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.TE_prediction Method
out_TE = TE_prediction( out, C0, KDs_database, dtb;
ZrSat_model :: String = "CB")Perform TE partitioning and zircon saturation calculation.
This function computes the partitioning of elements into different phases based on the provided KDs database and the initial composition C0. It also checks for zircon saturation and adjusts the composition if necessary.
sourceMAGEMin_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.compute_TE_partitioning Method
compute_TE_partitioning( KDs_database:: custom_KDs_database,
C0 :: Vector{Float64},
ph :: Vector{String},
ph_wt :: Vector{Float64},
liq_wt :: Float64,
sol_wt :: Float64)Compute the partitioning of elements into different phases based on the provided KDs database and the initial composition C0.
This function partitions the elements into liquid, solid, and other phases based on the provided KDs database and the initial composition C0. It returns the partitioned compositions along with normalized phase weights.
sourceMAGEMin_C.compute_Zr_sat_n_part Method
compute_Zr_sat_n_part( out :: MAGEMin_C.gmin_struct{Float64, Int64},
KDs_database:: custom_KDs_database,
Cliq, Csol, Cmin, ph_TE, ph_wt_norm, liq_wt_norm,
C0 :: Vector{Float64},
ph :: Vector{String},
ph_wt :: Vector{Float64},
liq_wt :: Float64,
sol_wt :: Float64;
ZrSat_model :: String = "CB")Compute zircon saturation and adjust bulk composition if necessary.
This function checks if the zirconium content in the liquid phase exceeds the saturation limit. If it does, it adjusts the bulk composition by removing the excess zirconium and adds a new phase for zircon.
sourceMAGEMin_C.compute_melt_viscosity_G08 Method
compute_melt_viscosity_G08(oxides, M_mol, T_C; A = -4.55)
Takes as input arguments:
oxides :: Vector{String} -> oxide list of the melt composition
M_mol :: Vector{Float64} -> melt composition in mol
T_C :: Float64 -> temperature in °C
returns melt viscosity in Pa.s
Formulation after Giordano et al., 2008MAGEMin_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_custom_KDs_database Method
KDs_database = custom_KDs_database(infos::String,
element_name::Vector{String},
phase_name::Vector{String},
KDs_expr::Matrix{Expr})Create a custom KDs database from the given information.
returns a custom_KDs_database object that can be used in the TE_partitioning.jl module.
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_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.mineral_classification Method
Classify the mineral output from MAGEMin to be able to be compared with partitioning coefficient databaseMAGEMin_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