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MAGEMin_v1.6.1
- Added frac_M_vol, frac_F_vol and frac_S_vol output for MAGEMin_C - Corrected wrong set of W's for spinel in the metapelite and metapelite extended database - Added molar mass of CO2 for MAGEMin_C (which was leading to failed mpe bulk loading in the App)
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‎Project.toml

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name = "MAGEMin_C"
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uuid = "e5d170eb-415a-4524-987b-12f1bce1ddab"
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authors = ["Boris Kaus <[email protected]> & Nicolas Riel <[email protected]>"]
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version = "1.6.0"
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version = "1.6.1"
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[deps]
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BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"

‎doc_raw/index.rst

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**MAGEMin v1.6.0**
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**MAGEMin v1.6.1**
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==================
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MAGEMin (Mineral Assemblage Gibbs Energy Minimization) is a parallel C library callable from any petrological/geodynamic tool. For a given set of pressure, temperature and bulk-rock composition MAGEMin uses a combination of linear programming, extended Partitioning Gibbs free Energy and gradient-based local minimization to compute the most stable mineral assemblage

‎docs/index.html

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<meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>MAGEMin v1.6.0 &mdash; MAGEMin 2022 documentation</title>
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<title>MAGEMin v1.6.1 &mdash; MAGEMin 2022 documentation</title>
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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<link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
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<div role="navigation" aria-label="Page navigation">
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<ul class="wy-breadcrumbs">
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<li><a href="#" class="icon icon-home"></a> &raquo;</li>
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<li><strong>MAGEMin v1.6.0</strong></li>
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<li><strong>MAGEMin v1.6.1</strong></li>
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<li class="wy-breadcrumbs-aside">
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<a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
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</li>
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<div class="line"><br /></div>
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</div>
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<section id="magemin-v1-5-0">
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<h1><strong>MAGEMin v1.6.0</strong><a class="headerlink" href="#magemin-v1-5-0" title="Permalink to this headline"></a></h1>
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<h1><strong>MAGEMin v1.6.1</strong><a class="headerlink" href="#magemin-v1-5-0" title="Permalink to this headline"></a></h1>
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<p>MAGEMin (Mineral Assemblage Gibbs Energy Minimization) is a parallel C library callable from any petrological/geodynamic tool. For a given set of pressure, temperature and bulk-rock composition MAGEMin uses a combination of linear programming, extended Partitioning Gibbs free Energy and gradient-based local minimization to compute the most stable mineral assemblage</p>
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<p>A full description of the minimization approach used in MAGEMin is given in:</p>
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<p>Riel, N., Kaus, B. J. P., Green, E. C. R., &amp; Berlie, N. (2022). MAGEMin, an efficient Gibbs energy minimizer: Application to igneous systems. Geochemistry, Geophysics, Geosystems, 23, e2022GC010427. <a class="reference external" href="https://doi.org/10.1029/2022GC010427">https://doi.org/10.1029/2022GC010427</a></p>

‎docs/searchindex.js

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‎docs/stp.html

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<link rel="index" title="Index" href="genindex.html" />
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<link rel="search" title="Search" href="search.html" />
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<link rel="next" title="External libraries" href="stp/Linux.html" />
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<link rel="prev" title="MAGEMin v1.6.0" href="index.html" />
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<link rel="prev" title="MAGEMin v1.6.1" href="index.html" />
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</head>
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<body class="wy-body-for-nav">
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</div>
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</div>
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<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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<a href="index.html" class="btn btn-neutral float-left" title="MAGEMin v1.6.0" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="index.html" class="btn btn-neutral float-left" title="MAGEMin v1.6.1" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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<a href="stp/Linux.html" class="btn btn-neutral float-right" title="External libraries" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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</div>
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‎gen/magemin_library.jl

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rho_F::Cdouble
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bulk_S_wt::Ptr{Cdouble}
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frac_S_wt::Cdouble
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frac_S_vol::Cdouble
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bulk_M_wt::Ptr{Cdouble}
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frac_M_wt::Cdouble
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frac_M_vol::Cdouble
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bulk_F_wt::Ptr{Cdouble}
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frac_F_wt::Cdouble
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frac_F_vol::Cdouble
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n_ph::Cint
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n_PP::Cint
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n_SS::Cint
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n_pp::Cint
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n_ss::Cint
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ox::NTuple{11, NTuple{20, Cchar}}
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PP::NTuple{23, NTuple{20, Cchar}}
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PP::NTuple{24, NTuple{20, Cchar}}
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SS::NTuple{18, NTuple{20, Cchar}}
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verifyPC::NTuple{18, Cint}
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n_SS_PC::NTuple{18, Cint}
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n_pp::Cint
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n_ss::Cint
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ox::NTuple{10, NTuple{20, Cchar}}
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PP::NTuple{23, NTuple{20, Cchar}}
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PP::NTuple{24, NTuple{20, Cchar}}
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SS::NTuple{17, NTuple{20, Cchar}}
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verifyPC::NTuple{17, Cint}
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n_SS_PC::NTuple{17, Cint}
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n_pp::Cint
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n_ss::Cint
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ox::NTuple{13, NTuple{20, Cchar}}
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PP::NTuple{25, NTuple{20, Cchar}}
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PP::NTuple{26, NTuple{20, Cchar}}
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SS::NTuple{23, NTuple{20, Cchar}}
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verifyPC::NTuple{23, Cint}
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n_SS_PC::NTuple{23, Cint}

‎julia/MAGEMin_wrappers.jl

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‎ref_database/.DS_Store

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‎ref_database/TC_ref_database/aq_min.jl

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#=
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Test for Aqueous minimizer
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=#
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species = ["H2O", "Al(OH)2+", "Al(OH)3@", "Al(OH)4-", "Al+3", "AlH3SiO4+2", "AlOH+2", "Ca+2", "CaHSiO3+", "CaOH+", "CaSiO3@", "HSiO3-", "K+", "KAlO2@", "KOH@", "Mg+2", "MgHSiO3+", "MgOH+", "MgSiO3@", "Na+", "NaAl(OH)4@", "NaHSiO3@", "NaOH@", "OH-", "SiO2@"]
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G0s = [-378.991999, -1012.553295, -1405.559155, -1669.882646, -260.382070, -2061.778806, -641.559594, -536.589068, -1772.464205, -761.449349, -1705.193764, -1154.160844, -375.639412, -1280.307808, -585.973831, -400.958279, -1617.254393, -701.376817, -1567.329979, -350.424257, -2035.360551, -1485.410150, -563.302949, -179.482769, -970.840788]
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oxide_names = ["SiO2", "Al2O3", "CaO", "MgO", "FeO", "K2O", "Na2O", "TiO2", "O", "MnO", "H2O"]
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gamma_pc = [-966.661516, -1766.267094, -808.803681, -688.195348, -369.432486, -936.439987, -876.096639, -1018.881760, -238.219822, -526.537851, -379.011475]
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matrix = [ 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0;
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0.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 -0.5 0.0 1.0;
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0.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.5;
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0.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.0 2.0;
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0.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 -1.5 0.0 0.0;
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1.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 1.5;
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0.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.5;
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0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0;
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1.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 -0.5 0.0 0.5;
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0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 -0.5 0.0 0.5;
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1.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0;
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1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.0 0.5;
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0.0 0.0 0.0 0.0 0.0 0.5 0.0 0.0 -0.5 0.0 0.0;
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0.0 0.5 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.0;
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0.0 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.0 0.5;
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0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0;
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1.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -0.5 0.0 0.5;
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0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 -0.5 0.0 0.5;
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1.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0;
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0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.0 -0.5 0.0 0.0;
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0.0 0.5 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 2.0;
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1.0 0.0 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5;
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0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.0 0.0 0.0 0.5;
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0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 0.0 0.5;
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1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0]
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# id_OHm = findfirst(species .== "OH-")
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# id_H2O = findfirst(species .== "H2O")
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# id_O2 = findfirst(oxide_names .== "O")
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# gO2 = gamma_pc[id_O2]
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# gO = gO2/2.0
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gH2 = G0s[id_H2O] - gO
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gH = gH2/2.0
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G_H2 = (G0s[id_H2O] - G0s[id_OHm])

‎ref_database/TC_ref_database/aqueous.md

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# Aqueous species formulation, using Miron et al., 2017 database.
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```math
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G_{aq} = \sum_{i=1}^{n^{em}} n_i \mu_i
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```
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where $n_i$ the molar fraction and $\mu_i$ is the chemical potential of the species $i$.
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```math
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\mu_i = G_i^0 + RT ln(\gamma_i m_i)
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```
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where $m_i$ is the molal fraction (!?)
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And then develops into:
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```math
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\mu_i = G_i^0 + RT( ln(\gamma_i) + ln(m_i))
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```
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```math
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\mu_i = G_i^0 + RT( ln(\gamma_i) + ln(\frac{n_i}{n_{H2O} M_{H2O}}))
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```
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```math
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\mu_i = G_i^0 + RT( ln(\gamma_i) + ln(\frac{n_i}{18.015 * n_{H2O}}))
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```
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---
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For solute (aqueous species, excluding water), and assuming $\gamma_i$ = 1 (for now)
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```math
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\mu_i = G_i^0 + RT ln(m_i)
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```
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where
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```math
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m_i = \frac{n_i}{m_{H2O}}
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```
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so here $n_i$ is again the molar fraction and $m_{H2O}$ is mass of water? Should it be water density?
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I could find the following definition:
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```math
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m_i = \frac{n_i}{n_{H2O} M_{H2O}}
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```
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and here $n_i$ is the molarity and $M_{H2O}$ is the Molar mass of water (18.015). However, here density of water like we discussed is not appearing, is that right?
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Should it simply be:
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```math
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m_i = \frac{n_i}{\rho_{H2O}}
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```
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---
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For solvant (water):
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```math
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\mu_{H2O} = G_{H2O }^0 + RT ln(\frac{1}{M_{H2O}})
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```
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!?

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