MAGEMin v1.5.9

- Corrected default ilmenite model for metapelite and metabasite database to be ilm instead of ilmm
- Added adaptive refinement for MAGEMin_C Julia wrapper

Makefile

@@ -51,13 +51,16 @@ SOURCES=src/MAGEMin.c 							\
 		src/SB_database/sb_gss_init_function.c	\
 		src/SB_database/sb_gss_function.c		\
 		src/TC_database/NLopt_opt_function.c 	\
+		src/SB_database/SB_NLopt_opt_function.c \
 		src/TC_database/objective_functions.c	\
+		src/SB_database/sb_objective_functions.c\
 		src/TC_database/SS_xeos_PC_mp.c			\
 		src/TC_database/SS_xeos_PC_mb.c			\
 		src/TC_database/SS_xeos_PC_ig.c			\
 		src/TC_database/SS_xeos_PC_igad.c		\
 		src/TC_database/SS_xeos_PC_um.c			\
 		src/TC_database/SS_xeos_PC_mtl.c		\
+		src/SB_database/SS_xeos_PC_sb11.c		\
 		src/pp_min_function.c 					\
 		src/ss_min_function.c 					\
 		src/simplex_levelling.c 				\

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 = "1.5.8"
+version = "1.5.9"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"

doc_raw/index.rst

@@ -10,7 +10,7 @@
 
 |
 
-**MAGEMin v1.5.8**
+**MAGEMin v1.5.9**
 ==================
 
 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

@@ -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 v1.5.8 &mdash; MAGEMin 2022 documentation</title>
+  <title>MAGEMin v1.5.9 &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 v1.5.8</strong></li>
+      <li><strong>MAGEMin v1.5.9</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 v1.5.8</strong><a class="headerlink" href="#magemin-v1-5-0" title="Permalink to this headline"></a></h1>
+<h1><strong>MAGEMin v1.5.9</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>

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 v1.5.8" href="index.html" /> 
+    <link rel="prev" title="MAGEMin v1.5.9" 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 v1.5.8" 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 v1.5.9" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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     </div>
 

gen/magemin_library.jl

@@ -68,15 +68,13 @@ struct PP_refs
     factor_norm::Cdouble
     phase_density::Cdouble
     phase_shearModulus::Cdouble
-    phase_shearModulus_v::Cdouble
+    phase_bulkModulus::Cdouble
     phase_cp::Cdouble
     phase_expansivity::Cdouble
     phase_isoTbulkModulus::Cdouble
-    volume_P0::Cdouble
     thetaExp::Cdouble
     phase_entropy::Cdouble
     phase_enthalpy::Cdouble
-    phase_bulkModulus::Cdouble
     volume::Cdouble
     mass::Cdouble
     charge::Cdouble
@@ -865,6 +863,11 @@ struct SS_refs
     mu_Ppc::Ptr{Ptr{Cdouble}}
     xeos_Ppc::Ptr{Ptr{Cdouble}}
     solvus_id::Ptr{Cint}
+    n_cat::Cint
+    C::Ptr{Ptr{Cdouble}}
+    N::Ptr{Ptr{Cdouble}}
+    Vec1::Ptr{Cdouble}
+    Vec2::Ptr{Cdouble}
     is_liq::Cint
     symmetry::Cint
     n_em::Cint
@@ -915,6 +918,7 @@ struct SS_refs
     sum_xi::Cdouble
     xeos::Ptr{Cdouble}
     ElShearMod::Ptr{Cdouble}
+    ElBulkMod::Ptr{Cdouble}
     density::Ptr{Cdouble}
     phase_density::Cdouble
     volume::Cdouble
@@ -1028,10 +1032,8 @@ struct csd_phase_sets
     phase_expansivity::Cdouble
     phase_bulkModulus::Cdouble
     phase_isoTbulkModulus::Cdouble
-    volume_P0::Cdouble
     thetaExp::Cdouble
     phase_shearModulus::Cdouble
-    phase_shearModulus_v::Cdouble
     phase_entropy::Cdouble
     phase_enthalpy::Cdouble
 end
@@ -1257,6 +1259,10 @@ function ReadCommandLineOptions(gv, z_b, argc, argv)
     ccall((:ReadCommandLineOptions, libMAGEMin), global_variable, (global_variable, Ptr{bulk_info}, Cint, Ptr{Ptr{Cchar}}), gv, z_b, argc, argv)
 end
 
+function SetupDatabase(gv, z_b)
+    ccall((:SetupDatabase, libMAGEMin), global_variable, (global_variable, Ptr{bulk_info}), gv, z_b)
+end
+
 function PrintOutput(gv, rank, l, DB, time_taken, z_b)
     ccall((:PrintOutput, libMAGEMin), Cvoid, (global_variable, Cint, Cint, Databases, Cdouble, bulk_info), gv, rank, l, DB, time_taken, z_b)
 end
@@ -1514,7 +1520,7 @@ mutable struct stx11_datasets
     n_pp::Cint
     n_ss::Cint
     ox::NTuple{6, NTuple{20, Cchar}}
-    PP::NTuple{9, NTuple{20, Cchar}}
+    PP::NTuple{10, NTuple{20, Cchar}}
     SS::NTuple{14, NTuple{20, Cchar}}
     verifyPC::NTuple{14, Cint}
     n_SS_PC::NTuple{14, Cint}
@@ -1560,6 +1566,7 @@ end
 mutable struct em_datas
     C::NTuple{14, Cdouble}
     ElShearMod::Cdouble
+    ElBulkMod::Cdouble
     gb::Cdouble
     charge::Cdouble
     em_datas() = new()
@@ -2126,13 +2133,6 @@ function TC_mtl_PC_init(PC_read, gv)
     ccall((:TC_mtl_PC_init, libMAGEMin), Cvoid, (Ptr{PC_type}, global_variable), PC_read, gv)
 end
 
-# typedef void ( * sf_type ) ( unsigned m , double * result , unsigned n , const double * x , double * grad , void * data )
-const sf_type = Ptr{Cvoid}
-
-function NLopt_global_opt_function(z_b, gv, PP_ref_db, SS_ref_db, cp)
-    ccall((:NLopt_global_opt_function, libMAGEMin), global_variable, (bulk_info, global_variable, Ptr{PP_ref}, Ptr{SS_ref}, Ptr{csd_phase_set}), z_b, gv, PP_ref_db, SS_ref_db, cp)
-end
-
 # typedef SS_ref ( * NLopt_type ) ( global_variable gv , SS_ref SS_ref_db )
 const NLopt_type = Ptr{Cvoid}
 
@@ -2212,6 +2212,90 @@ 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 SB_sb11_objective_init_function(SS_objective, gv)
+    ccall((:SB_sb11_objective_init_function, libMAGEMin), Cvoid, (Ptr{obj_type}, global_variable), SS_objective, gv)
+end
+
+function SB_SS_objective_init_function(SS_objective, gv)
+    ccall((:SB_SS_objective_init_function, libMAGEMin), Cvoid, (Ptr{obj_type}, global_variable), SS_objective, gv)
+end
+
+function SB_PC_init(PC_read, gv)
+    ccall((:SB_PC_init, libMAGEMin), Cvoid, (Ptr{PC_type}, global_variable), PC_read, gv)
+end
+
+function obj_sb11_plg(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_plg, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_sp(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_sp, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_ol(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_ol, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_wa(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_wa, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_ri(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_ri, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_opx(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_opx, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_cpx(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_cpx, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_hpcpx(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_hpcpx, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_ak(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_ak, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_gtmj(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_gtmj, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_pv(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_pv, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_ppv(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_ppv, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_mw(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_mw, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function obj_sb11_cf(n, x, grad, SS_ref_db)
+    ccall((:obj_sb11_cf, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
+end
+
+function SB_PC__function(gv, PC_read, SS_ref_db, z_b, ph_id)
+    ccall((:SB_PC__function, libMAGEMin), SS_ref, (global_variable, Ptr{PC_type}, SS_ref, bulk_info, Cint), gv, PC_read, SS_ref_db, z_b, ph_id)
+end
+
+function SB_sb11_PC_init(PC_read, gv)
+    ccall((:SB_sb11_PC_init, libMAGEMin), Cvoid, (Ptr{PC_type}, global_variable), PC_read, gv)
+end
+
+function SB_NLopt_opt_init(NLopt_opt, gv)
+    ccall((:SB_NLopt_opt_init, libMAGEMin), Cvoid, (Ptr{NLopt_type}, global_variable), NLopt_opt, gv)
+end
+
+function SB_sb11_pc_init_function(SS_pc_xeos, iss, name)
+    ccall((:SB_sb11_pc_init_function, libMAGEMin), Cvoid, (Ptr{PC_ref}, Cint, Ptr{Cchar}), SS_pc_xeos, iss, 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
@@ -2477,6 +2561,14 @@ function get_tests_bulks(gv)
     ccall((:get_tests_bulks, libMAGEMin), global_variable, (global_variable,), gv)
 end
 
+function vector_matrix_multiplication(v, M, result, vector_size, matrix_cols)
+    ccall((:vector_matrix_multiplication, libMAGEMin), Cvoid, (Ptr{Cdouble}, Ptr{Ptr{Cdouble}}, Ptr{Cdouble}, Cint, Cint), v, M, result, vector_size, matrix_cols)
+end
+
+function matrix_vector_multiplication(M, v, result, matrix_rows, matrix_cols)
+    ccall((:matrix_vector_multiplication, libMAGEMin), Cvoid, (Ptr{Ptr{Cdouble}}, Ptr{Cdouble}, Ptr{Cdouble}, Cint, Cint), M, v, result, matrix_rows, matrix_cols)
+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