Merge pull request ComputationalThermodynamics#63 from NicolasRiel/main

MAGEMin 1.3.3
Iddingsite · Sep 25, 2023 · 28b3d39 · 28b3d39
2 parents d4b1e20 + 5923a44
commit 28b3d39
Show file tree

Hide file tree

Showing 127 changed files with 5,931 additions and 86,994 deletions.
diff --git a/PlotPseudosection.mlapp b/PlotPseudosection.mlapp
diff --git a/Project.toml b/Project.toml
@@ -1,15 +1,16 @@
 name = "MAGEMin_C"
 uuid = "e5d170eb-415a-4524-987b-12f1bce1ddab"
 authors = ["Boris Kaus <[email protected]> & Nicolas Riel <[email protected]>"]
-version = "1.2.8"
+version = "1.3.3"
 
 [deps]
 CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82"
 MAGEMin_jll = "763ebaa8-b0d2-5f6b-90ef-4fc23b5db1c4"
+ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
 CEnum = "0.4"
+MAGEMin_jll = "1.3.1"
+ProgressMeter = "1"
 julia = "1.6"
-
-
diff --git a/doc_raw/ckbk.rst b/doc_raw/ckbk.rst
@@ -37,3 +37,11 @@ Pseudosection generator
    :maxdepth: 2
 
    ckbk/gui
+
+Predefined bulk-rocks
+=====================
+
+.. toctree::
+   :maxdepth: 2
+
+   ckbk/predef
diff --git a/doc_raw/ckbk/predef.rst b/doc_raw/ckbk/predef.rst
@@ -0,0 +1,9 @@
+.. MAGEMin documentation
+
+List of pre-defined bulk-rock composition
+=========================================
+
+.. csv-table:: Table Title
+   :file: /figs/predefined_bulks.csv
+   :widths: 10, 50, 10, 20, 20, 20
+   :header-rows: 1
diff --git a/doc_raw/figs/predefined_bulks.csv b/doc_raw/figs/predefined_bulks.csv
@@ -0,0 +1,30 @@
+title,comments,test,oxide,frac,db
+"FPWorldMedian pelite
+ Water oversaturated","Forshaw, J. B., & Pattison, D. R. (2023)",0,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, MnO, H2O","70.999, 12.805, 0.771, 3.978, 6.342, 2.7895, 1.481, 0.758, 0.72933, 0.075, 30.0",mp
+"FPWorldMedian pelite 
+ Water undersaturated","Forshaw, J. B., & Pattison, D. R. (2023)",1,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, MnO, H2O","70.999, 12.805, 0.771, 3.978, 6.342, 2.7895, 1.481, 0.758, 0.72933, 0.075, 5.0",mp
+"Pelite
+ Water oversaturated","White et al., 2014, Fig 8",2,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, MnO, H2O","64.578, 13.651, 1.586, 5.529, 8.025, 2.943, 2.0, 0.907, 0.65, 0.175, 40.0",mp
+"Pelite 
+ Water
+ undersaturated","White et al., 2014, Fig 8",3,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, MnO, H2O","64.578, 13.651, 1.586, 5.529, 8.025, 2.943, 2.0, 0.907, 0.65, 0.175, 6.244",mp
+"Garnet-migmatite
+ AV0832a","Riel et al., 2013",4,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, MnO, H2O","73.988, 8.6143, 2.0146, 2.7401, 3.8451, 1.7686, 2.482, 0.6393, 0.11, 0.063, 10.0",mp
+"SM89
+ MORB composition","Sun & McDonough, 1989",0,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, H2O","52.47, 9.1, 12.21, 12.71, 8.15, 0.23, 2.61, 1.05, 1.47, 20.0",mb
+"Natural amphibolite
+ LT  Granulite",unpublished,1,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, H2O","51.08, 9.68, 13.26, 11.21, 11.66, 0.16, 0.79, 1.37, 0.8, 20.0",mb
+"SQA
+ Synthetic amphibolite","Patino Douce & Beard, 1995",2,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, H2O","60.05, 6.62, 8.31, 9.93, 6.57, 0.44, 1.83, 1.27, 0.33, 4.64",mb
+BL478: Sample 478,"Beard & Lofgren, 1991",3,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, H2O","53.96, 9.26, 10.15, 8.11, 10.14, 0.11, 2.54, 1.35, 0.98, 3.42",mb
+"KLB1 Peridotite 
+ Anhydrous","Holland et al., 2018",0,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, Cr2O3, H2O","38.494, 1.776, 2.824, 50.566, 5.886, 0.01, 0.25, 0.1, 0.096, 0.109, 0.0",ig
+"RE46 
+ Icelandic basalt","Yang et al., 1996",1,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, Cr2O3, H2O","50.72, 9.16, 15.21, 16.25, 7.06, 0.01, 1.47, 0.39, 0.35, 0.01, 0.0",ig
+N_MORB - Basalt,"Gale et al., 2013",2,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, Cr2O3, H2O","53.21, 9.41, 12.21, 12.21, 8.65, 0.09, 2.9, 1.21, 0.69, 0.02, 0.0",ig
+MIX1-G - Pyroxenite,"Hirschmann et al., 2003",3,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, Cr2O3, H2O","45.25, 8.89, 12.22, 24.68, 6.45, 0.03, 1.39, 0.67, 0.11, 0.02, 0.0",ig
+High-Al basalt,"Baker, 1983",4,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, Cr2O3, H2O","54.4, 12.96, 11.31, 7.68, 8.63, 0.54, 3.93, 0.79, 0.41, 0.01, 0.0",ig
+Tonalite 101,"Piwinskii, 1968",5,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, Cr2O3, H2O","66.01, 11.98, 7.06, 4.16, 5.3, 1.57, 4.12, 0.66, 0.97, 0.01, 50.0",ig
+Wet Basalt,unpublished,6,"SiO2, Al2O3, CaO, MgO, FeOt, K2O, Na2O, TiO2, O, Cr2O3, H2O","50.081, 8.6901, 11.6698, 12.1438, 7.7832, 0.215, 2.4978, 1.0059, 0.467, 0.01, 5.4364",ig
+Serpentine oxidized,"Evans & Forst, 2021",0,"SiO2, Al2O3, MgO, FeOt, O, H2O, S","20.044, 0.6256, 29.24, 3.149, 0.7324, 46.755, 0.3",um
+Serpentine reduced,"Evans & Forst, 2021",1,"SiO2, Al2O3, MgO, FeOt, O, H2O, S","20.044, 0.6256, 29.24, 3.149, 0.1324, 46.755, 0.3",um
diff --git a/doc_raw/index.rst b/doc_raw/index.rst
@@ -10,7 +10,7 @@
 
 |
 
-**MAGEMin v1.3.2**
+**MAGEMin v1.3.3**
 ==================
 
 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/doc_raw/julia/Run.rst b/doc_raw/julia/Run.rst
@@ -1,7 +1,7 @@
 .. MAGEMin documentation
 
 
-Single point calculation Tutorial
+Serial point calculation Tutorial
 =================================
 
 First open a terminal and execute Julia, then type :literal:`using MAGEMin_C` to load the package.
@@ -12,22 +12,22 @@ Initialize database
 *******************
 .. code-block:: shell
 
-   db          = "ig"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
-   gv, z_b, DB, splx_data      = init_MAGEMin(db);
+   # 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);
 
 This initiatizes the global variables and the Database.
 
+|
+
 Set P-T-(pressure temperature)
 **********************************************************
 .. code-block:: shell
 
-   P           = 8.
-   T           = 800.
-   sys_in      = "mol"     # wt or mol, default is mol
-   test        = 0;
-   gv          = use_predefined_bulk_rock(gv, test, db)
+   P           =   8.0
+   T           =   800.0
 
-:literal:`get_bulk_rock` retrieves the saved bulk-rock composition 0, which corresponds to KLB-1 peridotite. 
+:literal:`use_predefined_bulk_rock` retrieves the saved bulk-rock composition 0 from database ig, which corresponds to KLB-1 peridotite. 
 
 |
 
@@ -41,24 +41,52 @@ Use a pre-defined bulk-rock "test" composition
    test        = 0;
    gv          = use_predefined_bulk_rock(gv, test, db)
 
+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"    
+
+Note that the system unit :literal:`[mol,wt]` has to be provided here.
+
+where :literal:`Xoxides` is a :literal:`Vector(String)` containing the oxide names and :literal:`X` is a :literal:`Vector(Float)` of the :literal:`[mol,wt]` fraction of the bulk-rock composition.
+The function converts
+
+ :literal:`SiO2`, ..., :literal:`FeO` and :literal:`Fe2O3` in system unit :literal:`[mol,wt]`
+
+to:
+
+ :literal:`SiO2`, ..., :literal:`FeOt` and :literal:`O` in system unit :literal:`[mol]`.
+
+Note that if the provided bulk-rock composition includes more oxides than supported, they will be ignored and the composition will be renormalized accordingly. Moreover, if both :literal:`Fe2O3` and :literal:`O` are provided, :literal:`O` will be recalculated as function of :literal:`Fe2O3`. Thus, if you want to prescribe a different :literal:`O` content, do not define :literal:`Fe2O3`!
+
 |
 
-Set the level of verbose :literal:`[-1,0,1]`
-********************************************
+Set the level of verbose :literal:`[false,true,1]`
+**************************************************
 .. code-block:: shell   
 
-   gv.verbose  = -1    # switch off any verbose
+   gv.verbose  = false    # switch off any verbose
 
-:literal:`-1`, none; :literal:`0`, stable phase assemblage; :literal:`1`, full verbose. By default :literal:`gv.verbose` = 0.
+: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   
 
-   gv.verbose  = -1    # switch off any verbose
-   out         = point_wise_minimization(P,T, gv, z_b, DB, splx_data, sys_in)
+   out     =   single_point_minimization(P, T, data, test=0);
+
+if a predefined test is used (see :doc:`/ckbk/predef`) or:
+
+.. code-block:: shell   
+
+   out     = single_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
+
+if a custom bulk-rock composition is provided.
 
 |
 
@@ -104,111 +132,120 @@ The full description of what contains the output structure is given in the CookB
 
 |
 
-Provide custom bulk rock composition
-====================================
-
+Examples of serial point calculation
+************************************
 
-To define and use your own bulk rock composition we provide a routine that converts bulk-rock composition into the right MAGEMin format.
-
-* For the igneous database:
 
 .. code-block:: shell
 
-   bulk_in_ox = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"]
-   bulk_in    = [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"
-   db         = "ig"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
-
-   gv         = define_bulk_rock(gv, bulk_in, bulk_in_ox, sys_in, db);
-
-* For the metapelite database
+   #load MAGEMin
+   using MAGEMin_C 
 
-.. code-block:: shell
+   data    = Initialize_MAGEMin("ig", verbose=false);
 
-   bulk_in_ox = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "MnO"; "H2O"]
-   bulk_in    = [69.64; 13.76; 1.77; 1.73; 4.32; 0.4; 2.61; 2.41; 0.80; 0.07; 10.0]
-   sys_in     = "wt"
-   db         = "mp"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
+   # One bulk rock for all points
+   P,T     = 10.0, 1100.0
+   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"    
+   out     = single_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
+   Finalize_MAGEMin(data)
 
-   gv         = define_bulk_rock(gv, bulk_in, bulk_in_ox, sys_in, db);
 
+for the metapelite database:
 
+.. code-block:: shell
 
-where :literal:`bulk_in_ox` is a :literal:`Vector(String)` containing the oxide names and :literal:`bulk_in` is a :literal:`Vector(Float)` of the :literal:`[mol,wt]` fraction of the bulk-rock composition.
-The function converts
+   #load MAGEMin
+   using MAGEMin_C 
 
- :literal:`SiO2`, ..., :literal:`FeO` and :literal:`Fe2O3` in system unit :literal:`[mol,wt]`
-
-to:
-
- :literal:`SiO2`, ..., :literal:`FeOt` and :literal:`O` in system unit :literal:`[mol]`.
+   #initialize
+   data    = Initialize_MAGEMin("mp", verbose=false);
 
-Note that if the provided bulk-rock composition includes more oxides than supported, they will be ignored and the composition will be renormalized accordingly. Moreover, if both :literal:`Fe2O3` and :literal:`O` are provided, :literal:`O` will be recalculated as function of :literal:`Fe2O3`. Thus, if you want to prescribe a different :literal:`O` content, do not define :literal:`Fe2O3`!
+   # provide bulk-rock composition
+   P,T      = 2.0, 650.0
+   Xoxides  = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "MnO"; "H2O"]
+   X        = [69.64; 13.76; 1.77; 1.73; 4.32; 0.4; 2.61; 2.41; 0.80; 0.07; 10.0]
+   sys_in   = "wt"    
+   out      = single_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
+   Finalize_MAGEMin(data)
 
-A full Julia script demonstrating how to use this function is provided below:
+for the ultramafic database:
 
 .. code-block:: shell
 
    #load MAGEMin
    using MAGEMin_C 
 
    #initialize
-   db          = "ig"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
-   gv, z_b, DB, splx_data      = init_MAGEMin(db);     
+   data    = Initialize_MAGEMin("um", verbose=false);
 
    # provide bulk-rock composition
-   bulk_in_ox = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
-   bulk_in    = [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"
+   P,T      = 2.0, 650.0
+   out      = single_point_minimization(P, T, data, test=0)
+   Finalize_MAGEMin(data)
 
-   # convert bulk rock
-   gv         = define_bulk_rock(gv, bulk_in, bulk_in_ox, sys_in, db);
 
-   # provide pressure and temperature conditions
-   P,T        = 10.0, 1100.0;
 
-   # switch off any verbose
-   gv.verbose = -1    
+Parallel point calculation Tutorial
+===================================
 
-   # perform minimization    
-   out        = point_wise_minimization(P,T, gv, z_b, DB, splx_data, sys_in)
+To compute a list of single point calculation in parallel your can use the native Julia multi-threading. To activate multi-threading simply launch the Julia terminal as:
 
-   # print output
-   print_info(out)
+.. code-block:: shell
 
-   # free memory
-   finalize_MAGEMin(gv,DB)
+   julia -t 4
 
-of for the metapelite database:
+or 
+
+.. code-block:: shell
+
+   julia --threads 4
+
+where the number of threads depends on your system, generally twice the number of cores. 
+
+|
+
+Examples of serial point calculation
+************************************
+
+To run :literal:`n` points, using database :literal:`ig` and :literal:`test 0` (see :doc:`/ckbk/predef`):
 
 .. code-block:: shell
 
    #load MAGEMin
    using MAGEMin_C 
 
    #initialize
-   db          = "mp"  # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
-   gv, z_b, DB, splx_data      = init_MAGEMin(db);     
+   data    =   Initialize_MAGEMin("ig", verbose=false);
+   n       =   100;
+   P       =   fill(8.0,n)
+   T       =   fill(800.0,n)
+   out     =   multi_point_minimization(P, T, data, test=1);
+   Finalize_MAGEMin(data)
 
-   # provide bulk-rock composition
-   bulk_in_ox = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "MnO"; "H2O"]
-   bulk_in    = [69.64; 13.76; 1.77; 1.73; 4.32; 0.4; 2.61; 2.41; 0.80; 0.07; 10.0]
-   sys_in     = "wt"
+Here the results are stored in :literal:`out` as :literal:`out[1:end]`. Various bulk-rock compositions can be prescribed as:
 
-   # convert bulk rock
-   gv         = define_bulk_rock(gv, bulk_in, bulk_in_ox, sys_in, db);
+.. code-block:: shell
 
-   # provide pressure and temperature conditions
-   P,T        = 4.0, 800.0;
+   #load MAGEMin
+   using MAGEMin_C 
 
-   # switch off any verbose
-   gv.verbose = -1    
+   #initialize
+   data    = Initialize_MAGEMin("ig", verbose=false);
 
-   # perform minimization    
-   out        = point_wise_minimization(P,T, gv, z_b, DB, splx_data, sys_in)
+   #set P-T-X conditions
+   P       = [10.0, 10.0];
+   T       = [1100.0, 1100.0];
+   Xoxides = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
+   X1      = [48.43; 15.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
+   X2      = [49.43; 14.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
+   X       = [X1,X2];
+   sys_in  = "wt"    
+   out     = multi_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
 
-   # print output
-   print_info(out)
 
-   # free memory
-   finalize_MAGEMin(gv,DB)
+Other examples
+==============
+
+Several additional tests are provided in :literal:`./test/runtests.jl`.