Merge pull request ComputationalThermodynamics#77 from NicolasRiel/main

MAGEMin v1.3.8

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 = "1.3.3"
+version = "1.3.8"
 
 [deps]
 CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82"

README.md

@@ -44,6 +44,9 @@ Then copy and paste the address `127.0.0.1:8050` in your web-browser
 
 <img src="https://raw.githubusercontent.com/ComputationalThermodynamics/repositories_pictures/main/MAGEMinApp/MAGEMin_app.png?raw=true" alt="drawing" width="640" alt="centered image"/>
 
+> [!CAUTION]
+> There is some issues with Windows machine (loading `Kaleido`). `] add MAGEMinApp` works well, however when `using MAGEMinApp` it may hang indefinitely. Currently, the current workaround is to cancel `CTRL+C` and try `using MAGEMinApp` a couple of time.
+
 \
 **With Matlab using Julia (not maintained anymore)**
 

doc_raw/index.rst

@@ -10,7 +10,7 @@
 
 |
 
-**MAGEMin v1.3.6**
+**MAGEMin v1.3.8**
 ==================
 
 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     

doc_raw/julia/Run.rst

@@ -13,8 +13,7 @@ Initialize database
 .. code-block:: shell
 
    # Initialize database  - new way
-   db          =   "ig"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b); um, ultramafic (Evans & Frost 2021)
-   data        =   Initialize_MAGEMin(db, verbose=true);
+   data        =   Initialize_MAGEMin("ig", verbose=true); # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b); mb, metabasite (Green et al.,2016); um, ultramafic (Evans & Frost 2021)
 
 This initiatizes the global variables and the Database.
 
@@ -37,17 +36,16 @@ Set bulk-rock composition
 Use a pre-defined bulk-rock "test" composition
 
 .. code-block:: shell
-
-   test        = 0;
-   gv          = use_predefined_bulk_rock(gv, test, db)
+   test        =   0         #KLB1
+   data        =   use_predefined_bulk_rock(data, test);
 
 or a custom bulk-rock composition:
 
 .. code-block:: shell
 
     Xoxides = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
     X       = [48.43; 15.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
-    sys_in  = "wt"    
+    sys_in  = "wt"
 
 Note that the system unit :literal:`[mol,wt]` has to be provided here.
 
@@ -64,21 +62,11 @@ Note that if the provided bulk-rock composition includes more oxides than suppor
 
 |
 
-Set the level of verbose :literal:`[false,true,1]`
-**************************************************
-.. code-block:: shell   
-
-   gv.verbose  = false    # switch off any verbose
-
-:literal:`false`, none; :literal:`true`, stable phase assemblage; :literal:`1`, full verbose. By default :literal:`gv.verbose` = true.
-
-|
-
 Call optimization routine for given P-T-X
 *****************************************
 .. code-block:: shell   
 
-   out     =   single_point_minimization(P, T, data, test=0);
+   out         =   point_wise_minimization(P,T, data);
 
 if a predefined test is used (see :doc:`/ckbk/predef`) or:
 

docs/_modules/MAGEMin.c.html

@@ -147,7 +147,6 @@
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#initialize-database">Initialize database</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-p-t-pressure-temperature">Set P-T-(pressure temperature)</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-bulk-rock-composition">Set bulk-rock composition</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-the-level-of-verbose-false-true-1">Set the level of verbose <code class="docutils literal notranslate"><span class="pre">[false,true,1]</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#call-optimization-routine-for-given-p-t-x">Call optimization routine for given P-T-X</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#display-minimized-point">Display minimized point</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#access-output-structure">Access output structure</a></li>

docs/_modules/NLopt_opt_function.c.html

@@ -147,7 +147,6 @@
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#initialize-database">Initialize database</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-p-t-pressure-temperature">Set P-T-(pressure temperature)</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-bulk-rock-composition">Set bulk-rock composition</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-the-level-of-verbose-false-true-1">Set the level of verbose <code class="docutils literal notranslate"><span class="pre">[false,true,1]</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#call-optimization-routine-for-given-p-t-x">Call optimization routine for given P-T-X</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#display-minimized-point">Display minimized point</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#access-output-structure">Access output structure</a></li>

docs/_modules/PGE_function.c.html

@@ -147,7 +147,6 @@
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#initialize-database">Initialize database</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-p-t-pressure-temperature">Set P-T-(pressure temperature)</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-bulk-rock-composition">Set bulk-rock composition</a></li>
-<li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#set-the-level-of-verbose-false-true-1">Set the level of verbose <code class="docutils literal notranslate"><span class="pre">[false,true,1]</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#call-optimization-routine-for-given-p-t-x">Call optimization routine for given P-T-X</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#display-minimized-point">Display minimized point</a></li>
 <li class="toctree-l3"><a class="reference internal" href="../julia/Run.html#access-output-structure">Access output structure</a></li>
@@ -1395,8 +1394,9 @@ <h1>Source code for PGE_function.c</h1><div class="highlight"><pre>
 
 <span class="w">	</span><span class="cm">/* get number of duplicated phases and their cp id */</span><span class="w"></span>
 <span class="w">	</span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o">&lt;</span><span class="w"> </span><span class="n">gv</span><span class="p">.</span><span class="n">len_cp</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="o">++</span><span class="p">){</span><span class="w"></span>
-<span class="w">		</span><span class="n">ph_id</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">cp</span><span class="p">[</span><span class="n">i</span><span class="p">].</span><span class="n">id</span><span class="p">;</span><span class="w"></span>
+<span class="w">		</span>
 <span class="w">		</span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">cp</span><span class="p">[</span><span class="n">i</span><span class="p">].</span><span class="n">ss_flags</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">1</span><span class="w"> </span><span class="p">){</span><span class="w"></span>
+<span class="w">			</span><span class="n">ph_id</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">cp</span><span class="p">[</span><span class="n">i</span><span class="p">].</span><span class="n">id</span><span class="p">;</span><span class="w"></span>
 <span class="w">			</span><span class="n">SS_ref_db</span><span class="p">[</span><span class="n">ph_id</span><span class="p">].</span><span class="n">solvus_id</span><span class="p">[</span><span class="n">gv</span><span class="p">.</span><span class="n">n_solvi</span><span class="p">[</span><span class="n">ph_id</span><span class="p">]]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">i</span><span class="p">;</span><span class="w"></span>
 <span class="w">			</span><span class="n">gv</span><span class="p">.</span><span class="n">n_solvi</span><span class="p">[</span><span class="n">ph_id</span><span class="p">]</span><span class="w"> </span><span class="o">+=</span><span class="w"> </span><span class="mi">1</span><span class="p">;</span><span class="w"></span>
 <span class="w">		</span><span class="p">}</span><span class="w"></span>