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fix: corrected rate parameters in carbonate system #9

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rrsettgast merged 7 commits into from
Oct 3, 2025
Merged

fix: corrected rate parameters in carbonate system #9

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d4cbd48
Update carbonate system reaction constants
jkgolla Jul 2, 2025
453dbc6
Update carbonate reaction system
jkgolla Jul 2, 2025
91464ae
Resolve redundant aqueous carbonate secondary species and update affe…
jkgolla Sep 4, 2025
f40b79b
Merge remote-tracking branch 'origin/main' into jon-frank/update-carb…
frankfeifan Sep 5, 2025
4ac3c00
uncrustify
frankfeifan Sep 5, 2025
67af45f
increased timestep in mixed reactions test
rrsettgast Oct 2, 2025
c5dcba6
corrected expected solutions in mixed reaction test
frankfeifan Oct 2, 2025
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134 changes: 62 additions & 72 deletions src/reactions/geochemistry/Carbonate.hpp
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Expand Up @@ -24,92 +24,80 @@ namespace geochemistry
namespace carbonate
{

constexpr CArrayWrapper<double, 11, 18> stoichMatrix =
{ // OH- CO2 CO3-2 H2CO3 CaHCO3+ CaSO4 CaCl+ CaCl2 MgSO4 NaSO4- CaCO3 H+ HCO3- Ca+2 SO4-2 Cl- Mg+2 Na+
{ -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0 }, // OH- + H+ = H2O
{ 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0 }, // CO2 + H2O = H+ + HCO3-
{ 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0 }, // CO3-2 + H+ = HCO3-
{ 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0 }, // H2CO3 = H+ + HCO3-
{ 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0 }, // CaHCO3+ = Ca+2 + HCO3-
{ 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0 }, // CaSO4 = Ca+2 + SO4-2
{ 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0 }, // CaCl+ = Ca+2 + Cl-
{ 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 2, 0, 0 }, // CaCl2 = Ca+2 + 2Cl-
{ 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 1, 0 }, // MgSO4 = Mg+2 + SO4-2
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 0, 1 }, // NaSO4- = Na+ + SO4-2
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, -1, 1, 1, 0, 0, 0, 0 } // CaCO3(s) + H+ = Ca+2 + HCO3- (kinetic)
// { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, 0, 1, 0, 0, 0, 0 } // Ca(OH)2​(s) + 2H+ = Ca2+ + 2H2​O (kinetic)
constexpr CArrayWrapper<double, 10, 17> stoichMatrix =
{ // OH- CO2 CO3-2 CaHCO3+ CaSO4 CaCl+ CaCl2 MgSO4 NaSO4- CaCO3 H+ HCO3- Ca+2 SO4-2 Cl- Mg+2 Na+
{ -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0 }, // OH- + H+ = H2O
{ 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0 }, // CO2 + H2O = H+ + HCO3-
{ 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0 }, // CO3-2 + H+ = HCO3-
{ 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0 }, // CaHCO3+ = Ca+2 + HCO3-
{ 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0 }, // CaSO4 = Ca+2 + SO4-2
{ 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0 }, // CaCl+ = Ca+2 + Cl-
{ 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 2, 0, 0 }, // CaCl2 = Ca+2 + 2Cl-
{ 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 1, 0 }, // MgSO4 = Mg+2 + SO4-2
{ 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 0, 1 }, // NaSO4- = Na+ + SO4-2
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, -1, 1, 1, 0, 0, 0, 0 } // CaCO3(s) + H+ = Ca+2 + HCO3- (kinetic)
};

constexpr CArrayWrapper<double, 11, 17> stoichMatrixNosolid =
{ // OH- CO2 CO3-2 H2CO3 CaHCO3+ CaSO4 CaCl+ CaCl2 MgSO4 NaSO4- H+ HCO3- Ca+2 SO4-2 Cl- Mg+2 Na+
{ -1, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0 }, // OH- + H+ = H2O
{ 0, -1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0 }, // CO2 + H2O = H+ + HCO3-
{ 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0 }, // CO3-2 + H+ = HCO3-
{ 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0 }, // H2CO3 = H+ + HCO3-
{ 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0 }, // CaHCO3+ = Ca+2 + HCO3-
{ 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0 }, // CaSO4 = Ca+2 + SO4-2
{ 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0 }, // CaCl+ = Ca+2 + Cl-
{ 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 2, 0, 0 }, // CaCl2 = Ca+2 + 2Cl-
{ 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 1, 0 }, // MgSO4 = Mg+2 + SO4-2
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 1, 0, 0, 1 }, // NaSO4- = Na+ + SO4-2
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 1, 1, 0, 0, 0, 0 } // CaCO3(s) + H+ = Ca+2 + HCO3- (kinetic)
// { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -2, 0, 1, 0, 0, 0, 0 } // Ca(OH)2​(s) + 2H+ = Ca2+ + 2H2​O (kinetic)
constexpr CArrayWrapper<double, 10, 16> stoichMatrixNosolid =
{ // OH- CO2 CO3-2 CaHCO3+ CaSO4 CaCl+ CaCl2 MgSO4 NaSO4- H+ HCO3- Ca+2 SO4-2 Cl- Mg+2 Na+
{ -1, 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0 }, // OH- + H+ = H2O
{ 0, -1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0 }, // CO2 + H2O = H+ + HCO3-
{ 0, 0, -1, 0, 0, 0, 0, 0, 0, -1, 1, 0, 0, 0, 0, 0 }, // CO3-2 + H+ = HCO3-
{ 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0 }, // CaHCO3+ = Ca+2 + HCO3-
{ 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0 }, // CaSO4 = Ca+2 + SO4-2
{ 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0 }, // CaCl+ = Ca+2 + Cl-
{ 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 2, 0, 0 }, // CaCl2 = Ca+2 + 2Cl-
{ 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1, 0, 1, 0 }, // MgSO4 = Mg+2 + SO4-2
{ 0, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 1, 0, 0, 1 }, // NaSO4- = Na+ + SO4-2
{ 0, 0, 0, 0, 0, 0, 0, 0, 0, -1, 1, 1, 0, 0, 0, 0 } // CaCO3(s) + H+ = Ca+2 + HCO3- (kinetic)
};

// C^{n+1} - C^n - r( C^{n+1} ) * dt = 0
constexpr CArrayWrapper<double, 11> equilibriumConstants =
// thermodynamic constants derived from 'llnl.tdat' used by Geochemists' Workbench (originally from EQ36)
constexpr CArrayWrapper<double, 10> equilibriumConstants =
{
9.77E+13, // OH- + H+ = H2O
4.37E-07, // CO2 + H2O = H+ + HCO3-
2.14E+10, // CO3-2 + H+ = HCO3-
1.70E-04, // H2CO3 = H+ + HCO3-
8.13E-02, // CaHCO3+ = Ca+2 + HCO3-
6.92E-03, // CaSO4 = Ca+2 + SO4-2
4.68E+00, // CaCl+ = Ca+2 + Cl-
3.98E+00, // CaCl2 = Ca+2 + 2Cl-
3.72E-03, // MgSO4 = Mg+2 + SO4-2
1.51E-01, // NaSO4- = Na+ + SO4-2
1.17E+07 // CaCO3 + H+ = Ca+2 + HCO3- (kinetic)
// 1
}; // Ca(OH)2​(s) + 2H+ = Ca2+ + 2H2​O (kinetic)
9.89E+13, // OH- + H+ = H2O
4.42E-07, // CO2 + H2O = H+ + HCO3-
2.21E+10, // CO3-2 + H+ = HCO3-
6.00E-02, // CaHCO3+ = Ca+2 + HCO3-
4.79E-03, // CaSO4 = Ca+2 + SO4-2
2.00E-01, // CaCl+ = Ca+2 + Cl-
3.98E+00, // CaCl2 = Ca+2 + 2Cl-
5.92E-03, // MgSO4 = Mg+2 + SO4-2
2.02E-01, // NaSO4- = Na+ + SO4-2
5.16E+01 // CaCO3 + H+ = Ca+2 + HCO3- (kinetic)
};

constexpr CArrayWrapper<double, 11> forwardRates =
constexpr CArrayWrapper<double, 10> forwardRates =
{
1.4e11, // OH- + H+ = H2O
0.039, // CO2 + H2O = H+ + HCO3-
1.0e10, // CO3-2 + H+ = HCO3-
0.57, // H2CO3 = H+ + HCO3-
1.0e10, // CO3-2 + H+ = HCO3-
1.5e6, // CaHCO3+ = Ca+2 + HCO3-
1.0e5, // CaSO4 = Ca+2 + SO4-2
1.0e8, // CaCl+ = Ca+2 + Cl-
1.0e7, // CaCl2 = Ca+2 + 2Cl-
1.0e5, // MgSO4 = Mg+2 + SO4-2
1.0e7, // NaSO4- = Na+ + SO4-2
1.0e5 // CaCO3 + H+ = Ca+2 + HCO3- (kinetic)

// 1
}; // Ca(OH)2​(s) + 2H+ = Ca2+ + 2H2​O (kinetic)
1.55E-06 // CaCO3 + H+ = Ca+2 + HCO3- (kinetic)
};

constexpr CArrayWrapper<double, 11> reverseRates =
{ 1.43E-03, // OH- + H+ = H2O
8.92E+04, // CO2 + H2O = H+ + HCO3-
4.67E-01, // CO3-2 + H+ = HCO3-
3.35E+03, // H2CO3 = H+ + HCO3-
1.85E+07, // CaHCO3+ = Ca+2 + HCO3-
1.45E+07, // CaSO4 = Ca+2 + SO4-2
2.14E+07, // CaCl+ = Ca+2 + Cl-
2.51E+06, // CaCl2 = Ca+2 + 2Cl-
2.69E+07, // MgSO4 = Mg+2 + SO4-2
6.62E+07, // NaSO4- = Na+ + SO4-2
8.55E-03 // CaCO3 + H+ = Ca+2 + HCO3-
// 1 // Ca(OH)2​(s) + 2H+ = Ca2+ + 2H2​O (kinetic)
constexpr CArrayWrapper<double, 10> reverseRates =
{ 1.43E-03, // OH- + H+ = H2O
8.92E+04, // CO2 + H2O = H+ + HCO3-
4.67E-01, // CO3-2 + H+ = HCO3-
1.85E+07, // CaHCO3+ = Ca+2 + HCO3-
1.45E+07, // CaSO4 = Ca+2 + SO4-2
2.14E+07, // CaCl+ = Ca+2 + Cl-
2.51E+06, // CaCl2 = Ca+2 + 2Cl-
2.69E+07, // MgSO4 = Mg+2 + SO4-2
6.62E+07, // NaSO4- = Na+ + SO4-2
3.00E-08 // CaCO3 + H+ = Ca+2 + HCO3-
};

constexpr CArrayWrapper<int, 11> mobileSpeciesFlag =
constexpr CArrayWrapper<int, 10> mobileSpeciesFlag =
{ 1, // OH- + H+ = H2O
1, // CO2 + H2O = H+ + HCO3-
1, // CO3-2 + H+ = HCO3-
1, // H2CO3 = H+ + HCO3-
1, // CaHCO3+ = Ca+2 + HCO3-
1, // CaSO4 = Ca+2 + SO4-2
1, // CaCl+ = Ca+2 + Cl-
Expand All @@ -118,14 +106,16 @@ constexpr CArrayWrapper<int, 11> mobileSpeciesFlag =
1, // NaSO4- = Na+ + SO4-2
1 // CaCO3 + H+ = Ca+2 + HCO3-
};
}
using carbonateSystemAllKineticType = reactionsSystems::MixedReactionsParameters< double, int, int, 18, 11, 0 >;
using carbonateSystemAllEquilibriumType = reactionsSystems::MixedReactionsParameters< double, int, int, 18, 11, 11 >;
using carbonateSystemType = reactionsSystems::MixedReactionsParameters< double, int, int, 17, 11, 10 >;

constexpr carbonateSystemAllKineticType carbonateSystemAllKinetic( carbonate::stoichMatrix, carbonate::equilibriumConstants, carbonate::forwardRates, carbonate::reverseRates, carbonate::mobileSpeciesFlag );
constexpr carbonateSystemAllEquilibriumType carbonateSystemAllEquilibrium( carbonate::stoichMatrix, carbonate::equilibriumConstants, carbonate::forwardRates, carbonate::reverseRates, carbonate::mobileSpeciesFlag );
constexpr carbonateSystemType carbonateSystem( carbonate::stoichMatrixNosolid, carbonate::equilibriumConstants, carbonate::forwardRates, carbonate::reverseRates, carbonate::mobileSpeciesFlag );
}

using carbonateSystemAllKineticType = reactionsSystems::MixedReactionsParameters< double, int, int, 17, 10, 0 >;
using carbonateSystemAllEquilibriumType = reactionsSystems::MixedReactionsParameters< double, int, int, 17, 10, 10 >;
using carbonateSystemType = reactionsSystems::MixedReactionsParameters< double, int, int, 16, 10, 9 >;

constexpr carbonateSystemAllKineticType carbonateSystemAllKinetic( carbonate::stoichMatrix, carbonate::equilibriumConstants, carbonate::forwardRates, carbonate::reverseRates, carbonate::mobileSpeciesFlag );
constexpr carbonateSystemAllEquilibriumType carbonateSystemAllEquilibrium( carbonate::stoichMatrix, carbonate::equilibriumConstants, carbonate::forwardRates, carbonate::reverseRates, carbonate::mobileSpeciesFlag );
constexpr carbonateSystemType carbonateSystem( carbonate::stoichMatrixNosolid, carbonate::equilibriumConstants, carbonate::forwardRates, carbonate::reverseRates, carbonate::mobileSpeciesFlag );

// *****UNCRUSTIFY-ON******
} // namespace geochemistry
Expand Down
55 changes: 27 additions & 28 deletions src/reactions/geochemistry/unitTests/testGeochemicalEquilibriumReactions.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -38,12 +38,12 @@ TEST( testEquilibriumReactions, testcarbonateSystemAllEquilibrium )
{
using namespace hpcReact::geochemistry;

double const initialSpeciesConcentration[18] =
double const initialSpeciesConcentration[17] =
{
1.0e-16, // OH-
1.0e-16, // CO2
1.0e-16, // CO3-2
1.0e-16, // H2CO3
//1.0e-16, // H2CO3
1.0e-16, // CaHCO3+
1.0e-16, // CaSO4
1.0e-16, // CaCl+
Expand All @@ -60,25 +60,24 @@ TEST( testEquilibriumReactions, testcarbonateSystemAllEquilibrium )
1.09 // Na+1
};

double const expectedSpeciesConcentrations[18] =
{ 2.327841695586879e-11, // OH-
3.745973700632716e-01, // CO2
3.956656978189456e-11, // CO3-2
9.629355924567627e-04, // H2CO3
6.739226982791492e-05, // CaHCO3+
5.298329882666738e-03, // CaSO4
5.844517547638333e-03, // CaCl+
1.277319392670652e-02, // CaCl2
6.618125707964991e-03, // MgSO4
1.769217213462983e-02, // NaSO4-
1.065032288527957e-09, // CaCO3
4.396954721488358e-04, // H+
3.723009698453808e-04, // HCO3-
1.471656530812871e-02, // Ca+2
2.491372274738741e-03, // SO4-2
1.858609094598949e+00, // Cl-
9.881874292035110e-03, // Mg+2
1.072307827865370e+00 // Na+1
double const expectedSpeciesConcentrations[17] =
{ 2.1579694253441686e-11, // OH-
0.3755789961165058, // CO2
3.4214835005538611e-11, // CO3-2
1.9160014879413049e-05, // CaHCO3+
0.0025013721967110923, // CaSO4
0.030083903919781853, // CaCl+
0.0028032598559295028, // CaCl2
0.0063383337566393907, // MgSO4
0.019567697287351467, // NaSO4-
4.754873524374959e-05, // CaCO3
0.00046855267453226469, // H+
0.00035429509915661095, // HCO3-
0.0032447552774548935, // Ca+2
0.0036925967592983458, // SO4-2
1.8543095763683592, // Cl-
0.01016166624336071, // Mg+2
1.0704323027126488 // Na+1
};

std::cout<<" RESIDUAL_FORM 0:"<<std::endl;
Expand Down Expand Up @@ -140,13 +139,13 @@ TEST( testEquilibriumReactions, testcarbonateSystemAllEquilibrium2 )

double const expectedPrimarySpeciesConcentrations[numPrimarySpecies] =
{
4.396954721488358e-04, // H+
3.723009698453808e-04, // HCO3-
1.471656530812871e-02, // Ca+2
2.491372274738741e-03, // SO4-2
1.858609094598949e+00, // Cl-
9.881874292035110e-03, // Mg+2
1.072307827865370e+00 // Na+1
0.00046855267453254149, // H+
0.00035429509915645743, // HCO3-
0.0032447552774548518, // Ca+2
0.0036925967592983211, // SO4-2
1.8543095763683592, // Cl-
0.010161666243360675, // Mg+2
1.0704323027126488 // Na+1
};

for( int r=0; r<numPrimarySpecies; ++r )
Expand Down
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