MAGEMin v1.5.7

- Added 1atom basis to output structure - Added buffer and buffer_n to output structure - Re-added consideration of pure-end member to the minimization, improves performance and accuracy
ComputationalThermodynamics · Nov 7, 2024 · 8a31103 · 8a31103
2 parents 21c7b72 + fb2c312
commit 8a31103
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diff --git a/Makefile b/Makefile
@@ -43,12 +43,13 @@ SOURCES=src/MAGEMin.c 							\
 		src/SB_database/SB_init_database.c		\
 		src/SB_database/SB_endmembers.c			\
 		src/SB_database/SB_gem_function.c		\
-		src/SB_database/sb_gss_init_function.c	\
 		src/toolkit.c							\
 		src/io_function.c						\
 		src/gem_function.c 						\
 		src/TC_database/tc_gss_init_function.c	\
 		src/TC_database/tc_gss_function.c		\
+		src/SB_database/sb_gss_init_function.c	\
+		src/SB_database/sb_gss_function.c		\
 		src/TC_database/NLopt_opt_function.c 	\
 		src/TC_database/objective_functions.c	\
 		src/TC_database/SS_xeos_PC_mp.c			\

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "MAGEMin_C"
 uuid = "e5d170eb-415a-4524-987b-12f1bce1ddab"
 authors = ["Boris Kaus <[email protected]> & Nicolas Riel <[email protected]>"]
-version = "1.5.6"
+version = "1.5.7"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"

diff --git a/doc_raw/index.rst b/doc_raw/index.rst
@@ -10,7 +10,7 @@
 
 |
 
-**MAGEMin v1.5.6**
+**MAGEMin v1.5.7**
 ==================
 
 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     

diff --git a/docs/index.html b/docs/index.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>MAGEMin v1.5.6 &mdash; MAGEMin 2022 documentation</title>
+  <title>MAGEMin v1.5.7 &mdash; MAGEMin 2022 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
@@ -247,7 +247,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="#" class="icon icon-home"></a> &raquo;</li>
-      <li><strong>MAGEMin v1.5.6</strong></li>
+      <li><strong>MAGEMin v1.5.7</strong></li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -263,7 +263,7 @@
 <div class="line"><br /></div>
 </div>
 <section id="magemin-v1-5-0">
-<h1><strong>MAGEMin v1.5.6</strong><a class="headerlink" href="#magemin-v1-5-0" title="Permalink to this headline"></a></h1>
+<h1><strong>MAGEMin v1.5.7</strong><a class="headerlink" href="#magemin-v1-5-0" title="Permalink to this headline"></a></h1>
 <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>
 <p>A full description of the minimization approach used in MAGEMin is given in:</p>
 <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>

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/stp.html b/docs/stp.html
@@ -20,7 +20,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="External libraries" href="stp/Linux.html" />
-    <link rel="prev" title="MAGEMin v1.5.6" href="index.html" /> 
+    <link rel="prev" title="MAGEMin v1.5.7" href="index.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -292,7 +292,7 @@ <h1>Optional (developers)<a class="headerlink" href="#optional-developers" title
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="index.html" class="btn btn-neutral float-left" title="MAGEMin v1.5.6" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="index.html" class="btn btn-neutral float-left" title="MAGEMin v1.5.7" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <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>
     </div>
 

diff --git a/gen/magemin_library.jl b/gen/magemin_library.jl
@@ -131,9 +131,9 @@ function rho_wat_calc(wat, Pbar, TK, opt)
 end
 
 mutable struct EM_db_sb_
-    Name::NTuple{20, Cchar}
-    FullName::NTuple{50, Cchar}
-    Equation::NTuple{50, Cchar}
+    Name::NTuple{50, Cchar}
+    FullName::NTuple{80, Cchar}
+    Equation::NTuple{90, Cchar}
     Comp::NTuple{6, Cdouble}
     input_1::NTuple{10, Cdouble}
     input_2::NTuple{3, Cdouble}
@@ -146,6 +146,10 @@ function Access_SB_EM_DB(id, EM_dataset)
     ccall((:Access_SB_EM_DB, libMAGEMin), EM_db_sb, (Cint, Cint), id, EM_dataset)
 end
 
+function SB_G_EM_function(EM_database, len_ox, id, bulk_rock, apo, P, T, name, state)
+    ccall((:SB_G_EM_function, libMAGEMin), PP_ref, (Cint, Cint, Ptr{Cint}, Ptr{Cdouble}, Ptr{Cdouble}, Cdouble, Cdouble, Ptr{Cchar}, Ptr{Cchar}), EM_database, len_ox, id, bulk_rock, apo, P, T, name, state)
+end
+
 # typedef double ( * nlopt_func ) ( unsigned n , const double * x , double * gradient , /* NULL if not needed */ void * func_data )
 const nlopt_func = Ptr{Cvoid}
 
@@ -1114,6 +1118,7 @@ const stb_PP_phase = stb_PP_phases
 struct stb_systems
     MAGEMin_ver::Ptr{Cchar}
     dataset::Ptr{Cchar}
+    database::Ptr{Cchar}
     bulk_res_norm::Cdouble
     n_iterations::Cint
     status::Cint
@@ -1125,6 +1130,8 @@ struct stb_systems
     X::Cdouble
     bulk::Ptr{Cdouble}
     bulk_wt::Ptr{Cdouble}
+    buffer::Ptr{Cchar}
+    buffer_n::Cdouble
     gamma::Ptr{Cdouble}
     G::Cdouble
     M_sys::Cdouble
@@ -1175,6 +1182,7 @@ struct stb_systems
     ph::Ptr{Ptr{Cchar}}
     ph_frac::Ptr{Cdouble}
     ph_frac_wt::Ptr{Cdouble}
+    ph_frac_1at::Ptr{Cdouble}
     ph_frac_vol::Ptr{Cdouble}
     ph_type::Ptr{Cint}
     ph_id::Ptr{Cint}
@@ -1506,7 +1514,7 @@ mutable struct stx11_datasets
     n_pp::Cint
     n_ss::Cint
     ox::NTuple{6, NTuple{20, Cchar}}
-    PP::NTuple{10, NTuple{20, Cchar}}
+    PP::NTuple{9, NTuple{20, Cchar}}
     SS::NTuple{14, NTuple{20, Cchar}}
     verifyPC::NTuple{14, Cint}
     n_SS_PC::NTuple{14, Cint}
@@ -2196,6 +2204,14 @@ function SS_mtl_pc_init_function(SS_pc_xeos, iss, name)
     ccall((:SS_mtl_pc_init_function, libMAGEMin), Cvoid, (Ptr{PC_ref}, Cint, Ptr{Cchar}), SS_pc_xeos, iss, name)
 end
 
+function SB_SS_init(SS_init, gv)
+    ccall((:SB_SS_init, libMAGEMin), Cvoid, (Ptr{SS_init_type}, global_variable), SS_init, gv)
+end
+
+function G_SS_sb11_EM_function(gv, SS_ref_db, EM_dataset, z_b, name)
+    ccall((:G_SS_sb11_EM_function, libMAGEMin), SS_ref, (global_variable, SS_ref, Cint, bulk_info, Ptr{Cchar}), gv, SS_ref_db, EM_dataset, z_b, name)
+end
+
 function PGE(z_b, gv, PC_read, SS_objective, NLopt_opt, splx_data, PP_ref_db, SS_ref_db, cp)
     ccall((:PGE, libMAGEMin), global_variable, (bulk_info, global_variable, Ptr{PC_type}, Ptr{obj_type}, Ptr{NLopt_type}, Ptr{simplex_data}, Ptr{PP_ref}, Ptr{SS_ref}, Ptr{csd_phase_set}), z_b, gv, PC_read, SS_objective, NLopt_opt, splx_data, PP_ref_db, SS_ref_db, cp)
 end
@@ -2287,22 +2303,20 @@ function read_in_data(gv, input_data, n_points)
     ccall((:read_in_data, libMAGEMin), Cvoid, (global_variable, Ptr{io_data}, Cint), gv, input_data, n_points)
 end
 
-mutable struct ketopt_t
+struct ketopt_t
     ind::Cint
     opt::Cint
     arg::Ptr{Cchar}
     longidx::Cint
     i::Cint
     pos::Cint
     n_args::Cint
-    ketopt_t() = new()
 end
 
-mutable struct ko_longopt_t
+struct ko_longopt_t
     name::Ptr{Cchar}
     has_arg::Cint
     val::Cint
-    ko_longopt_t() = new()
 end
 
 function ketopt_permute(argv, j, n)
@@ -2351,6 +2365,10 @@ function init_em_db(EM_database, z_b, gv, PP_ref_db)
     ccall((:init_em_db, libMAGEMin), global_variable, (Cint, bulk_info, global_variable, Ptr{PP_ref}), EM_database, z_b, gv, PP_ref_db)
 end
 
+function init_em_db_sb(EM_database, z_b, gv, PP_ref_db)
+    ccall((:init_em_db_sb, libMAGEMin), global_variable, (Cint, bulk_info, global_variable, Ptr{PP_ref}), EM_database, z_b, gv, PP_ref_db)
+end
+
 function update_dG(splx_data)
     ccall((:update_dG, libMAGEMin), Cvoid, (Ptr{simplex_data},), splx_data)
 end
@@ -2451,6 +2469,10 @@ function convert_system_comp(gv, sys_in, z_b)
     ccall((:convert_system_comp, libMAGEMin), Cvoid, (global_variable, Ptr{Cchar}, bulk_info), gv, sys_in, z_b)
 end
 
+function get_tests_bulks(gv)
+    ccall((:get_tests_bulks, libMAGEMin), global_variable, (global_variable,), gv)
+end
+
 function get_act_sf_id(result, A, n)
     ccall((:get_act_sf_id, libMAGEMin), Cvoid, (Ptr{Cint}, Ptr{Cdouble}, Cint), result, A, n)
 end