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feat: Separate Mobile and Immobile Parts of Aggregate Species Concentrations #10

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8 changes: 6 additions & 2 deletions src/reactions/exampleSystems/BulkGeneric.hpp
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Expand Up @@ -61,7 +61,9 @@ simpleKineticTestRateParams =
// forward rate constants
{ 1.0, 0.5 },
// reverse rate constants
{ 1.0, 0.5 }
{ 1.0, 0.5 },
// flag of mobile secondary species
{ 1, 1 }
};

using simpleTestType = reactionsSystems::MixedReactionsParameters< double, int, int, 5, 2, 2 >;
Expand All @@ -80,7 +82,9 @@ simpleTestRateParams =
// forward rate constants
{ 1.0, 0.5 },
// reverse rate constants
{ 1.0, 0.5 }
{ 1.0, 0.5 },
// flag of mobile secondary species
{ 1, 1 }
};

// *****UNCRUSTIFY-ON******
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10 changes: 10 additions & 0 deletions src/reactions/exampleSystems/MoMasBenchmark.hpp
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Expand Up @@ -67,6 +67,16 @@ namespace MomMasBenchmark
0.0,
0.0
},

// Flag of mobile secondary species
{ 1,
1,
1,
1,
1,
0,
0
}
};

// *****UNCRUSTIFY-ON******
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26 changes: 20 additions & 6 deletions src/reactions/geochemistry/Carbonate.hpp
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Expand Up @@ -69,7 +69,7 @@ constexpr CArrayWrapper<double, 11> equilibriumConstants =
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)
70.55 // CaCO3 + H+ = Ca+2 + HCO3- (kinetic)
// 1
}; // Ca(OH)2​(s) + 2H+ = Ca2+ + 2H2​O (kinetic)

Expand All @@ -85,7 +85,7 @@ constexpr CArrayWrapper<double, 11> forwardRates =
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)
1.55e-6 // CaCO3 + H+ = Ca+2 + HCO3- (kinetic)

// 1
}; // Ca(OH)2​(s) + 2H+ = Ca2+ + 2H2​O (kinetic)
Expand All @@ -101,17 +101,31 @@ constexpr CArrayWrapper<double, 11> reverseRates =
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-
2.197e-8 // CaCO3 + H+ = Ca+2 + HCO3-
// 1 // Ca(OH)2​(s) + 2H+ = Ca2+ + 2H2​O (kinetic)
};

constexpr CArrayWrapper<int, 11> 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-
1, // CaCl2 = Ca+2 + 2Cl-
1, // MgSO4 = Mg+2 + SO4-2
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 );
constexpr carbonateSystemAllEquilibriumType carbonateSystemAllEquilibrium( carbonate::stoichMatrix, carbonate::equilibriumConstants, carbonate::forwardRates, carbonate::reverseRates );
constexpr carbonateSystemType carbonateSystem( carbonate::stoichMatrixNosolid, carbonate::equilibriumConstants, carbonate::forwardRates, carbonate::reverseRates );
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
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25 changes: 24 additions & 1 deletion src/reactions/geochemistry/Forge.hpp
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Expand Up @@ -119,12 +119,35 @@ constexpr CArrayWrapper< double, 19 > reverseRateConstant =
1.0 // Albite: NaAlSi₃O₈(s) + 4H⁺ ⇌ Al³⁺ + Na⁺ + 3SiO₂(aq)
};

constexpr CArrayWrapper< int, 19 > mobileSpeciesFlag =
{
1, // CaCO₃(aq) + H⁺ ⇌ Ca²⁺ + HCO₃⁻
1, // CaHCO₃⁺ ⇌ Ca²⁺ + HCO₃⁻
1, // CaSO₄ ⇌ Ca²⁺ + SO₄²⁻
1, // CaCl⁺ ⇌ Ca²⁺ + Cl⁻
1, // CaCl₂ ⇌ Ca²⁺ + 2Cl⁻ (approximate, same source)
1, // MgHCO₃⁺ ⇌ Mg²⁺ + HCO₃⁻
1, // MgCO₃(aq) + H⁺ ⇌ Mg²⁺ + HCO₃⁻
1, // MgCl⁺ ⇌ Mg²⁺ + Cl⁻
1, // CO₂(aq) + H₂O ⇌ H⁺ + HCO₃⁻
1, // HSO₄⁻ ⇌ H⁺ + SO₄²⁻
1, // KHSO₄ ⇌ H⁺ + K⁺ + SO₄²⁻
1, // HSiO₃⁻ ⇌ H⁺ + SiO₂(aq)
1, // NaHSilO₃ ⇌ H⁺ + Na⁺ + SiO₂(aq)
1, // NaCl ⇌ Na⁺ + Cl⁻
1, // KCl ⇌ K⁺ + Cl⁻
1, // KSO₄⁻ ⇌ K⁺ + SO₄²⁻
1, // Dolomite: CaMg(CO₃)₂(s) + 2H⁺ ⇌ Ca²⁺ + Mg²⁺ + 2HCO₃⁻
1, // Microcline: KAlSi₃O₈(s) + 4H⁺ ⇌ Al³⁺ + K⁺ + 3SiO₂(aq)
1 // Albite: NaAlSi₃O₈(s) + 4H⁺ ⇌ Al³⁺ + Na⁺ + 3SiO₂(aq)
};

}

using forgeSystemType = reactionsSystems::MixedReactionsParameters< double, int, int, 26, 19, 16 >;


constexpr forgeSystemType forgeSystem( forge::soichMatrix, forge::equilibriumConstants, forge::fwRateConstant, forge::reverseRateConstant );
constexpr forgeSystemType forgeSystem( forge::soichMatrix, forge::equilibriumConstants, forge::fwRateConstant, forge::reverseRateConstant, forge::mobileSpeciesFlag );


// *****UNCRUSTIFY-ON******
Expand Down
31 changes: 28 additions & 3 deletions src/reactions/geochemistry/Ultramafics.hpp
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Expand Up @@ -126,15 +126,40 @@ constexpr CArrayWrapper<double, 21> reverseRates =
2.83E-44, // Mg3Si2O5(OH)4 + 6H+ = 3Mg++ + 2SiO2(aq) + 5H2O
2.10E-25 // Mg(OH)2 + 2H+ = Mg++ + 2H2O
};

constexpr CArrayWrapper<int, 21> mobileSpeciesFlag =
{
1, // OH- + H+ = H2O
1, // CO2(aq) + H2O = HCO3- + H+
1, // CO3-- + H+ = HCO3-
1, // Mg2OH+++ + H+ = 2Mg++ + H2O
1, // Mg4(OH)++++ + 4H+ = 4Mg++ + 4H2O
1, // MgOH+ + H+ = Mg++ + H2O
1, // Mg2CO3++ + H+ = 2Mg++ + HCO3-
1, // MgCO3 + H+ = Mg++ + HCO3-
1, // MgHCO3+ = Mg++ + HCO3-
1, // Mg(H3SiO4)2 + 2H+ = Mg++ + SiO2(aq) + 4H2O
1, // MgH2SiO4 + 2H+ = Mg++ + SiO2(aq) + 2H2O
1, // MgH3SiO4+ + H+ = Mg++ + SiO2(aq) + 2H2O
1, // H2SiO4-- + 2H+ = SiO2(aq) + 2H2O
1, // H3SiO4- + H+ = SiO2(aq) + 2H2O
1, // H4(H2SiO4)---- + 4H+ = 4SiO2(aq) + 8H2O
1, // H6(H2SiO4)-- + 2H+ = 4SiO2 + 8H2O
1, // Mg2SiO4 + 4H+ = 2Mg++ + SiO2(aq) + 2H2O
1, // MgCO3 + H+ = Mg++ + HCO3-
1, // SiO2 = SiO2(aq)
1, // Mg3Si2O5(OH)4 + 6H+ = 3Mg++ + 2SiO2(aq) + 5H2O
1 // Mg(OH)2 + 2H+ = Mg++ + 2H2O
};
};

using ultramaficSystemAllKineticType = reactionsSystems::MixedReactionsParameters< double, int, int, 25, 21, 0 >;
using ultramaficSystemAllEquilibriumType = reactionsSystems::MixedReactionsParameters< double, int, int, 25, 21, 21 >;
using ultramaficSystemType = reactionsSystems::MixedReactionsParameters< double, int, int, 25, 21, 16 >;

constexpr ultramaficSystemAllKineticType ultramaficSystemAllKinetic( ultramafics::stoichMatrix, ultramafics::equilibriumConstants, ultramafics::forwardRates, ultramafics::reverseRates );
constexpr ultramaficSystemAllEquilibriumType ultramaficSystemAllEquilibrium( ultramafics::stoichMatrix, ultramafics::equilibriumConstants, ultramafics::forwardRates, ultramafics::reverseRates );
constexpr ultramaficSystemType ultramaficSystem( ultramafics::stoichMatrix, ultramafics::equilibriumConstants, ultramafics::forwardRates, ultramafics::reverseRates );
constexpr ultramaficSystemAllKineticType ultramaficSystemAllKinetic( ultramafics::stoichMatrix, ultramafics::equilibriumConstants, ultramafics::forwardRates, ultramafics::reverseRates, ultramafics::mobileSpeciesFlag );
constexpr ultramaficSystemAllEquilibriumType ultramaficSystemAllEquilibrium( ultramafics::stoichMatrix, ultramafics::equilibriumConstants, ultramafics::forwardRates, ultramafics::reverseRates, ultramafics::mobileSpeciesFlag );
constexpr ultramaficSystemType ultramaficSystem( ultramafics::stoichMatrix, ultramafics::equilibriumConstants, ultramafics::forwardRates, ultramafics::reverseRates, ultramafics::mobileSpeciesFlag );

// *****UNCRUSTIFY-ON******
} // namespace geochemistry
Expand Down
63 changes: 63 additions & 0 deletions src/reactions/massActions/MassActions.hpp
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Expand Up @@ -210,5 +210,68 @@ void calculateAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA const & params,
}
}

template< typename REAL_TYPE,
typename INT_TYPE,
typename INDEX_TYPE,
typename PARAMS_DATA,
typename ARRAY_1D_TO_CONST,
typename ARRAY_1D_PRIMARY,
typename ARRAY_1D_SECONDARY,
typename ARRAY_2D >
HPCREACT_HOST_DEVICE
inline
void calculateTotalAndMobileAggregatePrimaryConcentrationsWrtLogC( PARAMS_DATA const & params,
ARRAY_1D_TO_CONST const & logPrimarySpeciesConcentrations,
ARRAY_1D_SECONDARY & logSecondarySpeciesConcentrations,
ARRAY_1D_PRIMARY & aggregatePrimarySpeciesConcentrations,
ARRAY_1D_PRIMARY & mobileAggregatePrimarySpeciesConcentrations,
ARRAY_2D & dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations,
ARRAY_2D & dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations )
{
constexpr int numPrimarySpecies = PARAMS_DATA::numPrimarySpecies();
constexpr int numSecondarySpecies = PARAMS_DATA::numSecondarySpecies();

calculateLogSecondarySpeciesConcentration< REAL_TYPE,
INT_TYPE,
INDEX_TYPE >( params,
logPrimarySpeciesConcentrations,
logSecondarySpeciesConcentrations );
for( INDEX_TYPE i = 0; i < numPrimarySpecies; ++i )
{
for( INDEX_TYPE j = 0; j < numPrimarySpecies; ++j )
{
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations[i][j] = 0.0;
dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations[i][j] = 0.0;
}
}

for( int i = 0; i < numPrimarySpecies; ++i )
{
REAL_TYPE const speciesConcentration_i = exp( logPrimarySpeciesConcentrations[i] );
aggregatePrimarySpeciesConcentrations[i] = speciesConcentration_i;
mobileAggregatePrimarySpeciesConcentrations[i] = speciesConcentration_i;
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = speciesConcentration_i;
dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, i ) = speciesConcentration_i;

for( int j = 0; j < numSecondarySpecies; ++j )
{
REAL_TYPE const secondarySpeciesConcentrations_j = exp( logSecondarySpeciesConcentrations[j] );
aggregatePrimarySpeciesConcentrations[i] += params.stoichiometricMatrix( j, i+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
mobileAggregatePrimarySpeciesConcentrations[i] += params.stoichiometricMatrix( j, i+numSecondarySpecies ) * secondarySpeciesConcentrations_j * params.mobileSecondarySpeciesFlag( j );
for( int k=0; k<numPrimarySpecies; ++k )
{
REAL_TYPE const dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration = params.stoichiometricMatrix( j, k+numSecondarySpecies ) * secondarySpeciesConcentrations_j;
dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j,
i+numSecondarySpecies ) *
dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration;

dMobileAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations( i, k ) += params.stoichiometricMatrix( j,
i+numSecondarySpecies ) *
dSecondarySpeciesConcentrations_dLogPrimarySpeciesConcentration * params.mobileSecondarySpeciesFlag( j );
}
}
}
}

} // namespace massActions
} // namespace hpcReact
10 changes: 10 additions & 0 deletions src/reactions/reactionsSystems/MixedEquilibriumKineticReactions.hpp
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Expand Up @@ -72,7 +72,9 @@ class MixedEquilibriumKineticReactions
* @param surfaceArea surface Aread for kinetic reactions
* @param logSecondarySpeciesConcentrations Output log concentrations for secondary species
* @param aggregatePrimarySpeciesConcentrations Output aggregate concentrations (per primary)
* @param mobileAggregatePrimarySpeciesConcentrations Output mobile aggregate concentrations (per primary)
* @param dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of aggregate concentrations w.r.t. log
* @param dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of mobile aggregate concentrations w.r.t. log
* primary
* @param reactionRates Output vector of kinetic reaction rates
* @param dReactionRates_dLogPrimarySpeciesConcentrations Derivatives of reaction rates w.r.t. log primary species
Expand All @@ -94,7 +96,9 @@ class MixedEquilibriumKineticReactions
ARRAY_1D_TO_CONST_KINETIC const & surfaceArea,
ARRAY_1D_SECONDARY & logSecondarySpeciesConcentrations,
ARRAY_1D_PRIMARY & aggregatePrimarySpeciesConcentrations,
ARRAY_1D_PRIMARY & mobileAggregatePrimarySpeciesConcentrations,
ARRAY_2D_PRIMARY & dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations,
ARRAY_2D_PRIMARY & dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations,
ARRAY_1D_KINETIC & reactionRates,
ARRAY_2D_KINETIC & dReactionRates_dLogPrimarySpeciesConcentrations,
ARRAY_1D_PRIMARY & aggregateSpeciesRates,
Expand All @@ -106,7 +110,9 @@ class MixedEquilibriumKineticReactions
surfaceArea,
logSecondarySpeciesConcentrations,
aggregatePrimarySpeciesConcentrations,
mobileAggregatePrimarySpeciesConcentrations,
dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations,
dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations,
reactionRates,
dReactionRates_dLogPrimarySpeciesConcentrations,
aggregateSpeciesRates,
Expand Down Expand Up @@ -219,7 +225,9 @@ class MixedEquilibriumKineticReactions
* @param logPrimarySpeciesConcentrations Log of primary species concentrations
* @param logSecondarySpeciesConcentrations Output log concentrations for secondary species
* @param aggregatePrimarySpeciesConcentrations Output aggregate concentrations (per primary)
* @param mobileAggregatePrimarySpeciesConcentrations Output mobile aggregate concentrations (per primary)
* @param dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of aggregate concentrations w.r.t. log
* @param dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations Derivatives of mobile aggregate concentrations w.r.t. log
* primary
* @param reactionRates Output vector of kinetic reaction rates
* @param dReactionRates_dLogPrimarySpeciesConcentrations Derivatives of reaction rates w.r.t. log primary species
Expand All @@ -241,7 +249,9 @@ class MixedEquilibriumKineticReactions
ARRAY_1D_TO_CONST_KINETIC const & surfaceArea,
ARRAY_1D_SECONDARY & logSecondarySpeciesConcentrations,
ARRAY_1D_PRIMARY & aggregatePrimarySpeciesConcentrations,
ARRAY_1D_PRIMARY & mobileAggregatePrimarySpeciesConcentrations,
ARRAY_2D_PRIMARY & dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations,
ARRAY_2D_PRIMARY & dMobileAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations,
ARRAY_1D_KINETIC & reactionRates,
ARRAY_2D_KINETIC & dReactionRates_dLogPrimarySpeciesConcentrations,
ARRAY_1D_PRIMARY & aggregateSpeciesRates,
Expand Down
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