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Merge pull request #71 from jannittayao/main
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Updating StatGeochem functions for Perplex v7.1.9
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@jannittayao
jannittayao authored Nov 12, 2024
2 parents 83c9d76 + dbd1102 commit 62701a1
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4 changes: 2 additions & 2 deletions Artifacts.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,9 @@ lazy = true
url = "https://github.com/brenhinkeller/statgeochem-artifacts/raw/main/litho1/litho1-gridded.tar.gz"

[perplex-datafiles]
git-tree-sha1 = "2330aa8d576c1123c1325f3b3036c5c1428f2276"
git-tree-sha1 = "1b7dff7d9e039af11e1809e12638a523e064c64b"
lazy = true

[[perplex-datafiles.download]]
sha256 = "54ff70b3e5e1c8c090b81c688113a9580926dff658d179dc4e6e4ef2fba61121"
sha256 = "9ad6b3aa2c67619446d0d10a119b74329468a9b38b566c6462c529d9775d410c"
url = "https://github.com/brenhinkeller/statgeochem-artifacts/raw/main/perplex-datafiles/perplex-datafiles.tar.gz"
147 changes: 107 additions & 40 deletions src/resources/Perplex.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -503,30 +503,47 @@ export perplex_query_point
"""
```julia
perplex_query_seismic(scratchdir::String;
\tdof::Integer=1, index::Integer=1, include_fluid="n")
\tdof::Integer=1, index::Integer=1, include_fluid="n",
\tmanual_grid::Bool=false, npoints::Integer=100)
```
Query perplex seismic results along a previously configured 1-d path (dof=1,
isobar or geotherm) or 2-d grid / pseudosection (dof=2).
Results are returned as a dictionary.
"""
function perplex_query_seismic(scratchdir::String;
dof::Integer=1, index::Integer=1, include_fluid::String="n", importas=:Dict)
dof::Integer=1, index::Integer=1, include_fluid::String="n", importas=:Dict,
manual_grid::Bool=false, npoints::Integer=100)
# Query a pre-defined path (isobar or geotherm)

werami = joinpath(Perple_X_jll.PATH[], "werami") # path to PerpleX werami
prefix = joinpath(scratchdir, "out$(index)/") # path to data files

# Create werami batch file
fp = open(prefix*"werami.bat", "w")
if dof == 1
write(fp,"$index\n3\n2\nn\n$include_fluid\n13\nn\n$include_fluid\n15\nn\n$include_fluid\n0\nn\n1\n0\n") # v7.1.6 1d path
# write(fp,"$index\n3\n2\nn\n$include_fluid\n13\nn\n$include_fluid\n15\nn\n$include_fluid\n0\n0\n") # v6.7.8 1d path
elseif dof == 2
# v6.7.8 2d grid
write(fp,"$index\n2\n2\nn\n$include_fluid\n13\nn\n$include_fluid\n15\nn\n$include_fluid\n0\nn\n1\n0\n")
else
error("Expecting dof = 1 (path) or 2 (grid/pseudosection) degrees of freedom")
if manual_grid
# Edit perplex_option.dat to specify a manual grid size
system("sed -e \"s/sample_on_grid .*|/sample_on_grid F |/\" -i.backup $(prefix)perplex_option.dat")
if dof == 1
write(fp,"$index\n3\n2\nn\n$include_fluid\n13\nn\n$include_fluid\n15\nn\n$include_fluid\n0\nn\n$npoints\n0\n") # v7.1.8+ 1d path
# write(fp,"$index\n3\n2\nn\n$include_fluid\n13\nn\n$include_fluid\n15\nn\n$include_fluid\n0\n0\n") # v6.7.8 1d path
elseif dof == 2
# v7.1.8+ 2d grid
write(fp,"$index\n2\n2\nn\n$include_fluid\n13\nn\n$include_fluid\n15\nn\n$include_fluid\n0\nn\n$npoints\n0\n")
else
error("Expecting dof = 1 (path) or 2 (grid/pseudosection) degrees of freedom")
end
else
# Edit perplex_option.dat to specify an automatic grid size
system("sed -e \"s/sample_on_grid .*|/sample_on_grid T |/\" -i.backup $(prefix)perplex_option.dat")
if dof == 1
write(fp,"$index\n3\n2\nn\n$include_fluid\n13\nn\n$include_fluid\n15\nn\n$include_fluid\n0\nn\n1\n0\n") # v7.1.6 1d path
elseif dof==2
# v6.7.8 2d grid
write(fp,"$index\n2\n2\nn\n$include_fluid\n13\nn\n$include_fluid\n15\nn\n$include_fluid\n0\nn\n1\n0\n")
else
error("Expecting dof = 1 (path) or 2 (grid/pseudosection) degrees of freedom")
end
end
close(fp)

Expand Down Expand Up @@ -660,35 +677,52 @@ export perplex_query_seismic
"""
```julia
perplex_query_phase(scratchdir::String, phase::String;
\tdof::Integer=1, index::Integer=1, include_fluid="y", clean_units::Bool=true)
\tdof::Integer=1, index::Integer=1, include_fluid="y", clean_units::Bool=true
\tmanual_grid::Bool=false, npoints::Integer=100)
```
Query all perplex-calculated properties for a specified phase (e.g. "Melt(G)")
along a previously configured 1-d path (dof=1, isobar, geotherm, or P–T path) or 2-d
grid / pseudosection (dof=2). Results are returned as a dictionary.
"""
function perplex_query_phase(scratchdir::String, phase::String;
dof::Integer=1, index::Integer=1, include_fluid="y", clean_units::Bool=true, importas=:Dict)
dof::Integer=1, index::Integer=1, include_fluid="y", clean_units::Bool=true, importas=:Dict,
manual_grid::Bool=false, npoints::Integer=100)
# Query a pre-defined path (isobar or geotherm)

werami = joinpath(Perple_X_jll.PATH[], "werami") # path to PerpleX werami
prefix = joinpath(scratchdir, "out$(index)/") # path to data files

# Create werami batch file
fp = open(prefix*"werami.bat", "w")
if dof == 1
# v7.1.6, 1d path
write(fp,"$index\n3\n36\n2\n$phase\n$include_fluid\nn\n1\n0\n")

# v6.7.8, 1d path
# write(fp,"$index\n3\n36\n2\n$phase\n$include_fluid\n5\n0\n")
# If a named phase (e.g. feldspar) has multiple immiscible phases, average them (5)
elseif dof == 2
# 2d grid
write(fp,"$index\n2\n36\n2\n$phase\n$include_fluid\nn\n1\n0\n") # v6.7.8/v7.1.6
else
error("Expecting dof = 1 (path) or 2 (grid/pseudosection) degrees of freedom")
if manual_grid
# Edit perplex_option.dat to specify a manual grid size
system("sed -e \"s/sample_on_grid .*|/sample_on_grid F |/\" -i.backup $(prefix)perplex_option.dat")
# if dof == 1
#v7.1.8+, 1d path
write(fp,"$index\n3\n36\n2\n$phase\n$include_fluid\nn\n$npoints\n0\n")

# v7.1.6, 1d path
# write(fp,"$index\n3\n36\n2\n$phase\n$include_fluid\nn\n1\n0\n")

# v6.7.8, 1d path
# write(fp,"$index\n3\n36\n2\n$phase\n$include_fluid\n5\n0\n")
# If a named phase (e.g. feldspar) has multiple immiscible phases, average them (5)
# elseif dof == 2
# 2d grid
# write(fp,"$index\n2\n36\n2\n$phase\n$include_fluid\nn\n1\n0\n") # v6.7.8/v7.1.6
# else
# error("Expecting dof = 1 (path) or 2 (grid/pseudosection) degrees of freedom")
# end
else
# Edit perplex_option.dat to specify an automatic grid size
system("sed -e \"s/sample_on_grid .*|/sample_on_grid T |/\" -i.backup $(prefix)perplex_option.dat")

#v7.1.8+, 1d path
write(fp,"$index\n3\n36\n2\n$phase\n$include_fluid\nn\n1\n0\n")
end

close(fp)

# Make sure there isn"t already an output
Expand Down Expand Up @@ -743,7 +777,7 @@ end
"""
```julia
perplex_query_phase(scratchdir::String, phase::String, P::NTuple{2,Number}, T::NTuple{2,Number};
\tindex::Integer=1, npoints::Integer=200, include_fluid="y", clean_units::Bool=true)
\tindex::Integer=1, npoints::Integer=200, include_fluid="y", clean_units::Bool=true, importas=:Dict)
```
Query all perplex-calculated properties for a specified phase (e.g. "Melt(G)")
Expand All @@ -759,7 +793,7 @@ function perplex_query_phase(scratchdir::String, phase::String, P::NTuple{2,Numb

# Create werami batch file
fp = open(prefix*"werami.bat", "w")
write(fp,"$index\n3\nn\n$(first(T))\n$(first(P))\n$(last(T))\n$(last(P))\n$npoints\n36\n2\n$phase\n$include_fluid\n0\n") # v7.1.6 pseudosection
write(fp,"$index\n3\nn\n$(first(T))\n$(first(P))\n$(last(T))\n$(last(P))\n$npoints\n36\n2\n$phase\n$include_fluid\n0\n") # v7.1.6+ pseudosection

# If a named phase (e.g. feldspar) has multiple immiscible phases, average them (5)
# write(fp,"$index\n3\nn\n$(first(T))\n$(first(P))\n$(last(T))\n$(last(P))\n$npoints\n36\n2\n$phase\n$include_fluid\n5\n0\n") # v6.7.8 pseudosection
Expand Down Expand Up @@ -891,7 +925,8 @@ export perplex_query_phase
"""
```julia
perplex_query_modes(scratchdir::String;
\tdof::Integer=1, index::Integer=1, include_fluid="y")
\tdof::Integer=1, index::Integer=1, include_fluid="y",
\tmanualgrid::Bool=false, npoints::Integer=100)
```
Query modal mineralogy (mass proportions) along a previously configured 1-d
Expand All @@ -901,22 +936,41 @@ Results are returned as a dictionary.
Currently returns wt%
"""
function perplex_query_modes(scratchdir::String;
dof::Integer=1, index::Integer=1, include_fluid="y", importas=:Dict)
dof::Integer=1, index::Integer=1, include_fluid="y", importas=:Dict,
manual_grid::Bool=false, npoints::Integer=100)
# Query a pre-defined path (isobar or geotherm)

werami = joinpath(Perple_X_jll.PATH[], "werami") # path to PerpleX werami
prefix = joinpath(scratchdir, "out$(index)/") # path to data files

# Create werami batch file
fp = open(prefix*"werami.bat", "w")
if dof == 1
write(fp,"$index\n3\n38\n3\n$include_fluid\n37\n0\n0\n1\n0\n") # v7.1.6 1d path
# write(fp,"$index\n3\n38\n3\nn\n37\n0\n0\n") # v6.7.8 1d path
elseif dof == 2
# v6.7.8 2d grid
write(fp,"$index\n2\n25\nn\n$include_fluid\nn\n1\n0\n")
if manual_grid
# Edit perplex_option.dat to specify a manual grid size
system("sed -e \"s/sample_on_grid .*|/sample_on_grid F |/\" -i.backup $(prefix)perplex_option.dat")
if dof == 1
write(fp,"$index\n3\n38\n3\n$include_fluid\n37\n0\nn\n$npoints\n0\n") # v7.1.8+ 1d path
# write(fp,"$index\n3\n38\n3\n$include_fluid\n37\n0\n0\n1\n0\n") # v7.1.6 1d path
# write(fp,"$index\n3\n38\n3\nn\n37\n0\n0\n") # v6.7.8 1d path
elseif dof == 2
# v6.7.8 2d grid
#TODO: check this with a pseudosection example
write(fp,"$index\n2\n25\nn\n$include_fluid\nn\n1\n0\n")
else
error("Expecting dof = 1 (path) or 2 (grid/pseudosection) degrees of freedom")
end
else
error("Expecting dof = 1 (path) or 2 (grid/pseudosection) degrees of freedom")
# Edit perplex_option.dat to specify an automatic grid size
system("sed -e \"s/sample_on_grid .*|/sample_on_grid T |/\" -i.backup $(prefix)perplex_option.dat")

if dof == 1
write(fp,"$index\n3\n38\n3\n$include_fluid\n37\n0\n0\n1\n0\n") # v7.1.6 1d path
elseif dof == 2
# v6.7.8 2d grid
write(fp,"$index\n2\n25\nn\n$include_fluid\nn\n1\n0\n")
else
error("Expecting dof = 1 (path) or 2 (grid/pseudosection) degrees of freedom")
end
end
close(fp)

Expand Down Expand Up @@ -1008,7 +1062,7 @@ end
"""
```julia
perplex_query_modes(scratchdir::String, P::NTuple{2,Number}, T::NTuple{2,Number};
\tindex::Integer=1, npoints::Integer=200, include_fluid="y")
\tindex::Integer=1, npoints::Integer=200, include_fluid="y", manual_grid::Bool=false)
```
Query modal mineralogy (mass proportions) along a specified P-T path using a
Expand Down Expand Up @@ -1105,7 +1159,8 @@ export perplex_query_modes
"""
```julia
perplex_query_system(scratchdir::String;
\tindex::Integer=1, include_fluid="y", clean_units::Bool=true)
\tindex::Integer=1, include_fluid="y", clean_units::Bool=true, dof::Integer=1, importas=:Dict,
\tmanual_grid::Bool=false, npoints::Integer=100)
```?
Query all perplex-calculated properties for the system (with or without fluid)
Expand All @@ -1114,16 +1169,28 @@ grid / pseudosection (dof=2). Results are returned as a dictionary.
Set include_fluid="n" to return solid+melt only.
"""
function perplex_query_system(scratchdir::String;
index::Integer=1, include_fluid="y", clean_units::Bool=true, dof::Integer=1, importas=:Dict)
index::Integer=1, include_fluid="y", clean_units::Bool=true, dof::Integer=1, importas=:Dict,
manual_grid::Bool=false, npoints::Integer=100)
# Query a pre-defined path (isobar or geotherm)
werami = joinpath(Perple_X_jll.PATH[], "werami")# path to PerpleX werami
prefix = joinpath(scratchdir, "out$(index)/") # path to data files

# Create werami batch file
fp = open(prefix*"werami.bat", "w")

# v 7.1.6 (same for both dof=1 and dof=2)
write(fp,"$index\n3\n36\n1\n$include_fluid\nn\n1\n0\n")
if manual_grid
# Edit perplex_option.dat to specify a manual grid size
system("sed -e \"s/sample_on_grid .*|/sample_on_grid F |/\" -i.backup $(prefix)perplex_option.dat")

# v 7.1.8+ (same for both dof=1 and dof=2)
write(fp,"$index\n3\n36\n1\n$include_fluid\nn\n$npoints\n0\n")
else
# Edit perplex_option.dat to specify an automatic grid size
system("sed -e \"s/sample_on_grid .*|/sample_on_grid T |/\" -i.backup $(prefix)perplex_option.dat")

# v 7.1.6+ (same for both dof=1 and dof=2)
write(fp,"$index\n3\n36\n1\n$include_fluid\nn\n1\n0\n") #uses coarsest grid option
end

# if dof == 1
# # v6.7.8, 1d path
Expand Down Expand Up @@ -1196,7 +1263,7 @@ function perplex_query_system(scratchdir::String, P::NTuple{2,Number}, T::NTuple

# Create werami batch file
fp = open(prefix*"werami.bat", "w")
# v6.7.8 pseudosection
# v6.7.8+ pseudosection
write(fp,"$index\n3\nn\n$(first(T))\n$(first(P))\n$(last(T))\n$(last(P))\n$npoints\n36\n1\n$include_fluid\n0\n")
close(fp)

Expand Down
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