertex)
@time perplex_configure_geotherm(perplexdir, scratchdir, composition, elements,
P_range, T_surf, geotherm, dataset=dataset, excludes=HP_excludes,
solution_phases=HP_solution_phases, npoints=200, index=10+i)
# Query perplex results
seismic = perplex_query_seismic(perplexdir, scratchdir, index=10+i)
# Plot results
plot!(h,seismic["P(bar)"],seismic[yelem], label="$geotherm K/bar")
display(h)
end
## --- Compare seismic properties for several different geotherms, as a function of temperature
# Input parameters
P_range = [280, 16000] # Pressure range to explore, bar (roughly 1-60 km depth)
T_surf = 273.15 # Temperature of surface (K)
dataset="hp02ver.dat"
yelem = "vp,km/s"
# yelem = "rho,kg/m3"
h = plot(xlabel="Temperature (K)", ylabel=yelem)
for i=1:5
geotherm = i/50
# Configure (run build and vertex)
@time perplex_configure_geotherm(perplexdir, scratchdir, composition, elements,
P_range, T_surf, geotherm, dataset=dataset, excludes=HP_excludes,
solution_phases=HP_solution_phases, npoints=200, index=10+i)
# Query perplex results
seismic = perplex_query_seismic(perplexdir, scratchdir, index=10+i)
# Plot results
plot!(h,seismic["T(K)"],seismic[yelem], label="$geotherm K/bar")
display(h)
end
## --- Build a pseudosection
# Input parameters
mingeotherm = 0.009 # Geothermal gradient, K/bar. For reference, 0.1 K/bar ≈ 28.4 K/km
max_lith_T = 1300 # Maximum temperature of the TBL lithosphere (no point calculating beyond that)
P_range = [280, (max_lith_T-273.15)/mingeotherm] # Pressure range to explore, bar (roughly 1-100 km depth)
T_range = [273.15, max_lith_T] # Temperature range to explore, K
melt_model = ""
# Configure (run build and vertex)
@time perplex_configure_pseudosection(perplexdir, scratchdir, composition,
elements, P_range, T_range, dataset="hpha02ver.dat", excludes=HP_excludes,
solution_phases=melt_model*HP_solution_phases, index=3, xnodes=200, ynodes=200)
## --- Query modes from a pseudosection
geotherm = 0.015 # Geothermal gradient, K/bar. For reference, 0.1 K/bar ≈ 28.4 K/km
@time modes = perplex_query_modes(perplexdir, scratchdir, [280, (max_lith_T-273.15)/geotherm], T_range, index=3, npoints=200)
h = plot(xlabel="T (C)", ylabel="Weight percent")
for m in modes["elements"][3:end]
plot!(h, modes["T(K)"] .- 273.15, modes[m], label=m)
end
plot!(h,fg_color_legend=:white, framestyle=:box)
savefig(h,"GeothermPhaseModesPseudosection.pdf")
display(h)
## --- Query seismic properties from a pseudosection
geotherm = 0.15 # Geothermal gradient, K/bar. For reference, 0.1 K/bar ≈ 28.4 K/km
@time seismic = perplex_query_seismic(perplexdir, scratchdir, [280, (max_lith_T-273.15)/geotherm], T_range, index=3, npoints=200)
h = plot(xlabel="Pressure", ylabel="Property")
plot!(h,seismic["P(bar)"],seismic["vp,km/s"], label="vp,km/s")
plot!(h,seismic["P(bar)"],seismic["vp/vs"], label="vp/vs")
plot!(h,seismic["P(bar)"],seismic["rho,kg/m3"]/1000, label="rho, g/cc")
plot!(h,seismic["P(bar)"],seismic["T(K)"]/1000, label="T(K)/1000")
# savefig(h,"GeothermSeismicProperties.pdf")
# display(h)
## ---
geotherm = 0.15 # Geothermal gradient, K/bar. For reference, 0.1 K/bar ≈ 28.4 K/km
@time bulk = perplex_query_system(perplexdir, scratchdir, [280, (max_lith_T-273.15)/geotherm], T_range, index=3, npoints=200, include_fluid="n")
h = plot(xlabel="Pressure", ylabel="Property")
plot!(h,bulk["P(bar)"],bulk["vp,km/s"], label="vp,km/s")
plot!(h,bulk["P(bar)"],bulk["vp/vs"], label="vp/vs")
plot!(h,bulk["P(bar)"],bulk["rho,kg/m3"]/1000, label="rho, g/cc")
plot!(h,bulk["P(bar)"],bulk["T(K)"]/1000, label="T(K)/1000")
# savefig(h,"GeothermSeismicProperties.pdf")
# display(h)
## --- End of File