API
MAGEMin_C.MAGEMin_Data Type
Holds the MAGEMin databases & required structures for every threadMAGEMin_C.W_data Type
Holds the overriding Ws parameters0 = "mp", 1 = "mb", 11 = "mbe",2 = "ig", 3 = "igad", 4 = "um", 5 = "ume", 6 = "mtl", 7 = "mpe", 8 = "sb11", 9 = "sb21"
sourceMAGEMin_C.AMR_minimization Method
AMR_minimization( init_sub :: Int64,
ref_lvl :: Int64,
Prange :: Union{T1, NTuple{2, T1}},
Trange :: Union{T1, NTuple{2, T1}},
MAGEMin_db :: MAGEMin_Data;
test :: Int64 = 0, # if using a build-in test case,
X :: VecOrMat = nothing,
B :: Union{Nothing, T1, Vector{T1}} = 0.0,
scp :: Int64 = 0,
iguess :: Union{Vector{Bool},Bool} = false,
rm_list :: Union{Nothing, Vector{Int64}} = nothing,
W :: Union{Nothing, Vector{MAGEMin_C.W_data{Float64, Int64}}} = nothing,
Xoxides = Vector{String},
sys_in :: String = "mol",
rg :: String = "tc",
progressbar :: Bool = true # show a progress bar or not?
) where {T1 <: Float64}
Performs an Adaptive Mesh Refinement (AMR) minimization for a range of points as a function of pressure `Prange`, temperature `Trange` and/or composition `X`. The database `MAGEMin_db` must be initialised before calling the routine.Example
data = Initialize_MAGEMin("mp", verbose=-1, solver=0);
init_sub = 1
ref_lvl = 2
Prange = (1.0,10.0)
Trange = (400.0,800.0)
Xoxides = ["SiO2","Al2O3","CaO","MgO","FeO","K2O","Na2O","TiO2","O","MnO","H2O"]
X = [70.999,12.805,0.771,3.978,6.342,2.7895,1.481,0.758,0.72933,0.075,30.0]
sys_in = "mol"
out = AMR_minimization(init_sub, ref_lvl, Prange, Trange, data, X=X, Xoxides=Xoxides, sys_in=sys_in)MAGEMin_C.Finalize_MAGEMin Method
Finalize_MAGEMin(dat::MAGEMin_Data)Finalizes MAGEMin and clears variables
sourceMAGEMin_C.Initialize_MAGEMin Function
Dat = Initialize_MAGEMin(db = "ig"; verbose::Union{Bool, Int64} = true)Initializes MAGEMin on one or more threads, for the database db. You can suppress all output with verbose=false. verbose=true will give a brief summary of the result, whereas verbose=1 will give more details about the computations.
MAGEMin_C.MAGEMin_data2dataframe Method
MAGEMin_data2dataframe( out:: Union{Vector{MAGEMin_C.gmin_struct{Float64, Int64}}, MAGEMin_C.gmin_struct{Float64, Int64}})
Transform MAGEMin output into a dataframe for quick(ish) saveMAGEMin_C.MAGEMin_data2dataframe_inlined Method
MAGEMin_data2dataframe( out:: Union{Vector{MAGEMin_C.gmin_struct{Float64, Int64}}, MAGEMin_C.gmin_struct{Float64, Int64}})
Transform MAGEMin output into a dataframe for quick(ish) saveMAGEMin_C.MAGEMin_dataTE2dataframe Method
MAGEMin_dataTE2dataframe( out:: Union{Vector{out_tepm}, out_tepm},dtb,fileout)
Transform MAGEMin trace-element output into a dataframe for quick(ish) saveMAGEMin_C.anhydrous_renormalization Method
bulk_dry = anhydrous_renormalization( bulk :: Vector{Float64},
oxide :: Vector{String})
This function renormalizes the bulk rock composition to remove water (H2O) if present.MAGEMin_C.convertBulk4MAGEMin Method
MAGEMin_bulk, MAGEMin_ox; = convertBulk4MAGEMin(bulk_in::T1,bulk_in_ox::Vector{String},sys_in::String,db::String) where {T1 <: AbstractVector{Float64}}receives bulk-rock composition in [mol,wt] fraction and associated oxide list and sends back bulk-rock composition converted for MAGEMin use
sourceMAGEMin_C.create_gmin_struct Method
out = create_gmin_struct(gv, z_b)This extracts the output of a pointwise MAGEMin optimization and adds it into a julia structure
sourceMAGEMin_C.create_light_gmin_struct Method
out = create_light_gmin_struct(gv, z_b)This extracts the output of a pointwise MAGEMin optimization and adds it into a julia structure
sourceMAGEMin_C.define_bulk_rock Method
gv = define_bulk_rock(gv, bulk_in, bulk_in_ox, sys_in, db)Defines the bulk-rock composition in gv structure using the input bulk_in and bulk_in_ox, converting it to the appropriate format for MAGEMin.
MAGEMin_C.get_AV_Nat_KDs_database Method
Get the partitioning coefficient database from Oliveira Da Costa, E. ...MAGEMin_C.get_B_Nat_KDs_database Method
Get the partitioning coefficient database from Oliveira Da Costa, E. ...MAGEMin_C.get_KP_Exp_KDs_database Method
Get the Li partitioning coefficient (Oliveira Da Costa, E. ...)MAGEMin_C.get_MM_KDs_database Method
Get the partitioning coefficient database from Matt Morris et ., 2025 ...MAGEMin_C.get_OL_KDs_database Method
Get the partitioning coefficient database from Laurent, O. ...MAGEMin_C.get_all_stable_phases Method
get_all_stable_phases(out:: Union{Vector{gmin_struct{Float64, Int64}}, gmin_struct{Float64, Int64}})
return ph_name
The function receives as an input a single/Vector of MAGEMin_C output structure and returns the list (Vector{String}) of unique stable phases
- Note that first the sorted solution phase names are provided, followed by the sorted pure phase names
e.g., ["amp", "bi", "chl", "cpx", "ep", "fl", "fsp", "liq", "opx", "sph"]MAGEMin_C.get_ss_from_mineral Method
This function returns the solution phase name given the mineral name (handling solvus -> solution phase)MAGEMin_C.init_MAGEMin Function
gv, DB = init_MAGEMin(;EM_database=0)Initializes MAGEMin (including setting global options) and loads the Database.
sourceMAGEMin_C.mol2wt Method
mol2wt(bulk_mol::Vector{Float64}, bulk_ox::Vector{String})
Converts bulk-rock composition from mol to wt fractionMAGEMin_C.multi_point_minimization Method
Out_PT =multi_point_minimization(P::T2,T::T2,MAGEMin_db::MAGEMin_Data;test::Int64=0,X::Union{Nothing, AbstractVector{Float64}, AbstractVector{<:AbstractVector{Float64}}}=nothing,B::Union{Nothing, T1, Vector{T1}}=nothing,W::Union{Nothing, Vector{MAGEMin_C.W_data{Float64, Int64}}}=nothing,Xoxides=Vector{String},sys_in="mol",progressbar=true, callback_fn ::Union{Nothing, Function}= nothing, callback_int::Int64 = 1) where {T1 <: Float64, T2 <: AbstractVector{T1}}
Perform (parallel) MAGEMin calculations for a range of points as a function of pressure P, temperature T and/or composition X. The database MAGEMin_db must be initialised before calling the routine. The bulk-rock composition can either be set to be one of the pre-defined build-in test cases, or can be specified specifically by passing X, Xoxides and sys_in (that specifies whether the input is in "mol" or "wt").
Below a few examples:
Example 1 - build-in test vs. pressure and temperature
julia> data = Initialize_MAGEMin("ig", verbose=false);
julia> n = 10
julia> P = rand(8:40.0,n)
julia> T = rand(800:1500.0,n)
julia> out = multi_point_minimization(P, T, data, test=0)
julia> Finalize_MAGEMin(data)Example 2 - Specify constant bulk rock composition for all points:
julia> data = Initialize_MAGEMin("ig", verbose=false);
julia> n = 10
julia> P = fill(10.0,n)
julia> T = fill(1100.0,n)
julia> Xoxides = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
julia> X = [48.43; 15.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
julia> sys_in = "wt"
julia> out = multi_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
julia> Finalize_MAGEMin(data)Example 3 - Different bulk rock composition for different points
julia> data = Initialize_MAGEMin("ig", verbose=false);
julia> P = [10.0, 20.0]
julia> T = [1100.0, 1200]
julia> Xoxides = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
julia> X1 = [48.43; 15.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
julia> X2 = [49.43; 14.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
julia> X = [X1,X2]
julia> sys_in = "wt"
julia> out = multi_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
julia> Finalize_MAGEMin(data)Activating multithreading on julia
To take advantage of multithreading, you need to start julia from the terminal with:
$ julia -t autowhich will automatically use all threads on your machine. Alternatively, use julia -t 4 to start it on 4 threads. If you are interested to see what you can do on your machine type:
julia> versioninfo()MAGEMin_C.point_wise_metastability Method
out = point_wise_metastability(out, P, T, data)
where out is a MAGEMin_C output structure of type MAGEMin_C.gmin_struct{Float64, Int64}, P is pressure, T is temperature and data is the MAGEMin_C working data structure.
This function computes the metastability of the solution phases in `out` at pressure `P` and temperature `T`.Example:
using MAGEMin_C
data = Initialize_MAGEMin("mp", verbose=-1; solver=0);
P,T = 6.0, 630.0
Xoxides = ["SiO2"; "TiO2"; "Al2O3"; "FeO"; "MnO"; "MgO"; "CaO"; "Na2O"; "K2O"; "H2O"; "O"];
X = [58.509, 1.022, 14.858, 4.371, 0.141, 4.561, 5.912, 3.296, 2.399, 10.0, 0.0];
sys_in = "wt"
out = single_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
Pmeta, Tmeta = 6.0, 500.0
out2 = point_wise_metastability(out, Pmeta, Tmeta, data)which gives:
julia> out = single_point_minimization(P, T, data, X=X, Xoxides=Xoxides, sys_in=sys_in)
Pressure : 6.0 [kbar]
Temperature : 630.0 [Celsius]
Stable phase | Fraction (mol fraction)
bi 0.18975
fsp 0.33769
opx 0.06615
q 0.14587
sph 0.01103
H2O 0.24952
Stable phase | Fraction (wt fraction)
bi 0.21347
fsp 0.44152
opx 0.07259
q 0.17078
sph 0.01404
H2O 0.0876
Stable phase | Fraction (vol fraction)
bi 0.16535
fsp 0.38301
opx 0.05008
q 0.1507
sph 0.00921
H2O 0.24165
Gibbs free energy : -806.707117 (23 iterations; 15.5 ms)
Oxygen fugacity : 11.422305637291458
Delta QFM : 29.789994195381436
julia> Pmeta, Tmeta = 6.0, 500.0
(6.0, 500.0)
julia> out2 = point_wise_metastability(out, Pmeta, Tmeta, data)
Pressure : 6.0 [kbar]
Temperature : 500.0 [Celsius]
Stable phase | Fraction (mol fraction)
bi 0.18975
fsp 0.33769
opx 0.06615
q 0.14587
sph 0.01103
H2O 0.24952
Stable phase | Fraction (wt fraction)
bi 0.21347
fsp 0.44152
opx 0.07259
q 0.17078
sph 0.01404
H2O 0.0876
Stable phase | Fraction (vol fraction)
bi 0.16819
fsp 0.39062
opx 0.05102
q 0.1528
sph 0.0094
H2O 0.22795
Gibbs free energy : -791.460287 (0 iterations; 0.04 ms)
Oxygen fugacity : 11.256905434522107
Delta QFM : 34.26950061699225MAGEMin_C.point_wise_minimization Method
point_wise_minimization(P::Float64,T::Float64, gv, z_b, DB, splx_data, sys_in::String="mol")Computes the stable assemblage at P [kbar], T [C] and for a given bulk rock composition
Example 1
This is an example of how to use it for a predefined bulk rock composition:
julia> db = "ig" # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
julia> gv, z_b, DB, splx_data = init_MAGEMin(db);
julia> test = 0;
julia> sys_in = "mol" #default is mol, if wt is provided conversion will be done internally (MAGEMin works on mol basis)
julia> gv = use_predefined_bulk_rock(gv, test, db)
julia> P = 8.0;
julia> T = 800.0;
julia> gv.verbose = -1; # switch off any verbose
julia> out = point_wise_minimization(P,T, gv, z_b, DB, splx_data, sys_in)
Pressure : 8.0 [kbar]
Temperature : 800.0 [Celsius]
Stable phase | Fraction (mol fraction)
opx 0.24229
ol 0.58808
cpx 0.14165
spl 0.02798
Stable phase | Fraction (wt fraction)
opx 0.23908
ol 0.58673
cpx 0.14583
spl 0.02846
Gibbs free energy : -797.749183 (26 iterations; 94.95 ms)
Oxygen fugacity : 9.645393319147175e-12Example 2
And here a case in which you specify your own bulk rock composition. We convert that in the correct format, using the convertBulk4MAGEMin function.
julia> db = "ig" # database: ig, igneous (Holland et al., 2018); mp, metapelite (White et al 2014b)
julia> gv, z_b, DB, splx_data = init_MAGEMin(db);
julia> bulk_in_ox = ["SiO2"; "Al2O3"; "CaO"; "MgO"; "FeO"; "Fe2O3"; "K2O"; "Na2O"; "TiO2"; "Cr2O3"; "H2O"];
julia> bulk_in = [48.43; 15.19; 11.57; 10.13; 6.65; 1.64; 0.59; 1.87; 0.68; 0.0; 3.0];
julia> sys_in = "wt"
julia> gv = define_bulk_rock(gv, bulk_in, bulk_in_ox, sys_in, db);
julia> P,T = 10.0, 1100.0;
julia> gv.verbose = -1; # switch off any verbose
julia> out = point_wise_minimization(P,T, gv, z_b, DB, splx_data, sys_in)
Pressure : 10.0 [kbar]
Temperature : 1100.0 [Celsius]
Stable phase | Fraction (mol fraction)
pl4T 0.01114
liq 0.74789
cpx 0.21862
opx 0.02154
Stable phase | Fraction (wt fraction)
pl4T 0.01168
liq 0.72576
cpx 0.23872
opx 0.02277
Gibbs free energy : -907.27887 (47 iterations; 187.11 ms)
Oxygen fugacity : 0.02411835177808492
julia> finalize_MAGEMin(gv,DB)MAGEMin_C.point_wise_minimization Method
out = point_wise_minimization(P::Number,T::Number, data::MAGEMin_Data)Performs a point-wise optimization for a given pressure P and temperature T for the data specified in the MAGEMin database MAGEMin_Data (where also compoition is specified)
MAGEMin_C.point_wise_minimization_with_guess Method
out = function point_wise_minimization_with_guess(mSS_vec :: Vector{mSS_data}, P, T, gv, z_b, DB, splx_data)MAGEMin_C.print_info Method
print_info(g::gmin_struct)Prints a more extensive overview of the simulation results
sourceMAGEMin_C.pwm_init Method
pwm_init(P::Float64,T::Float64, gv, z_b, DB, splx_data)
Function to provide single point minimization and give access to G0 and W's (Margules) parameters
The objective here is to be able to use MAGEMin for thermodynamic database inversion/calibrationExample
dtb = "mp"
gv, z_b, DB, splx_data = init_MAGEMin(dtb);
Xoxides = ["SiO2"; "TiO2"; "Al2O3"; "FeO"; "MnO"; "MgO"; "CaO"; "Na2O"; "K2O"; "H2O"; "O"];
X = [58.509, 1.022, 14.858, 4.371, 0.141, 4.561, 5.912, 3.296, 2.399, 10.0, 0.0];
sys_in = "wt"
gv = define_bulk_rock(gv, X, Xoxides, sys_in, dtb);
P, T = 6.0, 500.0
gv, z_b, DB, splx_data = pwm_init(P, T, gv, z_b, DB, splx_data);
# Modify gbase or W's here
out = pwm_run(gv, z_b, DB, splx_data);which gives:
julia> out = pwm_run(gv, z_b, DB, splx_data);
Status : 0
Mass residual : +3.23681e-15
Rank : 0
Point : 1
Temperature : +500.00000 [C]
Pressure : +6.00000 [kbar]
SOL = [G: -791.477] (12 iterations, 11.03 ms)
GAM = [-943.275969,-1739.945965,-770.603948,-668.434121,-339.621452,-886.160861,-804.045787,-992.801306,-480.273909,-480.273909]
Phase : bi chl g opx fsp q sph H2O zo
Mode : 0.18022 0.00161 0.00174 0.04239 0.33178 0.15155 0.01325 0.24445 0.03301MAGEMin_C.remove_phases Method
Function to retrieve the list of indexes of the solution phases to be removed from the minimizationMAGEMin_C.retrieve_solution_phase_information Method
Function to retrieve the general information of the databasesMAGEMin_C.use_predefined_bulk_rock Function
bulk_rock = use_predefined_bulk_rock(gv, test=-1, db="ig")
Returns the pre-defined bulk rock composition of a given test
sourceMAGEMin_C.use_predefined_bulk_rock Function
data = use_predefined_bulk_rock(data::MAGEMin_Data, test=0)Returns the pre-defined bulk rock composition of a given test
sourceMAGEMin_C.wt2mol Method
bulk_mol = wt2mol(bulk_wt, bulk_ox)Converts bulk-rock composition from wt to mol fraction
source