wip: add surfaceArea to test.

Author: CusiniM

src/reactions/bulkGeneric/KineticReactions.hpp

@@ -77,7 +77,7 @@ class KineticReactions
   computeReactionRates( RealType const & temperature,
                         PARAMS_DATA const & params,
                         ARRAY_1D_TO_CONST const & speciesConcentration,
-                        ARRAY_1D & reactionRates, )
+                        ARRAY_1D & reactionRates )
   {
     REAL_TYPE reactionRatesDerivatives[PARAMS_DATA::numReactions()][PARAMS_DATA::numSpecies()] = { {0.0} };
     computeReactionRates_impl< PARAMS_DATA, false >( temperature,
@@ -89,7 +89,8 @@ class KineticReactions
 
   template< typename PARAMS_DATA,
             typename ARRAY_1D_TO_CONST,
-            typename ARRAY_1D >
+            typename ARRAY_1D,
+            typename ARRAY_2D >
   static HPCREACT_HOST_DEVICE inline void
   computeReactionRates( RealType const & temperature,
                         PARAMS_DATA const & params,

src/reactions/bulkGeneric/Parameters.hpp

@@ -30,7 +30,6 @@ struct EquilibriumReactionsParameters
 
   static constexpr IndexType numSpecies() { return NUM_SPECIES; }
 
-<<<<<<< HEAD
   static constexpr IndexType numReactions() { return NUM_REACTIONS; }
 
   static constexpr IndexType numSurfaceReactions() { return NUM_SURFACE_REACTIONS; }
@@ -41,26 +40,12 @@ struct EquilibriumReactionsParameters
 
   static constexpr IndexType numSecondarySpecies() { return numSpecies() - numPrimarySpecies(); }
 
-=======
-  static constexpr IndexType numSpecies() { return NUM_SPECIES; }
-
-  static constexpr IndexType numReactions() { return NUM_REACTIONS; }
-
-  static constexpr IndexType numPrimarySpecies() { return numSpecies() - numReactions(); }
-
-  static constexpr IndexType numSecondarySpecies() { return numSpecies() - numPrimarySpecies(); }
->>>>>>> origin/main
 
   constexpr
   EquilibriumReactionsParameters( CArrayWrapper< RealType, NUM_REACTIONS, NUM_SPECIES > const & stoichiometricMatrix,
                                   CArrayWrapper< RealType, NUM_REACTIONS > equilibriumConstant ):
-<<<<<<< HEAD
-  m_stoichiometricMatrix( stoichiometricMatrix ),
-  m_equilibriumConstant( equilibriumConstant )
-=======
     m_stoichiometricMatrix( stoichiometricMatrix ),
     m_equilibriumConstant( equilibriumConstant )
->>>>>>> origin/main
   {}
 
 
@@ -89,15 +74,9 @@ struct KineticReactionsParameters
   constexpr KineticReactionsParameters( CArrayWrapper< RealType, NUM_REACTIONS, NUM_SPECIES > const & stoichiometricMatrix,
                                         CArrayWrapper< RealType, NUM_REACTIONS > const & rateConstantForward,
                                         CArrayWrapper< RealType, NUM_REACTIONS > const & rateConstantReverse ):
-<<<<<<< HEAD
-  m_stoichiometricMatrix( stoichiometricMatrix ),
-  m_rateConstantForward( rateConstantForward ),
-  m_rateConstantReverse( rateConstantReverse ) 
-=======
     m_stoichiometricMatrix( stoichiometricMatrix ),
     m_rateConstantForward( rateConstantForward ),
     m_rateConstantReverse( rateConstantReverse )
->>>>>>> origin/main
   {}
 
 
@@ -128,23 +107,13 @@ struct MixedReactionsParameters
   constexpr MixedReactionsParameters() = default;
 
   constexpr MixedReactionsParameters( CArrayWrapper< RealType, NUM_REACTIONS, NUM_SPECIES > const & stoichiometricMatrix,
-<<<<<<< HEAD
-                                      CArrayWrapper< RealType, NUM_REACTIONS > const & equilibriumConstant,                                  
-                                      CArrayWrapper< RealType, NUM_REACTIONS > const & rateConstantForward,
-                                      CArrayWrapper< RealType, NUM_REACTIONS > const & rateConstantReverse ):
-  m_stoichiometricMatrix( stoichiometricMatrix ),
-  m_equilibriumConstant( equilibriumConstant ),
-  m_rateConstantForward( rateConstantForward ),
-  m_rateConstantReverse( rateConstantReverse )
-=======
                                       CArrayWrapper< RealType, NUM_REACTIONS > const & equilibriumConstant,
                                       CArrayWrapper< RealType, NUM_REACTIONS > const & rateConstantForward,
                                       CArrayWrapper< RealType, NUM_REACTIONS > const & rateConstantReverse ):
     m_stoichiometricMatrix( stoichiometricMatrix ),
     m_equilibriumConstant( equilibriumConstant ),
     m_rateConstantForward( rateConstantForward ),
     m_rateConstantReverse( rateConstantReverse )
->>>>>>> origin/main
   {}
 
   static constexpr IndexType numReactions() { return NUM_REACTIONS; }
@@ -154,11 +123,7 @@ struct MixedReactionsParameters
   static constexpr IndexType numEquilibriumReactions() { return NUM_EQ_REACTIONS; }
 
   static constexpr IndexType numSpecies() { return NUM_SPECIES; }
-<<<<<<< HEAD
 
-=======
-
->>>>>>> origin/main
   static constexpr IndexType numPrimarySpecies() { return NUM_SPECIES - NUM_EQ_REACTIONS; }
 
   static constexpr IndexType numSecondarySpecies() { return NUM_EQ_REACTIONS; }
@@ -169,16 +134,6 @@ struct MixedReactionsParameters
   {
     CArrayWrapper< RealType, numEquilibriumReactions(), numSpecies() > eqMatrix{};
     CArrayWrapper< RealType, numEquilibriumReactions() > eqConstants{};
-<<<<<<< HEAD
-    
-    for (IntType i = 0; i < numEquilibriumReactions(); ++i)
-    {
-      for (IntType j = 0; j < numSpecies(); ++j)
-      {
-        eqMatrix(i, j) = m_stoichiometricMatrix(i, j);
-      }
-      eqConstants(i) = m_equilibriumConstant(i);
-=======
 
     for( IntType i = 0; i < numEquilibriumReactions(); ++i )
     {
@@ -187,7 +142,6 @@ struct MixedReactionsParameters
         eqMatrix( i, j ) = m_stoichiometricMatrix( i, j );
       }
       eqConstants( i ) = m_equilibriumConstant( i );
->>>>>>> origin/main
     }
 
     return { eqMatrix, eqConstants };
@@ -200,21 +154,12 @@ struct MixedReactionsParameters
     CArrayWrapper< RealType, numKineticReactions(), numSpecies() > kineticMatrix{};
     CArrayWrapper< RealType, numKineticReactions() > rateConstantForward{};
     CArrayWrapper< RealType, numKineticReactions() > rateConstantReverse{};
-<<<<<<< HEAD
-    
-    for ( IndexType i = 0; i < numKineticReactions(); ++i )
-    {
-      for ( IndexType j = 0; j < numSpecies(); ++j )
-      {
-        kineticMatrix(i, j) = m_stoichiometricMatrix( numEquilibriumReactions() + i, j );
-=======
 
     for( IndexType i = 0; i < numKineticReactions(); ++i )
     {
       for( IndexType j = 0; j < numSpecies(); ++j )
       {
         kineticMatrix( i, j ) = m_stoichiometricMatrix( numEquilibriumReactions() + i, j );
->>>>>>> origin/main
       }
       rateConstantForward( i ) = m_rateConstantForward( numEquilibriumReactions() + i );
       rateConstantReverse( i ) = m_rateConstantReverse( numEquilibriumReactions() + i );

src/reactions/geochemistry/unitTests/testGeochemicalMixedReactions.cpp

@@ -12,6 +12,11 @@ TEST( testMixedReactions, testTimeStep_carbonateSystem )
 
   constexpr int numPrimarySpecies = carbonateSystemType::numPrimarySpecies();
 
+  double const surfaceArea[carbonateSystemType::numKineticReactions()] =
+  {
+    1.0, // CaCO3
+  };
+
   double const initialAggregateSpeciesConcentration[numPrimarySpecies] =
   {
     3.76e-3, // CaCO3 
@@ -40,6 +45,7 @@ TEST( testMixedReactions, testTimeStep_carbonateSystem )
                                 0.2,
                                 10,
                                 initialAggregateSpeciesConcentration,
+                                surfaceArea,
                                 expectedSpeciesConcentrations );
 
 }