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feat: MoMaS Benchmark #11

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877df19
initial commit
frankfeifan Jul 14, 2025
952ba2e
revised notations in parameters
frankfeifan Jul 25, 2025
b172c96
Implement unit test for MoMaS benchmark easy case
jkgolla Jul 28, 2025
b0a8aed
cleanup of massActions...and change definition of K in the momas example
rrsettgast Jul 29, 2025
e7058a5
add new interface function to specify target aggregate concentrations…
rrsettgast Jul 30, 2025
9bddcd4
a few changes to make GEOS work
frankfeifan Aug 5, 2025
3a687e5
more iterations to solve equilibrium
frankfeifan Aug 13, 2025
6d0282a
fix gcc error
frankfeifan Aug 15, 2025
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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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30 changes: 20 additions & 10 deletions src/reactions/exampleSystems/MoMasBenchmark.hpp
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Expand Up @@ -28,9 +28,9 @@ namespace MomMasBenchmark
// Columns 7–11 are primary species: {X1, X2, X3, X4, S}
{
// C1 C2 C3 C4 C5 CS1 CS2 | X1 X2 X3 X4 S
{ -1, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0 }, // C1 = X2
{ 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0 }, // C2 = X2 * X3
{ 0, 0, -1, 0, 0, 0, 0, 0, -1, 0, 1, 0 }, // C3 = X2 * X4
{ -1, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0 }, // C1 = -X2
{ 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0 }, // C2 = X2 + X3
{ 0, 0, -1, 0, 0, 0, 0, 0, -1, 0, 1, 0 }, // C3 = X2 + X4
{ 0, 0, 0, -1, 0, 0, 0, 0, -4, 1, 3, 0 }, // C4 = -4X2 + X3 + 3X4
{ 0, 0, 0, 0, -1, 0, 0, 0, 4, 3, 1, 0 }, // C5 = 4X2 + 3X3 + X4
{ 0, 0, 0, 0, 0, -1, 0, 0, 3, 1, 0, 1 }, // CS1 = 3X2 + X3 + S
Expand All @@ -39,13 +39,13 @@ namespace MomMasBenchmark

// Equilibrium constants K
{
1.0e-12, // C1
1.0, // C2
1.0, // C3
0.1, // C4
1.0e35, // C5
1.0e6, // CS1
1.0e-1 // CS2
1.0e12, // C1 + X2 = ??
1.0, // C2 = X2 + X3
1.0, // C3 = X2 + X4
1.0e1, // C4 + 4X2 = X3 + 3X4
1.0e-35, // C5 = 4X2 + 3X3 + X4
1.0e-6, // CS1 = 3X2 + X3 + S
1.0e1 // CS2 + 3X2 = + X4 + 2S
},

// Forward rate constants
Expand All @@ -67,6 +67,16 @@ namespace MomMasBenchmark
0.0,
0.0
},

// Flag of mobile secondary species
{ 1, // C1 = - X2
1, // C2 = X2 + X3
1, // C3 = -X2 + X4
1, // C4 = -4X2 + X3 + 3X4
1, // C5 = 4X2 + 3X3 + X4
0, // CS1 = 3X2 + X3 + S
0 // CS2 = -3X2 + X4 + 2S
}
};

// *****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
93 changes: 93 additions & 0 deletions src/reactions/geochemistry/Momas.hpp
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@@ -0,0 +1,93 @@
/*
* ------------------------------------------------------------------------------------------------------------
* SPDX-License-Identifier: (BSD-3-Clause)
*
* Copyright (c) 2025- Lawrence Livermore National Security LLC
* All rights reserved
*
* See top level LICENSE files for details.
* ------------------------------------------------------------------------------------------------------------
*/

#pragma once

#include "../reactionsSystems/Parameters.hpp"

namespace hpcReact
{

namespace geochemistry
{
// turn off uncrustify to allow for better readability of the parameters
// *****UNCRUSTIFY-OFF******

namespace momas
{

constexpr CArrayWrapper<double, 7, 12> stoichMatrix =
{
// C1 C2 C3 C4 C5 CS1 CS2 | X1 X2 X3 X4 S
{ -1, 0, 0, 0, 0, 0, 0, 0, -1, 0, 0, 0 }, // C1 = -X2
{ 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0 }, // C2 = X2 + X3
{ 0, 0, -1, 0, 0, 0, 0, 0, -1, 0, 1, 0 }, // C3 = X2 + X4
{ 0, 0, 0, -1, 0, 0, 0, 0, -4, 1, 3, 0 }, // C4 = -4X2 + X3 + 3X4
{ 0, 0, 0, 0, -1, 0, 0, 0, 4, 3, 1, 0 }, // C5 = 4X2 + 3X3 + X4
{ 0, 0, 0, 0, 0, -1, 0, 0, 3, 1, 0, 1 }, // CS1 = 3X2 + X3 + S
{ 0, 0, 0, 0, 0, 0, -1, 0, -3, 0, 1, 2 } // CS2 = -3X2 + X4 + 2S
};

constexpr CArrayWrapper<double, 7> equilibriumConstants =
{
1.0e12, // C1 + X2 = ??
1.0, // C2 = X2 + X3
1.0, // C3 = X2 + X4
1.0e1, // C4 + 4X2 = X3 + 3X4
1.0e-35, // C5 = 4X2 + 3X3 + X4
1.0e-6, // CS1 = 3X2 + X3 + S
1.0e1 // CS2 + 3X2 = + X4 + 2S
};

constexpr CArrayWrapper<double, 7> forwardRates =
{
0.0, // C1 = -X2
0.0, // C2 = X2 + X3
0.0, // C3 = X2 + X4
0.0, // C4 = -4X2 + X3 + 3X4
0.0, // C5 = 4X2 + 3X3 + X4
0.0, // CS1 = 3X2 + X3 + S
0.0 // CS2 = -3X2 + X4 + 2S
};

constexpr CArrayWrapper<double, 7> reverseRates =
{
0.0, // C1 = -X2
0.0, // C2 = X2 + X3
0.0, // C3 = X2 + X4
0.0, // C4 = -4X2 + X3 + 3X4
0.0, // C5 = 4X2 + 3X3 + X4
0.0, // CS1 = 3X2 + X3 + S
0.0 // CS2 = -3X2 + X4 + 2S
};

constexpr CArrayWrapper<int, 7> mobileSpeciesFlag =
{
1, // C1 = -X2
1, // C2 = X2 + X3
1, // C3 = X2 + X4
1, // C4 = -4X2 + X3 + 3X4
1, // C5 = 4X2 + 3X3 + X4
0, // CS1 = 3X2 + X3 + S
0 // CS2 = -3X2 + X4 + 2S
};
}
using momasSystemAllKineticType = reactionsSystems::MixedReactionsParameters< double, int, int, 12, 7, 0 >;
using momasSystemAllEquilibriumType = reactionsSystems::MixedReactionsParameters< double, int, int, 12, 7, 7 >;
using momasSystemType = reactionsSystems::MixedReactionsParameters< double, int, int, 12, 7, 7 >;

constexpr momasSystemAllKineticType momasSystemAllKinetic( momas::stoichMatrix, momas::equilibriumConstants, momas::forwardRates, momas::reverseRates, momas::mobileSpeciesFlag );
constexpr momasSystemAllEquilibriumType momasSystemAllEquilibrium( momas::stoichMatrix, momas::equilibriumConstants, momas::forwardRates, momas::reverseRates, momas::mobileSpeciesFlag );
constexpr momasSystemType carbonateSystem( momas::stoichMatrix, momas::equilibriumConstants, momas::forwardRates, momas::reverseRates, momas::mobileSpeciesFlag );

// *****UNCRUSTIFY-ON******
} // namespace geochemistry
} // namespace hpcReact
33 changes: 29 additions & 4 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
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1 change: 1 addition & 0 deletions src/reactions/geochemistry/unitTests/CMakeLists.txt
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Expand Up @@ -3,6 +3,7 @@ set( testSourceFiles
testGeochemicalEquilibriumReactions.cpp
testGeochemicalKineticReactions.cpp
testGeochemicalMixedReactions.cpp
testMomasEasyCase.cpp
)

set( dependencyList hpcReact gtest )
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8 changes: 4 additions & 4 deletions src/reactions/geochemistry/unitTests/testGeochemicalEquilibriumReactions.cpp
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Expand Up @@ -133,10 +133,10 @@ TEST( testEquilibriumReactions, testcarbonateSystemAllEquilibrium2 )
};

double logPrimarySpeciesConcentration[numPrimarySpecies];
EquilibriumReactionsType::enforceEquilibrium_Aggregate( 0,
hpcReact::geochemistry::carbonateSystemAllEquilibrium.equilibriumReactionsParameters(),
logInitialPrimarySpeciesConcentration,
logPrimarySpeciesConcentration );
EquilibriumReactionsType::enforceEquilibrium_LogAggregate( 0,
hpcReact::geochemistry::carbonateSystemAllEquilibrium.equilibriumReactionsParameters(),
logInitialPrimarySpeciesConcentration,
logPrimarySpeciesConcentration );

double const expectedPrimarySpeciesConcentrations[numPrimarySpecies] =
{
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