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MAGEMin_C v1.5.7 #55

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Sep 10, 2024
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MAGEMin_C v1.5.7 #55

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55ee3fe
updated version number
NicolasRiel Aug 30, 2024
5641658
MAGEMin_C v1.5.7
NicolasRiel Sep 10, 2024
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4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "MAGEMin_C"
uuid = "e5d170eb-415a-4524-987b-12f1bce1ddab"
authors = ["Boris Kaus <[email protected]> & Nicolas Riel <[email protected]>"]
version = "1.5.6"
version = "1.5.7"

[deps]
CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82"
Expand All @@ -17,6 +17,6 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
CEnum = "0.4"
DataFrames = "1.6.1"
CSV = "0.10.14"
MAGEMin_jll = "1.5.2 - 1.5.2"
MAGEMin_jll = "1.5.3 - 1.5.3"
ProgressMeter = "1"
julia = "1.6"
10 changes: 8 additions & 2 deletions gen/epilogue.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ struct SS_data
Vs::Cdouble
Comp::Vector{Cdouble}
Comp_wt::Vector{Cdouble}
Comp_apfu::Vector{Cdouble}
compVariables::Vector{Cdouble}
compVariablesNames::Vector{String}
siteFractions::Vector{Cdouble}
Expand All @@ -29,12 +30,14 @@ struct SS_data
emChemPot::Vector{Cdouble}
emComp::Vector{Vector{Float64}}
emComp_wt::Vector{Vector{Float64}}
emComp_apfu::Vector{Vector{Float64}}
end

function Base.convert(::Type{SS_data}, a::stb_SS_phases)
return SS_data(a.f, a.G, a.deltaG, a.V, a.alpha, a.entropy, a.enthalpy, a.cp, a.rho, a.bulkMod, a.shearMod, a.Vp, a.Vs,
unsafe_wrap( Vector{Cdouble}, a.Comp, a.nOx),
unsafe_wrap( Vector{Cdouble}, a.Comp_wt, a.nOx),
unsafe_wrap( Vector{Cdouble}, a.Comp_apfu, a.nOx),
unsafe_wrap( Vector{Cdouble}, a.compVariables, a.n_xeos),
unsafe_string.( unsafe_wrap( Vector{Ptr{Int8}}, a.compVariablesNames,a.n_xeos)),
unsafe_wrap( Vector{Cdouble}, a.siteFractions, a.n_sf),
Expand All @@ -44,7 +47,8 @@ function Base.convert(::Type{SS_data}, a::stb_SS_phases)
unsafe_wrap( Vector{Cdouble}, a.emFrac_wt, a.n_em),
unsafe_wrap( Vector{Cdouble}, a.emChemPot, a.n_em),
unsafe_wrap.(Vector{Cdouble}, unsafe_wrap( Vector{Ptr{Cdouble}}, a.emComp, a.n_em), a.nOx),
unsafe_wrap.(Vector{Cdouble}, unsafe_wrap( Vector{Ptr{Cdouble}}, a.emComp_wt, a.n_em), a.nOx) )
unsafe_wrap.(Vector{Cdouble}, unsafe_wrap( Vector{Ptr{Cdouble}}, a.emComp_wt, a.n_em), a.nOx),
unsafe_wrap.(Vector{Cdouble}, unsafe_wrap( Vector{Ptr{Cdouble}}, a.emComp_apfu, a.n_em), a.nOx) )
end

# metastable phases
Expand Down Expand Up @@ -92,12 +96,14 @@ struct PP_data
Vs::Cdouble
Comp::Vector{Cdouble}
Comp_wt::Vector{Cdouble}
Comp_apfu::Vector{Cdouble}
end

function Base.convert(::Type{PP_data}, a::stb_PP_phases)
return PP_data(a.f, a.G, a.deltaG, a.V, a.alpha, a.entropy, a.enthalpy, a.cp, a.rho, a.bulkMod, a.shearMod, a.Vp, a.Vs,
unsafe_wrap(Vector{Cdouble},a.Comp, a.nOx),
unsafe_wrap(Vector{Cdouble},a.Comp_wt, a.nOx))
unsafe_wrap(Vector{Cdouble},a.Comp_wt, a.nOx),
unsafe_wrap(Vector{Cdouble},a.Comp_apfu, a.nOx))
end


Expand Down
77 changes: 75 additions & 2 deletions gen/magemin_library.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -638,6 +638,7 @@ mutable struct global_variables
numPoint::Cint
global_ite::Cint
H2O_id::Cint
S_id::Cint
Al2O3_id::Cint
K2O_id::Cint
O_id::Cint
Expand Down Expand Up @@ -1033,6 +1034,8 @@ struct stb_SS_phases
emComp::Ptr{Ptr{Cdouble}}
Comp_wt::Ptr{Cdouble}
emComp_wt::Ptr{Ptr{Cdouble}}
Comp_apfu::Ptr{Cdouble}
emComp_apfu::Ptr{Ptr{Cdouble}}
end

const stb_SS_phase = stb_SS_phases
Expand Down Expand Up @@ -1073,6 +1076,7 @@ struct stb_PP_phases
Vs::Cdouble
Comp::Ptr{Cdouble}
Comp_wt::Ptr{Cdouble}
Comp_apfu::Ptr{Cdouble}
end

const stb_PP_phase = stb_PP_phases
Expand Down Expand Up @@ -1170,6 +1174,10 @@ function get_bulk_ultramafic(gv)
ccall((:get_bulk_ultramafic, libMAGEMin), global_variable, (global_variable,), gv)
end

function get_bulk_ultramafic_ext(gv)
ccall((:get_bulk_ultramafic_ext, libMAGEMin), global_variable, (global_variable,), gv)
end

mutable struct Database
PP_ref_db::Ptr{PP_ref}
SS_ref_db::Ptr{SS_ref}
Expand Down Expand Up @@ -1237,6 +1245,10 @@ function TC_SS_init_um(SS_init, gv)
ccall((:TC_SS_init_um, libMAGEMin), Cvoid, (Ptr{SS_init_type}, global_variable), SS_init, gv)
end

function TC_SS_init_um_ext(SS_init, gv)
ccall((:TC_SS_init_um_ext, libMAGEMin), Cvoid, (Ptr{SS_init_type}, global_variable), SS_init, gv)
end

function TC_SS_init(SS_init, gv)
ccall((:TC_SS_init, libMAGEMin), Cvoid, (Ptr{SS_init_type}, global_variable), SS_init, gv)
end
Expand Down Expand Up @@ -1269,6 +1281,10 @@ function G_SS_um_EM_function(gv, SS_ref_db, EM_dataset, z_b, name)
ccall((:G_SS_um_EM_function, libMAGEMin), SS_ref, (global_variable, SS_ref, Cint, bulk_info, Ptr{Cchar}), gv, SS_ref_db, EM_dataset, z_b, name)
end

function G_SS_um_ext_EM_function(gv, SS_ref_db, EM_dataset, z_b, name)
ccall((:G_SS_um_ext_EM_function, libMAGEMin), SS_ref, (global_variable, SS_ref, Cint, bulk_info, Ptr{Cchar}), gv, SS_ref_db, EM_dataset, z_b, name)
end

mutable struct em_datas
C::NTuple{14, Cdouble}
ElShearMod::Cdouble
Expand Down Expand Up @@ -1303,6 +1319,10 @@ function TC_um_objective_init_function(SS_objective, gv)
ccall((:TC_um_objective_init_function, libMAGEMin), Cvoid, (Ptr{obj_type}, global_variable), SS_objective, gv)
end

function TC_um_ext_objective_init_function(SS_objective, gv)
ccall((:TC_um_ext_objective_init_function, libMAGEMin), Cvoid, (Ptr{obj_type}, global_variable), SS_objective, gv)
end

function TC_SS_objective_init_function(SS_objective, gv)
ccall((:TC_SS_objective_init_function, libMAGEMin), Cvoid, (Ptr{obj_type}, global_variable), SS_objective, gv)
end
Expand Down Expand Up @@ -1566,6 +1586,18 @@ function obj_um_po(n, x, grad, SS_ref_db)
ccall((:obj_um_po, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
end

function obj_ume_pl4tr(n, x, grad, SS_ref_db)
ccall((:obj_ume_pl4tr, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
end

function obj_ume_hb(n, x, grad, SS_ref_db)
ccall((:obj_ume_hb, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
end

function obj_ume_aug(n, x, grad, SS_ref_db)
ccall((:obj_ume_aug, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
end

function obj_aq17(n, x, grad, SS_ref_db)
ccall((:obj_aq17, libMAGEMin), Cdouble, (Cuint, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cvoid}), n, x, grad, SS_ref_db)
end
Expand All @@ -1590,6 +1622,10 @@ function TC_um_PC_init(PC_read, gv)
ccall((:TC_um_PC_init, libMAGEMin), Cvoid, (Ptr{PC_type}, global_variable), PC_read, gv)
end

function TC_um_ext_PC_init(PC_read, gv)
ccall((:TC_um_ext_PC_init, libMAGEMin), Cvoid, (Ptr{PC_type}, global_variable), PC_read, gv)
end

# typedef void ( * sf_type ) ( unsigned m , double * result , unsigned n , const double * x , double * grad , void * data )
const sf_type = Ptr{Cvoid}

Expand All @@ -1616,6 +1652,10 @@ function TC_um_NLopt_opt_init(NLopt_opt, gv)
ccall((:TC_um_NLopt_opt_init, libMAGEMin), Cvoid, (Ptr{NLopt_type}, global_variable), NLopt_opt, gv)
end

function TC_um_ext_NLopt_opt_init(NLopt_opt, gv)
ccall((:TC_um_ext_NLopt_opt_init, libMAGEMin), Cvoid, (Ptr{NLopt_type}, global_variable), NLopt_opt, gv)
end

function TC_NLopt_opt_init(NLopt_opt, gv)
ccall((:TC_NLopt_opt_init, libMAGEMin), Cvoid, (Ptr{NLopt_type}, global_variable), NLopt_opt, gv)
end
Expand Down Expand Up @@ -1678,6 +1718,7 @@ mutable struct oxide_datas
oxMass::NTuple{15, Cdouble}
atPerOx::NTuple{15, Cdouble}
ElEntropy::NTuple{15, Cdouble}
OPerOx::NTuple{15, Cdouble}
oxide_datas() = new()
end

Expand Down Expand Up @@ -1791,6 +1832,32 @@ end

const ultramafic_dataset = ultramafic_datasets

mutable struct ultramafic_ext_datasets
ds_version::Cint
n_ox::Cint
n_pp::Cint
n_ss::Cint
ox::NTuple{9, NTuple{20, Cchar}}
PP::NTuple{21, NTuple{20, Cchar}}
SS::NTuple{15, NTuple{20, Cchar}}
verifyPC::NTuple{15, Cint}
n_SS_PC::NTuple{15, Cint}
SS_PC_stp::NTuple{15, Cdouble}
PC_df_add::Cdouble
solver_switch_T::Cdouble
min_melt_T::Cdouble
inner_PGE_ite::Cdouble
max_n_phase::Cdouble
max_g_phase::Cdouble
max_fac::Cdouble
merge_value::Cdouble
re_in_n::Cdouble
obj_tol::Cdouble
ultramafic_ext_datasets() = new()
end

const ultramafic_ext_dataset = ultramafic_ext_datasets

function global_variable_TC_init(gv, z_b)
ccall((:global_variable_TC_init, libMAGEMin), global_variable, (global_variable, Ptr{bulk_info}), gv, z_b)
end
Expand Down Expand Up @@ -2328,6 +2395,7 @@ struct SS_data
Vs::Cdouble
Comp::Vector{Cdouble}
Comp_wt::Vector{Cdouble}
Comp_apfu::Vector{Cdouble}
compVariables::Vector{Cdouble}
compVariablesNames::Vector{String}
siteFractions::Vector{Cdouble}
Expand All @@ -2338,12 +2406,14 @@ struct SS_data
emChemPot::Vector{Cdouble}
emComp::Vector{Vector{Float64}}
emComp_wt::Vector{Vector{Float64}}
emComp_apfu::Vector{Vector{Float64}}
end

function Base.convert(::Type{SS_data}, a::stb_SS_phases)
return SS_data(a.f, a.G, a.deltaG, a.V, a.alpha, a.entropy, a.enthalpy, a.cp, a.rho, a.bulkMod, a.shearMod, a.Vp, a.Vs,
unsafe_wrap( Vector{Cdouble}, a.Comp, a.nOx),
unsafe_wrap( Vector{Cdouble}, a.Comp_wt, a.nOx),
unsafe_wrap( Vector{Cdouble}, a.Comp_apfu, a.nOx),
unsafe_wrap( Vector{Cdouble}, a.compVariables, a.n_xeos),
unsafe_string.( unsafe_wrap( Vector{Ptr{Int8}}, a.compVariablesNames,a.n_xeos)),
unsafe_wrap( Vector{Cdouble}, a.siteFractions, a.n_sf),
Expand All @@ -2353,7 +2423,8 @@ function Base.convert(::Type{SS_data}, a::stb_SS_phases)
unsafe_wrap( Vector{Cdouble}, a.emFrac_wt, a.n_em),
unsafe_wrap( Vector{Cdouble}, a.emChemPot, a.n_em),
unsafe_wrap.(Vector{Cdouble}, unsafe_wrap( Vector{Ptr{Cdouble}}, a.emComp, a.n_em), a.nOx),
unsafe_wrap.(Vector{Cdouble}, unsafe_wrap( Vector{Ptr{Cdouble}}, a.emComp_wt, a.n_em), a.nOx) )
unsafe_wrap.(Vector{Cdouble}, unsafe_wrap( Vector{Ptr{Cdouble}}, a.emComp_wt, a.n_em), a.nOx),
unsafe_wrap.(Vector{Cdouble}, unsafe_wrap( Vector{Ptr{Cdouble}}, a.emComp_apfu, a.n_em), a.nOx) )
end

# metastable phases
Expand Down Expand Up @@ -2401,12 +2472,14 @@ struct PP_data
Vs::Cdouble
Comp::Vector{Cdouble}
Comp_wt::Vector{Cdouble}
Comp_apfu::Vector{Cdouble}
end

function Base.convert(::Type{PP_data}, a::stb_PP_phases)
return PP_data(a.f, a.G, a.deltaG, a.V, a.alpha, a.entropy, a.enthalpy, a.cp, a.rho, a.bulkMod, a.shearMod, a.Vp, a.Vs,
unsafe_wrap(Vector{Cdouble},a.Comp, a.nOx),
unsafe_wrap(Vector{Cdouble},a.Comp_wt, a.nOx))
unsafe_wrap(Vector{Cdouble},a.Comp_wt, a.nOx),
unsafe_wrap(Vector{Cdouble},a.Comp_apfu, a.nOx))
end


Expand Down
43 changes: 36 additions & 7 deletions julia/MAGEMin_wrappers.jl
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4 changes: 2 additions & 2 deletions julia/export2CSV.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,7 @@ function MAGEMin_data2dataframe( out:: Union{Vector{gmin_struct{Float64, Int64}}
Symbol("aFeO") => Float64[],
Symbol("density[kg/m3]") => Float64[],
Symbol("volume[cm3/mol]") => Float64[],
Symbol("heatCapacity[kJ/K]")=> Float64[],
Symbol("heatCapacity[J/K]")=> Float64[],
Symbol("alpha[1/K]") => Float64[],
Symbol("Entropy[J/K]") => Float64[],
Symbol("Enthalpy[J]") => Float64[],
Expand Down Expand Up @@ -239,7 +239,7 @@ function MAGEMin_data2dataframe( out:: Union{Vector{gmin_struct{Float64, Int64}}
"aFeO" => out[k].aFeO,
"density[kg/m3]" => out[k].rho,
"volume[cm3/mol]" => out[k].V,
"heatCapacity[kJ/K]"=> out[k].cp,
"heatCapacity[J/K]"=> out[k].s_cp,
"alpha[1/K]" => out[k].alpha,
"Entropy[J/K]" => out[k].entropy,
"Enthalpy[J]" => out[k].enthalpy,
Expand Down
15 changes: 13 additions & 2 deletions src/MAGEMin.c
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Original file line number Diff line number Diff line change
Expand Up @@ -154,6 +154,7 @@ int runMAGEMin( int argc,
/*
get bulk rock composition parsed from args
*/

if (gv.EM_database == 0){
gv = get_bulk_metapelite( gv );
}
Expand All @@ -166,6 +167,9 @@ int runMAGEMin( int argc,
else if (gv.EM_database == 4){
gv = get_bulk_ultramafic( gv );
}
else if (gv.EM_database == 5){
gv = get_bulk_ultramafic_ext( gv );
}
else{
printf(" Wrong database...\n");
}
Expand Down Expand Up @@ -859,6 +863,9 @@ global_variable ReadCommandLineOptions( global_variable gv,
else if (strcmp(gv.db, "um") == 0){
gv.EM_database = 4;
}
else if (strcmp(gv.db, "ume") == 0){
gv.EM_database = 5;
}
else {
printf(" No or wrong database acronym has been provided, using default (Igneous [ig])\n");
gv.EM_database = 2;
Expand All @@ -882,12 +889,12 @@ Databases InitializeDatabases( global_variable gv,
/**
Allocate memory for each solution phase according to their specificities (n_em, sf etc)
*/

SS_init_type SS_init[gv.len_ss];

TC_SS_init( SS_init,
gv );


DB.SS_ref_db = malloc ((gv.len_ss) * sizeof(SS_ref));
for (int iss = 0; iss < gv.len_ss; iss++){

Expand Down Expand Up @@ -976,11 +983,13 @@ void FreeDatabases( global_variable gv,
for ( i = 0; i < n_ox; i++){
if (DB.sp[0].PP[i].Comp !=NULL) free( DB.sp[0].PP[i].Comp );
if (DB.sp[0].PP[i].Comp_wt !=NULL) free( DB.sp[0].PP[i].Comp_wt );
if (DB.sp[0].PP[i].Comp_apfu !=NULL) free( DB.sp[0].PP[i].Comp_apfu );
}

for ( i = 0; i < n_ox; i++){
if (DB.sp[0].SS[i].Comp !=NULL) free( DB.sp[0].SS[i].Comp );
if (DB.sp[0].SS[i].Comp_wt !=NULL) free( DB.sp[0].SS[i].Comp_wt );
if (DB.sp[0].SS[i].Comp_apfu !=NULL) free( DB.sp[0].SS[i].Comp_apfu );
if (DB.sp[0].SS[i].compVariables !=NULL) free( DB.sp[0].SS[i].compVariables );
if (DB.sp[0].SS[i].siteFractions !=NULL) free( DB.sp[0].SS[i].siteFractions );
if (DB.sp[0].SS[i].emFrac !=NULL) free( DB.sp[0].SS[i].emFrac );
Expand All @@ -991,13 +1000,15 @@ void FreeDatabases( global_variable gv,
if (DB.sp[0].SS[i].siteFractionsNames[j] !=NULL) free( DB.sp[0].SS[i].siteFractionsNames[j] );
if (DB.sp[0].SS[i].emNames[j] !=NULL) free( DB.sp[0].SS[i].emNames[j] );
if (DB.sp[0].SS[i].emComp[j] !=NULL) free( DB.sp[0].SS[i].emComp[j] );
if (DB.sp[0].SS[i].emComp_wt[j] !=NULL) free( DB.sp[0].SS[i].emComp_wt[j] );
if (DB.sp[0].SS[i].emComp_wt[j] !=NULL) free( DB.sp[0].SS[i].emComp_wt[j] );
if (DB.sp[0].SS[i].emComp_apfu[j] !=NULL) free( DB.sp[0].SS[i].emComp_apfu[j] );
}
if (DB.sp[0].SS[i].compVariablesNames !=NULL) free( DB.sp[0].SS[i].compVariablesNames );
if (DB.sp[0].SS[i].siteFractionsNames !=NULL) free( DB.sp[0].SS[i].siteFractionsNames );
if (DB.sp[0].SS[i].emNames !=NULL) free( DB.sp[0].SS[i].emNames );
if (DB.sp[0].SS[i].emComp !=NULL) free( DB.sp[0].SS[i].emComp );
if (DB.sp[0].SS[i].emComp_wt !=NULL) free( DB.sp[0].SS[i].emComp_wt );
if (DB.sp[0].SS[i].emComp_apfu !=NULL) free( DB.sp[0].SS[i].emComp_apfu );
}

/* free metastable assemblage */
Expand Down
9 changes: 8 additions & 1 deletion src/MAGEMin.h
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,7 @@ typedef struct global_variables {
int numPoint; /** the number of the current point */
int global_ite; /** global iteration increment */
int H2O_id;
int S_id;
int Al2O3_id;
int K2O_id;
int O_id;
Expand Down Expand Up @@ -607,7 +608,10 @@ typedef struct stb_SS_phases {

double *Comp_wt;
double **emComp_wt;


double *Comp_apfu;
double **emComp_apfu;

//double *siteFrac;

} stb_SS_phase;
Expand Down Expand Up @@ -657,6 +661,8 @@ typedef struct stb_PP_phases {
double *Comp;
double *Comp_wt;

double *Comp_apfu;

} stb_PP_phase;

/* structure to store informations of stable phase equilibria */
Expand Down Expand Up @@ -746,6 +752,7 @@ global_variable global_variable_init( global_variable gv,
global_variable get_bulk_igneous( global_variable gv );
global_variable get_bulk_metapelite( global_variable gv );
global_variable get_bulk_ultramafic( global_variable gv );
global_variable get_bulk_ultramafic_ext( global_variable gv );

/** Stores databases **/
typedef struct Database { PP_ref *PP_ref_db; /** Pure phases */
Expand Down
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