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restructure. separate geo and battery chemistry
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‎src/reactions/geochemistry/GeochemicalReactionsParameters.hpp‎

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#pragma once
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namespace hpcReact
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{
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template< typename REAL_TYPE,
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typename INT_TYPE,
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int NUM_PRIMARY_SPECIES,
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int NUM_SECONDARY_SPECIES >
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struct EquilibriumGeochemicalReactionsParameters
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{
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using RealType = REAL_TYPE;
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using IntType = INT_TYPE;
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static constexpr IntType numPrimarySpecies = NUM_PRIMARY_SPECIES;
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static constexpr IntType numSecondarySpecies = NUM_SECONDARY_SPECIES;
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RealType m_ionSizePrimary[numPrimarySpecies];
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RealType m_ionSizeSec[numSecondarySpecies];
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IntType m_chargePrimary[numPrimarySpecies];
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IntType m_chargeSec[numSecondarySpecies];
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RealType m_DebyeHuckelA;
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RealType m_DebyeHuckelB;
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RealType m_WATEQBDot;
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CArrayWrapper< RealType, numSecondarySpecies, numPrimarySpecies> m_StoichMatrix[numSecondarySpecies][numPrimarySpecies];
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RealType m_Log10EqConst[numSecondarySpecies];
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};
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template< typename REAL_TYPE,
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typename INT_TYPE,
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int NUM_PRIMARY_SPECIES,
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int NUM_SECONDARY_SPECIES,
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int NUM_KINETIC_REACTIONS >
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struct KineticGeochemicalReactionsParameters
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{
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using RealType = REAL_TYPE;
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using IntType = INT_TYPE;
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static constexpr IntType numPrimarySpecies = NUM_PRIMARY_SPECIES;
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static constexpr IntType numSecondarySpecies = NUM_SECONDARY_SPECIES;
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static constexpr IntType numKineticReactions = NUM_KINETIC_REACTIONS;
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RealType m_ionSizePrimary[numPrimarySpecies];
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RealType m_ionSizeSec[numSecondarySpecies];
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IntType m_chargePrimary[numPrimarySpecies];
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IntType m_chargeSec[numSecondarySpecies];
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RealType m_DebyeHuckelA;
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RealType m_DebyeHuckelB;
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RealType m_WATEQBDot;
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CArrayWrapper< RealType, numKineticReactions, numPrimarySpecies> m_StoichMatrix[numKineticReactions][numPrimarySpecies];
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RealType m_log10EqConst[numKineticReactions];
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RealType m_reactionRateConstant[numKineticReactions];
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RealType m_specificSurfaceArea;
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};
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template< typename REAL_TYPE,
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typename INT_TYPE,
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int NUM_PRIMARY_SPECIES,
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int NUM_SECONDARY_SPECIES,
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int NUM_KINETIC_REACTIONS >
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struct GeochemicalReactionsParameters
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{
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using RealType = REAL_TYPE;
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using IntType = INT_TYPE;
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static constexpr IntType numPrimarySpecies = NUM_PRIMARY_SPECIES;
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static constexpr IntType numSecondarySpecies = NUM_SECONDARY_SPECIES;
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static constexpr IntType numKineticReactions = NUM_KINETIC_REACTIONS;
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RealType m_ionSizePrimary[numPrimarySpecies];
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RealType m_ionSizeSec[numSecondarySpecies];
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IntType m_chargePrimary[numPrimarySpecies];
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IntType m_chargeSec[numSecondarySpecies];
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RealType m_DebyeHuckelA;
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RealType m_DebyeHuckelB;
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RealType m_WATEQBDot;
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CArrayWrapper< RealType, numSecondarySpecies, numPrimarySpecies> m_eqStoichMatrix;
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RealType m_eqLog10EqConst[numSecondarySpecies];
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CArrayWrapper< RealType, numKineticReactions, numPrimarySpecies > m_kineticStoichMatrix;
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RealType m_kineticlog10EqConst[numKineticReactions];
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RealType m_kineticReactionRateConstant[numKineticReactions];
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RealType m_kineticSpecificSurfaceArea;
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template< int ... PRIMARY_SPECIES,
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int ... SECONDARY_SPECIES,
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int ... SPECIES_PERMUTATIONS >
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constexpr EquilibriumGeochemicalReactionsParameters< REAL_TYPE, INT_TYPE, NUM_PRIMARY_SPECIES, NUM_SECONDARY_SPECIES >
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equilibriumReactionsParams_impl( std::integer_sequence< int, PRIMARY_SPECIES... >,
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std::integer_sequence< int, SECONDARY_SPECIES... >,
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std::integer_sequence< int, SPECIES_PERMUTATIONS... > )
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{
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return EquilibriumGeochemicalReactionsParameters< REAL_TYPE, INT_TYPE, NUM_PRIMARY_SPECIES, NUM_SECONDARY_SPECIES >{
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{m_ionSizePrimary[ PRIMARY_SPECIES ]...},
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{m_ionSizeSec[ SECONDARY_SPECIES ]...},
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{m_chargePrimary[ PRIMARY_SPECIES ]...},
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{m_chargeSec[ SECONDARY_SPECIES ]...},
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m_DebyeHuckelA,
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m_DebyeHuckelB,
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m_WATEQBDot,
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m_eqStoichMatrix,
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{m_eqLog10EqConst[ SECONDARY_SPECIES ]...}
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};
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}
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constexpr EquilibriumGeochemicalReactionsParameters< REAL_TYPE, INT_TYPE, NUM_PRIMARY_SPECIES, NUM_SECONDARY_SPECIES >
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equilibriumReactions()
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{
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return equilibriumReactionsParams_impl( std::make_integer_sequence< int, NUM_PRIMARY_SPECIES >{},
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std::make_integer_sequence< int, NUM_SECONDARY_SPECIES >{},
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std::make_integer_sequence< int, NUM_PRIMARY_SPECIES*NUM_SECONDARY_SPECIES >{} );
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}
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};
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}

‎src/reactions/geochemistry/GeochemicalReactionsParametersPredefined.hpp‎

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#pragma once
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#include "GeochemicalReactionsParameters.hpp"
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namespace hpcReact
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{
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constexpr
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GeochemicalReactionsParameters< double, int, 7, 11, 2 > chemicalReactionsParams =
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{
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// m_ionSizePrimary
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{ 9.00, 4.00, 6.00, 4.00, 3.00, 8.00, 4.00 },
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// m_ionSizeSec
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{ 3.50, 3.00, 4.50, 3.00, 4.00, 3.00, 3.00, 4.00, 3.00, 3.00, 4.00 },
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// m_chargePrimary
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{ 1, -1, 2, -2, -1, 2, 1 },
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// m_chargeSec
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{ -1, 0, -2, 0, 1, 0, 0, 1, 0, 0, -1 },
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// m_DebyeHuckelA
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0.5465,
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// m_DebyeHuckelB
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0.3346,
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// m_WATEQBDot
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0.0438,
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// m_eqStoichMatrix
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// First index: 0 = OH-, 1 = CO2, 2 = CO3-2, 3 = H2CO3, 4 = CaHCO3+, 5 = CaCO3, 6 = CaSO4, 7 = CaCl+, 8 = CaCl2, 9 = MgSO4, 10 = NaSO4-
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// Second index: 0 = H+, 1 = HCO3-, 2 = Ca+2, 3 = SO4-2, 4 = Cl-, 5 = Mg+2, 6 = Na+1
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{ { { -1, 0, 0, 0, 0, 0, 0 },
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{ 1, 1, 0, 0, 0, 0, 0 },
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{ -1, 1, 0, 0, 0, 0, 0 },
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{ 1, 1, 0, 0, 0, 0, 0 },
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{ 0, 1, 1, 0, 0, 0, 0 },
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{ -1, 1, 1, 0, 0, 0, 0 },
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{ 0, 0, 1, 1, 0, 0, 0 },
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{ 0, 0, 1, 1, 0, 0, 0 },
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{ 0, 0, 1, 0, 2, 0, 0 },
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{ 0, 0, 0, 1, 0, 1, 0 },
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{ 0, 0, 0, 1, 0, 0, 1 } }
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},
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// m_eqLog10EqConst
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{ 13.99, -6.36, 10.33, -3.77, -1.09, 7.07, -2.16, 0.67, 0.60, -2.43, -0.82 },
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// m_kineticStoichMatrix
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// First index: 0 = Ca(OH)2 dissolution, 1 = CaCO3 dissolution
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// Second index: 0 = H+, 1 = HCO3-, 2 = Ca+2, 3 = SO4-2, 4 = Cl-, 5 = Mg+2, 6 = Na+1
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{ { { -2, 0, 1, 0, 0, 0, 0 },
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{ -1, 1, 1, 0, 0, 0, 0 } }
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},
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// m_kineticLog10EqConst
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{ 20.19, 1.32 },
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// m_reactionRateConstant
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{ 9.95e-1, 9.95e-3 },
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// m_specificSurfaceArea
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1.0
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};
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} // namespace hpcReact

‎src/reactions/geochemistry/unitTests/testReactionsParameterData.cpp‎

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#include "../ReactionsBase_impl.hpp"
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#include "MultiVector.hpp"
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#include "common/CArrayWrapper.hpp"
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#include "../GeochemicalReactionsParametersPredefined.hpp"
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#include <gtest/gtest.h>
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using namespace hpcReact;
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template< typename T >
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constexpr bool nearEqual( T a, T b, T tol = 1e-7 )
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{
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return ( a - b ) * ( a - b ) < tol * tol;
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}
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TEST( testReactionsBase, testParamsInitialization )
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{
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static_assert( chemicalReactionsParams.numPrimarySpecies == 7, "Number of primary species is not 7" );
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static_assert( chemicalReactionsParams.numSecondarySpecies == 11, "Number of secondary species is not 11" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[0], 9.00 ), "Ion size for primary species 0 is not 9.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[1], 4.00 ), "Ion size for primary species 1 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[2], 6.00 ), "Ion size for primary species 2 is not 6.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[3], 4.00 ), "Ion size for primary species 3 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[4], 3.00 ), "Ion size for primary species 4 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[5], 8.00 ), "Ion size for primary species 5 is not 8.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizePrimary[6], 4.00 ), "Ion size for primary species 6 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[0] , 3.50 ), "Ion size for secondary species 0 is not 3.50" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[1] , 3.00 ), "Ion size for secondary species 1 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[2] , 4.50 ), "Ion size for secondary species 2 is not 4.50" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[3] , 3.00 ), "Ion size for secondary species 3 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[4] , 4.00 ), "Ion size for secondary species 4 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[5] , 3.00 ), "Ion size for secondary species 5 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[6] , 3.00 ), "Ion size for secondary species 6 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[7] , 4.00 ), "Ion size for secondary species 7 is not 4.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[8] , 3.00 ), "Ion size for secondary species 8 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[9] , 3.00 ), "Ion size for secondary species 9 is not 3.00" );
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static_assert( nearEqual( chemicalReactionsParams.m_ionSizeSec[10], 4.00 ), "Ion size for secondary species 10 is not 4.00" );
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static_assert( chemicalReactionsParams.m_chargePrimary[0] == 1, "Charge for primary species 0 is not 1" );
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static_assert( chemicalReactionsParams.m_chargePrimary[1] == -1, "Charge for primary species 1 is not -1" );
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static_assert( chemicalReactionsParams.m_chargePrimary[2] == 2, "Charge for primary species 2 is not 2" );
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static_assert( chemicalReactionsParams.m_chargePrimary[3] == -2, "Charge for primary species 3 is not -2" );
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static_assert( chemicalReactionsParams.m_chargePrimary[4] == -1, "Charge for primary species 4 is not -1" );
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static_assert( chemicalReactionsParams.m_chargePrimary[5] == 2, "Charge for primary species 5 is not 2" );
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static_assert( chemicalReactionsParams.m_chargePrimary[6] == 1, "Charge for primary species 6 is not 1" );
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static_assert( chemicalReactionsParams.m_chargeSec[0] == -1, "Charge for secondary species 0 is not -1" );
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static_assert( chemicalReactionsParams.m_chargeSec[1] == 0, "Charge for secondary species 1 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[2] == -2, "Charge for secondary species 2 is not -2" );
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static_assert( chemicalReactionsParams.m_chargeSec[3] == 0, "Charge for secondary species 3 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[4] == 1, "Charge for secondary species 4 is not 1" );
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static_assert( chemicalReactionsParams.m_chargeSec[5] == 0, "Charge for secondary species 5 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[6] == 0, "Charge for secondary species 6 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[7] == 1, "Charge for secondary species 7 is not 1" );
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static_assert( chemicalReactionsParams.m_chargeSec[8] == 0, "Charge for secondary species 8 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[9] == 0, "Charge for secondary species 9 is not 0" );
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static_assert( chemicalReactionsParams.m_chargeSec[10] == -1, "Charge for secondary species 10 is not -1" );
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static_assert( nearEqual( chemicalReactionsParams.m_DebyeHuckelA, 0.5465 ), "Debye Huckel A is not 0.5465" );
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static_assert( nearEqual( chemicalReactionsParams.m_DebyeHuckelB, 0.3346 ), "Debye Huckel B is not 0.3346" );
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static_assert( nearEqual( chemicalReactionsParams.m_WATEQBDot, 0.0438 ), "WATEQBDot is not 0.0438" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][0], -1.0 ), "Stoichiometry matrix for species 0 and 0 is not -1" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][1], 0.0 ), "Stoichiometry matrix for species 0 and 1 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][2], 0.0 ), "Stoichiometry matrix for species 0 and 2 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][3], 0.0 ), "Stoichiometry matrix for species 0 and 3 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][4], 0.0 ), "Stoichiometry matrix for species 0 and 4 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][5], 0.0 ), "Stoichiometry matrix for species 0 and 5 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[0][6], 0.0 ), "Stoichiometry matrix for species 0 and 6 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][0], 1.0 ), "Stoichiometry matrix for species 1 and 0 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][1], 1.0 ), "Stoichiometry matrix for species 1 and 1 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][2], 0.0 ), "Stoichiometry matrix for species 1 and 2 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][3], 0.0 ), "Stoichiometry matrix for species 1 and 3 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][4], 0.0 ), "Stoichiometry matrix for species 1 and 4 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][5], 0.0 ), "Stoichiometry matrix for species 1 and 5 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqStoichMatrix[1][6], 0.0 ), "Stoichiometry matrix for species 1 and 6 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[0], 13.99 ), "Log10 equilibrium constant for species 0 is not 13.99" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[1], -6.36 ) , "Log10 equilibrium constant for species 1 is not -6.36" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[2], 10.33 ), "Log10 equilibrium constant for species 2 is not 10.33" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[3], -3.77 ) , "Log10 equilibrium constant for species 3 is not -3.77" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[4], -1.09 ) , "Log10 equilibrium constant for species 4 is not -1.09" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[5], 7.07 ) , "Log10 equilibrium constant for species 5 is not 7.07" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[6], - 2.16 ) , "Log10 equilibrium constant for species 6 is not -2.16" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[7], + 0.67 ) , "Log10 equilibrium constant for species 7 is not 0.67" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[8], + 0.60 ) , "Log10 equilibrium constant for species 8 is not 0.60" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[9], - 2.43 ) , "Log10 equilibrium constant for species 9 is not -2.43" );
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static_assert( nearEqual( chemicalReactionsParams.m_eqLog10EqConst[10], - 0.82 ), "Log10 equilibrium constant for species 10 is not -0.82" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][0],-2.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 0 is not -2" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][1], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 1 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][2], 1.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 2 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][3], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 3 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][4], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 4 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][5], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 5 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[0][6], 0.0 ), "Stoichiometry matrix for kinetic reaction 0 and species 6 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][0],-1.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 0 is not -1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][1], 1.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 1 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][2], 1.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 2 is not 1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][3], 0.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 3 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][4], 0.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 4 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][5], 0.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 5 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticStoichMatrix[1][6], 0.0 ), "Stoichiometry matrix for kinetic reaction 1 and species 6 is not 0" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticlog10EqConst[0], 20.19 ), "Log10 equilibrium constant for kinetic reaction 0 is not 20.19" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticlog10EqConst[1], 1.32 ), "Log10 equilibrium constant for kinetic reaction 1 is not 1.32" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticReactionRateConstant[0], 9.95e-1 ), "Reaction rate constant for kinetic reaction 0 is not 9.95e-1" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticReactionRateConstant[1], 9.95e-3 ), "Reaction rate constant for kinetic reaction 1 is not 9.95e-3" );
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static_assert( nearEqual( chemicalReactionsParams.m_kineticSpecificSurfaceArea, 1.0 ), "Specific surface area is not 1.0" );
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}
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TEST( testReactionsBase, testEquilibriumParamsExtraction )
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{
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constexpr auto eqParams = chemicalReactionsParams.equilibriumReactions();
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static_assert( eqParams.numPrimarySpecies == 7, "Number of primary species is not 7" );
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static_assert( eqParams.numSecondarySpecies == 11, "Number of secondary species is not 11" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[0], 9.00 ), "Ion size for primary species 0 is not 9.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[1], 4.00 ), "Ion size for primary species 1 is not 4.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[2], 6.00 ), "Ion size for primary species 2 is not 6.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[3], 4.00 ), "Ion size for primary species 3 is not 4.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[4], 3.00 ), "Ion size for primary species 4 is not 3.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[5], 8.00 ), "Ion size for primary species 5 is not 8.00" );
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static_assert( nearEqual( eqParams.m_ionSizePrimary[6], 4.00 ), "Ion size for primary species 6 is not 4.00" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[0] , 3.50 ), "Ion size for secondary species 0 is not 3.50" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[1] , 3.00 ), "Ion size for secondary species 1 is not 3.00" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[2] , 4.50 ), "Ion size for secondary species 2 is not 4.50" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[3] , 3.00 ), "Ion size for secondary species 3 is not 3.00" );
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static_assert( nearEqual( eqParams.m_ionSizeSec[
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}
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int main( int argc, char * * argv )
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{
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::testing::InitGoogleTest( &argc, argv );
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int const result = RUN_ALL_TESTS();
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return result;
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}

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