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CusiniMCusiniM
committed
refactor
1 parent 6c6838e commit ee66f3e

19 files changed

+1180
-608
lines changed

‎src/CMakeLists.txt‎

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Original file line numberDiff line numberDiff line change
@@ -5,13 +5,16 @@ set( hpcReact_headers
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reactions/bulkGeneric/EquilibriumReactions.hpp
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reactions/bulkGeneric/EquilibriumReactionsAggregatePrimaryConcentration_impl.hpp
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reactions/bulkGeneric/EquilibriumReactionsReactionExtents_impl.hpp
8+
reactions/geochemistry/GeochemicalSystems.hpp
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reactions/bulkGeneric/KineticReactions.hpp
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reactions/bulkGeneric/KineticReactions_impl.hpp
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reactions/bulkGeneric/MixedEquilibriumKineticReactions.hpp
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reactions/bulkGeneric/MixedEquilibriumKineticReactions_impl.hpp
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reactions/bulkGeneric/Parameters.hpp
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reactions/bulkGeneric/ParametersPredefined.hpp
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reactions/bulkGeneric/SpeciesUtilities.hpp
16+
reactions/bulkGeneric/unitTestUtilities/kineticReactionsTest_utilities.hpp
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reactions/massActions/MassActions.hpp
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)
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set( hpcReact_sources)
@@ -60,6 +63,8 @@ message(STATUS "HPCReact/src CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DI
6063
# EXCLUDES "blt/*" )
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add_subdirectory( reactions/bulkGeneric/unitTests )
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add_subdirectory( reactions/geochemistry/unitTests )
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add_subdirectory( reactions/massActions/unitTests )
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add_subdirectory( common/unitTests )
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add_subdirectory( docs )
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‎src/common/printers.hpp‎

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@@ -1,6 +1,7 @@
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#pragma once
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#include <stdio.h>
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#include "CArrayWrapper.hpp"
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template< typename T, int N >
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void print( T const (&a)[N], char const * name, int const numDigits )

‎src/reactions/bulkGeneric/EquilibriumReactionsAggregatePrimaryConcentration_impl.hpp‎

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@@ -2,7 +2,7 @@
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#include "EquilibriumReactions.hpp"
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#endif
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5-
#include "SpeciesUtilities.hpp"
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#include "reactions/massActions/MassActions.hpp"
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namespace hpcReact
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{
@@ -35,10 +35,10 @@ EquilibriumReactions< REAL_TYPE,
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RealType aggregatePrimaryConcentrations[numPrimarySpecies] = {0.0};
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ARRAY_2D dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations = {{{0.0}}};
38-
calculateAggregatePrimaryConcentrationsWrtLogC< REAL_TYPE, INT_TYPE, INDEX_TYPE >( params,
39-
logPrimarySpeciesConcentration,
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aggregatePrimaryConcentrations,
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dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations );
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massActions::calculateAggregatePrimaryConcentrationsWrtLogC< REAL_TYPE, INT_TYPE, INDEX_TYPE >( params,
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logPrimarySpeciesConcentration,
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aggregatePrimaryConcentrations,
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dAggregatePrimarySpeciesConcentrationsDerivatives_dLogPrimarySpeciesConcentrations );
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for( IndexType i=0; i<numPrimarySpecies; ++i )

‎src/reactions/bulkGeneric/KineticReactions_impl.hpp‎

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Original file line numberDiff line numberDiff line change
@@ -273,9 +273,10 @@ KineticReactions< REAL_TYPE,
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reactionRatesDerivatives( r, i ) = 0.0;
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}
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}
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} // end of if constexpr ( CALCULATE_DERIVATIVES )
276+
} // end of if constexpr ( CALCULATE_DERIVATIVES )
277+
} // end of else
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reactionRates[r] = - rateConstant * surfaceArea[r] * ( 1 - quotient / equilibriumConstant );
278-
} // end of if constexpr ( LOGE_CONCENTRATION )
279+
}
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}
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// function to the reaction rate. Includes impact of temperature, concentration, surface area, volume fraction and porosity

‎src/reactions/bulkGeneric/MixedEquilibriumKineticReactions_impl.hpp‎

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Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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#include "common/constants.hpp"
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#include "common/CArrayWrapper.hpp"
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#include "SpeciesUtilities.hpp"
5+
#include "reactions/massActions/MassActions.hpp"
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/** @file MixedEquilibriumKineticReactions_impl.hpp
@@ -45,13 +45,13 @@ MixedEquilibriumKineticReactions< REAL_TYPE,
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{
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// 1. Compute new aggregate species from primary species
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calculateAggregatePrimaryConcentrationsWrtLogC< REAL_TYPE,
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INT_TYPE,
50-
INDEX_TYPE >( params.equilibriumReactionsParameters(),
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logPrimarySpeciesConcentrations,
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logSecondarySpeciesConcentrations,
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aggregatePrimarySpeciesConcentrations,
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dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations );
48+
massActions::calculateAggregatePrimaryConcentrationsWrtLogC< REAL_TYPE,
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INT_TYPE,
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INDEX_TYPE >( params.equilibriumReactionsParameters(),
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logPrimarySpeciesConcentrations,
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logSecondarySpeciesConcentrations,
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aggregatePrimarySpeciesConcentrations,
54+
dAggregatePrimarySpeciesConcentrations_dLogPrimarySpeciesConcentrations );
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if constexpr( PARAMS_DATA::numKineticReactions() > 0 )
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{

‎src/reactions/bulkGeneric/Parameters.hpp‎

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Original file line numberDiff line numberDiff line change
@@ -20,7 +20,8 @@ template< typename REAL_TYPE,
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typename INT_TYPE,
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typename INDEX_TYPE,
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int NUM_SPECIES,
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int NUM_REACTIONS >
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int NUM_REACTIONS,
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int NUM_SURFACE_REACTIONS = 0 >
2425
struct EquilibriumReactionsParameters
2526
{
2627
using RealType = REAL_TYPE;
@@ -31,9 +32,14 @@ struct EquilibriumReactionsParameters
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3233
static constexpr IndexType numReactions() { return NUM_REACTIONS; }
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35+
static constexpr IndexType numSurfaceReactions() { return NUM_SURFACE_REACTIONS; }
36+
37+
static constexpr IndexType numAqueousReactions() { return numReactions() - numSurfaceReactions(); }
38+
3439
static constexpr IndexType numPrimarySpecies() { return numSpecies() - numReactions(); }
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3641
static constexpr IndexType numSecondarySpecies() { return numSpecies() - numPrimarySpecies(); }
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3844
constexpr
3945
EquilibriumReactionsParameters( CArrayWrapper< RealType, NUM_REACTIONS, NUM_SPECIES > const & stoichiometricMatrix,
@@ -50,30 +56,6 @@ struct EquilibriumReactionsParameters
5056
CArrayWrapper< RealType, NUM_REACTIONS > m_equilibriumConstant;
5157
};
5258

53-
template< typename REAL_TYPE,
54-
typename INT_TYPE,
55-
typename INDEX_TYPE,
56-
int NUM_SPECIES,
57-
int NUM_REACTIONS >
58-
struct SurfaceReactionsParameters : public EquilibriumReactionsParameters< REAL_TYPE,
59-
INT_TYPE,
60-
INDEX_TYPE,
61-
NUM_SPECIES,
62-
NUM_REACTIONS >
63-
{
64-
using Base = EquilibriumReactionsParameters< REAL_TYPE, INT_TYPE, INDEX_TYPE, NUM_SPECIES, NUM_REACTIONS >;
65-
using RealType = Base::RealType;
66-
using IntType = Base::IntType;
67-
using IndexType = Base::IndexType
68-
69-
constexpr SurfaceReactionsParameters( CArrayWrapper< RealType, NUM_REACTIONS, NUM_SPECIES > const & stoichiometricMatrix,
70-
CArrayWrapper< RealType, NUM_REACTIONS > equilibriumConstant ) :
71-
Base( stoichiometricMatrix, equilibriumConstant )
72-
{}
73-
};
74-
75-
76-
7759
template< typename REAL_TYPE,
7860
typename INT_TYPE,
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typename INDEX_TYPE,

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