MAGEMin v1.5.8

- Corrected segfault problem affecting MAGEMin_C (julia wrapper)
ComputationalThermodynamics · Nov 8, 2024 · 6c625b4 · 6c625b4
2 parents a4e7de0 + dcf32d2
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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 = "1.5.7"
+version = "1.5.8"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"

diff --git a/doc_raw/index.rst b/doc_raw/index.rst
@@ -10,7 +10,7 @@
 
 |
 
-**MAGEMin v1.5.7**
+**MAGEMin v1.5.8**
 ==================
 
 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 v1.5.7 &mdash; MAGEMin 2022 documentation</title>
+  <title>MAGEMin v1.5.8 &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 v1.5.7</strong></li>
+      <li><strong>MAGEMin v1.5.8</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 v1.5.7</strong><a class="headerlink" href="#magemin-v1-5-0" title="Permalink to this headline"></a></h1>
+<h1><strong>MAGEMin v1.5.8</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 v1.5.7" href="index.html" /> 
+    <link rel="prev" title="MAGEMin v1.5.8" 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 v1.5.7" 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 v1.5.8" 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
@@ -2457,6 +2457,10 @@ function init_ss_db(EM_database, z_b, gv, SS_ref_db)
     ccall((:init_ss_db, libMAGEMin), global_variable, (Cint, bulk_info, global_variable, Ptr{SS_ref}), EM_database, z_b, gv, SS_ref_db)
 end
 
+function init_ss_db_sb(EM_database, z_b, gv, SS_ref_db)
+    ccall((:init_ss_db_sb, libMAGEMin), global_variable, (Cint, bulk_info, global_variable, Ptr{SS_ref}), EM_database, z_b, gv, SS_ref_db)
+end
+
 function print_help(gv)
     ccall((:print_help, libMAGEMin), Cvoid, (global_variable,), gv)
 end

diff --git a/ref_database/SB_ref_database/functions_ss.jl b/ref_database/SB_ref_database/functions_ss.jl
@@ -113,6 +113,7 @@ function get_sb_gss_init_function(sb_ver,ss)
         sb_gss_init_function *= "SS_ref G_SS_$(sb_ver)_$(ss[i].abbrev)_init_function(SS_ref SS_ref_db,  global_variable gv){\n\n"
         sb_gss_init_function *= "    SS_ref_db.is_liq    = 0;\n"
         sb_gss_init_function *= "    SS_ref_db.symmetry  = $sym;\n"
+        sb_gss_init_function *= "    SS_ref_db.n_xeos    = $(length(em));\n"
         sb_gss_init_function *= "    SS_ref_db.n_em      = $(length(em));\n"
         sb_gss_init_function *= "    SS_ref_db.n_sf      = $(length(mul));\n"
         sb_gss_init_function *= "    SS_ref_db.n_w       = $(length(W));\n"

diff --git a/src/MAGEMin.c b/src/MAGEMin.c
@@ -330,19 +330,27 @@ int runMAGEMin(			int    argc,
 								z_b,											/** bulk rock informations 			*/
 								gv,												/** global variables (e.g. Gamma) 	*/
 								PP_ref_db						);
+
+		/* Calculate solution phase data at given P-T conditions (G0 based on G0 of endmembers) */
+		gv = init_ss_db(		EM_database,
+								z_b,
+								gv,
+								SS_ref_db						);
 	}
 	else if ( strcmp(gv.research_group, "sb") 	== 0 ){
 		gv = init_em_db_sb(		EM_database,
 								z_b,											/** bulk rock informations 			*/
 								gv,												/** global variables (e.g. Gamma) 	*/
 								PP_ref_db						);
+
+		/* Calculate solution phase data at given P-T conditions (G0 based on G0 of endmembers) */
+		gv = init_ss_db_sb(		EM_database,
+								z_b,
+								gv,
+								SS_ref_db						);
 	}
 
-	/* Calculate solution phase data at given P-T conditions (G0 based on G0 of endmembers) */
-	gv = init_ss_db(		EM_database,
-							z_b,
-							gv,
-							SS_ref_db						);
+
 
 	return gv;
 }

diff --git a/src/SB_database/SB_gem_function.c b/src/SB_database/SB_gem_function.c
@@ -59,11 +59,12 @@ PP_ref SB_G_EM_function(	int 		 EM_dataset,
 							int         *id,
 							double 		*bulk_rock, 
 							double 		*apo, 
-							double 		 P, 
+							double 		 Pkbar, 
 							double 		 T, 
 							char 		*name, 
 							char		*state			
 ){
+
 	/* Get thermodynamic data */
 	EM_db_sb EM_return;
 	int i, p_id = find_EM_id(name);
@@ -76,11 +77,10 @@ PP_ref SB_G_EM_function(	int 		 EM_dataset,
 	}
 
 	double kbar2bar = 1e3;
-	double RTlnf 	= 0.0;
 	double T0 		= 298.15;
 	double P0 		= 0.001;
 	double R  		= 8.31446261815324;
-
+ 	double P       = Pkbar * kbar2bar;
 	/* declare the variables */
 	double nr9, nr9T0, c1, c2, c3, aii, aiikk2, aii2;
 	double r23, r59, t1, t2, nr9t, tht, thT0;
@@ -105,7 +105,7 @@ PP_ref SB_G_EM_function(	int 		 EM_dataset,
 
     nr9 	= -9.0 * n * R;
     nr9T0 	= nr9 * T0;
-    c1 		= -9.0 * V0 * K0;
+    c1 		= -9.0 * (-V0) * K0;
     c2 		= Kp / 2.0 - 2.0;
     c3 		= 3.0 * c1 * c2;
     aii 	= 6.0 * gamma0;
@@ -118,6 +118,7 @@ PP_ref SB_G_EM_function(	int 		 EM_dataset,
     t1 		= z00 / T;
     t2 		= T / T0;
     nr9t 	= nr9 * T;
+
 	tht 	= t1;
 	thT0 	= tht * t2;
 
@@ -136,7 +137,7 @@ PP_ref SB_G_EM_function(	int 		 EM_dataset,
 	else{
 		V = V0;
 	}
-	
+
 	ibad 	= 4;
 	bad 	= 1;
 
@@ -149,32 +150,27 @@ PP_ref SB_G_EM_function(	int 		 EM_dataset,
 		f 		= 0.5 * V23 - 0.5;
 		df 		= -V23 / V / 3.0;
 		d2f 	= r59 * V23 / pow(V,2.0);
-
 		dfc 	= (c3 * f + c1) * f * df;
 		d2fc 	= (2.0 * c3 * f + c1) * pow(df,2.0) + (c3 * f + c1) * f * d2f;
-
 		z 		= 1.0 + (aii + aiikk2 * f) * f;
 
 		if (z < 0.0 || V / V0 > 100.0 || V / V0 < 1e-2){
 			printf(" ERROR z or V/V0\n");
 		}
 
 		root 	= sqrt(z);
-
 		tht 	= t1 * root;
 		thT0 	= tht * T / T0;
-
 		a2f 	= aii2 + aiikk2 * f;
 		da 		= a2f / root;
 		dtht 	= t1 * da * df;
 		d2tht 	= t1 * ((aiikk2 / root - pow(a2f,2.0) / pow(z,1.5)) * pow(df,2.0) + da * d2f);
 
 		dthT0 	= dtht * t2;
-		d2thT0 	= d2tht * T;
+		d2thT0 	= d2tht * t2;
 
 		fpoly 	= 3.0 * plg(tht) / pow(tht,3.0);
 		fpoly0 	= 3.0 * plg(thT0) / pow(thT0,3.0);
-
 		etht 	= exp(-tht);
 
 		if (1.0 - etht < 0.0){
@@ -185,7 +181,6 @@ PP_ref SB_G_EM_function(	int 		 EM_dataset,
 
 		dfth 	= (letht - fpoly) * nr9t * dtht / tht;
 		d2fth 	= ((4.0 * pow(dtht,2.0) / tht - d2tht) * (fpoly - letht) + pow(dtht,2.0) * etht / (1.0 - etht)) * nr9t / tht;
-
 		ethT0 	= exp(-thT0);
 
 		if (1.0 - ethT0 < 0.0){

diff --git a/src/SB_database/sb_gss_function.c b/src/SB_database/sb_gss_function.c
@@ -966,7 +966,7 @@ SS_ref G_SS_sb11_cf_function(SS_ref SS_ref_db, char* research_group, int EM_data
     return SS_ref_db;
 }
 
-    SS_ref G_SS_sb11_EM_function(        global_variable        gv,
+    SS_ref G_SS_sb11_EM_function(       global_variable        gv,
                                         SS_ref            SS_ref_db,
                                         int            EM_dataset,
                                         bulk_info            z_b,

diff --git a/src/SB_database/sb_gss_init_function.c b/src/SB_database/sb_gss_init_function.c
@@ -22,14 +22,14 @@
 #include "../MAGEMin.h"
 #include "../all_solution_phases.h"
 #include "sb_gss_init_function.h"
-
 /**
     allocate memory for sb11_plg
 */
 SS_ref G_SS_sb11_plg_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 2;
     SS_ref_db.n_em      = 2;
     SS_ref_db.n_sf      = 1;
     SS_ref_db.n_w       = 1;
@@ -44,6 +44,7 @@ SS_ref G_SS_sb11_sp_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 2;
     SS_ref_db.n_em      = 2;
     SS_ref_db.n_sf      = 2;
     SS_ref_db.n_w       = 1;
@@ -58,6 +59,7 @@ SS_ref G_SS_sb11_ol_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 2;
     SS_ref_db.n_em      = 2;
     SS_ref_db.n_sf      = 1;
     SS_ref_db.n_w       = 1;
@@ -72,6 +74,7 @@ SS_ref G_SS_sb11_wa_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 2;
     SS_ref_db.n_em      = 2;
     SS_ref_db.n_sf      = 1;
     SS_ref_db.n_w       = 1;
@@ -86,6 +89,7 @@ SS_ref G_SS_sb11_ri_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 2;
     SS_ref_db.n_em      = 2;
     SS_ref_db.n_sf      = 1;
     SS_ref_db.n_w       = 1;
@@ -100,6 +104,7 @@ SS_ref G_SS_sb11_opx_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 4;
     SS_ref_db.n_em      = 4;
     SS_ref_db.n_sf      = 2;
     SS_ref_db.n_w       = 6;
@@ -114,6 +119,7 @@ SS_ref G_SS_sb11_cpx_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 0;
+    SS_ref_db.n_xeos    = 5;
     SS_ref_db.n_em      = 5;
     SS_ref_db.n_sf      = 3;
     SS_ref_db.n_w       = 10;
@@ -129,6 +135,7 @@ SS_ref G_SS_sb11_hpcpx_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 2;
     SS_ref_db.n_em      = 2;
     SS_ref_db.n_sf      = 1;
     SS_ref_db.n_w       = 1;
@@ -143,6 +150,7 @@ SS_ref G_SS_sb11_ak_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 3;
     SS_ref_db.n_em      = 3;
     SS_ref_db.n_sf      = 2;
     SS_ref_db.n_w       = 3;
@@ -157,6 +165,7 @@ SS_ref G_SS_sb11_gtmj_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 5;
     SS_ref_db.n_em      = 5;
     SS_ref_db.n_sf      = 3;
     SS_ref_db.n_w       = 10;
@@ -171,6 +180,7 @@ SS_ref G_SS_sb11_pv_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 0;
+    SS_ref_db.n_xeos    = 3;
     SS_ref_db.n_em      = 3;
     SS_ref_db.n_sf      = 2;
     SS_ref_db.n_w       = 3;
@@ -186,6 +196,7 @@ SS_ref G_SS_sb11_ppv_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 3;
     SS_ref_db.n_em      = 3;
     SS_ref_db.n_sf      = 2;
     SS_ref_db.n_w       = 3;
@@ -200,6 +211,7 @@ SS_ref G_SS_sb11_mw_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 2;
     SS_ref_db.n_em      = 2;
     SS_ref_db.n_sf      = 1;
     SS_ref_db.n_w       = 1;
@@ -214,6 +226,7 @@ SS_ref G_SS_sb11_cf_init_function(SS_ref SS_ref_db,  global_variable gv){
 
     SS_ref_db.is_liq    = 0;
     SS_ref_db.symmetry  = 1;
+    SS_ref_db.n_xeos    = 3;
     SS_ref_db.n_em      = 3;
     SS_ref_db.n_sf      = 2;
     SS_ref_db.n_w       = 3;

diff --git a/src/initialize.c b/src/initialize.c
@@ -122,7 +122,7 @@ global_variable global_variable_alloc( bulk_info  *z_b ){
 	}
 
 	strcpy(gv.outpath,"./output/");				/** define the outpath to save logs and final results file	 						*/
-	strcpy(gv.version,"1.5.7 [17/10/2024]");	/** MAGEMin version 																*/
+	strcpy(gv.version,"1.5.8 [7/11/2024]");	/** MAGEMin version 																*/
 
 	/* generate parameters        		*/
 	strcpy(gv.buffer,"none");

diff --git a/src/simplex_levelling.c b/src/simplex_levelling.c
@@ -1064,11 +1064,11 @@ void run_simplex_pseudocompounds(		bulk_info 	 		z_b,
 		k 		   += 1;
 		d->swp      = 0;
 		t 			= clock();
-		swap_pure_endmembers(				z_b,
-											splx_data,
-											gv,
-											PP_ref_db,
-											SS_ref_db	);	
+		// swap_pure_endmembers(				z_b,
+		// 									splx_data,
+		// 									gv,
+		// 									PP_ref_db,
+		// 									SS_ref_db	);	
 
 		swap_pure_phases(					z_b,
 											splx_data,