move stuff around to allow for separate geochem and battery chemistry approaches before we merge to a general form

Author: rrsettgast

src/CMakeLists.txt

@@ -2,9 +2,9 @@
 set( hpcReact_headers
      common/macros.hpp
      common/CArrayWrapper.hpp
-     reactions/EquilibriumReactions.hpp
-     reactions/KineticReactions.hpp
-     reactions/ReactionsBase.hpp
+     reactions/geochemistry/EquilibriumReactions.hpp
+     reactions/geochemistry/KineticReactions.hpp
+     reactions/geochemistry/ReactionsBase.hpp
      reactions/ReactionsParameterData.hpp
      reactions/ReactionsParameterDataPredefined.hpp
      )
@@ -52,7 +52,7 @@ target_include_directories( hpcReact
 # hpcReact_add_code_checks( PREFIX hpcReact
 #                        EXCLUDES "blt/*" )
 
-add_subdirectory( reactions/unitTests )
+add_subdirectory( reactions/geochemistry/unitTests )
 
 
 HPCReact_add_code_checks( PREFIX hpcReact

src/reactions/EquilibriumReactions.hpp …ns/geochemistry/EquilibriumReactions.hppsrc/reactions/EquilibriumReactions.hpp renamed to src/reactions/geochemistry/EquilibriumReactions.hpp src/reactions/EquilibriumReactions.hpp renamed to src/reactions/geochemistry/EquilibriumReactions.hpp

@@ -52,10 +52,10 @@ KineticReactions< REAL_TYPE,
 
     for( int iPri = 0; iPri < PARAMS_DATA::numPrimarySpecies; ++iPri )
     {
-      saturationIndex += params.m_stoichMatrix[iRxn][iPri] * log10( primarySpeciesConcentration[iPri] );
-      saturationIndex += params.m_stoichMatrix[iRxn][iPri] * log10PrimaryActCoeff[iPri];
+      saturationIndex = saturationIndex 
+                      + params.m_stoichMatrix[iRxn][iPri] * log10( primarySpeciesConcentration[iPri] ) 
+                      + params.m_stoichMatrix[iRxn][iPri] * log10PrimaryActCoeff[iPri];
     }
-
     reactionRates[iRxn] = params.m_specificSurfaceArea * (1.0 - pow( 10, saturationIndex ) ) * params.m_reactionRateConstant[iRxn];
   }
 }

…/reactions/EquilibriumReactions_impl.hpp …ochemistry/EquilibriumReactions_impl.hppsrc/reactions/EquilibriumReactions_impl.hpp renamed to src/reactions/geochemistry/EquilibriumReactions_impl.hpp src/reactions/EquilibriumReactions_impl.hpp renamed to src/reactions/geochemistry/EquilibriumReactions_impl.hpp

@@ -38,8 +38,6 @@ void ReactionsBase< REAL_TYPE,
                                                params.m_DebyeHuckelB /
                                                (1.0 + params.m_ionSizePrimary[i] * params.m_DebyeHuckelB * sqrt( ionicStrength )) /
                                                (1.0 + params.m_ionSizePrimary[i] * params.m_DebyeHuckelB * sqrt( ionicStrength )));
-//    log10PrimaryActCoeff[i] = 0;
-//    dLog10PrimaryActCoeff_dIonicStrength[i] = 0;
   }
   for( INDEX_TYPE i = 0; i < PARAMS_DATA::numSecondarySpecies; ++i )
   {
@@ -50,8 +48,6 @@ void ReactionsBase< REAL_TYPE,
                                            params.m_DebyeHuckelB /
                                            (1.0 + params.m_ionSizeSec[i] * params.m_DebyeHuckelB * sqrt( ionicStrength )) /
                                            (1.0 + params.m_ionSizeSec[i] * params.m_DebyeHuckelB * sqrt( ionicStrength )));
-//    log10SecActCoeff[i] = 0;
-//    dLog10SecActCoeff_dIonicStrength[i] = 0;
   }
 }