MAGEMin_C.jl: Output structures:
This part decribes the content of the output structure of MAGEMin_C. These structures save the results of the phase equilibrium prediction. The first one MAGEMin_C gmin_struct stores the result of the minimization while the second one out_TE_struct stores the results of the trace-element partitioning model.
Both of the structures can be (and should be) pre-allocated when performing multiple minimizations. Pre-allocation of the output structures is achieved as:
julia
Out_XY = Vector{out_struct}(undef,n_calc)
Out_TE_XY = Vector{out_TE_struct}(undef,n_calc)where n_calc is the number of calculations you want to perform (e.g., the number of steps of a fractional crystallization experiment).
In the most simple form (where we don't pre-allocate), the output structure out is simply returned when the single_point_minimization() function is called:
julia
using MAGEMin_C
data = Initialize_MAGEMin("ig", verbose=false);
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)How to navitage the (nested) structures?
The content of the output structure out can be accessed as any Julia structure:
julia
julia> out.
G_system Gamma MAGEMin_ver M_sys PP_syms PP_vec P_kbar SS_syms SS_vec T_C V
Vp Vp_S Vs Vs_S X aAl2O3 aFeO aH2O aMgO aSiO2 aTiO2
alpha buffer buffer_n bulk bulkMod bulkModulus_M bulkModulus_S bulk_F bulk_F_wt bulk_M bulk_M_wt
bulk_S bulk_S_wt bulk_res_norm bulk_wt dQFM database dataset elements enthalpy entropy fO2
frac_F frac_F_vol frac_F_wt frac_M frac_M_vol frac_M_wt frac_S frac_S_vol frac_S_wt iter mSS_vec
n_PP n_SS n_mSS oxides ph ph_frac ph_frac_1at ph_frac_vol ph_frac_wt ph_id ph_id_db
ph_type rho rho_F rho_M rho_S s_cp shearMod shearModulus_S sol_name status time_msNote
- To display the content of the structure in a
juliaterminal after perform the calculation simply typeout.and then hitTABkey. This will display the content of the structure as shown above.
The system oxides are stored in out.oxides:
julia
julia> out.oxides
11-element Vector{String}:
"SiO2"
"Al2O3"
"CaO"
"MgO"
"FeO"
"K2O"
"Na2O"
"TiO2"
"O"
"Cr2O3"
"H2O"The list of stable phases can be accessed as:
julia
julia> out.ph
4-element Vector{String}:
"ol"
"spl"
"cpx"
"opx"The phase fraction in weight fraction:
julia
julia> out.ph_frac_wt
4-element Vector{Float64}:
0.5828145797692089
0.0329389249905903
0.1489250586188556
0.23532143662134522and for instance the content of the solution phase ol (olivine) nested strucure as:
julia
julia> out.SS_vec[1].
Comp Comp_apfu Comp_wt G V Vp
Vs alpha bulkMod compVariables compVariablesNames cp
deltaG emChemPot emComp emComp_apfu emComp_wt emFrac
emFrac_wt emNames enthalpy entropy f rho
shearMod siteFractions siteFractionsNameswhere [1] is the index of olivine in the out.SS_vec structure. The composition of olivine in weight fraction can be retrieved using:
julia
julia> out.SS_vec[1].Comp_wt
11-element Vector{Float64}:
0.40825577403516533
0.0
0.00019320141395582851
0.4913560738016318
0.10019495074924696
0.0
0.0
0.0
0.0
0.0
0.0The index of a solution-phase can be retrieved using:
julia
id_ol = nothing
if haskey(out.SS_syms, :ol)
id_ol = out.SS_syms[:ol]
endand for a pure-phase
julia
id_ru = nothing
if haskey(id_ru, :ru)
id_ru = out.PP_syms[:ru]
endwere out.SS_syms and out.PP_syms are symbol dictionaries, linking a phase name to its proper structure index.
Note
In the latter case
ru(rutile) is not stable, thereforeid_ru = nothing.Accessing the phase structure using symbols can be useful for instance when extracting specific phases composition and/or to ease vizualisation.
(...)
The list of all entries is presented below and can be accessed (and used) in a similar manner.
Note that you can define the out structure as vector or a matrix (or any n-D array). In such cases the information of individual points can be accessed using their index:
julia
julia> out[i].or
julia
julia> out[i,j].where i and j are indices.
MAGEMin_C gmin_struct
The main structure stores the properties of the system.
julia
├─ MAGEMin_ver :: String # [-] MAGEMin version
├─ dataset :: String # [-] Used thermodynamic dataset
├─ database :: String # [-] Acronym of the thermodynamic database
├─ buffer :: String # [-] Used oxygen/activity buffer
├─ buffer_n :: Float64 # [RTlog] oxygen fugacity offset
├─ G_system :: Float64 # [kJ] Gibbs energy of the system
├─ Gamma :: Vector{Float64} # [kJ] Chemical potential of system components (oxides e.g, SiO2, Al2O3 etc.)
├─ P_kbar :: Float64 # [kbar] pressure
├─ T_C :: Float64 # [°C] temperature
├─ X :: Vector{Float64} # 0 -> 1 x coordinate used when computing T-X, P-X or PT-X diagrams
├─ M_sys :: Float64 # [g/mol] normalized molar mass of the bulk rock composition
├─ bulk :: Vector{Float64} # [mol_i] bulk rock composition
├─ bulk_M :: Vector{Float64} # [mol_i] bulk mole composition of melt part
├─ bulk_S :: Vector{Float64} # [mol_i] bulk mole composition of solid part
├─ bulk_F :: Vector{Float64} # [mol_i] bulk mole composition of fluid part
├─ bulk_wt :: Vector{Float64} # [wt_i] bulk rock composition
├─ bulk_M_wt :: Vector{Float64} # [wt_i] bulk weight composition of melt part
├─ bulk_S_wt :: Vector{Float64} # [wt_i] bulk weight composition of solid par
├─ bulk_F_wt :: Vector{Float64} # [wt_i] bulk weight composition of fluid part
├─ frac_M :: Float64 # [mol_i] melt mole fraction
├─ frac_S :: Float64 # [mol_i] solid mole fraction
├─ frac_F :: Float64 # [mol_i] fluid/H2O mole fraction
├─ frac_M_wt :: Float64 # [wt_i] melt weight fraction
├─ frac_S_wt :: Float64 # [wt_i] solid weight fraction
├─ frac_F_wt :: Float64 # [wt_i] fluid/H2O weight fraction
├─ frac_M_vol :: Float64 # [vol_i] melt volume fraction
├─ frac_S_vol :: Float64 # [vol_i] solid volume fraction
├─ frac_F_vol :: Float64 # [vol_i] fluid volume fraction
├─ alpha :: Vector{Float64} # [1/K] thermal expansivity
├─ V :: Float64 # [cm^3/mol]system volume
├─ s_cp :: Vector{Float64} # [kJ/K/kg] specific heat capacity
├─ rho :: Float64 # [kg/m^3] system density
├─ rho_M :: Float64 # [kg/m^3] melt density
├─ rho_S :: Float64 # [kg/m^3] solid density
├─ rho_F :: Float64 # [kg/m^3] fluid/H2O density
├─ eta_M :: Float64 # [Pa.s] viscosity of the melt (after Giordano et al., 2008)
├─ fO2 :: Float64 # [-] oxygen fugacity
├─ dQFM :: Float64 # [-] oxygen fugacity offset from QFM buffer
├─ aH2O :: Float64 # [-] system H2O activity
├─ aSiO2 :: Float64 # [-] system SiO2 activity
├─ aTiO2 :: Float64 # [-] system TiO2 activity
├─ aAl2O3 :: Float64 # [-] system Al2O3 activity
├─ aMgO :: Float64 # [-] system MgO activity
├─ aFeO :: Float64 # [-] system FeO activity
├─ n_PP :: Int64 # [-] number of stable pure phases
├─ n_SS :: Int64 # [-] number of stables solution phases
├─ n_mSS :: Int64 # [-] number of metastable phases (used for initial guess)
├─ ph_frac :: Vector{Float64} # [mol_i] phases mole fraction
├─ ph_frac_wt :: Vector{Float64} # [wt_i] phases weight fraction
├─ ph_frac_1at :: Vector{Float64} # [mol_i 1at] phase mole fraction on a 1 atom basis
├─ ph_frac_vol :: Vector{Float64} # [vol_i] phase volume fraction
├─ ph_type :: Vector{Int64} # [0,1] phase type: 0 -> pure phase, 1 -> solution phase
├─ ph_id :: Vector{Int64} # [0-n] phase id
├─ ph_id_db :: Vector{Int64} # [0-m] phase id as in the C code
├─ ph :: Vector{String} # [-] acronym of the stable phases
├─ sol_name :: Vector{String} # [-] stable solution phases acronym with version
├─ SS_syms :: Dict{Symbol, Int64} # [-] symbol list for stable solution phases, returns the ph_id number of corresponding solution phase
├─ PP_syms :: Dict{Symbol, Int64} # [-] symbol list for stable pure phases, returns the ph_id number of corresponding pure phase
├─ SS_vec :: Vector{MAGEMin_C.LibMAGEMin.SS_data} # [-] vector of solution phase structures, storing the informations related to solution phases
├─ mSS_vec :: Vector{MAGEMin_C.LibMAGEMin.mSS_data} # [-] vector of metastable phase structures, storing the informations related to metastable solution phases
├─ PP_vec :: Vector{MAGEMin_C.LibMAGEMin.PP_data} # [-] vector of pure phase structures, storing the informations related to pures phases
├─ oxides :: Vector{String} # [-] list of oxides names
├─ elements :: Vector{String} # [-] list of elements
├─ Vp :: Float64 # [km/s] P-wave system velocity
├─ Vs :: Float64 # [km/s] S-wave system velocity
├─ Vp_S :: Float64 # [km/s] P-wave solid velocity
├─ Vs_S :: Float64 # [km/s] S-wave solid velocity
├─ bulkMod :: Float64 # [GPa] system bulk modulus
├─ shearMod :: Float64 # [GPa] system shear modulus
├─ bulkModulus_M :: Float64 # [GPa] melt bulk modulus
├─ bulkModulus_S :: Float64 # [GPa] solid bulk modulus
├─ shearModulus_S :: Float64 # [GPa] solid shear modulus
├─ entropy :: Float64 # [J/K] system entropy
├─ enthalpy :: Float64 # [J] system enthalpy
├─ iter :: Int64 # [-] number of iterations to reach convergence
├─ bulk_res_norm :: Float64 # [-] bulk rock composition residual
├─ time_ms :: Float64 # [ms] solution time
├─ status :: Int64 # [-] status of the minimization (Success,Relaxed1,Relaxed2,Failure)SS_vec
This sub-structure stores the properties of the stable solution phases.
julia
├─ SS_vec :: Vector{MAGEMin_C.LibMAGEMin.SS_data}
├─ f :: Float64 # [-] normalization factor to convert from mole to mole on 1 atom basis
├─ G :: Float64 # [kJ/f] Gibbs energy, has to be multiplied by f (normalization factor) to be in [kJ]
├─ deltaG :: Float64 # [kJ] driving force (distance from the Gibbs hyperplane)
├─ V :: Float64 # [cm^3/mol]volume
├─ alpha :: Float64 # [1/K] thermal expansivity
├─ entropy :: Float64 # [J/K] entropy
├─ enthalpy :: Float64 # [J] enthalpy
├─ cp :: Float64 # [kJ/K/Kg] specific heat capacity
├─ rho :: Float64 # [kg/m^3] density
├─ bulkMod :: Float64 # [GPa] bulk modulus
├─ shearMod :: Float64 # [GPa] bulk modulus
├─ Vp :: Float64 # [km/s] P-wave system velocity
├─ Vs :: Float64 # [km/s] S-wave system velocity
├─ Comp :: Vector{Float64} # [mol_i] composition in mole fracton
├─ Comp_wt :: Vector{Float64} # [wt_i] composition in weight fraction
├─ Comp_apfu :: Vector{Float64} # [apfu] composition in atim per formula unit
├─ compVariables :: Vector{Float64} # [-] compositional variables as described in THERMOCALC (https://hpxeosandthermocalc.org/the-thermocalc-software/)
├─ compVariablesNames :: Vector{String} # [-] compositional names
├─ siteFractions :: Vector{Float64} # [-] site fractions
├─ siteFractionsNames :: Vector{String} # [-] site fractions names
├─ emNames :: Vector{String} # [-] names of the end-members
├─ emFrac :: Vector{Float64} # [mol_i] end-members fraction in mole
├─ emFrac_wt :: Vector{Float64} # [wt_i] end-members fraction in weight
├─ emChemPot :: Vector{Float64} # [kJ] driving force (distance from the Gibbs hyperplane)
├─ emComp :: Vector{Vector{Float64}} # [mol_i] composition of the endmembers in mole fracton
├─ emComp_wt :: Vector{Vector{Float64}} # [wt_i] composition of the endmembers in weight fracton
├─ emComp_apfu :: Vector{Vector{Float64}} # [-] composition of the endmembers in atom per formula unitPP_vec
This sub-structure stores the properties of the stable pure phases.
julia
├─ PP_vec :: Vector{MAGEMin_C.LibMAGEMin.PP_data}
├─ f :: Float64 # [-] normalization factor to convert from mole to mole on 1 atom basis
├─ G :: Float64 # [kJ/f] Gibbs energy, has to be multiplied by f (normalization factor) to be in [kJ]
├─ deltaG :: Float64 # [kJ] distance from the Gibbs hyperplane
├─ V :: Float64 # [cm^3/mol]volume
├─ alpha :: Float64 # [1/K] thermal expansivity
├─ entropy :: Float64 # [J/K] entropy
├─ enthalpy :: Float64 # [J] enthalpy
├─ cp :: Float64 # [kJ/K/Kg] specific heat capacity
├─ rho :: Float64 # [kg/m^3] density
├─ bulkMod :: Float64 # [GPa] bulk modulus
├─ shearMod :: Float64 # [GPa] bulk modulus
├─ Vp :: Float64 # [km/s] P-wave system velocity
├─ Vs :: Float64 # [km/s] S-wave system velocity
├─ Comp :: Vector{Float64} # [mol_i] composition in mole fracton
├─ Comp_wt :: Vector{Float64} # [wt_i] composition in weight fraction
├─ Comp_apfu :: Vector{Float64} # [apfu] composition in atim per formula unitmSS_vec
This sub-structure stores the properties of the metastable assemblage i.e., the informations of the phases not far from the Gibbs hyperplane.
julia
├─ mSS_vec :: Vector{MAGEMin_C.LibMAGEMin.mSS_data}
├─ ph_name :: String # [-] name of the phases
├─ ph_type :: String # [-] type of the phase "ss" or "pp"
├─ info :: String # [-] origin of the phase in terms of minimization stage
├─ ph_id :: Int32 # [-] id of the phase in the C code
├─ em_id :: Int32 # [-] if end-member, id of the end-member
├─ n_xeos :: Int32 # [-] number of compositional variables
├─ n_em :: Int32 # [-] number of endmembers (n_xeos +1)
├─ G_Ppc :: Float64 # [-] Gibbs energy of the pseudocompound
├─ DF_Ppc :: Float64 # [-] driving force of the pseudocompound (distance from the Gibbs hyperplane)
├─ comp_Ppc :: Vector{Float64} # [mol_i] composition of the pseudocompound
├─ p_Ppc :: Vector{Float64} # [mol_i] end-member fractions of the pseudocompound
├─ mu_Ppc :: Vector{Float64} # [kJ/f] chemical potentials of the end-members
├─ xeos_Ppc :: Vector{Float64} # [-] compositional variablesout_TE_struct
This sub-structure stores the properties of the trace elements and accessory minerals.
julia
├─ elements :: Union{Nothing, Vector{String}} # [-] trace-elements names
├─ C0 :: Union{Nothing, Vector{Float64}} # [ug/g] trace-elements concentration
├─ Cliq :: Union{Nothing, Vector{Float64}} # [ug/g] trace-elements concentration in the melt
├─ Csol :: Union{Nothing, Vector{Float64}} # [ug/g] trace-elements concentration in the solid
├─ Cmin :: Union{Nothing, Matrix{Float64}} # [ug/g] trace-elements concentration in the stable phases
├─ ph_TE :: Union{Nothing, Vector{String}} # [-] names of the trace-elements-bearing phases (defined when settings the KDs)
├─ ph_wt_norm :: Union{Nothing, Vector{Float64}} # [wt_i] normalized weight fraction of the trace-elements-bearing phases (renormalized as KDs are not necessarily given for all phases)
├─ liq_wt_norm :: Union{Nothing, Float64} # [wt_i] normalized weight melt fraction
├─ Cliq_Zr :: Union{Nothing, Float64} # [ug/g] zirconium concentration in the liq (if Zr provided)
├─ Sat_zr_liq :: Union{Nothing, Float64} # [ug/g] zirconium saturation of the melt (computed using several saturation models)
├─ zrc_wt :: Union{Nothing, Float64} # [wt%] calculated zircon weight%
├─ bulk_cor_wt :: Union{Nothing, Vector{Float64}} # [wt_i] corrected bulk rock composition after zircon crystallization