examples/PerplexExamples.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Julia-Perple_X interface demo\n",
    "\n",
    "This notebook runs the <a href=\"https://github.com/brenhinkeller/StatGeochem.jl\" target=\"_blank\">StatGeochem.jl</a> package, which implements an interface for interacting with <a href=\"https://www.perplex.ethz.ch\" target=\"_blank\">Perple_X</a> from the <a href=\"https://julialang.org\" target=\"_blank\">Julia programming language</a>, including from Jupyter notebooks such as this.\n",
    "\n",
    "StatGeochem.jl also includes some of the codes and utilities used in <a href=\"https://doi.org/10.1038/nature11024\" target=\"_blank\">Keller & Schoene 2012</a>, <a href=\"https://doi.org/10.1038/nature14584\" target=\"_blank\">Keller et al. 2015</a> and <a href=\"https://doi.org/10.1016/j.epsl.2017.10.031\" target=\"_blank\">Keller & Schoene 2018</a>.\n",
    "\n",
    "<a href=\"https://mybinder.org/v2/gh/brenhinkeller/StatGeochem.jl/master?filepath=examples%2FPerplexExamples.ipynb\" target=\"_blank\"><img src=\"https://mybinder.org/badge_logo.svg\" alt=\"Launch Binder notebook\" align=\"left\"></a> \n",
    "<p style=\"text-indent: 5px\">If running this notebook as an online Binder notebook and the webpage times out, click the badge at left to relaunch (refreshing will not work). Note that any changes will be lost!</p>\n",
    "\n",
    "Hint: `shift`-`enter` to run a single cell, or from the `Cell` menu select `Run All` to run the whole file. Any code from this notebook can be copied and pasted into the Julia REPL or a `.jl` script.\n",
    "***\n",
    "### Load required Julia packages"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "┌ Info: Recompiling stale cache file /Users/cbkeller/.julia/compiled/v1.1/StatGeochem/Ht7Cf.ji for StatGeochem [df4de05a-b714-11e8-3c2a-c30fb13e804c]\n",
      "└ @ Base loading.jl:1184\n"
     ]
    }
   ],
   "source": [
    "## --- Load (and install if neccesary) the StatGeochem package which has the resampling functions we'll want\n",
    "\n",
    "try\n",
    "    using StatGeochem\n",
    "catch\n",
    "    using Pkg\n",
    "    Pkg.add(PackageSpec(url=\"https://github.com/brenhinkeller/StatGeochem.jl\"))\n",
    "    using StatGeochem\n",
    "end\n",
    "\n",
    "using Statistics, StatsBase, DelimitedFiles\n",
    "using Plots; gr();"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Try to download and install Perple_X"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "## --- Configure\n",
    "\n",
    "# Absolute paths to perplex resources\n",
    "perplexdir = joinpath(resourcepath,\"perplex-stable\")\n",
    "scratchdir = \"./scratch/\" # Location of directory to store output files\n",
    "\n",
    "# Attempt to install perplex, if not already extant\n",
    "if !isfile(joinpath(perplexdir,\"vertex\"))\n",
    "    # Make sure resourcepath exists\n",
    "    run(`mkdir -p $resourcepath`)\n",
    "\n",
    "    # Try to compile PerpleX from source; if that fails, try to download linux binaries\n",
    "    try\n",
    "        # Check if there is a fortran compiler\n",
    "        run(`gfortran -v`)\n",
    "\n",
    "        # Download Perplex v6.8.7 -- known to work with interface used here\n",
    "        file = download(\"https://storage.googleapis.com/statgeochem/perplex-6.8.7-source.zip\", joinpath(resourcepath,\"perplex-stable.zip\"))\n",
    "\n",
    "        # # For a more updated perplex version, you might also try\n",
    "        # file = download(\"https://petrol.natur.cuni.cz/~ondro/perplex-sources-stable.zip\", joinpath(resourcepath,\"perplex-stable.zip\"))\n",
    "\n",
    "        run(`unzip -u $file -d $resourcepath`) # Extract\n",
    "        system(\"cd $perplexdir; make\") # Compile\n",
    "    catch\n",
    "        @warn \"Failed to compile from source, trying precompiled linux binaries instead\"\n",
    "        run(`mkdir -p $perplexdir`)\n",
    "        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\")\n",
    "        run(`tar -xzf $file -C $perplexdir`)\n",
    "    end\n",
    "end"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Configure Perple_X options"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "9-element Array{Float64,1}:\n",
       " 50.0956\n",
       " 15.3224\n",
       "  8.5103\n",
       "  9.252 \n",
       "  9.6912\n",
       "  2.5472\n",
       "  0.8588\n",
       "  2.0   \n",
       "  0.6   "
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## --- # # # # # # # # # # # # # Initial composition # # # # # # # # # # # # # #\n",
    "\n",
    "## McDonough Pyrolite\n",
    "#elements =    [ \"SIO2\", \"TIO2\", \"AL2O3\",  \"FEO\",  \"MNO\",  \"MGO\",  \"CAO\", \"NA2O\",  \"K2O\",  \"H2O\",  \"CO2\",]\n",
    "#composition = [45.1242, 0.2005, 4.4623, 8.0723, 0.1354, 37.9043, 3.5598, 0.3610, 0.0291, 0.1511, 0.0440,]\n",
    "\n",
    "## Kelemen (2014) primitive continental basalt. H2O and CO2 are guesses\n",
    "#elements =    [ \"SIO2\", \"TIO2\", \"AL2O3\",  \"FEO\",  \"MNO\",  \"MGO\",  \"CAO\", \"NA2O\",  \"K2O\",  \"H2O\",  \"CO2\",]\n",
    "#composition = [50.0956, 0.9564, 15.3224, 8.5103, 0.1659, 9.2520, 9.6912, 2.5472, 0.8588, 2.0000, 0.6000,]\n",
    "\n",
    "# Kelemen (2014) primitive continental basalt excluding Mn and Ti since most melt models can\"t handle them..\n",
    "elements =    [ \"SIO2\", \"AL2O3\",  \"FEO\",  \"MGO\",  \"CAO\", \"NA2O\",  \"K2O\",  \"H2O\",  \"CO2\",]\n",
    "composition = [50.0956, 15.3224, 8.5103, 9.2520, 9.6912, 2.5472, 0.8588, 2.0000, 0.6000,]\n",
    "\n",
    "## Average Archean basalt (EarthChem data)\n",
    "#elements =    [ \"SIO2\", \"TIO2\", \"AL2O3\",   \"FEO\",  \"MNO\",   \"MGO\",  \"CAO\", \"NA2O\",  \"K2O\",  \"H2O\",  \"CO2\",]\n",
    "#composition = [49.2054, 0.8401, 12.0551, 11.4018, 0.2198, 12.3997, 9.3113, 1.6549, 0.4630, 1.8935, 0.5555,]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\"\""
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     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
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   ],
   "source": [
    "## --- # # # # # # # # # # # Some solution model options # # # # # # # # # # # #\n",
    "\n",
    "# Emphasis on phases from Green (2016) -- developed for metabasites, includes what is probably the best (and most expensive) amphibole model. Use with hp11ver.dat\n",
    "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\"\n",
    "G_excludes =\"ged\\nfanth\\ngl\\nilm\\nilm_nol\\n\"\n",
    "\n",
    "# Emphasis on phases from White (2014) -- developed for metapelites. Use with hp11ver.dat (though can apparenty run with hp02ver.dat without crashing)\n",
    "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\"\n",
    "W_excludes = \"andr\\nts\\nparg\\ngl\\nged\\nfanth\\n\"\n",
    "\n",
    "# Emphasis on phases from Jennings and Holland (2015) -- developed for mantle melting. Use with hp11ver.dat\n",
    "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\"\n",
    "JH_excludes = \"ts\\nparg\\ngl\\nged\\nfanth\\n\"\n",
    "\n",
    "# Emphasis on phases from Holland and Powell -- all phases can be used with hp02ver.dat.\n",
    "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\"\n",
    "HP_excludes = \"\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Run Perple_X"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " 54.792925 seconds (464.08 k allocations: 23.311 MiB, 0.02% gc time)\n",
      "\n",
      "----------------------------------------\n",
      "\n",
      "Stable phases at:\n",
      "                             T(K)     =  1723.15    \n",
      "                             P(bar)   =  10000.0    \n",
      "\n",
      "Phase Compositions (molar  proportions):\n",
      "                   wt %      vol %     mol %     mol        H2O      CO2      FEO      MGO      CAO      NA2O     K2O      SIO2     AL2O3\n",
      " melt(G)           99.35     98.28     97.33    0.590      0.18379  0.00000  0.20071  0.38896  0.29283  0.06964  0.01545  1.41272  0.25463\n",
      " F                  0.65      1.72      2.67    0.162E-01  0.15752  0.84248  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000  0.00000\n",
      "\n",
      "Phase speciation (molar proportions):\n",
      "\n",
      " melt(G)           foTL: 0.11411, faTL: 0.05889, abL: 0.16344, silL: 0.02543, kspL: 0.03626, woL: 0.17010, q8L: 0.04254\n",
      "                   h2oL: 0.21569, oanL: 0.17354\n",
      " F                 H2O: 0.15752, CO2: 0.84248\n",
      "\n",
      "Molar Properties and Density:\n",
      "                    N(g)          G(J)     S(J/K)     V(J/bar)      Cp(J/K)       Alpha(1/K)  Beta(1/bar)    Cp/Cv    Density(kg/m3)\n",
      " melt(G)           166.44       -2819391   506.13       6.3017       256.47      0.87739E-04  0.40948E-05   1.0865       2641.2    \n",
      " F                  39.92        -647615   214.51       4.0329       60.884      0.26245E-03  0.43779E-04   1.2189       989.75    \n",
      " System             98.88       -1674426   302.18       3.7844       152.35      0.90752E-04  0.47792E-05   1.0796       2612.7    \n",
      " System - fluid     98.23       -1663946   298.71       3.7192       151.37      0.87739E-04  0.40948E-05   1.0865       2641.2    \n",
      "\n",
      "Seismic Properties:\n",
      "                 Gruneisen_T      Ks(bar)      Mu(bar)    V0(km/s)     Vp(km/s)     Vs(km/s)   Poisson ratio\n",
      " melt(G)           0.57200      0.26533E+06   88443.       3.1695       3.8093       1.8299      0.35000    \n",
      " F                 0.48403       27842.       0.0000       1.6772       1.6772       0.0000      0.50000    \n",
      " System            0.57049      0.24627E+06   43459.       3.0701       3.4123       1.2897      0.41667    \n",
      " System - fluid    0.57200      0.26533E+06   88443.       3.1695       3.8093       1.8299      0.35000    \n",
      "\n",
      "Bulk Composition:\n",
      "\n",
      "                     Complete Assemblage                            Solid+Melt Only\n",
      "              mol        g        wt %     mol/kg          mol        g        wt %     mol/kg\n",
      "    H2O       0.111     2.000     2.023     1.123          0.108     1.954     1.989     1.104\n",
      "    CO2       0.014     0.600     0.607     0.138          0.000     0.000     0.000     0.000\n",
      "    FEO       0.118     8.510     8.607     1.198          0.118     8.510     8.664     1.206\n",
      "    MGO       0.230     9.252     9.357     2.322          0.230     9.252     9.419     2.337\n",
      "    CAO       0.173     9.691     9.801     1.748          0.173     9.691     9.866     1.759\n",
      "    NA2O      0.041     2.547     2.576     0.416          0.041     2.547     2.593     0.418\n",
      "    K2O       0.009     0.859     0.869     0.092          0.009     0.859     0.874     0.093\n",
      "    SIO2      0.834    50.096    50.664     8.432          0.834    50.096    50.997     8.488\n",
      "    AL2O3     0.150    15.322    15.496     1.520          0.150    15.322    15.598     1.530\n",
      "\n",
      "Other Bulk Properties:\n",
      "\n",
      " Enthalpy (J/kg) = -.116682E+08\n",
      " Specific Enthalpy (J/m3) = -.304862E+11\n",
      " Entropy (J/K/kg) =  3056.09    \n",
      " Specific Entropy (J/K/m3) = 0.798480E+07\n",
      " Heat Capacity (J/K/kg) =  1540.80    \n",
      " Specific Heat Capacity (J/K/m3) = 0.402573E+07\n",
      "\n",
      "\n",
      " Solid Enthalpy (J/kg) = -.116992E+08\n",
      " Solid Secific Enthalpy (J/m3) (2) = -.309002E+11\n",
      " Solid Entropy (J/K/kg) =  3040.85    \n",
      " Solid Specific Entropy (J/K/m3) = 0.803158E+07\n",
      " Solid Heat Capacity (J/K/kg) (1) =  1557.70    \n",
      " Solid Specific Heat Capacity (J/K/m3) (1) = 0.406988E+07\n",
      "\n",
      "\n",
      "N.B.: Aggregate properties represent the entire stable assemblage.\n",
      "Solid aggregate properties represent solid and melt properties,\n",
      "but do not include molecular fluid properties.\n",
      "\n",
      "\n",
      "Chemical Potentials (J/mol):\n",
      "\n",
      "      H2O           CO2           FEO           MGO           CAO           NA2O          K2O           SIO2          AL2O3\n",
      "    -509890.      -673366.      -478356.      -738298.      -864198.     -0.102378E+07 -0.111639E+07 -0.106581E+07 -0.194481E+07\n",
      "\n",
      "Variance (c-p+2) =  9\n",
      "\n",
      "\n",
      "----------------------------------------\n",
      "\n"
     ]
    }
   ],
   "source": [
    "## --- # # # # # # # # # # # # # Isobaric example # # # # # # # # # # # # # # # #\n",
    "\n",
    "    # Input parameters\n",
    "    P = 10000 # Pressure, bar\n",
    "    T_range = [500+273.15, 1500+273.15] # Temperature range, Kelvin\n",
    "    melt_model = \"melt(G)\"\n",
    "\n",
    "    # Configure (run build and vertex)\n",
    "    @time perplex_configure_isobar(perplexdir, scratchdir, composition, elements,\n",
    "        P, T_range, dataset=\"hp11ver.dat\", npoints=100, excludes=G_excludes,\n",
    "        solution_phases=melt_model*\"\\n\"*G_solution_phases)\n",
    "\n",
    "## --- Query all properties at a single temperature -- results returned as text\n",
    "\n",
    "    T = 1450+273.15\n",
    "    data_isobaric = perplex_query_1d(perplexdir, scratchdir, T) |> print"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "┌ Warning: Perplex seems to be reporting mole fractions instead of weight percentages, attempting to correct\n",
      "└ @ StatGeochem /Users/cbkeller/Documents/julia/packages/StatGeochem.jl/src/utilities/Geochemistry.jl:649\n"
     ]
    }
   ],
   "source": [
    "## --- Query the full isobar -- results returned as dict\n",
    "\n",
    "bulk = perplex_query_system(perplexdir, scratchdir)             # Get system data for all temperatures. Set include_fluid = \"n\" to get solid+melt only\n",
    "modes = perplex_query_modes(perplexdir, scratchdir)             # || phase modes\n",
    "melt = perplex_query_phase(perplexdir, scratchdir, melt_model)  # || melt data\n",
    "\n",
    "# Melt wt.% seems to be slightly inaccurate; use values from modes instead\n",
    "melt[\"wt_pct\"] = modes[melt_model]\n",
    "\n",
    "# Create dictionary to hold solid composition and fill it using what we know from system and melt\n",
    "solid = Dict()\n",
    "solid[\"wt_pct\"] = 100 .- melt[\"wt_pct\"]\n",
    "for e in [\"SIO2\",\"AL2O3\",\"FEO\",\"MGO\",\"CAO\",\"NA2O\",\"K2O\"]\n",
    "    solid[e] = (bulk[e] - (melt[e] .* melt[\"wt_pct\"]/100)) ./ (solid[\"wt_pct\"]/100)\n",
    "end\n",
    "renormalize!(solid,[\"SIO2\",\"AL2O3\",\"FEO\",\"MGO\",\"CAO\",\"NA2O\",\"K2O\"],total=100)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Plot results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
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       "  606.77,1079.19 630.935,1077.09 646.469,1073.98 664.42,1073.74 681.21,1072.74 714.01,1072.06 736.361,1072.17 755.448,1071.05 789.415,1072.79 818.638,1073.31 \n",
       "  852.699,1074.63 886.471,1075.04 921.588,1075.47 958.567,1077.19 1003.11,1077.38 1043.47,1077.48 1087.78,1078.12 1134.3,1078.23 1188.08,1077.15 1237.71,1076.39 \n",
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       "  2047.36,1065.46 2064.96,1068.04 2085.05,1071.09 2104.17,1074 2123.25,1077.02 2142.68,1080.14 2166.69,1083.47 2187.11,1086.56 2209.27,1089.92 2232.62,1093.4 \n",
       "  2258.23,1097.21 2282,1100.71 2291.9,1102.14 2291.85,1102.14 2291.81,1102.14 2291.76,1102.14 2291.72,1102.15 2291.67,1102.15 2291.63,1102.15 2291.59,1102.15 \n",
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       "  606.77,1104.04 630.935,1104.03 646.469,1104.03 664.42,1104.03 681.21,1104.03 714.01,1104.03 736.361,1104.03 755.448,1104.03 789.415,1104.03 818.638,1104.03 \n",
       "  852.699,1104.03 886.471,1104.03 921.588,1104.03 958.567,1104.03 1003.11,1104.03 1043.47,1104.03 1087.78,1104.03 1134.3,1104.03 1188.08,1104.03 1237.71,1104.03 \n",
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       "  1775.41,1104.03 1835.48,1104.03 1893.74,1104.03 1914.06,1104.03 1935.64,1104.03 1956.77,1104.03 1975.98,1104.03 1994.13,1104.03 2011.68,1104.03 2029.41,1104.03 \n",
       "  2047.36,1104.03 2064.96,1104.03 2085.05,1104.03 2104.17,1104.03 2123.25,1104.03 2142.68,1104.03 2166.69,1104.03 2187.11,1104.03 2209.27,1104.03 2232.62,1104.03 \n",
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       "  2258.23,1231.32 2282,1231.32 2291.9,1231.32 2291.85,1231.32 2291.81,1231.32 2291.76,1231.32 2291.72,1231.32 2291.67,1231.32 2291.63,1231.32 2291.59,1231.32 \n",
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     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "## --- Plot melt composition as a function of melt percent\n",
    "\n",
    "h = plot(xlabel=\"Percent melt\", ylabel=\"Wt. % in melt\", title=\"$melt_model + G_solution_phases, $P bar\")\n",
    "i = 0\n",
    "for e in [\"SIO2\",\"AL2O3\",\"FEO\",\"MGO\",\"CAO\",\"NA2O\",\"K2O\"]\n",
    "    plot!(h, melt[\"wt_pct\"], melt[e], label=e, color=lines[global i += 1])\n",
    "    plot!(h, melt[\"wt_pct\"], bulk[e], label=\"\", color=lines[i], linestyle=:dot)\n",
    "end\n",
    "plot!(h,fg_color_legend=:white, framestyle=:box)\n",
    "# savefig(h,\"MeltComposition.pdf\")\n",
    "display(h)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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   ],
   "source": [
    "## --- Plot solid composition as a function of melt percent\n",
    "\n",
    "h = plot(xlabel=\"Percent melt\", ylabel=\"Wt. % in solid\", title=\"$melt_model + G_solution_phases, $P bar\")\n",
    "i = 0\n",
    "for e in [\"SIO2\",\"AL2O3\",\"FEO\",\"MGO\",\"CAO\",\"NA2O\",\"K2O\"]\n",
    "    plot!(h, melt[\"wt_pct\"], solid[e], label=e, color=lines[global i +=1])\n",
    "end\n",
    "plot!(h,fg_color_legend=:white, framestyle=:box, legend=:topleft)\n",
    "# savefig(h,\"SolidComposition.pdf\")\n",
    "display(h)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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     "metadata": {},
     "output_type": "display_data"
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   ],
   "source": [
    "## --- Plot modes of all phases as a function of temperature\n",
    "\n",
    "h = plot(xlabel=\"T (C)\", ylabel=\"Weight percent\", title=\"$melt_model + G_solution_phases, $P bar\")\n",
    "for m in modes[\"elements\"][3:end]\n",
    "    plot!(h, modes[\"T(K)\"] .- 273.15, modes[m], label=m)\n",
    "end\n",
    "plot!(h,fg_color_legend=:white, framestyle=:box)\n",
    "# savefig(h,\"PhaseModes.pdf\")\n",
    "display(h)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "ename": "MethodError",
     "evalue": "MethodError: no method matching perplex_configure_geotherm(::String, ::String, ::Array{Float64,1}, ::Array{String,1}, ::Array{Int64,1}, ::Float64, ::Float64; dataset=\"hp02ver.dat\", excludes=\"\", 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\", npoints=200, index=2)\nClosest candidates are:\n  perplex_configure_geotherm(::String, ::String, ::Array{#s47,N} where N where #s47<:Number; elements, P_range, T_surf, geotherm, dataset, solution_phases, excludes, index, npoints) at /Users/cbkeller/Documents/julia/packages/StatGeochem.jl/src/utilities/Geochemistry.jl:427",
     "output_type": "error",
     "traceback": [
      "MethodError: no method matching perplex_configure_geotherm(::String, ::String, ::Array{Float64,1}, ::Array{String,1}, ::Array{Int64,1}, ::Float64, ::Float64; dataset=\"hp02ver.dat\", excludes=\"\", 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\", npoints=200, index=2)\nClosest candidates are:\n  perplex_configure_geotherm(::String, ::String, ::Array{#s47,N} where N where #s47<:Number; elements, P_range, T_surf, geotherm, dataset, solution_phases, excludes, index, npoints) at /Users/cbkeller/Documents/julia/packages/StatGeochem.jl/src/utilities/Geochemistry.jl:427",
      "",
      "Stacktrace:",
      " [1] top-level scope at util.jl:156",
      " [2] top-level scope at In[10]:8"
     ]
    }
   ],
   "source": [
    "## --- # # # # # # # # # # # Geothermal gradient example # # # # # # # # # # # #\n",
    "\n",
    "# Input parameters\n",
    "P_range = [280, 28000] # Pressure range to explore, bar (roughly 1-100 km depth)\n",
    "T_surf = 273.15 # Temperature of surface (K)\n",
    "geotherm = 0.1 # Geothermal gradient of 0.1 K/bar == about 28.4 K/km\n",
    "melt_model = \"\"\n",
    "\n",
    "# Configure (run build and vertex)\n",
    "@time perplex_configure_geotherm(perplexdir, scratchdir, composition, elements,\n",
    "    P_range, T_surf, geotherm, dataset=\"hp02ver.dat\", excludes=HP_excludes,\n",
    "    solution_phases=HP_solution_phases, npoints=200, index=2)\n",
    "\n",
    "# # Alternative configuration, using hpha02ver.dat\n",
    "# @time perplex_configure_geotherm(perplexdir, scratchdir, composition, elements,\n",
    "#     P_range, T_surf, geotherm, dataset=\"hpha02ver.dat\", excludes=\"qGL\\n\"*HP_excludes,\n",
    "#     solution_phases=HP_solution_phases, npoints=200, index=2)\n",
    "\n",
    "# # Alternative configuration, using hpha02ver.dat and new phases for metapelites\n",
    "# @time perplex_configure_geotherm(perplexdir, scratchdir, composition, elements,\n",
    "#     P_range, T_surf, geotherm, dataset=\"hpha02ver.dat\", excludes=\"qGL\\n\"*W_excludes,\n",
    "#     solution_phases=W_solution_phases, npoints=200, index=2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
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   "source": [
    "## --- Plot modes of all phases as a function of temperature\n",
    "\n",
    "# Get phase modes\n",
    "modes = perplex_query_modes(perplexdir, scratchdir, index=2)\n",
    "\n",
    "h = plot(xlabel=\"T (C)\", ylabel=\"Weight percent\")\n",
    "for m in modes[\"elements\"][3:end]\n",
    "    plot!(h, modes[\"T(K)\"] .- 273.15, modes[m], label=m)\n",
    "end\n",
    "plot!(h,fg_color_legend=:white, framestyle=:box)\n",
    "# savefig(h,\"GeothermPhaseModes.pdf\")\n",
    "display(h)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
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       "<text style=\"fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;\" transform=\"rotate(0, 2018.75, 329.704)\" x=\"2018.75\" y=\"329.704\">rho, g/cc</text>\n",
       "</g>\n",
       "<polyline clip-path=\"url(#clip7300)\" style=\"stroke:#c271d2; stroke-width:4; stroke-opacity:1; fill:none\" points=\"\n",
       "  1850.75,372.684 1994.75,372.684 \n",
       "  \"/>\n",
       "<g clip-path=\"url(#clip7300)\">\n",
       "<text style=\"fill:#000000; fill-opacity:1; font-family:Arial,Helvetica Neue,Helvetica,sans-serif; font-size:48px; text-anchor:start;\" transform=\"rotate(0, 2018.75, 390.184)\" x=\"2018.75\" y=\"390.184\">T(K)/1000</text>\n",
       "</g>\n",
       "</svg>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "## --- Plot seismic properties\n",
    "\n",
    "# Query seismic properties along the whole profile\n",
    "seismic = perplex_query_seismic(perplexdir, scratchdir, index=2)\n",
    "seismic[\"vp/vs\"][seismic[\"vp/vs\"] .> 100] .= NaN # Exclude cases where vs drops to zero\n",
    "\n",
    "h = plot(xlabel=\"Pressure\", ylabel=\"Property\")\n",
    "plot!(h,seismic[\"P(bar)\"],seismic[\"vp,km/s\"], label=\"vp,km/s\")\n",
    "plot!(h,seismic[\"P(bar)\"],seismic[\"vp/vs\"], label=\"vp/vs\")\n",
    "plot!(h,seismic[\"P(bar)\"],seismic[\"rho,kg/m3\"]/1000, label=\"rho, g/cc\")\n",
    "plot!(h,seismic[\"P(bar)\"],seismic[\"T(K)\"]/1000, label=\"T(K)/1000\")\n",
    "# savefig(h,\"GeothermSeismicProperties.pdf\")\n",
    "display(h)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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